Zinc Deficiency via a Splice Switch in Zinc Importer ZIP2/SLC39A2 Causes Cystic Fibrosis-Associated MUC5AC Hypersecretion in Airway Epithelial Cells☆
Airway mucus hyperproduction and fluid imbalance are important hallmarks of cystic fibrosis (CF), the most common life-shortening genetic disorder in Caucasians. Dysregulated expression and/or function of airway ion transporters, including cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC), have been implicated as causes of CF-associated mucus hypersecretory phenotype. However, the contributory roles of other substances and transporters in the regulation of CF airway pathogenesis remain unelucidated. Here, we identified a novel connection between CFTR/ENaC expression and the intracellular Zn2 + concentration in the regulation of MUC5AC, a major secreted mucin that is highly expressed in CF airway. CFTR-defective and ENaC-hyperactive airway epithelial cells specifically and highly expressed a unique, alternative splice isoform of the zinc importer ZIP2/SLC39A2 (ΔC-ZIP2), which lacks the C-terminal domain. Importantly, ΔC-ZIP2 levels correlated inversely with wild-type ZIP2 and intracellular Zn2 + levels. Moreover, the splice switch to ΔC-ZIP2 as well as decreased expression of other ZIPs caused zinc deficiency, which is sufficient for induction of MUC5AC; while ΔC-ZIP2 expression per se induced ENaC expression and function. Thus, our findings demonstrate that the novel splicing switch contributes to CF lung pathology via the novel interplay of CFTR, ENaC, and ZIP2 transporters.
Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed
Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.
Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification
Infection with Zika virus (ZIKV) is of growing concern since infection is associated with the development of congenital neurological disease. Quantitative reverse transcription PCR (qRT-PCR) has been the standard for ZIKV detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper testing. Studies have suggested that ZIKV detection in urine is more sensitive and has a longer window of detection compared to serum and saliva. The objective of this study was to develop a urine diagnostic test that could be completed in under 30 minutes. Urine samples spiked with ZIKV or dengue virus were tested using RT-LAMP as well as by conventional quantitative qRT-PCR. These techniques were then validated using crude lysates made from ZIKV infected mosquitoes in addition to urine and serum samples from ZIKV infected patients. RT-LAMP specifically detected ZIKV in urine and serum for ZIKV infected patients and crude mosquito lysates. This test was performed in under 30 minutes and did not require RNA extraction from urine nor mosquitos. This approach could be used for monitoring of exposed individuals, especially pregnant women, couples wanting to conceive, or individuals with suspicious symptoms as well as surveillance of mosquito populations.
Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau
Soil microbes provide important ecosystem services. Zoige Plateau wetland, the largest alpine peat wetland in the world, has suffered from serious degradation in the past 30 years. We studied the composition of the Zoige Plateau alpine wetland soil microbiota and relations among specific taxa using 16S rRNA amplicon sequencing combined with association network analysis. Compared to the pristine swamp soil, taxons DA101, Aeromicrobium, Bradyrhizobium, and Candidatus Nitrososphaera were enriched and several methanogenic Euryarchaeota were depleted in the moderately degraded meadow soil and highly degraded sandy soil. Soil total potassium contents in soils with different degradation levels were significantly different, being the highest in meadow soil and lowest in swamp soil. The association network analysis showed that total potassium positively correlated with specific bacterial and archaeal taxa. Jiangella, Anaerolinea, Desulfobulbus, Geobacter, Flavobacterium, Methanobacterium and Methanosaeta were identified as the keystone genera in the networks. Soil degradation affected soil properties, and caused changes in the bacterial and archaeal community composition and the association patterns of community members. The changes could serve as early warning signals of soil degradation in alpine wetlands.
Support for viral persistence in bats from age-specific serology and models of maternal immunity
Spatiotemporally-localised prediction of virus emergence from wildlife requires focused studies on the ecology and immunology of reservoir hosts in their native habitat. Reliable predictions from mathematical models remain difficult in most systems due to a dearth of appropriate empirical data. Our goal was to study the circulation and immune dynamics of zoonotic viruses in bat populations and investigate the effects of maternally-derived and acquired immunity on viral persistence. Using rare age-specific serological data from wild-caught Eidolon helvum fruit bats as a case study, we estimated viral transmission parameters for a stochastic infection model. We estimated mean durations of around 6 months for maternally-derived immunity to Lagos bat virus and African henipavirus, whereas acquired immunity was long-lasting (Lagos bat virus: mean 12 years, henipavirus: mean 4 years). In the presence of a seasonal birth pulse, the effect of maternally-derived immunity on virus persistence within modelled bat populations was highly dependent on transmission characteristics. To explain previous reports of viral persistence within small natural and captive E. helvum populations, we hypothesise that some bats must experience prolonged infectious periods or within-host latency. By further elucidating plausible mechanisms of virus persistence in bat populations, we contribute to guidance of future field studies.
Swimming mechanics and propulsive efficiency in the chambered nautilus
The chambered nautilus (Nautilus pompilius) encounters severe environmental hypoxia during diurnal vertical movements in the ocean. The metabolic cost of locomotion (Cmet) and swimming performance depend on how efficiently momentum is imparted to the water and how long on-board oxygen stores last. While propulsive efficiency is generally thought to be relatively low in jet propelled animals, the low Cmet in Nautilus indicates that this is not the case. We measured the wake structure in Nautilus during jet propulsion swimming, to determine their propulsive efficiency. Animals swam with either an anterior-first or posterior-first orientation. With increasing swimming speed, whole cycle propulsive efficiency increased during posterior-first swimming but decreased during anterior-first swimming, reaching a maximum of 0.76. The highest propulsive efficiencies were achieved by using an asymmetrical contractile cycle in which the fluid ejection phase was relatively longer than the refilling phase, reducing the volume flow rate of the ejected fluid. Our results demonstrate that a relatively high whole cycle propulsive efficiency underlies the low Cmet in Nautilus, representing a strategy to reduce the metabolic demands in an animal that spends a significant part of its daily life in a hypoxic environment.
Phosphotyrosine-Mediated Regulation of Enterohemorrhagic Escherichia coli Virulence
ABSTRACTEnteric pathogens with low infectious doses rely on the ability to orchestrate the expression of virulence and metabolism-associated genes in response to environmental cues for successful infection. Accordingly, the human pathogen enterohemorrhagic Escherichia coli (EHEC) employs a complex multifaceted regulatory network to link the expression of type III secretion system (T3SS) components to nutrient availability. While phosphorylation of histidine and aspartate residues on two-component system response regulators is recognized as an integral part of bacterial signaling, the involvement of phosphotyrosine-mediated control is minimally explored in Gram-negative pathogens. Our recent phosphotyrosine profiling study of E. coli identified 342 phosphorylated proteins, indicating that phosphotyrosine modifications in bacteria are more prevalent than previously anticipated. The present study demonstrates that tyrosine phosphorylation of a metabolite-responsive LacI/GalR family regulator, Cra, negatively affects T3SS expression under glycolytic conditions that are typical for the colonic lumen environment where production of the T3SS is unnecessary. Our data suggest that Cra phosphorylation affects T3SS expression by modulating the expression of ler, which encodes the major activator of EHEC virulence gene expression. Phosphorylation of the Cra Y47 residue diminishes DNA binding to fine-tune the expression of virulence-associated genes, including those of the locus of enterocyte effacement pathogenicity island that encode the T3SS, and thereby negatively affects the formation of attaching and effacing lesions. Our data indicate that tyrosine phosphorylation provides an additional mechanism to control the DNA binding of Cra and other LacI/GalR family regulators, including LacI and PurR. This study describes an initial effort to unravel the role of global phosphotyrosine signaling in the control of EHEC virulence potential.
Arithmetic learning in advanced age
Acquisition of numerical knowledge and understanding of numerical information are crucial for coping with the changing demands of our digital society. In this study, we assessed arithmetic learning in older and younger individuals in a training experiment including brain imaging. In particular, we assessed age-related effects of training intensity, prior arithmetic competence, and neuropsychological variables on the acquisition of new arithmetic knowledge and on the transfer to new, unknown problems. Effects were assessed immediately after training and after 3 months. Behavioural results showed higher training effects for younger individuals than for older individuals and significantly better performance after 90 problem repetitions than after 30 repetitions in both age groups. A correlation analysis indicated that older adults with lower memory and executive functions at baseline could profit more from intensive training. Similarly, training effects in the younger group were higher for those individuals who had lower arithmetic competence and executive functions prior to intervention. In younger adults, successful transfer was associated with higher executive functions. Memory and set-shifting emerged as significant predictors of training effects in the older group. For the younger group, prior arithmetic competence was a significant predictor of training effects, while cognitive flexibility was a predictor of transfer effects. After training, a subgroup of participants underwent an MRI assessment. A voxel-based morphometry analysis showed a significant interaction between training effects and grey matter volume of the right middle temporal gyrus extending to the angular gyrus for the younger group relative to the older group. The reverse contrast (older group vs. younger group) did not yield any significant results. These results suggest that improvements in arithmetic competence are supported by temporo-parietal areas in the right hemisphere in younger participants, while learning in older people might be more widespread. Overall, our study indicates that arithmetic learning depends on the training intensity as well as on person-related factors including individual age, arithmetic competence before training, memory, and executive functions. In conclusion, we suggest that major progress can be also achieved by older participants, but that interventions have to take into account individual variables in order to provide maximal benefit.
Three-dimensional analysis of synapses in the transentorhinal cortex of Alzheimer’s disease patients
Synaptic dysfunction or loss in early stages of Alzheimer’s disease (AD) is thought to be a major structural correlate of cognitive dysfunction. Early loss of episodic memory, which occurs at the early stage of AD, is closely associated with the progressive degeneration of medial temporal lobe (MTL) structures of which the transentorhinal cortex (TEC) is the first affected area. However, no ultrastructural studies have been performed in this region in human brain samples from AD patients.In the present study, we have performed a detailed three-dimensional (3D) ultrastructural analysis using focused ion beam/scanning electron microscopy (FIB/SEM) to investigate possible synaptic alterations in the TEC of patients with AD. Surprisingly, the analysis of the density, morphological features and spatial distribution of synapses in the neuropil showed no significant differences between AD and control samples. However, light microscopy studies showed that cortical thickness of the TEC was severely reduced in AD samples, but there were no changes in the volume occupied by neuronal and glial cell bodies, blood vessels, and neuropil. Thus, the present results indicate that there is a dramatic loss of absolute number of synapses, while the morphology of synaptic junctions and synaptic spatial distribution are maintained. How these changes affect cognitive impairment in AD remains to be elucidated.Electronic supplementary materialThe online version of this article (10.1186/s40478-018-0520-6) contains supplementary material, which is available to authorized users.
Diffusion tensor imaging in metachromatic leukodystrophy
ObjectiveWe aimed to gain more insight into the pathomechanisms of metachromatic leukodystrophy (MLD), by comparing magnitude and direction of diffusion between patients and controls at diagnosis and during follow-up.MethodsFour late-infantile, 16 juvenile and 8 adult onset MLD patients [of which 13 considered eligible for hematopoietic cell transplantation (HCT)] and 47 controls were examined using diffusion tensor imaging. Fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were quantified and compared between groups using tract-based spatial statistics (TBSS). Diffusion measures were determined for normal-appearing white matter (NAWM), corpus callosum, thalamus (all based on subject-wise segmentation), and pyramidal tracts, determined with probabilistic tractography. Measures were compared between HCT-eligible patients, non-eligible patients and controls using general linear model and nonparametric permutation analyses (randomise) for TBSS data, considering family-wise error corrected p < 0.05 significant.ResultsThroughout white matter (WM), FA was decreased and MD and RD increased in both patient groups compared to controls, while AD was decreased in NAWM and corpus callosum. In the thalamus, no differences in FA were observed, but all diffusivities were increased in both patient groups. Differences were most pronounced between controls and patients non-eligible for HCT. Longitudinally (median follow-up 3.9 years), diffusion measures remained relatively stable for HCT-treated patients, but were progressively abnormal for non-eligible patients.InterpretationThe observed diffusion measures confirm that brain microstructure is changed in MLD, reflecting different pathological processes including loss of myelin and sulfatide accumulation. The observation of both increased and decreased AD probably reflects a balance between myelin and axonal loss vs. intracellular sulfatide storage in macrophages, depending on region and disease stage.Electronic supplementary materialThe online version of this article (10.1007/s00415-018-8765-3) contains supplementary material, which is available to authorized users.
Gray Matter Volume of a Region in the Thalamic Pulvinar Is Specifically Associated with Novelty Seeking
Personality reflects the set of psychological traits and mechanisms characteristic for an individual. Geno-neuro-biologically inspired personality accounts have proposed a set of temperaments and characters that jointly compose personality profiles. The present study addresses the link between neurobiology and personality and investigates the association between temperament traits and regional gray matter volume. Furthermore, the specificity of these associations as well as the underlying components that drive the association are addressed. One hundred and four participants completed the Temperament and Character Inventory (TCI) and underwent structural magnetic resonance brain imaging. The participants included premanifest carriers of Huntington's disease, as this population is associated with temperament-related neuropsychiatric symptoms. Whole brain voxel-based multiple regression analyses on gray matter volume revealed a significant specific positive correlation between a region in the left thalamic pulvinar and novelty seeking score, controlled for the other traits (Pheight < 0.05, FWE-corrected). No significant associations were observed for the other temperament traits. Region of interest analyses showed that this association is driven by the subscale NS2: impulsiveness. The results increase the knowledge of the structural neurobiology of personality and indicate that individual differences in novelty seeking reflect the structural differences observed in the brain in an area that is widely and densely connected, which is in line with the typically domain-general behavioral influence of personality traits on a wide range of affective, perceptual, mnemotic, executive, and other cognitive functions.
Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers
Pharmaceutical interventions can slow aging in animals, and have advantages because their dose can be tightly regulated and the timing of the intervention can be closely controlled. They also may complement environmental interventions like caloric restriction by acting additively. A fertile source for therapies slowing aging is FDA approved drugs whose safety has been investigated. Because drugs bind to several protein targets, they cause multiple effects, many of which have not been characterized. It is possible that some of the side effects of drugs prescribed for one therapy may have benefits in retarding aging. We used computationally guided drug screening for prioritizing drug targets to produce a short list of candidate compounds for in vivo testing. We applied the virtual ligand screening approach FINDSITEcomb for screening potential anti-aging protein targets against FDA approved drugs listed in DrugBank. A short list of 31 promising compounds was screened using a multi-tiered approach with rotifers as an animal model of aging. Primary and secondary survival screens and cohort life table experiments identified four drugs capable of extending rotifer lifespan by 8–42%. Exposures to 1 µM erythromycin, 5 µM carglumic acid, 3 µM capecitabine, and 1 µM ivermectin, extended rotifer lifespan without significant effect on reproduction. Some drugs also extended healthspan, as estimated by mitochondria activity and mobility (swimming speed). Our most promising result is that rotifer lifespan was extended by 7–8.9% even when treatment was started in middle age.
