bluuebunny/crossref_metadata_2025 huggingface dataset:
SalmonellaEnteritidis Effector AvrA suppresses autophagy by reducing Beclin-1 protein
Authors: Jiao Yang , Zhang Yong-guo , Lin Zhijie , Lu Rong , Xia Yinglin , Meng Chuang , Pan Zhimin , Xu Xiulong , Jiao Xinan , Sun Jun
Published: January 2020

Autophagy is a cellular process to clear pathogens.Salmonella entericaserovar Enteritidis (S.E) has emerged as one of the most important food-borne pathogens. However, major studies still focus onSalmonella entericaserovar Typhimurium. Here, we reported that AvrA, aS. Enteritidis effector, inhibited autophagy to promote bacterial survival in the host. We found that AvrA regulates the conversion of LC3 I into LC3 II and the enrichment of lysosomes. Beclin-1, a key molecular regulator of autophagy, was decreased after AvrA expressed strain colonization. InS.E-AvrA--infected cells, we found the increases of protein levels of p-JNK and p-c-Jun and the transcription level of AP-1. AvrA-reduction of Beclin-1 protein expression is through the JNK pathway. The JNK inhibitor abolished the AvrA-reduced Beclin-1 protein expression. Moreover, we identified that the AvrA mutation C186A abolished its regulation of Beclin-1 expression. In addition, AvrA protein interacted with Beclin-1. In organoids and infected mice, we explored the physiologically related effects and mechanism of AvrA in reducing Beclin-1 through the JNK pathway, thus attenuating autophagic responses.

Importance

SalmonellaEnteritidis is an important pathogen with a public health concern and farm production risk, yet the host-pathogen interactions that govern the survival ofS. Enteritidis infections are incompletely understood. Anti-bacterial autophagy provides potent cell-autonomous immunity against bacterial colonization. Here, we report that a new role for effector AvrA ofS. Enteritidis in the reduction of Beclin-1 protein expression through the JNK pathway and the attenuation of the autophagic response in intestinal epithelial cells. This finding not only indicates an important role ofS. Enteritidis effector in reducing host protein as a strategy to suppress autophagy, but also suggests manipulating autophagy as a new strategy to treat infectious diseases.
Natural infection withGiardiais associated with altered community structure of the human and canine gut microbiome
Authors: Berry Alexander S.F. , Johnson Kaylynn , Martins Rene , Sullivan Megan , Amorim Camila Farias , Putre Alexandra , Scott Aiysha , Wang Shuai , Lindsay Brianna , Baldassano Robert , Nolan Thomas J. , Beiting Daniel P.
Published: January 2020

Enteric parasitic infections are among the most prevalent infections in lower- and middle-income countries (LMICs), and have a profound impact on global public health. While the microbiome is increasingly recognized as a key determinant of gut health and human development, the impact of naturally-acquired parasite infections on microbial community structure in the gut, and the extent to which parasite-induced changes in the microbiome may contribute to gastrointestinal symptoms, is poorly understood. Enteric parasites are routinely identified in companion animals in the United States, presenting a unique opportunity to leverage this animal model to investigate the impact of naturally-acquired parasite infections on the microbiome. Clinical, parasitological, and microbiome profiling of a cohort of 258 dogs revealed a significant correlation between parasite infection and composition of the bacterial community in the gut. Relative to other enteric pathogens,Giardiawas associated with a more pronounced perturbation of the microbiome. Using a database mining approach that allowed us to compare our findings to a large-scale epidemiological study of enteric diseases in humans, we also observed a substantial alteration to microbiome structure inGiardia-infected children. Importantly, infection was associated with a reduction in the relative abundance of potential pathobionts, includingGammaproteobacteria, and an increase inPrevotella- a profile often associated with gut health. Taken together, our data show that widespreadGiardiainfection in young animals and humans is associated with significant remodeling of the gut microbiome, and provide a possible explanation for the high prevalence of asymptomaticGiardiainfections observed across host species.

Importance

While enteric parasitic infections are among the most important infections in lower- and middle-income countries, their impact on gut microbiota is poorly understood. We reasoned that clinical symptoms associated with these infections may be influenced by alterations of the microbiome that occur during infection. To explore this notion, we took a two-pronged approach. First, we studied a cohort of dogs naturally infected with various enteric parasites and found a strong association between parasite infection and altered gut microbiota composition.Giardia, one of the most prevalent parasite infections globally, had a particularly large impact on the microbiome. Second, we took a database-driven strategy to integrate microbiome data with clinical data from large human field studies and found thatGiardiainfection is also associated with marked alteration of the gut microbiome of children, suggesting a possible explanation for whyGiardiahas been reported to be associated with protection from moderate-to-severe diarrhea.
A Genetics-First Approach to Dissecting the Heterogeneity of Autism: Phenotypic Comparison of Autism Risk Copy Number Variants
Authors: Chawner Samuel J.R.A. , Doherty Joanne L. , Anney Richard , Antshel Kevin M. , Bearden Carrie E. , Bernier Raphael , Chung Wendy K. , Clements Caitlin C. , Curran Sarah R. , Cuturilo Goran , Fiksinski Ania M. , Gallagher Louise , Goin-Kochel Robin P. , Kushan Leila , Gur Raquel E. , Hanson Ellen , Jacquemont Sebastien , Kates Wendy R. , Maillard Anne M. , McDonald-McGinn Donna M. , Mihaljevic Marina , Miller Judith S , Moss Hayley , Pejovic-Milovancevic Milica , Schultz Robert T. , Green-Snyder LeeAnne , Vorstman Jacob A. , Wenger Tara L. ,   IMAGINE-ID Consortium, Hall Jeremy , Owen Michael J. , van den Bree Marianne
Published: January 2020

