title: Interleukin-17A causes osteoarthritis-like transcriptional changes in human osteoarthritis-derived chondrocytes and synovial fibroblasts in vitro

abstract: Increased interleukin (IL)-17A has been identified in joints affected by osteoarthritis (OA), but it is unclear how IL-17A, and its family members IL-17AF and IL-17F, can contribute to human OA pathophysiology. Therefore, we aimed to evaluate the gene expression and signalling pathway activation effects of the different IL-17 family members in fibroblasts derived from cartilage and synovium of patients with end-stage knee OA. Immunohistochemistry staining confirmed that IL-17 receptors A (IL-17RA) and IL-17RC are expressed in end-stage OA-derived cartilage and synovium. Chondrocytes and synovial fibroblasts derived from end-stage OA patients were treated with IL-17A, IL-17AF, or IL-17F, and gene expression was assessed with bulk RNA-Seq. Hallmark pathway analysis showed that IL-17 cytokines regulated several OA pathophysiology-related pathways including immune-, angiogenesis-, and complement-pathways in both chondrocytes and synovial fibroblasts derived from end-stage OA patients. While overall IL-17A induced the strongest transcriptional response, followed by IL-17AF and IL-17F, not all genes followed this pattern. Disease-Gene Network analysis revealed that IL-17A-related changes in gene expression in these cells are associated with experimental arthritis, knee arthritis, and musculoskeletal disease gene-sets. Western blot analysis confirmed that IL-17A significantly activates p38 and p65 NF-{kappa}B. Incubation of chondrocytes and synovial fibroblasts with IL-17A antibody secukinumab significantly inhibited IL-17A-induced gene expression. In conclusion, the association of IL-17-induced transcriptional changes with arthritic gene-sets supports a role for IL-17A in OA pathophysiology. Therefore, secukinumab could be investigated as a potential therapeutic option in OA patients.


title: TCRβ rearrangements without D-segment are common, abundant and public

abstract: T cells play an important role in adaptive immunity. An enormous clonal diversity of T-cells with a different specificity, encoded by the T-cell receptor (TCR), protect the body against infection. Most TCR{beta} chains are generated from a V-, D-, and J-segment during recombination in the thymus. Although complete absence of the D-segment is not easily detectable from sequencing data, we find convincing evidence for a substantial proportion of TCR{beta} rearrangements lacking a D-segment. Additionally, sequences without a D-segment are more likely to be abundant within individuals and/or shared between individuals. We find that such sequences are preferentially generated during fetal development and persist within the elderly. Summarizing, TCR{beta} rearrangements without a D-segment are not uncommon, and tend to allow for TCR{beta} chains with a high abundance in the naive repertoire.

category: immunology


title: Invasive Earthworms Alter Forest Soil Microbiomes and Nitrogen Cycling

abstract: Northern hardwood forests in formerly glaciated areas had been free of earthworms until exotic European earthworms were introduced by human activities. The invasion of exotic earthworms is known to dramatically alter soil physical, geochemical, and biological properties, but its impacts on soil microbiomes are still unclear. Here we show that the invasive earthworms alter soil microbiomes and ecosystem functioning, especially for nitrogen cycling. We collected soil samples at different depths from three sites across an active earthworm invasion chronosequence in a hardwood forest in Minnesota, USA. We analyzed the structures and the functional potentials of the soil microbiomes by using amplicon sequencing, high-throughput nitrogen cycle gene quantification (NiCE chip), and shotgun metagenomics. Both the levels of earthworm invasion and soil depth influenced the microbiome structures. In the most recently and minimally invaded soils, Nitrososphaera and Nitrospira as well as the genes related to nitrification were more abundant than in the heavily invaded soils. By contrast, genes related to denitrification and nitrogen fixation were more abundant in the heavily invaded than the minimally invaded soils. Our results suggest that the N cycling in forest soils is mostly nitrification driven before earthworm invasion, whereas it becomes denitrification driven after earthworm invasion.

category: microbiology


title: Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha Genes

abstract: Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDH genes. Thus, REST/NRSF represses PCDH gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.