Imaging Aβ and tau in early stage Alzheimer’s disease with [18F]AV45 and [18F]AV1451
BackgroundAD is a progressive neurodegenerative disorder that is associated with the accumulation of two different insoluble protein aggregates, Aβ plaques and hyperphosphorylated tau. This study aimed to investigate the optimal acquisition and quantification of [18F]AV45 and [18F]AV1451 to image Aβ and tau, respectively, in subjects with AD.Fifteen subjects with early stage AD underwent a T1-weighted structural MRI and two dynamic PET scans to image Aβ (60 min, [18F]AV45) and tau (120 min, [18F]AV1451). Both dynamic BPND and static SUVR outcome measures were calculated and compared for 12 out of 15 subjects who completed 60 min of the Aβ PET scan and at least 110 min of the tau PET scan. The SRTM and reference Logan graphical analysis were applied to the dynamic data to estimate regional BPND values and SUVR ratios from the static data. Optimal acquisition windows were explored for both the dynamic and static acquisitions. In addition, the spatial correlation between regional Aβ and tau signals was explored.ResultsBoth the SRTM and graphical analysis methods showed a good fit to the dynamic data for both Aβ and tau dynamic PET scans. Mean regional BPND estimates became stable 30 min p.i. for [18F]AV45 and 80 min p.i. for [18F]AV1451.Time stability analysis of static SUVR data showed that the outcome measure starts to become stable for scan windows of 30–50 min p.i. for [18F]AV45 and 80–100 min p.i. for [18F]AV1451. The results from these time windows correlated well with the results from the full dynamic analysis for both tracers (R2 = 0.74 for [18F]AV45 and R2 = 0.88 for [18F]AV1451). There was a high correlation between amyloid uptake estimate using both dynamic analysis methods in thalamus and tau uptake in thalamus, hippocampus and amygdala.ConclusionsShort static PET scans at appropriate time windows provided SUVR values which were in reasonable agreement with BPND values calculated from dynamic scans using SRTM and reference Logan. These simplified methods may be appropriate for classification and intervention studies, although caution should be employed when considering interventional studies where blood flow and extraction could change.
Brd4 regulates the expression of essential autophagy genes and Keap1 in AML cells
We have recently reported that activation of Brd4 is associated with the presence of autophagy in NPMc+ and MLL AML cells. In order to determine the mechanisms underlying this relationship, we have examined the role of Brd4 in regulating the expression of several genes that are central to the process of autophagy. We found that Brd4 binds to the promoters of ATG 3, 7 and CEBPβ, and expression of these genes is markedly reduced by inhibitors of Brd4, as well as by Brd4-shRNA and depletion of CEBPβ. Inhibitors of Brd4 also dramatically suppress the transcription of Keap1, thereby increasing the expression of anti-oxidant genes through the Nrf2 pathway and reducing the cytotoxicity induced by Brd4 inhibitors. Elimination of ATG3 or KEAP1 expression using CRISPR-cas9 mediated genomic editing markedly reduced autophagy. We conclude that Brd4 plays a significant role in autophagy activation through the direct transcriptional regulation of genes essential for it, as well as through the Keap1-Nrf2 axis in NPMc+ and MLL-fusion AML cells.
The dynamic recruitment of TRBP to neuronal membranes mediates dendritogenesis during development
AbstractMicroRNAs are important regulators of local protein synthesis during neuronal development. We investigated the dynamic regulation of microRNA production and found that the majority of the microRNA‐generating complex, consisting of Dicer, TRBP, and PACT, specifically associates with intracellular membranes in developing neurons. Stimulation with brain‐derived neurotrophic factor (BDNF), which promotes dendritogenesis, caused the redistribution of TRBP from the endoplasmic reticulum into the cytoplasm, and its dissociation from Dicer, in a Ca2+‐dependent manner. As a result, the processing of a subset of neuronal precursor microRNAs, among them the dendritically localized pre‐miR16, was impaired. Decreased production of miR‐16‐5p, which targeted the BDNF mRNA itself, was rescued by expression of a membrane‐targeted TRBP. Moreover, miR‐16‐5p or membrane‐targeted TRBP expression blocked BDNF‐induced dendritogenesis, demonstrating the importance of neuronal TRBP dynamics for activity‐dependent neuronal development. We propose that neurons employ specialized mechanisms to modulate local gene expression in dendrites, via the dynamic regulation of microRNA biogenesis factors at intracellular membranes of the endoplasmic reticulum, which in turn is crucial for neuronal dendrite complexity and therefore neuronal circuit formation and function.
Microhomology-assisted scarless genome editing in human iPSCs
Gene-edited induced pluripotent stem cells (iPSCs) provide relevant isogenic human disease models in patient-specific or healthy genetic backgrounds. Towards this end, gene targeting using antibiotic selection along with engineered point mutations remains a reliable method to enrich edited cells. Nevertheless, integrated selection markers obstruct scarless transgene-free gene editing. Here, we present a method for scarless selection marker excision using engineered microhomology-mediated end joining (MMEJ). By overlapping the homology arms of standard donor vectors, short tandem microhomologies are generated flanking the selection marker. Unique CRISPR-Cas9 protospacer sequences nested between the selection marker and engineered microhomologies are cleaved after gene targeting, engaging MMEJ and scarless excision. Moreover, when point mutations are positioned unilaterally within engineered microhomologies, both mutant and normal isogenic clones are derived simultaneously. The utility and fidelity of our method is demonstrated in human iPSCs by editing the X-linked HPRT1 locus and biallelic modification of the autosomal APRT locus, eliciting disease-relevant metabolic phenotypes.
Serological survey of neutralizing antibodies to eight major enteroviruses among healthy population
Human enteroviruses (EVs) are the most common causative agents infecting human, causing many harmful diseases, such as hand, foot, and mouth disease (HFMD), herpangina (HA), myocarditis, encephalitis, and aseptic meningitis. EV-related diseases pose a serious worldwide threat to public health. To gain comprehensive insight into the seroepidemiology of major prevalent EVs in humans, we firstly performed a serological survey for neutralizing antibodies (nAbs) against Enterovirus A71 (EV-A71), Coxsackie virus A16 (CV-A16), Coxsackie virus A6 (CV-A6), Coxsackie virus A10 (CV-A10), Coxsackie virus B3 (CV-B3), Coxsackie virus B5 (CV-B5), Echovirus 25 (ECHO25), and Echovirus 30 (ECHO30) among the healthy population in Xiamen City in 2016, using micro-neutralization assay. A total of 515 subjects aged 5 months to 83 years were recruited by stratified random sampling. Most major human EVs are widely circulated in Xiamen City and usually infect infants and children. The overall seroprevalence of these eight EVs were ranged from 14.4% to 42.7%, and most of them increased with age and subsequently reached a plateau. The co-existence of nAbs against various EVs are common among people ≥ 7 years of age, due to the alternate infections or co-infections with different serotypes of EVs, while most children were negative for nAb against EVs, especially those < 1 year of age. This is the first report detailing the seroepidemiology of eight prevalent EVs in the same population, which provides scientific data supporting further studies on the improvement of EV-related disease prevention and control.
A simple rocker‐induced mechanical stimulus upregulates mineralization by human osteoprogenitor cells in fibrous scaffolds
AbstractBiodegradable electrospun polycaprolactone scaffolds can be used to support bone‐forming cells and could fill a thin bony defect, such as in cleft palate. Oscillatory fluid flow has been shown to stimulate bone production in human progenitor cells in monolayer culture. The aim of this study was to examine whether bone matrix production by primary human mesenchymal stem cells from bone marrow or jaw periosteal tissue could be stimulated using oscillatory fluid flow supplied by a standard see‐saw rocker. This was investigated for cells in two‐dimensional culture and within electrospun polycaprolactone scaffolds. From day 4 of culture onwards, samples were rocked at 45 cycles/min for 1 h/day, 5 days/week (rocking group). Cell viability, calcium deposition, collagen production, alkaline phosphatase activity and vascular endothelial growth factor secretion were evaluated to assess the ability of the cells to undergo bone differentiation and induce vascularisation. Both cell types produced more mineralized tissue when subjected to rocking and supplemented with dexamethasone. Mesenchymal progenitors and primary human mesenchymal stem cells from bone marrow in three‐dimensional scaffolds upregulated mineral deposition after rocking culture as assessed by micro‐computed tomography and alizarin red staining. Interestingly, vascular endothelial growth factor secretion, which has previously been shown to be mechanically sensitive, was not altered by rocking in this system and was inhibited by dexamethasone. Rocker culture may be a cost effective, simple pretreatment for bone tissue engineering for small defects such as cleft palate.
Low intensity repetitive transcranial magnetic stimulation modulates skilled motor learning in adult mice
Repetitive transcranial magnetic stimulation (rTMS) is commonly used to modulate cortical plasticity in clinical and non-clinical populations. Clinically, rTMS is delivered to targeted regions of the cortex at high intensities (>1 T). We have previously shown that even at low intensities, rTMS induces structural and molecular plasticity in the rodent cortex. To determine whether low intensity rTMS (LI-rTMS) alters behavioural performance, daily intermittent theta burst LI-rTMS (120 mT) or sham was delivered as a priming or consolidating stimulus to mice completing 10 consecutive days of skilled reaching training. Relative to sham, priming LI-rTMS (before each training session), increased skill accuracy (~9%) but did not alter the rate of learning over time. In contrast, consolidating LI-rTMS (after each training session), resulted in a small increase in the rate of learning (an additional ~1.6% each day) but did not alter the daily skill accuracy. Changes in behaviour with LI-rTMS were not accompanied with long lasting changes in brain-derived neurotrophic factor (BDNF) expression or in the expression of plasticity markers at excitatory and inhibitory synapses for either priming or consolidation groups. These results suggest that LI-rTMS can alter specific aspects of skilled motor learning in a manner dependent on the timing of intervention.
Obligatory and facultative brain regions for voice-identity recognition
The brain structures critical for recognising another person’s voice remain unclear. Roswandowitz et al. report lesion-behaviour results showing that the right posterior/mid temporal lobe is obligatory for voice-identity recognition. The right inferior parietal lobe, in contrast, is required for voice-identity recognition only when face-identity information must also be processed.
Choosing to regulate: does choice enhance craving regulation?
AbstractGoal-directed behavior and lifelong well-being often depend on the ability to control appetitive motivations, such as cravings. Cognitive reappraisal is an effective way to modulate emotional states, including cravings, but is often studied under explicit instruction to regulate. Despite the strong prediction from Self-Determination Theory that choice should enhance task engagement and regulation success, little is known empirically about whether and how regulation is different when participants choose (vs are told) to exert control. To investigate how choice affects neural activity and regulation success, participants reappraised their responses to images of personally-craved foods while undergoing functional neuroimaging. Participants were either instructed to view or reappraise (‘no-choice’) or chose freely to view or reappraise (‘yes-choice’). Choice increased activity in the frontoparietal control network. We expected this activity would be associated with increased task engagement, resulting in better regulation success. However, contrary to this prediction, choice slightly reduced regulation success. Follow-up multivariate functional neuroimaging analyses indicated that choice likely disrupted allocation of limited cognitive resources during reappraisal. While unexpected, these results highlight the importance of studying upstream processes such as regulation choice, as they may affect the ability to regulate cravings and other emotional states.
Forgetting emotional material in working memory
AbstractProactive interference (PI) is the tendency for information learned earlier to interfere with more recently learned information. In the present study, we induced PI by presenting items from the same category over several trials. This results in a build-up of PI and reduces the discriminability of the items in each subsequent trial. We introduced emotional (e.g. disgust) and neutral (e.g. furniture) categories and examined how increasing levels of PI affected performance for both stimulus types. Participants were scanned using functional magnetic resonance imaging (fMRI) performing a 5-item probe recognition task. We modeled responses and corresponding response times with a hierarchical diffusion model. Results showed that PI effects on latent processes (i.e. reduced drift rate) were similar for both stimulus types, but the effect of PI on drift rate was less pronounced PI for emotional compared to neutral stimuli. The decline in the drift rate was accompanied by an increase in neural activation in parahippocampal regions and this relationship was more strongly observed for neutral stimuli compared to emotional stimuli.
Minocycline reduces chronic microglial activation after brain trauma but increases neurodegeneration
Head injury survivors can develop neurodegeneration associated with persistent neuroinflammation, but whether the latter is harmful or beneficial is unclear. Scott et al. report that minocycline reduces neuroinflammation months and years after injury but increases a blood marker of neurodegeneration, suggesting that persistent neuroinflammation has reparative effects long after injury.
Spatio-temporal models to determine association between Campylobacter cases and environment
AbstractBackgroundCampylobacteriosis is a major cause of gastroenteritis in the UK, and although 70% of cases are associated with food sources, the remainder are probably associated with wider environmental exposure.MethodsIn order to investigate wider environmental transmission, we conducted a spatio-temporal analysis of the association of human cases of Campylobacter in the Tyne catchment with weather, climate, hydrology and land use. A hydrological model was used to predict surface-water flow in the Tyne catchment over 5 years. We analysed associations between population-adjusted Campylobacter case rate and environmental factors hypothesized to be important in disease using a two-stage modelling framework. First, we investigated associations between temporal variation in case rate in relation to surface-water flow, temperature, evapotranspiration and rainfall, using linear mixed-effects models. Second, we used the random effects for the first model to quantify how spatial variation in static landscape features of soil and land use impacted on the likely differences between subcatchment associations of case rate with the temporal variables.ResultsPopulation-adjusted Campylobacter case rates were associated with periods of high predicted surface-water flow, and during above average temperatures. Subcatchments with cattle on stagnogley soils, and to a lesser extent sheep plus cattle grazing, had higher Campylobacter case rates.ConclusionsAreas of stagnogley soils with mixed livestock grazing may be more vulnerable to both Campylobacter spread and exposure during periods of high rainfall, with resultant increased risk of human cases of the disease.
Striatal abnormalities in trichotillomania: A multi-site MRI analysis
Trichotillomania (hair-pulling disorder) is characterized by the repetitive pulling out of one's own hair, and is classified as an Obsessive-Compulsive Related Disorder. Abnormalities of the ventral and dorsal striatum have been implicated in disease models of trichotillomania, based on translational research, but direct evidence is lacking. The aim of this study was to elucidate subcortical morphometric abnormalities, including localized curvature changes, in trichotillomania. De-identified MRI scans were pooled by contacting authors of previous peer-reviewed studies that examined brain structure in adult patients with trichotillomania, following an extensive literature search. Group differences on subcortical volumes of interest were explored (t-tests) and localized differences in subcortical structure morphology were quantified using permutation testing. The pooled sample comprised N = 68 individuals with trichotillomania and N = 41 healthy controls. Groups were well-matched in terms of age, gender, and educational levels. Significant volumetric reductions were found in trichotillomania patients versus controls in right amygdala and left putamen. Localized shape deformities were found in bilateral nucleus accumbens, bilateral amygdala, right caudate and right putamen. Structural abnormalities of subcortical regions involved in affect regulation, inhibitory control, and habit generation, play a key role in the pathophysiology of trichotillomania. Trichotillomania may constitute a useful model through which to better understand other compulsive symptoms. These findings may account for why certain medications appear effective for trichotillomania, namely those modulating subcortical dopamine and glutamatergic function. Future work should study the state versus trait nature of these changes, and the impact of treatment.
Elevated (Pro)renin Receptor Expression Contributes to Maintaining Aerobic Metabolism in Growth Hormone Deficiency
AbstractContextGrowth hormone deficiency (GHD) leads to obesity and may induce tissue hypoxia. As (pro)renin receptor [(P)RR] is reported to contribute to the aerobic metabolism by stabilizing pyruvate dehydrogenase (PDH), it may play a substantial role in GHD.ObjectiveWe aimed to investigate serum soluble (P)RR [s(P)RR] concentration, the origin of s(P)RR, and significance of (P)RR in GHD.Design, Setting, and ParticipantsSerum s(P)RR concentration was examined in 72 patients with pituitary diseases, including 32 patients with severe GHD (SGHD) and after GH replacement in 16 SGHD patients. Leptin-deficient ob/ob obese mice were treated with pegvisomant, a GH receptor antagonist, to explore the source of elevated serum s(P)RR in GHD. Adipocytes were cultured with 5% O2 to examine the effects of hypoxia.ResultsSerum s(P)RR concentration was higher in patients with SGHD than in those without SGHD. Obesity was the important determinant of s(P)RR concentration. Serum s(P)RR concentration significantly decreased after GH replacement in SGHD patients. (P)RR mRNA expression was increased specifically in the adipose tissue (AT) of pegvisomant-treated obese mice compared with that of control obese mice. Hypoxia in cultured adipocytes increased (P)RR expression without affecting the PDH E1 β subunit (PDHB) expression; however, with (P)RR knockdown by small interfering RNA, hypoxia significantly decreased the expression of PDHB.ConclusionGHD patients showed increased serum s(P)RR concentration, possibly caused by obesity and hypoxia. (P)RR expression in AT of GHD patients may be elevated to help maintain aerobic metabolism under hypoxia. Thus, the elevated serum s(P)RR level may reflect hypoxia in ATs.