Objective

Certain copy number variants (CNVs) greatly increase risk of autism. We conducted a genetics-first study to investigate whether heterogeneity in the clinical presentation of autism is underpinned by specific genotype-phenotype relationships.

Methods

This international study included 547 individuals (12.3 years (SD=4.2), 54% male) who were ascertained on the basis of having a genetic diagnosis of a rare CNV associated with high risk of autism (82 16p11.2 deletion carriers, 50 16p11.2 duplication carriers, 370 22q11.2 deletion carriers and 45 22q11.2 duplication carriers), as well as 2027 individuals (9.1 years (SD=4.9), 86% male) with autism of heterogeneous aetiology. The Autism Diagnostic Interview-Revised (ADI-R) and IQ testing were conducted.

Results

The four genetic variant groups differed in autism severity, autism subdomain profile as well as IQ profile. However, we found substantial variability in phenotypic outcome within individual genetic variant groups (74% to 97% of the variance depending on the trait), whereas variability between groups was low (1% to 21% depending on trait). We compared CNV carriers who met autism criteria, to individuals with heterogeneous autism, and a range of profile differences were identified. Using clinical cut-offs, we found that 54% of individuals with one of the 4 CNVs who did not meet full autism diagnostic criteria nonetheless had elevated levels of autistic traits.

Conclusion

Many CNV carriers do not meet full diagnostic criteria for autism, but nevertheless meet clinical cut-offs for autistic traits. Although we find profile differences between variants, there is considerable variability in clinical symptoms within the same variant.
The interdomain helix between the kinase and RNase domains of IRE1α transmits the conformational change that underlies ER stress-induced activation
Authors: Ricci Daniela , Tutton Stephen , Marrocco Ilaria , Ying Mingjie , Blumenthal Daniel , Eletto Daniela , Vargas Jade , Boyle Sarah , Fazelinia Hossein , Paton James C. , Paton Adrienne W. , Anthony Tang Chih-Hang , Andrew Hu Chih-Chi , Gidalevitz Tali , Argon Yair
Published: January 2020

The unfolded protein response (UPR) plays an evolutionarily conserved role in homeostasis, and its dysregulation often leads to human disease, including diabetes and cancer. IRE1α is a major transducer that conveys endoplasmic reticulum (ER) stress to biochemical signals, yet major gaps persist in our understanding of how the detection of stress is converted to one of several molecular outcomes. It is known that upon sensing unfolded proteins via its ER luminal domain, IRE1α dimerizes and oligomerizes (often visualized as clustering), and then trans-autophosphorylates. The IRE1α kinase activity is required for activation of its RNase effector domain and for clustering of IRE1α. It is not yet clear if IRE1α clustering is a platform for the RNase activity, or if the two represent distinct biological functions. Here, we uncover a previously unrecognized role for helix αK between IRE1α kinase and RNase domains in conveying critical conformational changes. Using mutants within this inter-domain helix, we show for the first time that: 1) distinct substitutions (specifically, of Leu827) selectively affect oligomerization, RNase activity, and, unexpectedly, the kinase activity of IRE1α; 2) RNase activation can be uncoupled from IRE1α oligomerization, and phosphorylation of S729 marks the former but not the latter; 3) The nature of residue 827 determines the conformation that the IRE1α protein adopts, leading to different patterns of biochemical activities. In summary, this work reveals a previously unappreciated role for the inter-domain helix as a pivotal conduit for attaining the stress-responsive conformation of IRE1α.
Modulation of white matter bundle connectivity in the presence of axonal truncation pathologies
Authors: Smith Robert E. , Calamante Fernando , Gajamange Sanuji , Kolbe Scott , Connelly Alan
Published: January 2020

Endpoint-to-endpoint fibre bundle connectivity estimated using spherical deconvolution & streamlines tractography in diffusion MRI may be excessive in the presence of pathologies that involve truncation of axons within the white matter. Here we propose a simple modification to an existing method that directly quantifies and corrects for this over-estimation.
Conceptual knowledge affects early stages of visual mental imagery and object perception
Authors: Maier Martin , Frömer Romy , Rost Johannes , Sommer Werner , Rahman Rasha Abdel
Published: January 2020