category: molecular biology


title: Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development

abstract: Mammalian nephrons originate from a population of nephron progenitor cells (NPCs), and it is known that NPCs transcriptomes change throughout nephrogenesis during healthy kidney development. To characterize chromatin accessibility and microRNA (miRNA) expression throughout this process, we collected NPCs from mouse kidneys at embryonic day 14.5 (E14.5) and postnatal day zero (P0) and assayed cells for transposase-accessible chromatin and small RNA expression. We observe 46,374 genomic regions of accessible chromatin, with 2,103 showing significant changes in accessibility between E14.5 and P0. In addition, we detect 1,104 known microRNAs, with 114 showing significant changes in expression. Genome-wide, changes in DNA accessibility and microRNA expression highlight biological processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways such as Notch. Furthermore, our data identify novel candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in NPC differentiation; we also associate expression-changing microRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements. Overall, our data characterize NPCs during kidney development and point out new candidate regulatory elements for genes and microRNA with key roles in nephrogenesis.

category: developmental biology


title: Nano-CT characterization reveals coordinated growth of a rudimentary organ necessary for soldier development in the ant Pheidole hyatti

abstract: The growth of imaginal discs in holometabolous insects is coordinated with larval growth to ensure the symmetrical and proportional development of the adult appendages. In ants, the differential growth of these discs generates distinct castes - the winged male and queen castes and the wingless worker caste. In the hyperdiverse ant genus Pheidole, the worker caste is composed of two morphologically distinct subcastes: small minor workers and larger, big-headed soldiers. Although these worker subcastes are completely wingless, soldier larvae develop rudimentary forewing discs that are necessary for generating the disproportionate head-to-body scaling of the big-headed soldier subcaste. However, it remains unclear whether rudimentary forewing discs in soldier larvae are coordinated with other imaginal discs, and whether disc growth and coordination patterns vary between the minor worker and soldier subcastes. Here we show, using quantitative nano-CT three-dimensional analyses, that growth of the soldier rudimentary forewing discs is coordinated with the increase in volume of the leg and eye-antennal (head) discs as well as with larval size. We found that the growth rate of the rudimentary forewing discs differs from the leg discs but is similar to the growth of the head (eye-antennal) discs relative to larval size, suggesting that growth of each type of imaginal disc may be differentially regulated. In addition to their larger size, the soldier eye-antennal discs increase in width as they undergo morphogenesis to generate the characteristic shape of the large soldier head, suggesting that the rudimentary forewing discs may regulate their patterning in addition to their growth. Finally, we observe little growth of the leg and eye-antennal discs during the bipotential stage, while in minor worker development these discs grow at similar rates to one another in coordination with larval size to generate the smaller minor worker subcaste. Our results suggest that rudimentary organs with regulatory functions may participate in new patterns of inter-organ coordination and regulation to produce novel phenotypes and complex worker caste systems. We provide characterization of larval development and imaginal disc growth and morphogenesis with the aim of highlighting this as an emerging system for the study of rudimentary organs during development and evolution.


title: Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays

abstract: Family and population studies indicate clear heritability of major depressive disorder (MDD), though its underlying biology remains unclear. The majority of single-nucleotide polymorphism (SNP) linkage blocks associated with MDD by genome-wide association studies (GWASes) are believed to alter transcriptional regulators (e.g., enhancers, promoters), based on enrichment of marks correlated with these functions. A key to understanding MDD pathophysiology will be elucidation of which SNPs are functional and how such functional variants biologically converge to elicit the disease. Furthermore, retinoids can elicit MDD in patients, and promote depressive behaviors in rodent models, acting via a regulatory system of retinoid receptor transcription factors (TFs). We therefore sought to simultaneously identify functional genetic variants and assess retinoid pathway regulation of MDD risk loci. Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1 000 SNPs prioritized from 39 neuropsychiatric trait/disease GWAS loci, with SNPs selected based on overlap with predicted regulatory features--including expression quantitative trait loci (eQTL) and histone marks--from human brains and cell cultures. We identified >100 SNPs with allelic effects on expression in a retinoid-responsive model system. Further, functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs); with additional allelic differences unmasked by treatment with all-trans retinoic acid (ATRA). Finally, motifs overrepresented across functional SNPs corresponded to TFs highly specific to serotonergic neurons, suggesting an in vivo site of action. Our application of MPRAs to screen MDD-associated SNPs suggests a shared transcriptional regulatory program across loci, a subset of which are unmasked by retinoids.