Cerebral blood flow predicts differential neurotransmitter activity
Application of metabolic magnetic resonance imaging measures such as cerebral blood flow in translational medicine is limited by the unknown link of observed alterations to specific neurophysiological processes. In particular, the sensitivity of cerebral blood flow to activity changes in specific neurotransmitter systems remains unclear. We address this question by probing cerebral blood flow in healthy volunteers using seven established drugs with known dopaminergic, serotonergic, glutamatergic and GABAergic mechanisms of action. We use a novel framework aimed at disentangling the observed effects to contribution from underlying neurotransmitter systems. We find for all evaluated compounds a reliable spatial link of respective cerebral blood flow changes with underlying neurotransmitter receptor densities corresponding to their primary mechanisms of action. The strength of these associations with receptor density is mediated by respective drug affinities. These findings suggest that cerebral blood flow is a sensitive brain-wide in-vivo assay of metabolic demands across a variety of neurotransmitter systems in humans.
Structure-Activity Relationship Analysis of 3-Phenylcoumarin-Based Monoamine Oxidase B Inhibitors
Monoamine oxidase B (MAO-B) catalyzes deamination of monoamines such as neurotransmitters dopamine and norepinephrine. Accordingly, small-molecule MAO-B inhibitors potentially alleviate the symptoms of dopamine-linked neuropathologies such as depression or Parkinson's disease. Coumarin with a functionalized 3-phenyl ring system is a promising scaffold for building potent MAO-B inhibitors. Here, a vast set of 3-phenylcoumarin derivatives was designed using virtual combinatorial chemistry or rationally de novo and synthesized using microwave chemistry. The derivatives inhibited the MAO-B at 100 nM−1 μM. The IC50 value of the most potent derivative 1 was 56 nM. A docking-based structure-activity relationship analysis summarizes the atom-level determinants of the MAO-B inhibition by the derivatives. Finally, the cross-reactivity of the derivatives was tested against monoamine oxidase A and a specific subset of enzymes linked to estradiol metabolism, known to have coumarin-based inhibitors. Overall, the results indicate that the 3-phenylcoumarins, especially derivative 1, present unique pharmacological features worth considering in future drug development.
The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity
AbstractEpigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.
Influence of cerebrovascular disease on brain networks in prodromal and clinical Alzheimer’s disease
Little is known about the interaction between Alzheimer’s disease and cerebrovascular disease with respect to network degeneration. Chong et al. demonstrate differential functional and structural network changes in patients with Alzheimer’s disease with and without cerebrovascular disease, suggesting that the two groups may have different underlying pathologies.
Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw.
The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two restoration plantations (27 and 62 years old) and two forest remnants. We prepared and sequenced a genotyping-by-sequencing library, SNP markers were identified de novo using Stacks pipeline, and genetic parameters and structure analyses were then estimated for populations. The sequencing step was successful for 80 sampled individuals. Neutral genetic diversity was similar among restored and natural populations (AR = 1.72 ± 0.005; HO = 0.135 ± 0.005; HE = 0.167 ± 0.005; FIS = 0.16 ± 0.022), which were not genetically structured by population subdivision. In spite of this absence of genetic structure by population we found genetic structure within populations but even so there is not spatial genetic structure in any population studied. Less than 1% of the neutral alleles were exclusive to a population. In general, contrary to our expectations, restoration plantations were then effective for conserving tree genetic diversity in human-modified tropical landscapes. Furthermore, we demonstrate that genotyping-by-sequencing can be a useful tool in restoration genetics.
Could Arterial Spin Labeling Distinguish Patients in Minimally Conscious State from Patients in Vegetative State?
PurposeDiagnostic error is common among patients with vegetative state (VS) and minimally conscious state (MCS). The purpose of this article is to use three-dimensional pseudo-continuous arterial spin labeling (pcASL) to compare cerebral blood flow (CBF) patterns in patients in MCS with those in VS.MethodsPatients meeting MCS and VS criteria were identified. Two post-labeling delay (PLD) time pcASL on 3.0-Tesla magnetic resonance imaging scanner system were performed with patients in the resting awake state. After registration to T1WI structure imaging, multiple brain regions of interest of ASL CBF map were automatically separated. The average CBF value of every brain region was calculated and compared between the MCS and VS groups with t-tests.ResultsFifteen patients with VS were identified, with ages ranging from 33 to 71 years. Eight patients who met the MCS criteria ranged in age from 23 to 61 years. Compared with VS, the regional CBF for MCS had a pattern of significantly increased CBF in the regions including the putamen, anterior cingulate gyrus, and medial frontal cortex. A left-lateralized pattern was observed to differentiate MCS from VS. CBF with PLD 2.5 s could find more regions of pattern differentiating MCS from VS than with PLD 1.5 s, except for the pallidum.ConclusionMCS might be differentiated from VS by different ranges of regional CBF as measured by ASL. Multi-PLD ASL may serve as an adjunct method to separate MCS from VS and assess functional reserve in patients recovering from severe brain injuries.
MAP4K3 mediates amino acid-dependent regulation of autophagy via phosphorylation of TFEB
Autophagy is the major cellular pathway by which macromolecules are degraded, and amino acid depletion powerfully activates autophagy. MAP4K3, or germinal-center kinase-like kinase, is required for robust cell growth in response to amino acids, but the basis for MAP4K3 regulation of cellular metabolic disposition remains unknown. Here we identify MAP4K3 as an amino acid-dependent regulator of autophagy through its phosphorylation of transcription factor EB (TFEB), a transcriptional activator of autophagy, and through amino acid starvation-dependent lysosomal localization of MAP4K3. We document that MAP4K3 physically interacts with TFEB and MAP4K3 inhibition is sufficient for TFEB nuclear localization, target gene transactivation, and autophagy, even when mTORC1 is activated. Moreover, MAP4K3 serine 3 phosphorylation of TFEB is required for TFEB interaction with mTORC1-Rag GTPase-Ragulator complex and TFEB cytosolic sequestration. Our results uncover a role for MAP4K3 in the control of autophagy and reveal MAP4K3 as a central node in nutrient-sensing regulation.
A sophisticated, differentiated Golgi in the ancestor of eukaryotes
BackgroundThe Golgi apparatus is a central meeting point for the endocytic and exocytic systems in eukaryotic cells, and the organelle’s dysfunction results in human disease. Its characteristic morphology of multiple differentiated compartments organized into stacked flattened cisternae is one of the most recognizable features of modern eukaryotic cells, and yet how this is maintained is not well understood. The Golgi is also an ancient aspect of eukaryotes, but the extent and nature of its complexity in the ancestor of eukaryotes is unclear. Various proteins have roles in organizing the Golgi, chief among them being the golgins.ResultsWe address Golgi evolution by analyzing genome sequences from organisms which have lost stacked cisternae as a feature of their Golgi and those that have not. Using genomics and immunomicroscopy, we first identify Golgi in the anaerobic amoeba Mastigamoeba balamuthi. We then searched 87 genomes spanning eukaryotic diversity for presence of the most prominent proteins implicated in Golgi structure, focusing on golgins. We show some candidates as animal specific and others as ancestral to eukaryotes.ConclusionsNone of the proteins examined show a phyletic distribution that correlates with the morphology of stacked cisternae, suggesting the possibility of stacking as an emergent property. Strikingly, however, the combination of golgins conserved among diverse eukaryotes allows for the most detailed reconstruction of the organelle to date, showing a sophisticated Golgi with differentiated compartments and trafficking pathways in the common eukaryotic ancestor.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0492-9) contains supplementary material, which is available to authorized users.
Flight speed and performance of the wandering albatross with respect to wind
BackgroundAlbatrosses and other large seabirds use dynamic soaring to gain sufficient energy from the wind to travel large distances rapidly and with little apparent effort. The recent development of miniature bird-borne tracking devices now makes it possible to explore the physical and biological implications of this means of locomotion in detail. Here we use GPS tracking and concurrent reanalyzed wind speed data to model the flight performance of wandering albatrosses Diomedea exulans soaring over the Southern Ocean. We investigate the extent to which flight speed and performance of albatrosses is facilitated or constrained by wind conditions encountered during foraging trips.ResultsWe derived simple equations to model observed albatross ground speed as a function of wind speed and relative wind direction. Ground speeds of the tracked birds in the along-wind direction varied primarily by wind-induced leeway, which averaged 0.51 (± 0.02) times the wind speed at a reference height of 5 m. By subtracting leeway velocity from ground velocity, we were able to estimate airspeed (the magnitude of the bird’s velocity through the air). As wind speeds increased from 3 to 18 m/s, the airspeed of wandering albatrosses flying in an across-wind direction increased by 0.42 (± 0.04) times the wind speed (i.e. ~ 6 m/s). At low wind speeds, tracked birds increased their airspeed in upwind flight relative to that in downwind flight. At higher wind speeds they apparently limited their airspeeds to a maximum of around 20 m/s, probably to keep the forces on their wings in dynamic soaring well within tolerable limits. Upwind airspeeds were nearly constant and downwind leeway increased with wind speed. Birds therefore achieved their fastest upwind ground speeds (~ 9 m/s) at low wind speeds (~ 3 m/s).ConclusionsThis study provides insights into which flight strategies are optimal for dynamic soaring. Our results are consistent with the prediction that the optimal range speed of albatrosses is higher in headwind than tailwind flight but only in wind speeds of up to ~ 7 m/s. Our models predict that wandering albatrosses have oval-shaped airspeed polars, with the fastest airspeeds ~ 20 m/s centered in the across-wind direction. This suggests that in upwind flight in high winds, albatrosses can increase their ground speed by tacking like sailboats.
Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells
The Tasmanian devil faces extinction due to devil facial tumour disease (DFTD), a highly transmittable clonal form of cancer without available treatment. In this study, we report the cell-autonomous antiproliferative and cytotoxic activities exhibited by the spider peptide gomesin (AgGom) and gomesin-like homologue (HiGom) in DFTD cells. Mechanistically, both peptides caused a significant reduction at G0/G1 phase, in correlation with an augmented expression of the cell cycle inhibitory proteins p53, p27, p21, necrosis, exacerbated generation of reactive oxygen species and diminished mitochondrial membrane potential, all hallmarks of cellular stress. The screening of a novel panel of AgGom-analogues revealed that, unlike changes in the hydrophobicity and electrostatic surface, the cytotoxic potential of the gomesin analogues in DFTD cells lies on specific arginine substitutions in the eight and nine positions and alanine replacement in three, five and 12 positions. In conclusion, the evidence supports gomesin as a potential antiproliferative compound against DFTD disease.
Increased insula-putamen connectivity in X-linked dystonia-parkinsonism☆
Preliminary evidence from postmortem studies of X-linked dystonia-parkinsonism (XDP) suggests tissue loss may occur first and/or most severely in the striatal striosome compartment, followed later by cell loss in the matrix compartment. However, little is known about how this relates to pathogenesis and pathophysiology. While MRI cannot visualize these striatal compartments directly in humans, differences in relative gradients of afferent cortical connectivity across compartments (weighted toward paralimbic versus sensorimotor cortex, respectively) can be used to infer potential selective loss in vivo. In the current study we evaluated relative connectivity of paralimbic versus sensorimotor cortex with the caudate and putamen in 17 individuals with XDP and 17 matched controls. Although caudate and putamen volumes were reduced in XDP, there were no significant reductions in either “matrix-weighted”, or “striosome-weighted” connectivity. In fact, paralimbic connectivity with the putamen was elevated, rather than reduced, in XDP. This was driven most strongly by elevated putamen connectivity with the anterior insula. There was no relationship of these findings to disease duration or striatal volume, suggesting insula and/or paralimbic connectivity in XDP may develop abnormally and/or increase in the years before symptom onset.
On geographic barriers and Pleistocene glaciations: Tracing the diversification of the Russet-crowned Warbler (Myiothlypis coronata) along the Andes
We studied the phylogeography and plumage variation of the Russet-crowned Warbler (Myiothlypis coronata), from Venezuela to Bolivia, with focus on populations from Ecuador and northern Peru. We analyzed sequences of mitochondrial and nuclear genes, geographic distributions, as well as photographs of specimens deposited at museum collections. Phylogenetic analyses identified three major lineages formed by populations from: Venezuela and Colombia (M. c. regulus), Ecuador and northern Peru (M. elata, M. castaneiceps, M. orientalis, M. c. chapmani), and central Peru and Bolivia (M. c. coronata). We found further population structure within M. c. regulus and M. c. coronata, and population structure and complexity of plumage variation within the Ecuador-northern Peru lineage. Time-calibrated trees estimated that most intraspecific variation originated during the Pleistocene; however, this pattern may not be attributed to an increase in diversification rate during that period. We discuss these results in the context of the importance of geographic-ecological barriers in promoting lineage diversification along the Andes and put forward a preliminary taxonomic proposal for major lineages identified in this study.
Age-related functional brain changes in FMR1 premutation carriers
The FMR1 premutation confers a 40–60% risk for males of developing a neurodegenerative disease called the Fragile X-associated Tremor Ataxia Syndrome (FXTAS). FXTAS is a late-onset disease that primarily involves progressive symptoms of tremor and ataxia, as well as cognitive decline that can develop into dementia in some patients. At present, it is not clear whether changes to brain function are detectable in motor regions prior to the onset of frank symptomatology. The present study therefore aimed to utilize an fMRI motor task for the first time in an asymptomatic premutation population.Premutation carriers without a diagnosis of FXTAS (n = 17) and a group of healthy male controls (n = 17), with an age range of 24–68 years old, were recruited for this cross-sectional study. This study utilized neuroimaging, molecular and clinical measurements, employing an fMRI finger-tapping task with a block design consisting of sequential finger-tapping, random finger-tapping and rest conditions. The imaging analysis contrasted the sequential and random conditions to investigate activation changes in response to a change in task demand. Additionally, measurements were obtained of participant tremor, co-ordination and balance using the CATSYS-2000 system and measures of FMR1 mRNA were quantified from peripheral blood samples using quantitative real-time PCR methodology.Premutation carriers demonstrated significantly less cerebellar activation than controls during sequential versus random finger tapping (FWEcorr < 0.001). In addition, there was a significant age by group interaction in the hippocampus, inferior parietal cortex and temporal cortex originating from a more negative relationship between brain activation and age in the carrier group compared to the controls (FWEcorr < 0.001).Here, we present for the first time functional imaging-based evidence for early movement-related neurodegeneration in Fragile X premutation carriers. These changes pre-exist the diagnosis of FXTAS and are greatest in older carriers suggesting that they may be indicative of FXTAS vulnerability.
Alteration of brain network topology in HIV-associated neurocognitive disorder: A novel functional connectivity perspective
HIV is capable of invading the brain soon after seroconversion. This ultimately can lead to deficits in multiple cognitive domains commonly referred to as HIV-associated neurocognitive disorders (HAND). Clinical diagnosis of such deficits requires detailed neuropsychological assessment but clinical signs may be difficult to detect during asymptomatic injury of the central nervous system (CNS). Therefore neuroimaging biomarkers are of particular interest in HAND. In this study, we constructed brain connectivity profiles of 40 subjects (20 HIV positive subjects and 20 age-matched seronegative controls) using two different methods: a non-linear mutual connectivity analysis approach and a conventional method based on Pearson's correlation. These profiles were then summarized using graph-theoretic methods characterizing their topological network properties. Standard clinical and laboratory assessments were performed and a battery of neuropsychological (NP) tests was administered for all participating subjects. Based on NP testing, 14 of the seropositive subjects exhibited mild neurologic impairment. Subsequently, we analyzed associations between the network derived measures and neuropsychological assessment scores as well as common clinical laboratory plasma markers (CD4 cell count, HIV RNA) after adjusting for age and gender. Mutual connectivity analysis derived graph-theoretic measures, Modularity and Small Worldness, were significantly (p < 0.05, FDR adjusted) associated with the Executive as well as Overall z-score of NP performance. In contrast, network measures derived from conventional correlation-based connectivity did not yield any significant results. Thus, changes in connectivity can be captured using advanced time-series analysis techniques. The demonstrated associations between imaging-derived graph-theoretic properties of brain networks with neuropsychological performance, provides opportunities to further investigate the evolution of HAND in larger, longitudinal studies. Our analysis approach, involving non-linear time-series analysis in conjunction with graph theory, is promising and it may prove to be useful not only in HAND but also in other neurodegenerative disorders.