When we imagine an object and when we actually see that object, similar brain regions become active. Yet, the time course and mechanisms with which imagery engages perceptual networks remain to be better understood. An emerging view holds that imagery and perception follow distinct dynamics during early visual processing with similarities arising only during later, high-level visual processing. However, confounds of visual stimulation and paradigms favoring observation of high-level processes associated with subjective imagery strength may have precluded evidence of earlier shared mechanisms. We therefore manipulated prior knowledge that informs early-stage top-down predictions and tracked electrophysiological brain responses while fully controlling visual stimulation. Participants saw and imagined objects associated with varying amounts of semantic knowledge. Imagery and perception were equally influenced by knowledge at an early stage (P1 component), revealing shared mechanisms that support low-level visual processing. This finding complements previous research by showing that imagery is not merely perception in reverse. Instead, in line with the predictive processing framework, both, perception and imagery are active and constructive processes that share top-down mechanisms already in early phases of processing.
Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations
Authors: Wang Ying , Guo Jing , Ni Guiyan , Yang Jian , Visscher Peter M. , Yengo Loic
Published: January 2020

Polygenic scores (PGS) have been widely used to predict complex traits and risk of diseases using variants identified from genome-wide association studies (GWASs). To date, most GWASs have been conducted in populations of European ancestry, which limits the use of GWAS-derived PGS in non-European populations. Here, we develop a new theory to predict the relative accuracy (RA, relative to the accuracy in populations of the same ancestry as the discovery population) of PGS across ancestries. We used simulations and real data from the UK Biobank to evaluate our results. We found across various simulation scenarios that the RA of PGS based on trait-associated SNPs can be predicted accurately from modelling linkage disequilibrium (LD), minor allele frequencies (MAF), cross-population correlations of SNP effect sizes and heritability. Altogether, we find that LD and MAF differences between ancestries explain alone up to ~70% of the loss of RA using European-based PGS in African ancestry for traits like body mass index and height. Our results suggest that causal variants underlying common genetic variation identified in European ancestry GWASs are mostly shared across continents.
From thoughtless awareness to effortful cognition: alpha - theta cross-frequency dynamics in experienced meditators during meditation, rest and arithmetic
Authors: Rodriguez-Larios Julio , Faber Pascal , Achermann Peter , Tei Shisei , Alaerts Kaat
Published: January 2020

Neural activity is known to oscillate within discrete frequency bands and the synchronization between these rhythms is hypothesized to underlie information integration in the brain. Since strict synchronization is only possible for harmonic frequencies, a recent theory proposes that the interaction between different brain rhythms is facilitated by transient harmonic frequency arrangements. In this line, it has been recently shown that the transient occurrence of 2:1 harmonic cross-frequency relationships between alpha and theta rhythms (i.e. falpha≈12 Hz; ftheta≈6 Hz) is enhanced during effortful cognition. In this study, we tested whether achieving a state of ‘mental emptiness’ during meditation is accompanied by a relative decrease in the occurrence of 2:1 harmonic cross-frequency relationships between alpha and theta rhythms. Continuous EEG recordings (19 electrodes) were obtained from 43 highly experienced meditators during meditation practice, rest and an arithmetic task. We show that the occurrence of transient alpha:theta 2:1 harmonic relationships increased linearly from a meditative to an active cognitive processing state (i.e. meditation< rest< arithmetic task). It is argued that transient EEG cross-frequency arrangements that prevent alpha:theta cross-frequency coupling could facilitate the experience of ‘mental emptiness’ by avoiding the interaction between the memory and executive components of cognition.
Evolutionary and ecological processes influencing chemical defense variation in an aposematic and mimeticHeliconiusbutterfly
Authors: Mattila Anniina L. K. , Jiggins Chris D. , Opedal Øystein H. , Montejo-Kovacevich Gabriela , de Castro Érika , McMillan William O. , Bacquet Caroline , Saastamoinen Marjo
Published: January 2020

Chemical defences against predators underlie the evolution of aposematic coloration and mimicry, which are classic examples of adaptive evolution. Surprisingly little is known about the roles of ecological and evolutionary processes maintaining defence variation, and how they may feedback to shape the evolutionary dynamics of species. CyanogenicHeliconiusbutterflies exhibit diverse warning color patterns and mimicry, thus providing a useful framework for investigating these questions. We studied intraspecific variation inde novobiosynthesized cyanogenic toxicity and its potential ecological and evolutionary sources in wild populations ofHeliconius eratoalong environmental gradients, in common-garden broods and with feeding treatments. Our results demonstrate substantial intraspecific variation, including detectable variation among broods reared in a common garden. The latter estimate suggests considerable evolutionary potential in this trait, although predicting the response to selection is likely complicated due to the observed skewed distribution of toxicity values and the signatures of maternal contributions to the inheritance of toxicity. Larval diet contributed little to toxicity variation. Furthermore, toxicity profiles were similar along steep rainfall and altitudinal gradients, providing little evidence for these factors explaining variation in biosynthesized toxicity in natural populations. In contrast, there were striking differences in the chemical profiles ofH. eratofrom geographically distant populations, implying potential local adaptation in the acquisition mechanisms and levels of defensive compounds. The results highlight the extensive variation and potential for adaptive evolution in defense traits for aposematic and mimetic species, which may contribute to the high diversity often found in these systems.
Maternal genome dominance in early plant embryogenesis
Authors: Alaniz-Fabián Jaime , Xiang Daoquan , Toro-De León Gerardo Del , Orozco-Nieto Axel , Gao Peng , Sharpe Andrew , Kochian Leon V. , Selvaraj Gopalan , Springer Nathan , Abreu-Goodger Cei , Datla Raju , Gillmor C. Stewart
Published: January 2020