category: genetics


title: Multi-Modality Machine Learning Predicting Parkinsons Disease

abstract:
BackgroundPersonalized medicine promises individualized disease prediction and treatment. The convergence of machine learning (ML) and available multi-modal data is key moving forward. We build upon previous work to deliver multi-modal predictions of Parkinsons Disease (PD).

MethodsWe performed automated ML on multi-modal data from the Parkinsons Progression Marker Initiative (PPMI). After selecting the best performing algorithm, all PPMI data was used to tune the selected model. The model was validated in the Parkinsons Disease Biomarker Program (PDBP) dataset. Finally, networks were built to identify gene communities specific to PD.

FindingsOur initial model showed an area under the curve (AUC) of 89.72% for the diagnosis of PD. The tuned model was then tested for validation on external data (PDBP, AUC 85.03%). Optimizing thresholds for classification, increased the diagnosis prediction accuracy (balanced accuracy) and other metrics. Combining data modalities outperforms the single biomarker paradigm. UPSIT was the largest contributing predictor for the classification of PD. The transcriptomic data was used to construct a network of disease-relevant transcripts.

InterpretationWe have built a model using an automated ML pipeline to make improved multi-omic predictions of PD. The model developed improves disease risk prediction, a critical step for better assessment of PD risk. We constructed gene expression networks for the next generation of genomics-derived interventions. Our automated ML approach allows complex predictive models to be reproducible and accessible to the community.

FundingNational Institute on Aging, National Institute of Neurological Disorders and Stroke, the Michael J. Fox Foundation, and the Global Parkinsons Genetics Program.

RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPrior research into predictors of Parkinsons disease (PD) has either used basic statistical methods to make predictions across data modalities, or they have focused on a single data type or biomarker model. We have done this using an open-source automated machine learning (ML) framework on extensive multi-modal data, which we believe yields robust and reproducible results. We consider this the first true multi-modality ML study of PD risk classification.

Added value of this studyWe used a variety of linear, non-linear, kernel, neural networks, and ensemble ML algorithms to generate an accurate classification of both cases and controls in independent datasets using data that is not involved in PD diagnosis itself at study recruitment. The model built in this paper significantly improves upon our previous models that used the entire training dataset in previous work1. Building on this earlier work, we showed that the PD diagnosis can be refined using improved algorithmic classification tools that may yield potential biological insights. We have taken careful consideration to develop and validate this model using public controlled-access datasets and an open-source ML framework to allow for reproducible and transparent results.

Implications of all available evidenceTraining, validating, and tuning a diagnostic algorithm for PD will allow us to augment clinical diagnoses or risk assessments with less need for complex and expensive exams. Going forward, these models can be built on remote or asynchronously collected data which may be important in a growing telemedicine paradigm. More refined diagnostics will also increase clinical trial efficiency by potentially refining phenotyping and predicting onset, allowing providers to identify potential cases earlier. Early detection could lead to improved treatment response and higher efficacy. Finally, as part of our workflow, we built new networks representing communities of genes correlated in PD cases in a hypothesis-free manner, showing how new and existing genes may be connected and highlighting therapeutic opportunities.