Callous-unemotional traits and brain structure: Sex-specific effects in anterior insula of typically-developing youths
Callous-unemotional traits are characterized by a lack of empathy, a disregard for others' feelings and shallow or deficient affect, such as a lack of remorse or guilt. Neuroanatomical correlates of callous-unemotional traits have been demonstrated in clinical samples (i.e., adolescents with disruptive behavior disorders). However, it is unknown whether callous-unemotional traits are associated with neuroanatomical correlates within normative populations without clinical levels of aggression or antisocial behavior. Here we investigated the relationship between callous-unemotional traits and gray matter volume using voxel-based morphometry in a large sample of typically-developing boys and girls (N = 189). Whole-brain multiple regression analyses controlling for site, total intracranial volume, and age were conducted in the whole sample and in boys and girls individually. Results revealed that sex and callous-unemotional traits interacted to predict gray matter volume when considering the whole sample. This interaction was driven by a significant positive correlation between callous-unemotional traits and bilateral anterior insula volume in boys, but not girls. Insula gray matter volume explained 19% of the variance in callous-unemotional traits for boys. Our results demonstrate that callous-unemotional traits are related to variations in brain structure beyond psychiatric samples. This association was observed for boys only, underlining the importance of considering sex as a factor in future research designs. Future longitudinal studies should determine whether these findings hold over childhood and adolescence, and whether the neuroanatomical correlates of callous-unemotional traits are predictive of future psychiatric vulnerability.General scientific summaryThis study suggests that callous-unemotional traits have a neuroanatomical correlate within typically developing boys, but not girls. Bilateral anterior insula volume explains up to 19% of the variance in callous-unemotional traits in boys.
Connectome-wide investigation of altered resting-state functional connectivity in war veterans with and without posttraumatic stress disorder
Altered resting-state functional connectivity in posttraumatic stress disorder (PTSD) suggests neuropathology of the disorder. While seed-based fMRI connectivity analysis is often used for the studies, such analysis requires defining a seed location a priori, which restricts search scope and could bias findings toward presupposed areas. Recently, a comprehensive exploratory voxel-wise connectivity analysis, the connectome-wide association approach, has been introduced using multivariate distance matrix regression (MDMR) for resting-state functional connectivity analysis. The current study performed a connectome-wide investigation of resting-state functional connectivity for war veterans with and without PTSD compared to non-trauma-exposed healthy controls using MDMR.Thirty-five male combat veterans with PTSD (unmedicated), 18 male combat veterans without PTSD (veterans control, VC), and 28 age-matched non-trauma-exposed healthy males (NC) participated in a resting-state fMRI scan. MDMR analysis was used to identify between-groups differences in regions with altered connectivity. The identified regions were used as a seed for post-hoc functional connectivity analysis.The analysis revealed that PTSD patients had hypoconnectivity between the left lateral prefrontal regions and the salience network regions as well as hypoconnectivity between the parahippocampal gyrus and the visual cortex areas. Connectivity between the ventromedial prefrontal cortex and the middle frontal gyrus and between the parahippocampal gyrus and the anterior insula were negatively correlated with PTSD symptom severity. VC subjects also had altered functional connectivity compared to NC, including increased connectivity between the posterior insula and several brain regions and decreased connectivity between the precuneus region and several other brain areas.The decreased connectivity between the lateral prefrontal regions and the salience network regions in PTSD was consistent with previous reports that indicated lowered emotion-regulation function in these regions. The decreased connectivity between the parahippocampal gyrus and visual cortex supported the dual representation theory of PTSD, which suggests dissociation between sensory and contextual memory representations in PTSD. The theory also supposes that the precuneus is a region that triggers retrieval of sensory memory of traumatic events. The decreased connectivity at the precuneus for VC might be associated with suppressing such a process.
Fibre-specific white matter changes in multiple sclerosis patients with optic neuritis
Long term irreversible disability in multiple sclerosis (MS) is thought to be primarily driven by axonal degeneration. Axonal degeneration leads to degenerative atrophy, therefore early markers of axonal degeneration are required to predict clinical disability and treatment efficacy. Given that additional pathologies such as inflammation, demyelination and oedema are also present in MS, it is essential to develop axonal markers that are not confounded by these processes. The present study investigated a novel method for measuring axonal degeneration in MS based on high angular resolution diffusion magnetic resonance imaging. Unlike standard methods, this novel method involved advanced acquisition and modelling for improved axonal sensitivity and specificity. Recent work has developed analytical methods, two novel axonal markers, fibre density and cross-section, that can be estimated for each fibre direction in each voxel (termed a “fixel”). This technique, termed fixel-based analysis, thus simultaneously estimates axonal density and white matter atrophy from specific white matter tracts. Diffusion-weighted imaging datasets were acquired for 17 patients with a history of acute unilateral optic neuritis (35.3 ± 10.2 years, 11 females) and 14 healthy controls (32.7 ± 4.8 years, 8 females) on a 3 T scanner. Fibre density values were compared to standard diffusion tensor imaging parameters (fractional anisotropy and mean diffusivity) in lesions and normal appearing white matter. Group comparisons were performed for each fixel to assess putative differences in fibre density and fibre cross-section. Fibre density was observed to have a comparable sensitivity to fractional anisotropy for detecting white matter pathology in MS, but was not affected by crossing axonal fibres. Whole brain fixel-based analysis revealed significant reductions in fibre density and fibre cross-section in the inferior fronto-occipital fasciculus (including the optic radiations) of patients compared to controls. We interpret this result to indicate that this fixel-based approach is able to detect early loss of fibre density and cross-section in the optic radiations in MS patients with a history of optic neuritis. Fibre-specific markers of axonal degeneration should be investigated further for use in early stage therapeutic trials, or to monitor axonal injury in early stage MS.
Benthic meiofaunal community response to the cascading effects of herbivory within an algal halo system of the Great Barrier Reef
Benthic fauna play a crucial role in organic matter decomposition and nutrient cycling at the sediment-water boundary in aquatic ecosystems. In terrestrial systems, grazing herbivores have been shown to influence below-ground communities through alterations to plant distribution and composition, however whether similar cascading effects occur in aquatic systems is unknown. Here, we assess the relationship between benthic invertebrates and above-ground fish grazing across the ‘grazing halos’ of Heron Island lagoon, Australia. Grazing halos, which occur around patch reefs globally, are caused by removal of seagrass or benthic macroalgae by herbivorous fish that results in distinct bands of unvegetated sediments surrounding patch reefs. We found that benthic algal canopy height significantly increased with distance from patch reef, and that algal canopy height was positively correlated with the abundances of only one invertebrate taxon (Nematoda). Both sediment carbon to nitrogen ratios (C:N) and mean sediment particle size (μm) demonstrated a positive correlation with Nematoda and Arthropoda (predominantly copepod) abundances, respectively. These positive correlations indicate that environmental conditions are a major contributor to benthic invertebrate community distribution, acting on benthic communities in conjunction with the cascading effects of above-ground algal grazing. These results suggest that benthic communities, and the ecosystem functions they perform in this system, may be less responsive to changes in above-ground herbivorous processes than those previously studied in terrestrial systems. Understanding how above-ground organisms, and processes, affect their benthic invertebrate counterparts can shed light on how changes in aquatic communities may affect ecosystem function in previously unknown ways.
Molecular phylogeny of Panicum s. str. (Poaceae, Panicoideae, Paniceae) and insights into its biogeography and evolution
Panicum sensu stricto is a genus of grasses (Poaceae) with nearly, according to this study, 163 species distributed worldwide. This genus is included in the subtribe Panicinae together with Louisiella, the latter with 2 species. Panicum and subtribe Panicinae are characterized by including annual or perennial taxa with open and lax panicles, and spikelets with the lower glume reduced; all taxa also share a basic chromosome number of x = 9 and a Kranz leaf blade anatomy typical of the NAD-me subtype photosynthetic pathway. Nevertheless, the phylogenetic placements of many Panicum species, and the circumscription of the genus, remained untested. Therefore, phylogenetic analyses were conducted using sequence data from the ndhF plastid region, in an extensive worldwide sampling of Panicum and related genera, in order to infer evolutionary relationships and to provide a phylogenetic framework to review the classification of the genus. Diversification times, historical biogeography and evolutionary patterns of the life history (annual vs. perennial) in the subtribe and Panicum were also studied. Results obtained provide strong support for a monophyletic Panicum including 71 species and 7 sections, of which sections Arthragrostis and Yakirra are new in the genus; 7 new combinations are made here. Furthermore, 32 species traditionally assigned to Panicum were excluded from the genus, and discussed in other subtribes of Paniceae. Our study suggested that early diversification in subtribe Panicinae and Panicum occurred through the Early-Mid Miocene in the Neotropics, while the subsequent diversification of its sections mainly occurred in the Late Miocene-Pleistocene, involving multiple dispersals to all continents. Our analyses also showed that transition rates and changes between annual and perennial life history in Panicum were quite frequent, suggesting considerable lability of this trait. Changes of the life history, together with C4 photosynthesis, and the multiple dispersal events since the Mid Miocene, seem to have facilitated a widespread distribution of the genus. All these findings contribute to a better understanding of the systematics and evolution of Panicum.
Pharmacological Inhibition of Necroptosis Protects from Dopaminergic Neuronal Cell Death in Parkinson’s Disease Models
SummaryDysfunctions in mitochondrial dynamics and metabolism are common pathological processes associated with Parkinson’s disease (PD). It was recently shown that an inherited form of PD and dementia is caused by mutations in the OPA1 gene, which encodes for a key player in mitochondrial fusion and structure. iPSC-derived neural cells from these patients exhibited severe mitochondrial fragmentation, respiration impairment, ATP deficits, and heightened oxidative stress. Reconstitution of normal levels of OPA1 in PD-derived neural cells normalized mitochondria morphology and function. OPA1-mutated neuronal cultures showed reduced survival in vitro. Intriguingly, selective inhibition of necroptosis effectively rescued this survival deficit. Additionally, dampening necroptosis in MPTP-treated mice protected from DA neuronal cell loss. This human iPSC-based model captures both early pathological events in OPA1 mutant neural cells and the beneficial effects of blocking necroptosis, highlighting this cell death process as a potential therapeutic target for PD.
Regional association of pCASL-MRI with FDG-PET and PiB-PET in people at risk for autosomal dominant Alzheimer's disease
Autosomal dominant Alzheimer's disease (ADAD) is a small subset of Alzheimer's disease that is genetically determined with 100% penetrance. It provides a valuable window into studying the course of pathologic processes that leads to dementia. Arterial spin labeling (ASL) MRI is a potential AD imaging marker that non-invasively measures cerebral perfusion. In this study, we investigated the relationship of cerebral blood flow measured by pseudo-continuous ASL (pCASL) MRI with measures of cerebral metabolism (FDG PET) and amyloid deposition (Pittsburgh Compound B (PiB) PET). Thirty-one participants at risk for ADAD (age 39 ± 13 years, 19 females) were recruited into this study, and 21 of them received both MRI and FDG and PiB PET scans. Considerable variability was observed in regional correlations between ASL-CBF and FDG across subjects. Both regional hypo-perfusion and hypo-metabolism were associated with amyloid deposition. Cross-sectional analyses of each biomarker as a function of the estimated years to expected dementia diagnosis indicated an inverse relationship of both perfusion and glucose metabolism with amyloid deposition during AD development. These findings indicate that neurovascular dysfunction is associated with amyloid pathology, and also indicate that ASL CBF may serve as a sensitive early biomarker for AD. The direct comparison among the three biomarkers provides complementary information for understanding the pathophysiological process of AD.
The ERβ4 variant induces transformation of the normal breast mammary epithelial cell line MCF-10A; the ERβ variants ERβ2 and ERβ5 increase aggressiveness of TNBC by regulation of hypoxic signaling
Triple negative breast cancer (TNBC) still remains a challenge to treat in the clinic due to a lack of good targets for treatment. Although TNBC lacks expression of ERα, the expression of ERβ and its variants are detected quite frequently in this cancer type and can represent an avenue for treatment. We show that two of the variants of ERβ, namely ERβ2 and ERβ5, control aggressiveness of TNBC by regulating hypoxic signaling through stabilization of HIF-1α. RNA-seq of patient derived xenografts (PDX) from TNBC shows expression of ERβ2, ERβ4 and ERβ5 variants in more than half of the samples. Furthermore, expression of ERβ4 in the immortalized, normal mammary epithelial cell line MCF-10A that is resistant to tumorsphere formation caused transformation and development of tumorspheres. By contrast, ERβ1, ERβ2 or ERβ5 were unable to support tumorsphere formation. We have previously shown that all variants except ERβ1 stabilize HIF-1α but only ERβ4 appears to have the ability to transform normal mammary epithelial cells, pointing towards a unique property of ERβ4. We propose that ERβ variants may be good diagnostic tools and also serve as novel targets for treatment of breast cancer.
Co-circulation of different A. phagocytophilum variants within cattle herds and possible reservoir role for cattle
BackgroundAnaplasma phagocytophilum is a zoonotic tick-borne intracellular alpha-proteobacterium causing tick-borne fever, which leads to significant economic losses in domestic ruminants in Europe. Its epidemiological cycles are complex and reservoir host species of bovine strains have not yet been identified. Given that little genetic information is available on strains circulating within a defined bovine environment, our objective was to assess the genetic diversity of A. phagocytophilum obtained from the same farms over time.MethodsBlood samplings were performed several times in two European herds. In the French herd, 169 EDTA-blood samples were obtained from 115 cows (32 were sampled two to four times). In the German herd, 20 cows were sampled six times (120 EDTA-blood samples). The presence of A. phagocytophilum DNA was assessed using a qPCR targeting msp2. The positive DNA samples underwent MLST at nine genetic markers (typA, ctrA, msp4, pleD, recG, polA, groEL, gyrA, and ankA). For each locus, sequences were aligned with available bacterial sequences derived from cattle, horse, dog, and roe deer hosts, and concatenated neighbor joining trees were constructed using three to six loci.ResultsAround 20% (57/289) of samples were positive. Forty positive samples from 23 French and six German cows (11 of them being positive at two time points) were sequenced. Six loci (typA, ctrA, msp4, pleD, recG, and polA) allowed to build concatenated phylogenetic trees, which led to two distinct groups of bovine variants in the French herd (hereafter called A and B), whereas only group A was detected in the German herd. In 42% of French samples, double chromatogram peaks were encountered in up to four loci. Eleven cows were found infected three weeks to 17 months after first sampling and harboured a new variant belonging to one or the other group.ConclusionsOur results demonstrate the occurrence of two major bovine strain groups and the simultaneous infection of single cows by more than one A. phagocytophilum strain. This challenges the role of cattle as reservoirs for A. phagocytophilum. This role may be facilitated via long-term bacterial persistence in individual cows and active circulation at the herd scale.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-2661-7) contains supplementary material, which is available to authorized users.