Previous studies have alternately supported and discounted the hypothesis that the maternal genome plays a predominant role in early embryogenesis in plants. We used 24embryo defective (emb)mutants ofArabidopsis thalianato test for maternal and paternal effects in early embryogenesis. 5embmutants had equal maternal and paternal effects, 5 showed maternal effects and weak paternal effects, and the remaining 14embmutants conditioned only maternal effects, demonstrating a more important role for the maternal allele for most of theseEMBgenes. To assess genome-wide maternal and paternal contributions to early embryos, we produced allele-specific transcriptomes from zygote to mature stage embryos derived from reciprocal crosses of Columbia-0 and Tsu-1, a hybrid combination we show to be a faithful proxy for isogenic Columbia-0. Parent-of-origin analysis of these transcriptomes revealed a reciprocal maternal bias in thousands of genes from the zygote to octant stage. This bias greatly diminished by the globular stage, and was absent at later stages. Comparison with egg cell transcriptomes revealed no correlation between transcript levels in the egg and maternal bias in pre-globular embryos, suggesting that the maternal bias observed in early embryos is due to preferential zygotic transcription of maternal alleles. Taken together, the functional and transcriptome data presented here support a predominant role for the maternal genome in early Arabidopsis embryogenesis.

Significance

In both animals and plants, the zygote is produced by the union of the egg and sperm cells. In animals, it is well accepted that mRNAs and proteins from the egg direct the first steps of embryogenesis. Here we present genetic and genomic experiments that support a predominant role for the maternal genome in early embryogenesis of plants, as well. In contrast to animals, our data suggest that this maternal influence is primarily derived not from inheritance of egg transcripts, but from preferential transcription of maternal alleles in the zygote and early embryo. This transient maternal zygotic bias may reflect an ancestral condition to diminish paternal influence on early embryogenesis in outcrossing plants.
Development of Microstructural and Morphological Cortical Profiles in the Neonatal Brain
Authors: Fenchel Daphna , Dimitrova Ralica , Seidlitz Jakob , Robinson Emma C. , Batalle Dafnis , Hutter Jana , Christiaens Daan , Pietsch Maximilian , Brandon Jakki , Hughes Emer J. , Allsop Joanna , O’Keeffe Camilla , Price Anthony N. , Cordero-Grande Lucilio , Schuh Andreas , Makropoulos Antonios , Passerat-Palmbach Jonathan , Bozek Jelena , Rueckert Daniel , Hajnal Jo V. , Raznahan Armin , McAlonan Grainne , Edwards A. David , O’Muircheartaigh Jonathan
Published: January 2020

In the perinatal brain, regional cortical architecture and connectivity lay the foundations for functional circuits and emerging behaviour. Interruptions or atypical development during or before this period may therefore have long-lasting consequences. However, to be able to investigate these deviations, we need a measure of how this architecture evolves in the typically developing brain. To this end, in a large cohort of 241 term-born infants we used Magnetic Resonance Imaging to estimate cortical profiles based on morphometry and microstructure over the perinatal period (37-44 weeks post-menstrual age, PMA). Using the covariance of these profiles as a measure of inter-areal network similarity (Morphometric Similarity Networks; MSN), we clustered these networks into distinct modules. The resulting modules were consistent and symmetric, and corresponded to known functional distinctions, including sensory-motor, limbic and association regions and were spatially mapped onto known cytoarchitectonic tissue classes. Posterior (parietal, occipital) regions became more morphometrically similar with increasing PMA, while peri-cingulate and medial temporal regions became more dissimilar. Network strength was associated with PMA: Within-network similarity increased over PMA suggesting emerging network distinction. These changes in cortical network architecture over an eight-week period are consistent with, and likely underpin, the highly dynamic behavioural and cognitive development occurring during this critical period. The resulting cortical profiles might provide normative reference to investigate atypical early brain development.
Transcriptional profile of pyramidal neurons in chronic schizophrenia reveals lamina-specific dysfunction of neuronal immunity
Authors: Wu Xiaojun , Shukla Rammohan , Alganem Khaled , Depasquale Erica , Reigle James , Simmons Micah , Hahn Chang-Gyu , Haroutunian Vahram , Meller Jarek , Meador-Woodruff James , McCullumsmith Robert
Published: January 2020