category: genomics


title: Genomic Prediction In An Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding

abstract: Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop, with expanding production and consumption worldwide. The blueberry breeding program at the University of Florida (UF) has greatly contributed to the expansion of production areas by developing low-chilling cultivars better adapted to subtropical and Mediterranean climates of the globe. The breeding program has historically focused on phenotypic recurrent selection. As an autopolyploid, outcrossing, perennial, long juvenile phase crop, blueberrys breeding cycles are costly and time-consuming, which results in low genetic gains per unit of time. Motivated by the application of molecular markers for a more accurate selection in early stages of breeding, we performed pioneering genomic prediction studies and optimization for implementation in the blueberry breeding program. We have also addressed some complexities of sequence-based geno- typing and model parametrization for an autopolyploid crop, providing empirical contributions that can be extended to other polyploid species. We herein revisited some of our previous genomic prediction studies and described the current achievements in the crop. In this paper, our contribution for genomic prediction in an autotetraploid crop is three-fold: i) summarize previous results on the relevance of model parametrizations, such as diploid or polyploid methods, and inclusion of dominance effects; ii) assess the importance of sequence depth of coverage and genotype dosage calling steps; iii) demonstrate the real impact of genomic selection on leveraging breeding decisions by using an independent validation set. Altogether, we propose a strategy for the use of genomic selection in blueberry, with potential to be applied to other polyploid species of a similar background.


title: Placenta DNA methylation at ZNF300 is associated with fetal sex and placental morphology

abstract: Fetal sex-specific differences in placental morphology and physiology have been associated with sexually dimorphic health outcomes. However, the molecular mechanisms underlying these sex differences are not well understood. We performed whole genome bisulfite sequencing in 133 placenta samples and discovered a significant difference in DNA methylation (DNAm) at the ZNF300 gene locus between male and female offspring and replicated this result in 6 independent datasets. Additionally, the sex-specific pattern appears to be placenta-specific, is robust to a wide range of gestational ages and adverse health outcomes and is present in sorted placenta villous cytotrophoblast cells. Integration of DNAm, genetic, and placental morphology data from the same individuals revealed ZNF300 methylation is also associated with placenta area, perimeter, and max diameter, genetic variants on chromosomes 5 and X, and may mediate the effects of genetic variation on placental area.


title: Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development

abstract:
Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process for all flowering plants. Current knowledge of cell specification and differentiation during plant embryogenesis is largely based on studies of the dicot model plant Arabidopsis thaliana. However, the major crops are monocots and the transcriptional programs associated with the differentiation processes during embryogenesis in this clade were largely unknown. Here, we combined analysis of cell division patterns with development of a temporal transcriptomic resource during embryogenesis of the monocot model plant Brachypodium distachyon. We found that early divisions of the Brachypodium embryo were highly regular, while later stages were marked by less stereotypic patterns. Comparative transcriptomic analysis between Brachypodium and Arabidopsis revealed that the early and late embryogenesis shared a common transcriptional program, whereas mid-embryogenesis was divergent between species. Analysis of orthology groups revealed widespread heterochronic expression of potential developmental regulators between the species. Interestingly, Brachypodium genes tend to be expressed at earlier stages than Arabidopsis counterparts, which suggests that embryo patterning may occur early during Brachypodium embryogenesis. Detailed investigation of auxin-related genes shows that the capacity to synthesize, transport, and respond to auxin is established early in the embryo. However, while early PIN1 polarity could be confirmed, it is unclear if an active response is mounted. This study presents a resource for studying Brachypodium and grass embryogenesis, and shows that divergent angiosperms share a conserved genetic program that is marked by heterochronic gene expression.

Key messageDevelopmental and transcriptomic analysis of Brachypodium embryogenesis, and comparison with Arabidopsis, identifies conserved and divergent phases of embryogenesis, and reveals widespread heterochrony of developmental gene expression.

category: plant biology


title: Scarcity of hosts for gregarious parasitoids indicates an increase of individual offspring fertility by reducing their own fertility

abstract: The gregarious parasitoid strategy allows multiple larvae to complete development in a single host due to their tolerance and/or lower mobility and thus flexibly adjust their reproductive potential amidst changing environmental conditions. Reproductive success is generally measured as the number of each mothers offspring. We propose that with scarcity of host, for gregarious parasitoids is important the view on the fertility not only of a mother but also of her offspring (F1 generation). Due to the body size-fitness correlation, each female deliberately adjusts the clutch size, determining the offspring body size and their reproductive potential. In our study, using Anaphes flavipes as a model species, we showed that under a limited number of hosts, the females reduced their fertility. We propose that the lower fertility of mothers can cause higher fertility in the F2 generation using a larger offspring body while halving fertility. The females increase their individual offsprings fertility by reducing their own fertility. Moreover, we showed that with a scarcity of hosts, the mothers increased the number of their female offspring, and thus, they obtained more offspring in the F2 generation. Additionally, other costs and benefits of the gregarious strategy in relation to superparasitism were tested and discussed.