Comparative genomic analysis of Lactobacillus plantarum GB-LP4 and identification of evolutionarily divergent genes in high-osmolarity environment
Lactobacillus plantarum is one of the widely-used probiotics and there have been a large number of advanced researches on the effectiveness of this species. However, the difference between previously reported plantarum strains, and the source of genomic variation among the strains were not clearly specified. In order to understand further on the molecular basis of L. plantarum on Korean traditional fermentation, we isolated the L. plantarum GB-LP4 from Korean fermented vegetable and conducted whole genome assembly. With comparative genomics approach, we identified the candidate genes that are expected to have undergone evolutionary acceleration. These genes have been reported to associate with the maintaining homeostasis, which are generally known to overcome instability in external environment including low pH or high osmotic pressure. Here, our results provide an evolutionary relationship between L. plantarum species and elucidate the candidate genes that play a pivotal role in evolutionary acceleration of GB-LP4 in high osmolarity environment. This study may provide guidance for further studies on L. plantarum.Electronic supplementary materialThe online version of this article (doi:10.1007/s13258-017-0555-2) contains supplementary material, which is available to authorized users.
Insect pathogenic fungi and bed bugs: behaviour, horizontal transfer and the potential contribution to IPM solutions
The increasing problem of bed bugs requires the development of new control strategies, and insect pathogenic fungi can contribute towards management. We used laboratory bioassays with Isaria fumosoroseus, Lecanicillium muscarium and Beauveria bassiana to evaluate their virulence to the bed bug. Only B. bassiana significantly affected bed bug survival and was dependent on dose and formulation. A 2% B. bassiana oil formulation induced horizontal transfer to elevate mortality in a 10-day arena bioassay. Temporal distribution of contagious individuals and increasing the dose from 2 to 4% did not increase mortality. Horizontal transfer mainly occurred between adults, and only partly between adults and nymphs. Bed bugs showed activity peaks during the night, and activity was increased by elevated levels of CO2. Distribution between harbourages was not affected by CO2 activation, level of infection or the bio-pesticide, and horizontal transfer was not dependent on the degree of aggregation. Movement in the arenas negatively affected horizontal transfer when the number of susceptible individuals was large. Level of infection also influenced behaviour as the bed bug movement increased with elevated disease burden. The use of fungi as a part of an integrated pest management strategy seems to be an interesting option that should be investigated further. B. bassiana kills bed bugs and can be carried to harbourages to target hidden individuals.
Lysozyme Counteracts β-Lactam Antibiotics by Promoting the Emergence of L-Form Bacteria
Summaryβ-lactam antibiotics inhibit bacterial cell wall assembly and, under classical microbiological culture conditions that are generally hypotonic, induce explosive cell death. Here, we show that under more physiological, osmoprotective conditions, for various Gram-positive bacteria, lysis is delayed or abolished, apparently because inhibition of class A penicillin-binding protein leads to a block in autolytic activity. Although these cells still then die by other mechanisms, exogenous lytic enzymes, such as lysozyme, can rescue viability by enabling the escape of cell wall-deficient “L-form” bacteria. This protective L-form conversion was also observed in macrophages and in an animal model, presumably due to the production of host lytic activities, including lysozyme. Our results demonstrate the potential for L-form switching in the host environment and highlight the unexpected effects of innate immune effectors, such as lysozyme, on antibiotic activity. Unlike previously described dormant persisters, L-forms can continue to proliferate in the presence of antibiotic.
Neural Networks Mediating High-Level Mentalizing in Patients With Right Cerebral Hemispheric Gliomas
Mentalizing is the ability to understand others’ mental state through external cues. It consists of two networks, namely low-level and high-level metalizing. Although it is an essential function in our daily social life, surgical resection of right cerebral hemisphere disturbs mentalizing processing with high possibility. In the past, little was known about the white matter related to high-level mentalizing, and the conservation of high-level mentalizing during surgery has not been a focus of attention. Therefore, the main purpose of this study was to examine the neural networks underlying high-level mentalizing and then, secondarily, investigate the usefulness of awake surgery in preserving the mentalizing network. A total of 20 patients with glioma localized in the right hemisphere who underwent awake surgery participated in this study. All patients were assigned to two groups: with or without intraoperative assessment of high-level mentalizing. Their high-level mentalizing abilities were assessed before surgery and 1 week and 3 months after surgery. At 3 months after surgery, only patients who received the intraoperative high-level mentalizing test showed the same score as normal healthy volunteers. The tract-based lesion symptom analysis was performed to confirm the severity of damage of associated fibers and high-level mentalizing accuracy. This analysis revealed the superior longitudinal fascicles (SLF) III and fronto-striatal tract (FST) to be associated with high-level mentalizing processing. Moreover, the voxel-based lesion symptom analysis demonstrated that resection of orbito-frontal cortex (OFC) causes persistent mentalizing dysfunction. Our study indicates that damage of the OFC and structural connectivity of the SLF and FST causes the disorder of mentalizing after surgery, and assessing high-level mentalizing during surgery may be useful to preserve these pathways.
Capture Hi-C identifies putative target genes at 33 breast cancer risk loci
Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. Here, we use Capture Hi-C (CHi-C) to annotate 63 loci; we identify 110 putative target genes at 33 loci. To assess the support for these target genes in other data sources we test for associations between levels of expression and SNP genotype (eQTLs), disease-specific survival (DSS), and compare them with somatically mutated cancer genes. 22 putative target genes are eQTLs, 32 are associated with DSS and 14 are somatically mutated in breast, or other, cancers. Identifying the target genes at GWAS risk loci will lead to a greater understanding of the mechanisms that influence breast cancer risk and prognosis.
Outcome of Pediatric Cataract Surgeries in a Tertiary Center in Switzerland
Purpose To determine and to analyze the outcome of pediatric cataract surgery. Methods A retrospective chart review of individuals aged up to 10 years who underwent cataract surgery between January 1, 2004, and December 31, 2014, at the UniversityHospital Zurich, Switzerland. Results 63 children (94 affected eyes) with bilateral (68/94) or unilateral (26/94) cataract were identified. Surgery was performed at a median age of 1.5 months (IQR: 1.3–2.6 months) for the aphakic group (45/94) and of 50.7 months (IQR: 38.0–78.4 months) for the IOL group (49/94). At the last follow-up visit (median 31.1 months, IQR: 18.4–50.2 months), visual acuity was better in bilateral than in unilateral cataract cases. Posterior capsular opacification (PCO) was diagnosed in 30.9% of eyes without a significant difference in the IOL and aphakic groups (p = 0.12). Aphakic glaucoma was diagnosed in 12/45 eyes at a median of 6.8 months (IQR 2.1–13.3 months) after surgery. Microcornea (5/12) and anterior segment anomalies (8/12) were associated with glaucoma development (p < 0.05). Conclusion Laterality and timing of surgery influence the outcome of pediatric cataract surgery. PCO was the most frequent postoperative complication. Aphakic glaucoma is often associated with ocular developmental abnormalities and a poor visual outcome.
Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China
Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing tropical microbial resources.
Altered Brain Functional Hubs and Connectivity in Type 2 Diabetes Mellitus Patients: A Resting-State fMRI Study
Type 2 diabetes mellitus (T2DM) affects a vast population and is closely associated with cognitive impairment. However, the mechanisms of cognitive impairment in T2DM patients have not been unraveled. Research on the basic units (nodes or hubs and edges) of the brain functional network on the basis of neuroimaging may advance our understanding of the network change pattern in T2DM patients. This study investigated the change patterns of brain functional hubs using degree centrality (DC) analysis and the connectivity among these hubs using functional connectivity and Granger causality analysis. Compared to healthy controls, the DC values were higher in the left anterior cingulate gyrus (ACG) and lower in the bilateral lateral occipital cortices (LOC) and right precentral gyrus (PreCG) in T2DM patients. The functional connectivity between the left ACG and the right PreCG was stronger in T2DM patients, whereas the functional connectivity among the right PreCG and bilateral LOC was weaker. A negative causal effect from the left ACG to left LOC and a positive effect from the left ACG to right LOC were observed in T2DM patients, while in healthy controls, the opposite occurred. Additionally, the reserve of normal brain function in T2DM patients was negatively associated with the elevated glycemic parameters. This study demonstrates that there are brain functional hubs and connectivity alterations that may reflect the aberrant information communication in the brain of T2DM patients. The findings may advance our understanding of the mechanisms of T2DM-related cognitive impairment.
Long-term health in recipients of transplanted in vitro propagated spermatogonial stem cells
AbstractSTUDY QUESTIONIs testicular transplantation of in vitro propagated spermatogonial stem cells associated with increased cancer incidence and decreased survival rates in recipient mice?SUMMARY ANSWERCancer incidence was not increased and long-term survival rate was not altered after transplantation of in vitro propagated murine spermatogonial stem cells (SSCs) in busulfan-treated recipients as compared to non-transplanted busulfan-treated controls.WHAT IS KNOWN ALREADYSpermatogonial stem cell autotransplantation (SSCT) is a promising experimental reproductive technique currently under development to restore fertility in male childhood cancer survivors. Most preclinical studies have focused on the proof-of-principle of the functionality and efficiency of this technique. The long-term health of recipients of SSCT has not been studied systematically.STUDY DESIGN, SIZE, DURATIONThis study was designed as a murine equivalent of a clinical prospective study design. Long-term follow-up was performed for mice who received a busulfan treatment followed by either an intratesticular transplantation of in vitro propagated enhanced green fluorescent protein (eGFP) positive SSCs (cases, n = 34) or no transplantation (control, n = 37). Using a power calculation, we estimated that 36 animals per group would be sufficient to provide an 80% power and with a 5% level of significance to demonstrate a 25% increase in cancer incidence in the transplanted group. The survival rate and cancer incidence was investigated until the age of 18 months.PARTICIPANTS/MATERIALS, SETTING, METHODSNeonatal male B6D2F1 actin-eGFP transgenic mouse testis were used to initiate eGFP positive germline stem (GS) cell culture, which harbor SSCs. Six-week old male C57BL/6 J mice received a single dose busulfan treatment to deplete the testis from endogenous spermatogenesis. Half of these mice received a testicular transplantation of cultured eGFP positive GS cells, while the remainder of mice served as a control group. Mice were followed up until the age of 18 months (497–517 days post-busulfan) or sacrificed earlier due to severe discomfort or illness. Survival data were collected. To evaluate cancer incidence a necropsy was performed and tissues were collected. eGFP signal in transplanted testis and in benign and malignant lesions was assessed by standard PCR.MAIN RESULTS AND THE ROLE OF CHANCEWe found 9% (95% CI: 2–25%) malignancies in the transplanted busulfan-treated animals compared to 26% (95% CI: 14–45%) in the busulfan-treated control group, indicating no statistically significant difference in incidence of malignant lesions in transplanted and control mice (OR: 0.3, 95% CI: 0.1–1.1). Furthermore, none of the malignancies that arose in the transplanted animals contained eGFP signal, suggesting that they are not derived from the in vitro propagated transplanted SSCs. Mean survival time after busulfan treatment was found to be equal, with a mean survival time for transplanted animals of 478 days and 437 days for control animals (P = 0.076).LARGE SCALE DATANA.LIMITATIONS, REASONS FOR CAUTIONAlthough we attempted to mimic the future clinical application of SSCT in humans as close as possible, the mouse model that we used might not reflect all aspects of the future clinical setting.WIDER IMPLICATIONS OF THE FINDINGSThe absence of an increase in cancer incidence and a decrease in survival of mice that received a testicular transplantation of in vitro propagated SSCs is reassuring in light of the future clinical application of SSCT in humans.STUDY FUNDING/COMPETING INTEREST(S)This study was funded by KiKa (Kika86) and ZonMw (TAS 116003002). The authors report no financial or other conflict of interest relevant to the subject of this article.
Hidden species diversity in Sylvirana nigrovittata (Amphibia: Ranidae) highlights the importance of taxonomic revisions in biodiversity conservation
Accurately delimiting species and their geographic ranges is imperative for conservation, especially in areas experiencing rapid habitat loss. Southeast Asia currently has one of the highest rates of deforestation in the world, is home to multiple biodiversity hotspots, and the majority of its countries have developing economies with limited resources for biodiversity conservation. Thus, accurately delimiting species and their ranges is particularly important in this region. We examined genetic and morphological variation in the widespread frog species Sylvirana nigrovittata (and its long-treated junior synonym S. mortenseni) with the goal of clarifying its taxonomic content and geographic range boundaries for conservation. We present evidence that the current concept of S. nigrovittata contains at least eight species, two of which are each known from only two localities, but that S. mortenseni is more geographically widespread than currently realized. Five of these species are described as new to science.
Temperature stress deteriorates bed bug (Cimex lectularius) populations through decreased survival, fecundity and offspring success
Sublethal heat stress may weaken bed bug infestations to potentially ease control. In the present study, experimental populations exposed to 34, 36 or 38°C for 2 or 3 weeks suffered significant mortality during exposure. Among survivors, egg production, egg hatching, moulting success and offspring proliferation decreased significantly in the subsequent 7 week recovery period at 22°C. The overall population success was negatively impacted by increasing temperature and duration of the stress. Such heat stress is inadequate as a single tool for eradication, but may be included as a low cost part of an integrated pest management protocol. Depending on the time available and infestation conditions, the success of some treatments can improve if sublethal heat is implemented prior to the onset of more conventional pest control measures.
The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors
Meristems contain groups of indeterminate stem cells, which are maintained by a feedback loop between CLAVATA (CLV) and WUSCHEL (WUS) signaling. CLV signaling involves the secretion of the CLV3 peptide and its perception by a number of Leucine-Rich-Repeat (LRR) receptors, including the receptor-like kinase CLV1 and the receptor-like protein CLV2 coupled with the CORYNE (CRN) pseudokinase. CLV2, and its maize ortholog FASCIATED EAR2 (FEA2) appear to function in signaling by CLV3 and several related CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide ligands. Nevertheless, how signaling specificity is achieved remains unknown. Here we show that FEA2 transmits signaling from two distinct CLE peptides, the maize CLV3 ortholog ZmCLE7 and ZmFON2-LIKE CLE PROTEIN1 (ZmFCP1) through two different candidate downstream effectors, the alpha subunit of the maize heterotrimeric G protein COMPACT PLANT2 (CT2), and ZmCRN. Our data provide a novel framework to understand how diverse signaling peptides can activate different downstream pathways through common receptor proteins.
Plasma and Mucosal Immunoglobulin M, Immunoglobulin A, and Immunoglobulin G Responses to the Vibrio cholerae O1 Protein Immunome in Adults With Cholera in Bangladesh
SummaryThis study is the first unbiased antibody-based immunoprofiling of immune responses against the Vibrio cholerae proteome, and has identified immunogenic antigens that induce systemic, mucosal, and memory responses.
Effects of gender, digit ratio, and menstrual cycle on intrinsic brain functional connectivity: A whole‐brain, voxel‐wise exploratory study using simultaneous local and global functional connectivity mapping
AbstractIntroductionGender and sex hormones influence brain function, but their effects on functional network organization within the brain are not yet understood.MethodsWe investigated the influence of gender, prenatal sex hormones (estimated by the 2D:4D digit ratio), and the menstrual cycle on the intrinsic functional network organization of the brain (as measured by 3T resting‐state functional MRI (rs‐fMRI)) using right‐handed, age‐matched university students (100 males and 100 females). The mean (±SD) age was 20.9 ± 1.5 (range: 18–24) years and 20.8 ± 1.3 (range: 18–24) years for males and females, respectively. Using two parameters derived from the normalized alpha centrality analysis (one for local and another for global connectivity strength), we created mean functional connectivity strength maps.ResultsThere was a significant difference between the male mean map and female mean map in the distributions of network properties in almost all cortical regions and the basal ganglia but not in the medial parietal, limbic, and temporal regions and the thalamus. A comparison between the mean map for the low 2D:4D digit ratio group (indicative of high exposure to testosterone during the prenatal period) and that for the high 2D:4D digit ratio group revealed a significant difference in the network properties of the medial parietal region for males and in the temporal region for females. The menstrual cycle affected network organization in the brain, which varied with the 2D:4D digit ratio. Most of these findings were reproduced with our other datasets created with different preprocessing steps.ConclusionsThe results suggest that differences in gender, prenatal sex hormone exposure, and the menstrual cycle are useful for understanding the normal brain and investigating the mechanisms underlying the variable prevalence and symptoms of neurological and psychiatric diseases.