While the pathophysiology of schizophrenia has been extensively investigated using homogenized postmortem brain samples, few studies have examined changes in brain samples with techniques that may attribute perturbations to specific cell types. To fill this gap, we performed microarray assays on mRNA isolated from anterior cingulate cortex (ACC) superficial and deep pyramidal neurons from 12 schizophrenia and 12 control subjects using laser capture microdissection. Among all the annotated genes, we identified 134 significantly increased and 130 decreased genes in superficial pyramidal neurons, while 93 significantly increased and 101 decreased genes were found in deep pyramidal neurons, in schizophrenia compared to control subjects. In these differentially expressed genes, we detected lamina-specific changes of 55 and 31 genes in superficial and deep neurons in schizophrenia, respectively. Gene set enrichment analysis (GSEA) was applied to the entire pre-ranked differential expression gene lists to gain a complete pathway analysis throughout all annotated genes. Our analysis revealed over-represented groups of gene sets in schizophrenia, particularly in immunity and synapse related pathways in pyramidal neurons, suggesting the disruption of these pathways plays an important role in schizophrenia. We also detected pathways previously demonstrated in schizophrenia pathophysiology, including cytokine and chemotaxis, post-synaptic signaling, and glutamatergic synapses. In addition, we observed several novel pathways, including ubiquitin-independent protein catabolic process. By comparing our differential expression gene profiles with 51 antipsychotic treatment datasets, we demonstrated that our results were not influenced by antipsychotic treatment of our subjects. Taken together, we found pyramidal neuron-specific changes in neuronal immunity, synaptic dysfunction, and olfactory dysregulation in schizophrenia, providing new insights for the cell-subtype specific pathophysiology of chronic schizophrenia.
Interaction of 14-3-3I and CDPK1 mediates the growth of human malaria parasite
Authors: Jain Ravi , Dey Pinki , Gupta Sakshi , Pati Soumya , Bhattacherjee Arnab , Munde Manoj , Singh Shailja
Published: January 2020

Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs of target proteins and confer conformational changes leading to modulation of their functional parameters. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have characterizedPlasmodium falciparum14-3-3 and its interaction with key kinase of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Towards this, we annotated PF3D7_0818200 as 14-3-3 isoform I through extensive phylogenetic and comparative sequence analysis. Molecular dynamics simulation studies indicated that phosphoSer64present in CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The protein-protein interaction was validatedin vitrowith ELISA and SPR, which confirmed that CDPK1 interacts with 14-3-3I in a phosphorylation dependent manner, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: ARSHpSYPA and RLYHpSLPA as CDPK1 mimetics, by simulation studies and ITC. Further, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy.
Atf-6regulates lifespan through ER-mitochondrial calcium homeostasis
Authors: Burkewitz Kristopher , Dutta Sneha , Kelley Charlotte A. , Steinbaugh Michael , Cram Erin J. , Mair William B.
Published: January 2020

Functional crosstalk between organelles is critical for maintaining cellular homeostasis. Individually, dysfunction of both endoplasmic reticulum (ER) and mitochondria have been linked to cellular and organismal aging, but little is known about how mechanisms of inter-organelle communication might be targeted to extended longevity. The metazoan unfolded protein response (UPR) maintains ER health through a variety of mechanisms beyond its canonical role in proteostasis, including calcium storage and lipid metabolism. Here we provide evidence that inC. elegans, inhibition of the conserved UPR mediator, activating transcription factor (atf)-6increases lifespan via modulation of calcium homeostasis and signaling to the mitochondria. Loss ofatf-6confers long life via downregulation of the ER calcium buffering protein, calreticulin. Function of the ER calcium release channel, the inositol triphosphate receptor (IP3R/itr-1), is required foratf-6mutant longevity while a gain-of-function IP3R/itr-1mutation is sufficient to extend lifespan. IP3R dysfunction leads to altered mitochondrial behavior and hyperfused morphology, which is sufficient to suppress long life inatf-6mutants. Highlighting a novel and direct role for this inter-organelle coordination of calcium in longevity, the mitochondrial calcium import channel,mcu-1, is also required foratf-6mutant longevity. Altogether this study reveals the importance of organellar coordination of calcium handling in determining the quality of aging, and highlights calcium homeostasis as a critical output for the UPR andatf-6in particular.
Neuronal LXR Regulates Neuregulin-1 Expression and Sciatic Nerve-Associated Cell signaling
Authors: Gavini Chaitanya K. , Bonomo Raiza , Mansuy-Aubert Virginie
Published: January 2020

Neuropathic pain caused by peripheral nerve injury significantly affects sensory perception and quality of life. Accumulating evidence strongly link cholesterol and inflammation with development and progression of Obesity and Diabetes associated-neuropathies. However, the exact mechanisms of how lipid metabolism in peripheral nervous system (PNS) contributes to the pathogenesis of neuropathy remains poorly understood. Dysregulation of LXR pathways have been identified in many transcriptomic analyses in neuropathy models. LXR α/β expressed in sensory neurons are necessary for proper peripheral nerve function. Deletion of LXR α/β from sensory neurons lead to pain-like behaviors. In this study, we identified that LXR α/β expressed in sensory neurons regulates neuronal neuregulin-1 (Nrg1). Using in vivo cell-specific approaches, we observed that loss of LXR from sensory neurons altered genes regulating lipid metabolism in non-neuronal cells potentially representing Schwann cells (SC). Our data suggest that neuronal LXR may regulates SC function via a Nrg1-dependent mechanism. The decrease in Nrg1 expression in DRG neurons of WD-fed mice may suggest an altered Nrg1-dependent neuron-SC communication in Obesity. The communication between neurons and non-neuronal cell such as SC could be a new biological pathway to study and to treat Obesity-associated neuropathy and PNS dysfunction.
Pseudoreplication bias in single-cell studies; a practical solution
Authors: Zimmerman Kip D. , Espeland Mark A. , Langefeld Carl D.
Published: January 2020