category: zoology


title: Within-sibship GWAS improve estimates of direct genetic effects

abstract: Estimates from genome-wide association studies (GWAS) represent a combination of the effect of inherited genetic variation (direct effects), demography (population stratification, assortative mating) and genetic nurture from relatives (indirect genetic effects). GWAS using family-based designs can control for demography and indirect genetic effects, but large-scale family datasets have been lacking. We combined data on 159,701 siblings from 17 cohorts to generate population (between-family) and within-sibship (within-family) estimates of genome-wide genetic associations for 25 phenotypes. We demonstrate that existing GWAS associations for height, educational attainment, smoking, depressive symptoms, age at first birth and cognitive ability overestimate direct effects. We show that estimates of SNP-heritability, genetic correlations and Mendelian randomization involving these phenotypes substantially differ when calculated using within-sibship estimates. For example, genetic correlations between educational attainment and height largely disappear. In contrast, analyses of most clinical phenotypes (e.g. LDL-cholesterol) were generally consistent between population and within-sibship models. We also report compelling evidence of polygenic adaptation on taller human height using within-sibship data. Large-scale family datasets provide new opportunities to quantify direct effects of genetic variation on human traits and diseases.


title: A global multiregional proteomic map of the human cerebral cortex

abstract: The Brodmann area (BA)-based map is one of the most widely used cortical maps for studies of human brain functions and in clinical practice; however, the molecular architecture of BAs remain unknown. The present study provided a global multiregional proteomic map of the human cerebral cortex by analyzing 29 BAs. These 29 BAs were grouped into 6 clusters based on similarities in proteomic patterns: the motor and sensory cluster, vision cluster, auditory cluster and Brocas area, Wernickes area cluster, cingulate cortex cluster, and heterogeneous function cluster. We identified 474 cluster-specific and 134 BA-specific signature proteins whose functions are closely associated with specialized functions and disease vulnerability of the corresponding cluster or BA. The findings of the present study could provide explanations for the functional connections between the anterior cingulate cortex and sensorimotor cortex and for anxiety-related function in the sensorimotor cortex. The brain transcriptomic and proteomic comparison indicated that they both could reflect the function of cerebral cortex, but showed different characteristics. These proteomic data are publicly available at the Human Brain Proteome Atlas (www.brain-omics.com). Our results may enhance our understanding of the molecular basis of brain functions and provide an important resource to support human brain research.

category: neuroscience


title: Differential Expression of α,β, and γ Protocadherin Isoforms During Differentiation, Aging, and Cancer

abstract: The cadherin family of cell surface glycoproteins plays a fundamental role in cell-cell recognition, thereby participating in diverse biological process such as embryonic morphogenesis and oncogenic transformation. The subset of clustered protocadherin (PCDH) genes generated from the , {beta}, and {gamma} loci, have been widely studied for their potential role in neuronal cell-cell recognition and neurogenesis, however their broader role in normal embryonic development and cancer has not been examined in detail. We utilized human embryonic stem (hES) cells to model early human development in vitro, comparing PCDH isoform transcription in diverse types of embryonic progenitors with normal adult-derived and cancer counterparts. Embryonic progenitors express genes from the  and {beta} cluster at levels comparable to that seen in the CNS, while fetal and adult-derived cells express primarily from the {gamma} cluster. Replicative senescence left fibroblasts with markedly lower expression of all isoforms. We observe that an embryonic pattern of clustered protocadherin gene expression and associated CpG island methylation is commonly associated with cancer cell lines from diverse tissue types. The differential regulation of the , {beta}, and {gamma} loci coincide with alternate regions of DNA accessibility at CTCF binding sites and lamina-associated domains and CPL expression correlated with the expression of LMNA and LMNB1. These observations support a potential role for the differential regulation of genes within the clustered protocadherin locus in selective cell-cell adhesion during embryogenesis, regeneration, cancer and aging.