Enhanced Amygdala-Striatal Functional Connectivity during the Processing of Cocaine Cues in Male Cocaine Users with a History of Childhood Trauma
Background and aimsChildhood trauma is associated with increased levels of anxiety later in life, an increased risk for the development of substance use disorders, and neurodevelopmental abnormalities in the amygdala and frontostriatal circuitry. The aim of this study was to investigate the (neurobiological) link among childhood trauma, state anxiety, and amygdala-frontostriatal activity in response to cocaine cues in regular cocaine users.MethodsIn this study, we included 59 non-treatment seeking regular cocaine users and 58 non-drug using controls. Blood oxygenation level-dependent responses were measured using functional magnetic resonance imaging while subjects performed a cue reactivity paradigm with cocaine and neutral cues. Psychophysiological interaction analyses were applied to assess functional connectivity between the amygdala and other regions in the brain. Self-report questionnaires were used to measure childhood trauma, state anxiety, drug use, drug use severity, and craving.ResultsNeural activation was increased during the presentation of cocaine cues, in a widespread network including the frontostriatal circuit and amygdala in cocaine users but not in controls. Functional coupling between the amygdala and medial prefrontal cortex was reduced in response to cocaine cues, in both cocaine users and controls, which was further diminished with increasing state anxiety. Importantly, amygdala-striatal connectivity was positively associated with childhood trauma in regular cocaine users, while there was a negative association in controls. At the behavioral level, state anxiety was positively associated with cocaine use severity and craving related to negative reinforcement.ConclusionChildhood trauma is associated with enhanced amygdala-striatal connectivity during cocaine cue reactivity in regular cocaine users, which may contribute to increased habit behavior and poorer cognitive control. While we cannot draw conclusions on causality, this study provides novel information on how childhood trauma may contribute to the development and persistence of cocaine use disorder.
Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens
Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.
Targeting experimental orthotopic glioblastoma with chitosan-based superparamagnetic iron oxide nanoparticles (CS-DX-SPIONs)
BackgroundGlioblastoma is the most devastating primary brain tumor of the central nervous system in adults. Magnetic nanocarriers may help not only for a targeted delivery of chemotherapeutic agents into the tumor site but also provide contrast enhancing properties for diagnostics using magnetic resonance imaging (MRI).MethodsSynthesized hybrid chitosan-dextran superparamagnetic nanoparticles (CS-DX-SPIONs) were characterized using transmission electron microscopy (TEM) and relaxometry studies. Nonlinear magnetic response measurements were employed for confirming the superparamagnetic state of particles. Following in vitro analysis of nanoparticles cellular uptake tumor targeting was assessed in the model of the orthotopic glioma in rodents.ResultsCS-DX-SPIONs nanoparticles showed a uniform diameter of 55 nm under TEM and superparamagentic characteristics as determined by T1 (spin-lattice relaxation time) and T2 (spin-spin relaxation time) proton relaxation times. Application of the chitosan increased the charge from +8.9 to +19.3 mV of the dextran-based SPIONs. The nonlinear magnetic response at second harmonic of CS-DX-SPIONs following the slow change of stationary magnetic fields with very low hysteresis evidenced superparamagnetic state of particles at ambient temperatures. Confocal microscopy and flow cytometry studies showed an enhanced internalization of the chitosan-based nanoparticles in U87, C6 glioma and HeLa cells as compared to dextran-coated particles. Cytotoxicity assay demonstrated acceptable toxicity profile of the synthesized nanoparticles up to a concentration of 10 μg/ml. Intravenously administered CS-DX-SPIONs in orthotopic C6 gliomas in rats accumulated in the tumor site as shown by high-resolution MRI (11.0 T). Retention of nanoparticles resulted in a significant contrast enhancement of the tumor image that was accompanied with a dramatic drop in T2 values (P<0.001). Subsequent histological studies proved the accumulation of the nanoparticles inside glioblastoma cells.ConclusionHybrid chitosan-dextran magnetic particles demonstrated high MR contrast enhancing properties for the delineation of the brain tumor. Due to a significant retention of the particles in the tumor an application of the CS-DX-SPIONs could not only improve the tumor imaging but also could allow a targeted delivery of chemotherapeutic agents.
Resistance to the Antiproliferative In Vitro Effect of PI3K-Akt-mTOR Inhibition in Primary Human Acute Myeloid Leukemia Cells Is Associated with Altered Cell Metabolism
Constitutive signaling through the phosphatidylinositol-3-kinase-Akt-mechanistic target of rapamycin (PI3K-Akt-mTOR) pathway is present in acute myeloid leukemia (AML) cells. However, AML is a heterogeneous disease, and we therefore investigated possible associations between cellular metabolism and sensitivity to PI3K-Akt-mTOR pathway inhibitors. We performed non-targeted metabolite profiling to compare the metabolome differences of primary human AML cells derived from patients susceptible or resistant to the in vitro antiproliferative effects of mTOR and PI3K inhibitors. In addition, the phosphorylation status of 18 proteins involved in PI3K-Akt-mTOR signaling and the effect of the cyclooxygenase inhibitor indomethacin on their phosphorylation status was investigated by flow cytometry. Strong antiproliferative effects by inhibitors were observed only for a subset of patients. We compared the metabolite profiles for responders and non-responders towards PI3K-mTOR inhibitors, and 627 metabolites could be detected. Of these metabolites, 128 were annotated and 15 of the annotated metabolites differed significantly between responders and non-responders, including metabolites involved in energy, amino acid, and lipid metabolism. To conclude, leukemia cells that are susceptible or resistant to PI3K-Akt-mTOR inhibitors differ in energy, amino acid, and arachidonic acid metabolism, and modulation of arachidonic acid metabolism alters the activation of mTOR and its downstream mediators.
Histone Deacetylase Inhibitor Induced Radiation Sensitization Effects on Human Cancer Cells after Photon and Hadron Radiation Exposure
Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor, which has been widely utilized throughout the cancer research field. SAHA-induced radiosensitization in normal human fibroblasts AG1522 and lung carcinoma cells A549 were evaluated with a combination of γ-rays, proton, and carbon ion exposure. Growth delay was observed in both cell lines during SAHA treatment; 2 μM SAHA treatment decreased clonogenicity and induced cell cycle block in G1 phase but 0.2 μM SAHA treatment did not show either of them. Low LET (Linear Energy Transfer) irradiated A549 cells showed radiosensitization effects on cell killing in cycling and G1 phase with 0.2 or 2 μM SAHA pretreatment. In contrast, minimal sensitization was observed in normal human cells after low and high LET radiation exposure. The potentially lethal damage repair was not affected by SAHA treatment. SAHA treatment reduced the rate of γ-H2AX foci disappearance and suppressed RAD51 and RPA (Replication Protein A) focus formation. Suppression of DNA double strand break repair by SAHA did not result in the differences of SAHA-induced radiosensitization between human cancer cells and normal cells. In conclusion, our results suggest SAHA treatment will sensitize cancer cells to low and high LET radiation with minimum effects to normal cells.
Relationship between muscarinic M1 receptor binding and cognition in medication-free subjects with psychosis☆
BackgroundIt is still unclear which underlying mechanisms are involved in cognitive deficits of psychotic disorders. Pro-cognitive effects of muscarinic M1 receptor agonists suggest alterations in M1 receptor functioning may modulate these symptoms. Post mortem studies in patients with schizophrenia have shown significantly reduced M1 receptor expression rates in the dorsolateral prefrontal cortex (DLPFC) compared to controls. To date no in-vivo examinations of M1 receptor binding in relation to cognitive impairments have been done. As cognitive deficits have similar course and prognostic relevance across psychotic disorders, the current study assessed M1 receptor binding in the DLPFC and hippocampus in relation to cognitive functioning.MethodsMuscarinic M1 receptor binding potential (BPND) was measured using 123I-IDEX, single photon emission computed tomography (SPECT) in 30 medication-free subjects diagnosed with a psychotic disorder. A computerized neuropsychological test battery was used to assess cognition, and the positive and negative syndrome scale (PANSS) to assess severity of psychotic symptoms.ResultsAssessment of cognitive domains showed that lower M1 BPND in the DLPFC was related to overall lower performance in verbal learning and memory. In addition, lower M1 BPND in the DLPFC was related to greater negative symptom severity. Lastly, lower M1 BPND in the hippocampus was related to worse delayed recognition of verbal memory.ConclusionThis is the first study to show that variation in M1 receptors in the DLPFC is related to cognitive and negative symptom outcome in psychotic disorders. The M1 receptor may be an important biomarker in biological stratification of patients with psychotic disorders.
Effectiveness of a complex intervention on Prioritising Multimedication in Multimorbidity (PRIMUM) in primary care: results of a pragmatic cluster randomised controlled trial
ObjectivesInvestigate the effectiveness of a complex intervention aimed at improving the appropriateness of medication in older patients with multimorbidity in general practice.DesignPragmatic, cluster randomised controlled trial with general practice as unit of randomisation.Setting72 general practices in Hesse, Germany.Participants505 randomly sampled, cognitively intact patients (≥60 years, ≥3 chronic conditions under pharmacological treatment, ≥5 long-term drug prescriptions with systemic effects); 465 patients and 71 practices completed the study.InterventionsIntervention group (IG): The healthcare assistant conducted a checklist-based interview with patients on medication-related problems and reconciled their medications. Assisted by a computerised decision support system, the general practitioner optimised medication, discussed it with patients and adjusted it accordingly. The control group (CG) continued with usual care.Outcome measuresThe primary outcome was a modified Medication Appropriateness Index (MAI, excluding item 10 on cost-effectiveness), assessed in blinded medication reviews and calculated as the difference between baseline and after 6 months; secondary outcomes after 6 and 9 months’ follow-up: quality of life, functioning, medication adherence, and so on.ResultsAt baseline, a high proportion of patients had appropriate to mildly inappropriate prescriptions (MAI 0–5 points: n=350 patients). Randomisation revealed balanced groups (IG: 36 practices/252 patients; CG: 36/253). Intervention had no significant effect on primary outcome: mean MAI sum scores decreased by 0.3 points in IG and 0.8 points in CG, resulting in a non-significant adjusted mean difference of 0.7 (95% CI −0.2 to 1.6) points in favour of CG. Secondary outcomes showed non-significant changes (quality of life slightly improved in IG but continued to decline in CG) or remained stable (functioning, medication adherence).ConclusionsThe intervention had no significant effects. Many patients already received appropriate prescriptions and enjoyed good quality of life and functional status. We can therefore conclude that in our study, there was not enough scope for improvement.Trial registration numberISRCTN99526053. NCT01171339; Results.
Targeted metabolomic profiling in rat tissues reveals sex differences
Sex differences affect several diseases and are organ-and parameter-specific. In humans and animals, sex differences also influence the metabolism and homeostasis of amino acids and fatty acids, which are linked to the onset of diseases. Thus, the use of targeted metabolite profiles in tissues represents a powerful approach to examine the intermediary metabolism and evidence for any sex differences. To clarify the sex-specific activities of liver, heart and kidney tissues, we used targeted metabolomics, linear discriminant analysis (LDA), principal component analysis (PCA), cluster analysis and linear correlation models to evaluate sex and organ-specific differences in amino acids, free carnitine and acylcarnitine levels in male and female Sprague-Dawley rats. Several intra-sex differences affect tissues, indicating that metabolite profiles in rat hearts, livers and kidneys are organ-dependent. Amino acids and carnitine levels in rat hearts, livers and kidneys are affected by sex: male and female hearts show the greatest sexual dimorphism, both qualitatively and quantitatively. Finally, multivariate analysis confirmed the influence of sex on the metabolomics profiling. Our data demonstrate that the metabolomics approach together with a multivariate approach can capture the dynamics of physiological and pathological states, which are essential for explaining the basis of the sex differences observed in physiological and pathological conditions.
Effect of leukocyte-reduced platelet-rich plasma on osteoarthritis caused by cranial cruciate ligament rupture: A canine gait analysis model
The goal of this study was to objectively assess the effect of a platelet-rich plasma (PRP) derivate in English bulldogs with stifle degenerative joint disease secondary to cranial cruciate ligament rupture (CCLR). We used a force platform and affixed electrogoniometers to measure peak vertical force (PVF), vertical impulse (VI), stance time (ST), and angular range of motion (AROM), from 12 lame client-owned English bulldogs with post-CCLR stifle joint abnormalities. The 12 affected subjects were treated with 4 intra-articular injections of PRP, at 30-day intervals. Ten untreated, sound English bulldogs were used as a reference group. Clinical outcomes were evaluated using a linear mixed effects model. Mean values of PVF, VI, ST, and AROM were improved within the first 3 months post-treatment in the CCLR group, with mean measured changes increasing to maximum 4.56% body weight gain, 1.5% body weight/second, 0.07 seconds, and 6.18 degrees, respectively. The effects declined progressively after the treatment interval, ending at nearly initial levels after 6 months. This study demonstrates that dogs with CCLR treated with intra-articular PRP had improved PVF, VI, ST, and AROM over time; the duration of effect was waning by the end of the post-treatment period.
From cellulose to kerogen: molecular simulation of a geological process††Electronic supplementary information (ESI) available: Fig. S1–S6 and Tables S1 and S2. See DOI: 10.1039/c7sc03466k
Accelerated reactive molecular dynamics simulations reveal the complex geological conversion path of organic matter into porous carbon (kerogen) and gas.
IL-6 and IL-10 are associated with good prognosis in early stage invasive breast cancer patients
Macrophage-associated cytokines play an important role in cancer metastasis; however, the functions of interleukins (IL) 6 and 10 in breast cancer (BC) progression and metastasis are not clear. In this study the roles of IL-6/IL-10 in regulating vascular invasion and their prognostic significance in BC are investigated. MDA-MB-231 and MCF-7 migration (± IL-6 or IL-10) was assessed by scratch wound assay. Cancer cell adhesion to IL-6/IL-10 stimulated blood and lymphatic endothelial cells (EC) was investigated. Expression of IL-6 /IL-10 was assessed using immunohistochemistry in an annotated cohort of early stage BC (n = 1380) and associations with clinicopathological variables and clinical outcome evaluated. IL-6 did not alter BC cell migration however a dose-dependent inhibition in MDA-MB-231 migration with IL-10 treatment was observed (P = 0.03). BC cells were more adhesive to blood vs lymphatic EC, however, IL-6/IL-10 had no effect on adhesion patterns. High expression of IL-6/IL-10 was associated with clinicopathological criteria (e.g. hormone receptor status, all P < 0.05), improved disease-free survival (DFS; P < 0.05) and improved BC-specific survival (BCSS; only IL-6, P = 0.017). However, neither IL-6 nor IL-10 expression were independent prognostic factors from multivariate analysis. In BC subgroups, IL-6 and IL-10 were good prognosticators in terms of DFS in non-basal, non-triple-negative (non-TN), ER-positive, PgR-positive (only IL-10), and Her-2-negative (only IL-6) BC (all P < 0.05). IL-6 was associated with improved BCSS in non-basal, ER-positive and non-TN BC (all P < 0.05).Electronic supplementary materialThe online version of this article (10.1007/s00262-017-2106-8) contains supplementary material, which is available to authorized users.
Functional Hemispheric (A)symmetries in the Aged Brain—Relevance for Working Memory
Functional hemispheric asymmetries have been described in different cognitive processes, such as decision-making and motivation. Variations in the pattern of left/right activity have been associated with normal brain functioning, and with neuropsychiatric diseases. Such asymmetries in brain activity evolve throughout life and are thought to decrease with aging, but clear associations with cognitive function have never been established. Herein, we assessed functional laterality during a working memory task (N-Back) in a healthy aging cohort (over 50 years old) and associated these asymmetries with performance in the test. Activity of lobule VI of the cerebellar hemisphere and angular gyrus was found to be lateralized to the right hemisphere, while the precentral gyrus presented left > right activation during this task. Interestingly, 1-Back accuracy was positively correlated with left > right superior parietal lobule activation, which was mostly due to the influence of the left hemisphere. In conclusion, although regions were mostly symmetrically activated during the N-Back task, performance in working memory in aged individuals seems to benefit from lateralized involvement of the superior parietal lobule.