Cells from the same individual share a common genetic and environmental background and are not independent, therefore they are subsamples or pseudoreplicates. Thus, single-cell data have a hierarchical structure that many current single-cell methods do not address, leading to biased inference, highly inflated type 1 error rates, and reduced robustness and reproducibility. This includes methods that use a batch effect correction for individual as a means of accounting for within sample correlation. Here, we document this dependence across a range of cell types and show that ‘pseudo-bulk’ aggregation methods are overly conservative and underpowered relative to mixed models. We propose applying two-part hurdle generalized linear mixed models with a random effect for individual to properly account for both zero inflation and the correlation structure among measures from cells within an individual. Finally, we provide power estimates across a range of experimental conditions to assist researchers in designing appropriately powered studies.
Reward modulates cortical representations of action
Authors: Adkins Tyler J. , Lee Taraz G.
Published: January 2020

People are capable of rapid on-line improvements in performance when they are offered a reward. The neural mechanism by which this performance enhancement occurs remains unclear. We investigated this phenomenon by offering monetary reward to human participants, contingent on successful performance in a sequence production task. We found that people performed actions more quickly and accurately when they were offered large rewards. Increasing reward magnitude was associated with elevated activity throughout the brain prior to movement. Multivariate patterns of activity in these reward-responsive regions encoded information about the upcoming action. Follow-up analyses provided evidence that action decoding in pre-SMA and other motor planning areas was improved for large reward trials and successful action decoding was associated with improved performance. These results suggest that reward may enhance performance by enhancing neural representations of action used in motor planning.

Highlights

Reward enhances behavioral performance.

Reward enhances action decoding in motor planning areas prior to movement.

Enhanced action decoding coincides with improved behavioral performance.
Molecular packing structure of fibrin fibers resolved by X-ray scattering and molecular modeling
Authors: Jansen Karin A. , Zhmurov Artem , Vos Bart E. , Portale Giuseppe , Merino D. Hermida , Litvinov Rustem I. , Tutwiler Valerie , Kurniawan Nicholas A. , Bras Wim , Weisel John W. , Barsegov Valeri , Koenderink Gijsje H.
Published: January 2020

Fibrin is the major extracellular component of blood clots and a proteinaceous hydrogel used as a versatile biomaterial. Fibrin forms branched networks of polymeric fibers, built of laterally associated double-stranded protofibrils. This multiscale hierarchical structure is crucial for the extraordinary mechanical resilience of blood clots. Yet, the structural basis of clot mechanical properties remains largely unclear due, in part, to the unresolved molecular packing structure of fibrin fibers. Here we quantitatively assess the packing structure of fibrin fibers by combining Small Angle X-ray Scattering (SAXS) measurements of fibrin networks reconstituted under a wide range of conditions with computational molecular modeling of fibrin oligomers. The number, positions, and intensities of the Bragg peaks observed in the SAXS experiments were reproduced computationally based on the all-atom molecular structure of reconstructed fibrin protofibrils. Specifically, the model correctly predicts the intensities of the reflections of the 22.5 nm axial repeat, corresponding to the half-staggered longitudinal arrangement of fibrin molecules. In addition, the SAXS measurements showed that protofibrils within fibrin fibers have a partially ordered lateral arrangement with a characteristic transverse repeat distance of 13 nm, irrespective of the fiber thickness. These findings provide fundamental insights into the molecular structure of fibrin clots that underlies their biological and physical properties.
A bead-based method for the removal of the amino acid lysine from cell-free transcription-translation systems
Authors: Finkler Marc , Kurt Ömer , Grimm Florent , Hartz Philip , Ott Albrecht
Published: January 2020

Cell-free transcription-translation systems are a versatile tool to study gene expression, enzymatic reactions and biochemical regulation mechanisms. Because cell-free transcription-translation systems are often derived from cell lysates, many different substances, among them amino acids, are present. However, experiments concerning the incorporation of non-canonical amino acids into proteins require a system with negligible amounts of canonical analogs. Here we propose a two-step method for the removal of residual free lysine in an allEscherichia coli-based cell-free expression system. The first step consists of the expression of a high-lysine dummy protein. The second step consists of direct removal via binding between lysine and DNA. The presented method is an efficient, fast and simple way to remove residual lysine without altering the system ability to perform gene expression.
Protein kinase Cε activation induces EHD-dependent degradation and downregulation of KATPchannels: Implications for glucose stimulated insulin secretion
Authors: Cockcroft Christopher J , Manna Paul , Karnik Rucha , Taneja Tarvinder K , Wrighton David , Mankouri Jamel , Rong Hong-Lin , Sivaprasadarao Asipu
Published: January 2020