A Set of Functional Brain Networks for the Comprehensive Evaluation of Human Characteristics
Many human characteristics must be evaluated to comprehensively understand an individual, and measurements of the corresponding cognition/behavior are required. Brain imaging by functional MRI (fMRI) has been widely used to examine brain function related to human cognition/behavior. However, few aspects of cognition/behavior of individuals or experimental groups can be examined through task-based fMRI. Recently, resting state fMRI (rs-fMRI) signals have been shown to represent functional infrastructure in the brain that is highly involved in processing information related to cognition/behavior. Using rs-fMRI may allow diverse information about the brain through a single MRI scan to be obtained, as rs-fMRI does not require stimulus tasks. In this study, we attempted to identify a set of functional networks representing cognition/behavior that are related to a wide variety of human characteristics and to evaluate these characteristics using rs-fMRI data. If possible, these findings would support the potential of rs-fMRI to provide diverse information about the brain. We used resting-state fMRI and a set of 130 psychometric parameters that cover most human characteristics, including those related to intelligence and emotional quotients and social ability/skill. We identified 163 brain regions by VBM analysis using regression analysis with 130 psychometric parameters. Next, using a 163 × 163 correlation matrix, we identified functional networks related to 111 of the 130 psychometric parameters. Finally, we made an 8-class support vector machine classifiers corresponding to these 111 functional networks. Our results demonstrate that rs-fMRI signals contain intrinsic information about brain function related to cognition/behaviors and that this set of 111 networks/classifiers can be used to comprehensively evaluate human characteristics.
Chronic voluntary oral methamphetamine induces deficits in spatial learning and hippocampal protein kinase Mzeta with enhanced astrogliosis and cyclooxygenase-2 levels
Methamphetamine (MA) is an addictive drug with neurotoxic effects on the brain producing cognitive impairment and increasing the risk for neurodegenerative disease. Research has focused largely on examining the neurochemical and behavioral deficits induced by injecting relatively high doses of MA [30 mg/kg of body weight (bw)] identifying the upper limits of MA-induced neurotoxicity. Accordingly, we have developed an appetitive mouse model of voluntary oral MA administration (VOMA) based on the consumption of a palatable sweetened oatmeal mash containing a known amount of MA. This VOMA model is useful for determining the lower limits necessary to produce neurotoxicity in the short-term and long-term as it progresses over time. We show that mice consumed on average 1.743 mg/kg bw/hour during 3 hours, and an average of 5.23 mg/kg bw/day over 28 consecutive days on a VOMA schedule. Since this consumption rate is much lower than the neurotoxic doses typically injected, we assessed the effects of long-term chronic VOMA on both spatial memory performance and on the levels of neurotoxicity in the hippocampus. Following 28 days of VOMA, mice exhibited a significant deficit in short-term spatial working memory and spatial reference learning on the radial 8-arm maze (RAM) compared to controls. This was accompanied by a significant decrease in memory markers protein kinase Mzeta (PKMζ), calcium impermeable AMPA receptor subunit GluA2, and the post-synaptic density 95 (PSD-95) protein in the hippocampus. Compared to controls, the VOMA paradigm also induced decreases in hippocampal levels of dopamine transporter (DAT) and tyrosine hydroxylase (TH), as well as increases in dopamine 1 receptor (D1R), glial fibrillary acidic protein (GFAP) and cyclooxygenase-2 (COX-2), with a decrease in prostaglandins E2 (PGE2) and D2 (PGD2). These results demonstrate that chronic VOMA reaching 146 mg/kg bw/28d induces significant hippocampal neurotoxicity. Future studies will evaluate the progression of this neurotoxic state.
Connectomic markers of symptom severity in sport-related concussion: Whole-brain analysis of resting-state fMRI
Concussion is associated with significant adverse effects within the first week post-injury, including physical complaints and altered cognition, sleep and mood. It is currently unknown whether these subjective disturbances have reliable functional brain correlates. Resting-state functional magnetic resonance imaging (rs-fMRI) has been used to measure functional connectivity of individuals after traumatic brain injury, but less is known about the relationship between functional connectivity and symptom assessments after a sport concussion. In this study, rs-fMRI was used to evaluate whole-brain functional connectivity for seventy (70) university-level athletes, including 35 with acute concussion and 35 healthy matched controls. Univariate analyses showed that greater symptom severity was mainly associated with lower pairwise connectivity in frontal, temporal and insular regions, along with higher connectivity in a sparser set of cerebellar regions. A novel multivariate approach also extracted two components that showed reliable covariation with symptom severity: (1) a network of frontal, temporal and insular regions where connectivity was negatively correlated with symptom severity (replicating the univariate findings); and (2) a network with anti-correlated elements of the default-mode network and sensorimotor system, where connectivity was positively correlated with symptom severity. These findings support the presence of connectomic signatures of symptom complaints following a sport-related concussion, including both increased and decreased functional connectivity within distinct functional brain networks.
Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation
A congeneric series of 21 phosphodiesterase 2 (PDE2) inhibitors are reported. Crystal structures show how the molecules can occupy a ‘top-pocket’ of the active site. Molecules with small substituents do not enter the pocket, a critical leucine (Leu770) is closed and water molecules are present. Large substituents enter the pocket, opening the Leu770 conformation and displacing the waters. We also report an X-ray structure revealing a new conformation of the PDE2 active site domain. The relative binding affinities of these compounds were studied with free energy perturbation (FEP) methods and it represents an attractive real-world test case. In general, the calculations could predict the energy of small-to-small, or large-to-large molecule perturbations. However, accurately capturing the transition from small-to-large proved challenging. Only when using alternative protein conformations did results improve. The new X-ray structure, along with a modelled dimer, conferred stability to the catalytic domain during the FEP molecular dynamics (MD) simulations, increasing the convergence and thereby improving the prediction of ΔΔG of binding for some small-to-large transitions. In summary, we found the most significant improvement in results when using different protein structures, and this data set is useful for future free energy validation studies.
Executive control processes are associated with individual fitness outcomes following regular exercise training: blood lactate profile curves and neuroimaging findings
Cardiovascular training has been associated with neuroimaging correlates of executive control functions (ECF) in seniors and children/adolescents, while complementary studies in middle-aged populations are lacking. Ascribing a prominent role to cardiorespiratory fitness improvements, most studies concentrated on training-induced gains in maximal oxygen uptake (VO2max), although other fitness indices may provide complementary information. Here, we investigated the impact of long-term sub-maximal exercise training on interference control, considering individual training-induced shifts in blood lactate profile curves (BLC) and VO2max. Twenty-three middle-aged sedentary males (M = 49 years) underwent a six-month exercise program (intervention group, IG). Additionally, 14 individuals without exercise training were recruited (control group, CG, M = 52 years). Interference control was assessed before and after the intervention, using a functional magnetic resonance imaging (fMRI) flanker paradigm. Task performance and brain activations showed no significant group-by-time interactions. However, regression analyses in the IG revealed significant associations between individual fitness gains and brain activation changes in frontal regions, which were not evident for VO2max, but for BLC. In conclusion, training-induced plasticity of ECF-related brain activity can be observed in late middle adulthood, but depends on individual fitness gains. For moderate training intensities, BLC shifts may provide sensitive markers for training-induced adaptations linked to ECF-related brain function.
Mps1 Phosphorylates Its N-Terminal Extension to Relieve Autoinhibition and Activate the Spindle Assembly Checkpoint
SummaryMonopolar spindle 1 (Mps1) is a conserved apical kinase in the spindle assembly checkpoint (SAC) that ensures accurate segregation of chromosomes during mitosis. Mps1 undergoes extensive auto- and transphosphorylation, but the regulatory and functional consequences of these modifications remain unclear. Recent findings highlight the importance of intermolecular interactions between the N-terminal extension (NTE) of Mps1 and the Hec1 subunit of the NDC80 complex, which control Mps1 localization at kinetochores and activation of the SAC. Whether the NTE regulates other mitotic functions of Mps1 remains unknown. Here, we report that phosphorylation within the NTE contributes to Mps1 activation through relief of catalytic autoinhibition that is mediated by the NTE itself. Moreover, we find that this regulatory NTE function is independent of its role in Mps1 kinetochore recruitment. We demonstrate that the NTE autoinhibitory mechanism impinges most strongly on Mps1-dependent SAC functions and propose that Mps1 activation likely occurs sequentially through dimerization of a “prone-to-autophosphorylate” Mps1 conformer followed by autophosphorylation of the NTE prior to maximal kinase activation segment trans-autophosphorylation. Our observations underline the importance of autoregulated Mps1 activity in generation and maintenance of a robust SAC in human cells.
Neonatal exposure to hyperoxia leads to persistent disturbances in pulmonary histone signatures associated with NOS3 and STAT3 in a mouse model
BackgroundEarly pulmonary oxygen exposure is one of the most important factors implicated in the development of bronchopulmonary dysplasia (BPD).MethodsHere, we analyzed short- and long-term effects of neonatal hyperoxia on NOS3 and STAT3 expression and corresponding epigenetic signatures using a hyperoxia-based mouse model of BPD.ResultsEarly hyperoxia exposure led to a significant increase in NOS3 (median fold change × 2.37, IQR 1.54–3.68) and STAT3 (median fold change × 2.83, IQR 2.21–3.88) mRNA levels in pulmonary endothelial cells with corresponding changes in histone modification patterns such as H2aZac and H3K9ac hyperacetylation at the respective gene loci. No complete restoration in histone signatures at these loci was observed, and responsivity to later hyperoxia was altered in mouse lungs. In vitro, histone signatures in human aortic endothelial cells (HAEC) remained altered for several weeks after an initial long-term exposure to trichostatin A. This was associated with a substantial increase in baseline eNOS (median 27.2, IQR 22.3–35.6) and STAT3α (median 5.8, IQR 4.8–7.3) mRNA levels with a subsequent significant reduction in eNOS expression upon exposure to hypoxia.ConclusionsEarly hyperoxia induced permanent changes in histones signatures at the NOS3 and STAT3 gene locus might partly explain the altered vascular response patterns in children with BPD.
PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
BackgroundWith the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important. So far, there are no suitable toolkits that can effectively link the chemical and biological space in view of molecular representation. To further explore these complex data, an integrated toolkit for various molecular representation is urgently needed which could be easily integrated with data mining algorithms to start a full data analysis pipeline.ResultsHerein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions. PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. The current version of PyBioMed could calculate 775 chemical descriptors and 19 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA descriptors from nucleotide sequences, and interaction descriptors from pairwise samples using three different combining strategies. Several examples and five real-life applications were provided to clearly guide the users how to use PyBioMed as an integral part of data analysis projects. By using PyBioMed, users are able to start a full pipelining from getting molecular data, pretreating molecules, molecular representation to constructing machine learning models conveniently.ConclusionPyBioMed provides various user-friendly and highly customized APIs to calculate various features of biological molecules and complex interaction samples conveniently, which aims at building integrated analysis pipelines from data acquisition, data checking, and descriptor calculation to modeling. PyBioMed is freely available at http://projects.scbdd.com/pybiomed.html.
Brain Volume Differences Associated With Hearing Impairment in Adults
Speech comprehension depends on the successful operation of a network of brain regions. Processing of degraded speech is associated with different patterns of brain activity in comparison with that of high-quality speech. In this exploratory study, we studied whether processing degraded auditory input in daily life because of hearing impairment is associated with differences in brain volume. We compared T1-weighted structural magnetic resonance images of 17 hearing-impaired (HI) adults with those of 17 normal-hearing (NH) controls using a voxel-based morphometry analysis. HI adults were individually matched with NH adults based on age and educational level. Gray and white matter brain volumes were compared between the groups by region-of-interest analyses in structures associated with speech processing, and by whole-brain analyses. The results suggest increased gray matter volume in the right angular gyrus and decreased white matter volume in the left fusiform gyrus in HI listeners as compared with NH ones. In the HI group, there was a significant correlation between hearing acuity and cluster volume of the gray matter cluster in the right angular gyrus. This correlation supports the link between partial hearing loss and altered brain volume. The alterations in volume may reflect the operation of compensatory mechanisms that are related to decoding meaning from degraded auditory input.
Methotrexate sensitizes drug-resistant metastatic melanoma cells to BRAF V600E inhibitors dabrafenib and encorafenib
Acquired resistance of metastatic melanoma (MM) tumors to BRAF V600E inhibitors (BRAFi’s) is commonplace in the clinic. Habitual relapse of patients contributes to <20% 5-year survival rates in MM. We previously identified serine synthesis as a critical detrminant of late-stage cancer cell resistance to BRAFi’s. Pre-treatment with DNA damaging agent gemcitabine (a nucleoside analog) re-sensitized drug-resistant cancer cells to BRAFi’s dabrafenib and vemurafenib. Importantly, the combination treatments were effective against BRAF wild type cancer cells potentially expanding the clinical reach of BRAFi’s. In this study, we identify the antifolate methotrexate (MTX) as a sensitizer of acquired- and intrinsically-resistant MM cells to BRAFi’s dabrafenib and encorafenib. We identify a novel, positive correlation between dabrafenib treatments and repair delay of MTX induced single-strand DNA (ssDNA) breaks. Cells arrest in G1 phase following simultaneous MTX + dabrafenib treatments and eventually die via apoptosis. Importantly, we identify RAS codon 12 activating mutations as prognostic markers for MTX + BRAFi treatment efficacy. We describe a method of killing drug-resistant MM cells that if translated has the potential to improve MM patient survival.
Preferential binding of fullerene and fullerenol with the N-terminal and middle regions of amyloid beta peptide: an in silico investigation
Amyloid beta (Aβ) deposits are implicated in the pathogenesis of debilitating neurodegenerative disorders such as Alzheimer’s disease. In the present study, the interactions of carbon-based nanoparticles (NPs) such as fullerene and fullerenol having different surface chemistry with Aβ were investigated using molecular dynamics simulations and docking studies. A detailed analysis of docking results showed that in 68% of the Aβ conformations, fullerene and fullerenol showed interactions with the N-terminal region of the peptide. However, the high-affinity binding site (E=−48.31 kJ/mol) of fullerene resides in the hydrophobic middle region of the peptide, whereas fullerenol interacts favorably with the charged N-terminal region with a binding energy of −50.42 kJ/mol. The above differences in binding could be attributed to the surface chemistry of fullerene and fullerenol. Moreover, the N-terminal and middle regions of Aβ play an important role in Aβ aggregation. Therefore, the binding of fullerene and fullerenol could inhibit amyloid aggregation. This information will be helpful in designing NPs for targeting amyloid-related disorders.
Structural insights into drug development strategy targeting EGFR T790M/C797S
Treatment of non-small-cell lung cancers (NSCLCs) harboring primary EGFR oncogenic mutations such as L858R and exon 19 deletion delE746_A750 (Del-19) using gefitinib/erlotinib ultimately fails due to the emergence of T790M mutation. Though WZ4002/CO-1686/AZD9291 are effective in overcoming EGFR T790M by targeting Cys797 via covalent bonding, their efficacy is again limited due to the emergence of C797S mutation. New agents effectively inhibiting EGFR T790M without covalent linkage through Cys 797 may solve this problem. We presented here crystal structures of EGFR activating/drug-resistant mutants in complex with a panel of reversible inhibitors along with mutagenesis and enzyme kinetic data. These data revealed a previously un-described hydrophobic clamp structure in the EGFR kinase which may be exploited to facilitate development of next generation drugs targeting EGFR T790M with or without concomitant C797S. Interestingly, mutations in the hydrophobic clamp that hinder drug binding often also weaken ATP binding and/or abolish kinase activity, thus do not readily result in resistance to the drugs.