Pancreatic β-cells have the unique ability to couple glucose metabolism to insulin secretion. This capacity is generally attributed to the ability of ATP to inhibit KATPchannels, and the consequent β-cell membrane depolarization and excitation. This notion has recently been challenged by a study which demonstrated that high glucose (HG) downregulates the cell surface KATPchannels, and thereby leads to β-cell depolarisation and excitation. The authors attributed the downregulation to HG-induced protein kinase C (PKC) activation and the consequent increase in channel endocytosis. This interpretation, however, is inconsistent with our previous findings that PKC activation does not affect endocytosis. To address this controversy, we revisited the problem: we have used cell biological and electrophysiological approaches combined with the pharmacological activator of PKC, PMA (phorbol 12-myristate 13-acetate). We first confirm that PKC does not play a role in KATPchannel endocytosis; instead, it downregulates the channel by promoting lysosomal degradation coupled with reduced recycling. We then show that (i) mutation of the dileucine motif (355LL356) in the C-terminal domain of the Kir6.2 subunit of the KATPchannel complex prevents lysosomal degradation; (ii) lysosomal targeting is mediated by the EHD (Eps15 homology domain– containing) proteins; and (iii) the PKC isoform responsible for channel degradation is PKCε. Taken together with the published data, we suggest that HG promotes β-cell excitability via two mechanisms: ATP-dependent channel inhibition and ATP-independent, PKCε-dependent channel degradation. The results likely have implications for glucose induced biphasic insulin secretion.
Harnessing intrinsic fluorescence for typing of secondary structures of DNA
Authors: Zuffo Michela , Gandolfini Aurélie , Heddi Brahim , Granzhan Anton
Published: January 2020

DNA is polymorphic since, despite its ubiquitous presence as a double-stranded helix, it is able to fold into a plethora of other secondary structures bothin vitroand in cells. Despite the considerable advances that have been made in understanding this structural diversity, its high-throughput investigation still faces severe limitations. This mainly stems from the lack of suitable label-free methods, combining a fast and cheap experimental workflow with high information content. Here, we explore the use of intrinsic fluorescence emitted by nucleic acids for this scope. After a preliminary assessment of the suitability of this phenomenon for tracking the conformational changes of DNA, we examined the intrinsic steady-state emission spectra of an 89-membered set of synthetic oligonucleotides with reported conformation (G-quadruplexes, i-motifs, single- and double stranded DNA) by means of multivariate analysis. Specifically, principal component analysis of emission spectra resulted in successful clustering of oligonucleotides into three corresponding conformational groups, albeit without discrimination between single- and double-stranded structures. Linear discriminant analysis of the same training set was exploited for the assessment of new sequences, allowing the evaluation of their G4-forming propensity. Our method does not require any labelling agent or dye, avoiding the related intrinsic bias, and can be utilized to screen novel sequences of interest in a high-throughput and cost-effective manner. In addition, we observed that left-handed (Z-) G4 structures were systematically more fluorescent than most other G4 structures, almost reaching the quantum yield of 5′-d[(G3T)3G3]-3′ (G3T), the most fluorescent G4 structure reported to date. This property is likely to arise from the similar base-stacking geometry in both types of structures.
Pathogens, endosymbionts, and blood-meal sources of host-seeking ticks in the fast-changing Maasai Mara wildlife ecosystem
Authors: Oundo Joseph Wang’ang’a , Villinger Jandouwe , Jeneby Maamun , Ong’amo George , Otiende Moses Yongo , Makhulu Edward Edmond , Musa Ali Abdulahi , Ouso Daniel Obado , Wambua Lillian
Published: January 2020

Background

The role of questing ticks in the epidemiology of tick-borne diseases in Kenya’s Maasai Mara National Reserve (MMNR), an ecosystem with intensified human-wildlife-livestock interactions, remains poorly understood. Therefore, we carried out a survey of the diversity of questing ticks, their blood-meal hosts, and tick-borne pathogens to understand potential effects to human and livestock health.

Methods

Questing ticks were collected by flagging and hand picks from vegetation in 25 localities and identified based on morphologic and molecular criteria. We used PCR with high-resolution melting (HRM) analysis, and sequencing to identifyAnaplasma, Babesia, Coxiella, Ehrlichia, Rickettsia, andTheileriapathogen diversities and blood meals in 231 tick pools.

Results

A total of 1,465 host-seeking ticks were collected, includingRhipicephalus appendiculatus(n = 1,125),Rhipicephalus pulchellus(n = 6),Rhipicephalus evertsi(n = 5),Amblyommacf.gemma(n = 178),Amblyomma gemma(n = 145),Amblyomma variegatum(n = 4),Amblyommasp. (n = 1), andHaemaphysalis leachi(n = 1). Remnant blood-meals from humans, wildebeest, and African buffalo were detected inRh. appendiculatus, goat inRh. evertsi, sheep inAm. gemma, and cattle inAm. variegatum. Rickettsia africaewas detected inAm. gemma(1/25 pools) that had blood-meal remnant from sheep andAm. variegatum(4/25 pools) that had fed on cattle.Rickettsiaspp. were found inAm. gemma(4/25 pools) andRh. evertsi(1/4 pools).Anaplasma oviswas detected inRh. appendiculatus(1/172 pools) andRh. evertsi(1/4 pools), whileAnaplasma boviswas detected inRh. appendiculatus(1/172 pools).Theileria parvawas detected inRh. appendiculatus(27/172 pools).Babesia, EhrlichiaandCoxiellapathogens were not found in any ticks. Unexpectedly, diverseCoxiellasp. endosymbionts were detected in all tick genera (174/231 pools).