Clinical Application of Foci Contralateral Facial Artery Myomucosal Flap for Tongue Defect Repair
Summary:This study aims to investigate the clinical efficacy of foci contralateral facial artery myomucosal flap (FAMF) in repairing the defect of tongue after tumor resection. There were 10 cases who received the operation to repair tongue tissue defects caused by tumor resection from January 2010 to January 2016. FAMF flap size ranged from 2.5 × 3 cm to 5 × 5 cm. All flaps survived after surgery, and no local necrosis occurred. For the donor and receptor sites of 10 cases, 8 cases got wounds healed at stage I, wound dehiscence of donor site occurred in 2 cases, and the dehisced wounds were healed after local cleaning. All 10 patients were followed up for 13 months to 5 years, with an average of 2 years and 4 months. No obvious deformity appeared on face after surgery, and there was no mouth floor leakage. After surgery, 3 cases had clinical manifestations of facial nerve marginal mandibular branch injury and returned to normal in 3 months. All patients had a limitation for mouth opening after surgery, 9 cases returned to normal after 1 year, and 1 case still had a mild limitation for mouth opening. There was no impact on patients’ eating, swallowing, language, or other functions. The foci contralateral FAMF surgery is simple and brings ideal plastic effect, high survival rate of flap, less donor site lesion, simple postoperative care, no breaking after surgery, and no impact on radical cure of tumor, which is suitable for repairing defect of tongue.
Linear and inverted U-shaped dose-response functions describe estrogen effects on hippocampal activity in young women
In animals, 17-beta-estradiol (E2) enhances hippocampal plasticity in a dose-dependent, monotonically increasing manner, but this relationship can also exhibit an inverted U-shaped function. To investigate E2’s dose-response function in the human hippocampus, we pharmacologically increased E2 levels in 125 naturally cycling women (who were in their low-hormone menstruation phase) to physiological (equivalent to menstrual cycle peak) and supraphysiological (equivalent to levels during early pregnancy) concentrations in a placebo-controlled design. Twenty-four hours after first E2 intake, we measured brain activity during encoding of neutral and negative pictures and then tested recognition memory 24 h after encoding. Here we report that E2 exhibits both a monotonically increasing relationship with hippocampal activity as well as an inverted U-shaped relationship, depending on the hippocampal region. Hippocampal activity exhibiting a U-shaped relationship inflects at supraphysiological E2 levels, suggesting that while E2 within physiological ranges stimulates hippocampal activity, supraphysiological ranges show opposite effects.
Spatial distribution of leprosy in India: an ecological study
BackgroundAs leprosy elimination becomes an increasingly realistic goal, it is essential to determine the factors that contribute to its persistence. We evaluate social and economic factors as predictors of leprosy annual new case detection rates within India, where the majority of leprosy cases occur.MethodsWe used correlation and linear mixed effect regressions to assess whether poverty, illiteracy, nighttime satellite radiance (an index of development), and other covariates can explain district-wise annual new case detection rate and Grade 2 disability diagnoses.ResultsWe find only weak evidence of an association between poverty and annual new case detection rates at the district level, though illiteracy and satellite radiance are statistically significant predictors of leprosy at the district level. We find no evidence of rapid decline over the period 2008–2015 in either new case detection or new Grade 2 disability.ConclusionsOur findings suggest a somewhat higher rate of leprosy detection, on average, in poorer districts; the overall effect is weak. The divide between leprosy case detection and true incidence of clinical leprosy complicates these results, particularly given that the detection rate is likely disproportionately lower in impoverished settings. Additional information is needed to distinguish the determinants of leprosy case detection and transmission during the elimination epoch.
Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains
Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8–89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes (hsrA and dfrG, respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus. Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis.
Evolutionary Mechanisms of Varying Chromosome Numbers in the Radiation of Erebia Butterflies
The evolution of intrinsic barriers to gene flow is a crucial step in the process of speciation. Chromosomal changes caused by fusion and fission events are one such barrier and are common in several groups of Lepidoptera. However, it remains unclear if and how chromosomal changes have contributed to speciation in this group. I tested for a phylogenetic signal of varying chromosome numbers in Erebia butterflies by combining existing sequence data with karyological information. I also compared different models of trait evolution in order to infer the underlying evolutionary mechanisms. Overall, I found significant phylogenetic signals that are consistent with non-neutral trait evolution only when parts of the mitochondrial genome were included, suggesting cytonuclear discordances. The adaptive evolutionary model tested in this study consistently outperformed the neutral model of trait evolution. Taken together, these results suggest that, unlike other Lepidoptera groups, changes in chromosome numbers may have played a role in the diversification of Erebia butterflies.
Threat of predation alters aggressive interactions among spotted salamander (Ambystoma maculatum) larvae
AbstractIntraspecific aggression represents a major source of mortality for many animals and is often experienced alongside the threat of predation. The presence of predators can strongly influence ecological systems both directly by consuming prey and indirectly by altering prey behavior or habitat use. As such, the threat of attack by higher level predators may strongly influence agonistic interactions among conspecifics via nonconsumptive (e.g., behaviorally mediated) predator effects. We sought to investigate these interactions experimentally using larval salamanders (Ambystoma maculatum) as prey and dragonfly nymphs (Anax junius) as predators. Specifically, we quantified salamander behavioral responses to perceived predation risk (PPR) from dragonfly nymphs and determined the degree to which PPR influenced intraspecific aggression (i.e., intraspecific biting and cannibalism) among prey. This included examining the effects of predator exposure on the magnitude of intraspecific biting (i.e., extent of tail damage) and the resulting change in performance (i.e., burst swim speed). Salamander larvae responded to PPR by reducing activity and feeding, but did not increase refuge use. Predator exposure did not significantly influence overall survival; however, the pattern of survival differed among treatments. Larvae exposed to PPR experienced less tail damage from conspecifics, and maximum burst swim speed declined as tail damage became more extensive. Thus, escape ability was more strongly compromised by intraspecific aggression occurring in the absence of predation risk. We conclude that multitrophic indirect effects may importantly modulate intraspecific aggression and should be considered when evaluating the effects of intraspecific competition.
A method combining a random forest-based technique with the modeling of linkage disequilibrium through latent variables, to run multilocus genome-wide association studies
BackgroundGenome-wide association studies (GWASs) have been widely used to discover the genetic basis of complex phenotypes. However, standard single-SNP GWASs suffer from lack of power. In particular, they do not directly account for linkage disequilibrium, that is the dependences between SNPs (Single Nucleotide Polymorphisms).ResultsWe present the comparative study of two multilocus GWAS strategies, in the random forest-based framework. The first method, T-Trees, was designed by Botta and collaborators (Botta et al., PLoS ONE 9(4):e93379, 2014). We designed the other method, which is an innovative hybrid method combining T-Trees with the modeling of linkage disequilibrium. Linkage disequilibrium is modeled through a collection of tree-shaped Bayesian networks with latent variables, following our former works (Mourad et al., BMC Bioinformatics 12(1):16, 2011). We compared the two methods, both on simulated and real data. For dominant and additive genetic models, in either of the conditions simulated, the hybrid approach always slightly performs better than T-Trees. We assessed predictive powers through the standard ROC technique on 14 real datasets. For 10 of the 14 datasets analyzed, the already high predicted power observed for T-Trees (0.910-0.946) can still be increased by up to 0.030. We also assessed whether the distributions of SNPs’ scores obtained from T-Trees and the hybrid approach differed. Finally, we thoroughly analyzed the intersections of top 100 SNPs output by any two or the three methods amongst T-Trees, the hybrid approach, and the single-SNP method.ConclusionsThe sophistication of T-Trees through finer linkage disequilibrium modeling is shown beneficial. The distributions of SNPs’ scores generated by T-Trees and the hybrid approach are shown statistically different, which suggests complementary of the methods. In particular, for 12 of the 14 real datasets, the distribution tail of highest SNPs’ scores shows larger values for the hybrid approach. Thus are pinpointed more interesting SNPs than by T-Trees, to be provided as a short list of prioritized SNPs, for a further analysis by biologists. Finally, among the 211 top 100 SNPs jointly detected by the single-SNP method, T-Trees and the hybrid approach over the 14 datasets, we identified 72 and 38 SNPs respectively present in the top25s and top10s for each method.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2054-0) contains supplementary material, which is available to authorized users.
Controlling Within-Field Sheep Movement Using Virtual Fencing
Simple SummaryVirtual fencing has the potential to increase the implementation of spatial grazing management and targeted grazing without the use of conventional fencing. Current virtual fencing that uses an algorithm that is patented through CSIRO involves a collar that emits a warning audio when an animal approaches a set boundary. If the animal continues walking towards the boundary, an electric stimulus is applied. Using manually operated collars to implement a similar virtual fence, a small group of sheep were restricted from accessing a section of a small paddock. Sheep were successfully kept out of the excluded zone of the paddock. By the third day, the sheep were able to avoid receiving an electrical stimulus by turning away from the boundary when the warning audio was applied. When the sheep were allowed full access to the paddock again, then they were quick to use the once restricted area.AbstractVirtual fencing has the potential to greatly improve livestock movement, grazing efficiency, and land management by farmers; however, relatively little work has been done to test the potential of virtual fencing with sheep. Commercial dog training equipment, comprising of a collar and GPS hand-held unit were used to implement a virtual fence in a commercial setting. Six, 5–6 year-old Merino wethers, which were naïve to virtual fencing were GPS tracked for their use of a paddock (80 × 20 m) throughout the experiment. The virtual fence was effective at preventing a small group of sheep from entering the exclusion zone. The probability of a sheep receiving an electrical stimulus following an audio cue was low (19%), and declined over the testing period. It took an average of eight interactions with the fence for an association to be made between the audio and stimulus cue, with all of the animals responding to the audio alone by the third day. Following the removal of the virtual fence, sheep were willing to cross the previous location of the virtual fence after 30 min of being in the paddock. This is an important aspect in the implementation of virtual fencing as a grazing management tool and further enforces that the sheep in this study were able to associate the audio with the virtual fence and not the physical location itself.
Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development
Protein folding and degradation are both required for protein quality control, an essential cellular activity that underlies normal growth and development. We investigated how BOB1, an Arabidopsis thaliana small heat shock protein, maintains normal plant development. bob1 mutants exhibit organ polarity defects and have expanded domains of KNOX gene expression. Some of these phenotypes are ecotype specific suggesting that other genes function to modify them. Using a genetic approach we identified an interaction between BOB1 and FIL, a gene required for abaxial organ identity. We also performed an EMS enhancer screen using the bob1-3 allele to identify pathways that are sensitized by a loss of BOB1 function. This screen identified genetic, but not physical, interactions between BOB1 and the proteasome subunit RPT2a. Two other proteasome subunits, RPN1a and RPN8a, also interact genetically with BOB1. Both BOB1 and the BOB1-interacting proteasome subunits had previously been shown to interact genetically with the transcriptional enhancers AS1 and AS2, genes known to regulate both organ polarity and KNOX gene expression. Our results suggest a model in which BOB1 mediated protein folding and proteasome mediated protein degradation form a functional proteostasis module required for ensuring normal plant development.
Anti-Inflammatory and Anti-Apoptotic Effects of Acer Palmatum Thumb. Extract, KIOM-2015EW, in a Hyperosmolar-Stress-Induced In Vitro Dry Eye Model
The aim of this study was to assess the anti-inflammatory and anti-apoptotic effects of KIOM-2015EW, the hot-water extract of maple leaves in hyperosmolar stress (HOS)-induced human corneal epithelial cells (HCECs). HCECs were exposed to hyperosmolar medium and exposed to KIOM-2015EW with or without the hyperosmolar media. Tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6 production and apoptosis were observed, and the activation of mitogen-activated protein kinases (MAPKs) including extracellular signal regulated kinase (ERK), p38 and c-JUN N-terminal kinase (JNK) signaling and nuclear factor (NF)-κB was confirmed. Compared to isomolar medium, the induction of cell cytotoxicity significantly increased in HCECs exposed to hyperosmolar medium in a time-dependent manner. KIOM-2015EW-treatment significantly reduced the mRNA and protein expression of pro-inflammatory mediators and apoptosis. KIOM-2015EW-treatment inhibited HOS-induced MAPK signaling activation. Additionally, the HOS-induced increase in NF-κB phosphorylation was attenuated by KIOM-2015EW. The results demonstrated that KIOM-2015EW protects the ocular surface by suppressing inflammation in dry eye disease, and suggest that KIOM-2015EW may be used to treat several ocular surface diseases where inflammation plays a key role.
Chronic health conditions and school performance in first graders: A prospective cohort study
ObjectiveChildren with chronic health conditions may perform poorer at school. Associations may be confounded by numerous social factors. We aimed to estimate the effects of a chronic health condition on overall school performance in first graders with an emphasis on rigorous adjustment for potential confounders.MethodsA population-based cohort study was performed in the area of Mainz-Bingen (Germany). In 2015 all preschoolers were approached and the presence of a chronic health condition was assessed by parental questionnaires and preschool health examination data. The identification of a chronic health condition was based on special health care needs and presence of a doctor’s diagnosis out of 24 school-relevant diseases. At the end of the first school year, overall school performance was assessed by teachers and rated on a 5-item scale ranging from -10 to +10.ResultsOf 3683 children approached, 2003 were enrolled. Overall school performance was available for 1462 children (51% boys). Of these, 52% suffered from a chronic health condition. Compared to children without a chronic health condition, children with special health care needs (15%) performed worse at school (adjusted mean difference: -0.95, 95% CI: [-1.55; -0.35], P = 0.002). Children with a doctor’s diagnosis but without special health care needs (37%) did not perform worse at school. The effect was further analysed considering the extent of special health care needed.ConclusionsChronic health conditions affect overall school performance early in primary school. To identify academically at-risk children, a chronic health condition identification based on special health care needs may be used.
The Anti-Cancer Multikinase Inhibitor Sorafenib Impairs Cardiac Contractility by Reducing Phospholamban Phosphorylation and Sarcoplasmic Calcium Transients
Tyrosine-kinase inhibitors (TKIs) have revolutionized cancer therapy in recent years. Although more targeted than conventional chemotherapy, TKIs exhibit substantial cardiotoxicity, often manifesting as hypertension or heart failure. Here, we assessed myocyte intrinsic cardiotoxic effects of the TKI sorafenib and investigated underlying alterations of myocyte calcium homeostasis. We found that sorafenib reversibly decreased developed force in auxotonically contracting human myocardia (3 µM: −25 ± 4%, 10 µM: −29 ± 7%, 30 µM: −43 ± 12%, p < 0.01), reduced peak cytosolic calcium concentrations in isolated cardiomyocytes (10 µM: 52 ± 8.1% of baseline, p < 0.001), and slowed cytosolic calcium removal kinetics (RT50, RT10, Tau, p < 0.05). Beta-adrenergic stimulation induced augmentation of calcium transient (CaT) amplitude was attenuated in sorafenib-treated cells (2.7 ± 0.3-fold vs. 3.6 ± 0.2-fold in controls, p < 0.001). Sarcoplasmic reticulum (SR) calcium content was reduced to 67 ± 4% (p < 0.01), and SR calcium re-uptake slowed (p < 0.05). Sorafenib significantly reduced serine 16 phosphorylation of phospholamban (PLN, p < 0.05), while PLN threonine 17 and CaMKII (T286) phosphorylation were not altered. Our data demonstrate that sorafenib acutely impairs cardiac contractility by reducing S16 PLN phosphorylation, leading to reduced SR calcium content, CaT amplitude, and slowed cytosolic calcium removal. These results indicate myocyte intrinsic cardiotoxicity irrespective of effects on the vasculature and chronic cardiac remodeling.
Genome-wide analysis of codon usage bias in four sequenced cotton species
Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.