Conclusions

The data shows that ticks from the rapidly-changing MMNR are infected with zoonoticR.africaeand unclassifiedRickettsiaspp, demonstrating the persistent risk of African tick-bite fever and other and Spotted Fever Group rickettsioses to local dwellers and visitors to the Maasai Mara ecosystem. Protozoan pathogens that may pose risk to livestock production were also identified. We also highlight possible existence of morphotypic variants ofAmblyommaspecies, based on the observation ofAmbyommacf.gemma, which may be potential human parasites or emergent disease vectors. Our findings also demonstrate that questing ticks in this ecosystem have dynamic vertebrate blood sources including humans, wildlife and domestic animals, which may amplify transmission of tickborne zoonoses and livestock diseases. Further studies are needed to determine the role ofCoxiellaendosymbionts in tick physiology and vector competence.
Testing for functional organization of three-dimensional surface tilt encoding within visual cortex
Authors: Rideaux Reuben , Welchman Andrew E
Published: January 2020

Visual perception of three-dimensional (3D) structure is important for object recognition, grasping, and manipulation. The 3D structure of a surface can be defined in terms of its slant and tilt. Previous work has shown that slant and tilt are represented in the posterior and ventral intraparietal sulcus of the human brain; however, it is unclear whether the representation of these features is functionally organized within this region. Here we use phase-encoded presentation of 3D planar surfaces with linear gradients defined by horizontal binocular disparity while measuring fMRI activity to test whether the representation of 3D surface tilt is functionally organized within visual cortex. We find functionally defined structures within V3A and V7. Most notably, in one participant we find that the tilt preference is unilaterally organized in a pinwheel-like structure, similar to those observed for orientation preference in V1, which encompasses most of area V3A. These findings indicate that 3D orientation is functionally organized within the human visual cortex, and the evidence suggesting the presence of a large pinwheel-like structure indicates that this type of organization may be applied canonically within the brain at multiple scales.
Diversified Learning Environment Alleviates Learning Impairment Caused by Contextual Stress
Authors: Gong Chen , Zhang Meng , Zhang Yanjie , Liu Xiang , Liu Pan , Liao Xiaoling , Zhou Yi , Shi Zhiyue , Liu Xue
Published: January 2020

Environment is capable of affecting our learning ability. Existing studies reported that learning ability can be enhanced by enriched environment and impaired by stressful context. However, it is still unclear whether diversified environment can reverse or ameliorate the learning difficulty caused by stressful context. In this study, several behavioral tasks were designed to test the role of diversified environment in active avoidance learning. In the present study, sound-cued active avoidance (two-way shuttle box) acted as learning paradigm. Multiple shuttle boxes with the identical size but different designs were employed to mimic diversified environment in learning tasks. Mild but inevitable foot shocking was adopted to increase animal’s stress to certain context. To quantify the depression/anxiety level of animals, open field test, forced swimming test, light-dark box test, and elevated plus maze were performed. The following findings were reported. First, diversified learning environment could improve learning ability in active avoidance, as manifested by higher successful rate and sharper learning curve. Second, elevating the stress level of animal to a certain context could noticeably reduce its performance in active avoidance learning. Third, the learning impairment attributed to stressful context can be improved by training in diversified environments. Thus, as revealed from the results, learning impairment caused by stressful context can be alleviated by diversified learning environment which may facilitate further medical and education applications.
Roles of the medial prefrontal cortex, mediodorsal thalamus, and their combined circuit for performance of the odor span task in rats: analysis of memory capacity and foraging behavior
Authors: Scott Gavin A. , Liu Max C. , Tahir Nimra B. , Zabder Nadine K. , Song Yuanyi , Greba Quentin , Howland John G.
Published: January 2020

Working memory (WM), the capacity for short-term storage of small quantities of information for immediate use, is thought to depend on activity within the prefrontal cortex. Recent evidence indicates that the prefrontal neuronal activity supporting WM is driven by thalamocortical connections arising in mediodorsal thalamus (mdThal). However, the role of these connections has not been studied using olfactory stimuli leaving open the question of whether this circuit extends to all sensory modalities. Additionally, manipulations of the mdThal in olfactory memory tasks have yielded mixed results. In the present experiment, we investigated the role of connections between the rat medial prefrontal cortex (mPFC) and mdThal in the odor span task (OST) using a pharmacological contralateral disconnection technique. Inactivation of either the mPFC or mdThal alone both significantly impaired memory performance in the OST, replicating previous findings with the mPFC and confirming that the mdThal plays an essential role in intact OST performance. Contralateral disconnection of the two structures impaired OST performance in support of the idea that the OST relies on mPFC-mdThal connections, but ipsilateral control infusions also impaired performance, complicating this interpretation. We also performed a detailed analysis of rats’ errors and foraging behavior and found a dissociation between mPFC and mdThal inactivation conditions. Inactivation of the mdThal and mPFC caused a significant reduction in the number of approaches rats made per odor, whereas only mdThal inactivation or mPFC-mdThal disconnection caused significant increases in choice latency. Our results confirm that the mdThal is necessary for performance of the OST and that it may critically interact with the mPFC to mediate OST performance. Additionally, we have provided evidence that the mPFC and mdThal play dissociable roles in mediating foraging behavior.