title: MicroRNA binding site variation is enriched inpsychiatric disorders

abstract: Psychiatric disorders and other complex traits have a polygenic architecture, often associated with dozens or even hundreds of independent genomic loci. As each of these have a relatively small influence on the trait, the dissection of their biological components is a non-trivial task. For psychiatric disorders in particular, the majority of associated loci lie within non-coding regions of the genome, suggesting that most of the genetic risk for disease originates from the disruption of regulatory sequences. While previously exploration of the heritability of these sequences has focused on variants that modify DNA elements, those that alter cis-acting RNA sequences, such as miRNA binding sites, are also likely to have a significant impact in these disorders. MiRNA have already been shown to be dysregulated in these disorders through both genetic and environmental influence, so it is reasonable to suspect their target genes may also be affected by common variation. In this study, we investigated the distribution of miRNA binding site variants (MBSVs) predicted to alter miRNA binding affinity in psychiatric disorders and observed significant enrichment in schizophrenia, depression, bipolar disorder, and anorexia nervosa. We also observed significant enrichment of MBSVs in genes targeted by several miRNA families, including miR-335-5p, miR-21-5p/590-5p, miR-361-5p, and miR-557 in both schizophrenia and depression, and nominally significant enrichment of MBSV for miR-323b-3p in schizophrenia. We also identified a significant association between MBSVs in gene sets involved in regulation of the synapse and synaptic depression in schizophrenia. While these observations support the role of miRNA in the pathophysiology of psychiatric disorders, we also observed significant association of MBSVs in other complex traits suggesting that MBSVs are an important class of regulatory variants that have functional implications for many disorders.


title: Combined landscape of single-nucleotide variants and copy-number alterations in clonal hematopoiesis

abstract: Implicated in the development of hematological malignancies (HM) and cardiovascular mortality, clonal hematopoiesis (CH) in apparently healthy individuals has been investigated by detecting either single-nucleotide variants and indels (SNVs/indels) or copy number alterations (CNAs), but not both. Here by combining targeted sequencing of 23 CH-related genes and array-based CNA detection of blood-derived DNA, we have delineated the landscape of CH-related SNVs/indels and CNAs in a general population of 11,234 individuals, including 672 with subsequent HM development. Both CH-related lesions significantly co-occurred, which combined, affected blood count, hypertension, and the mortality from HM and cardiovascular diseases depending on the total number of both lesions, highlighting the importance of detecting both lesions in the evaluation of CH.

category: cancer biology


title: Rapid and automated quantification of TDP-43 and FUS mislocalisation for screening of frontotemporal dementia and amyotrophic lateral sclerosis gene variants

abstract:
BackgroundIdentified genetic mutations cause 20% of frontotemporal dementia (FTD) and 5-10% of amyotrophic lateral sclerosis (ALS) cases: however, for the remainder of patients the origin of the disease is uncertain. The overlap in genetic, clinical and pathological presentation of FTD and ALS suggests these two diseases are related. Post-mortem, 97% of ALS and [~]50% of FTD patients show redistribution of the nuclear proteins TDP-43 or FUS to the cytoplasm within affected neurons. We exploited this predominant neuropathological feature to develop an automated method for the quantification of cytoplasmic TDP-43 and FUS in human cell lines.

ResultsUtilising fluorescently-tagged cDNA constructs to identify cells of interest, the fluorescence intensity of TDP-43 or FUS was measured in the nucleus and cytoplasm of HEK293 and SH-SY5Y cells. Confocal microscope images were input into the freely available software CellProfiler, which was used to isolate and measure the two cellular compartments. Significant increases in the amount of cytoplasmic TDP-43 and FUS were detectable in cells expressing known ALS-causative TARDBP and FUS gene mutations. Pharmacological intervention with the apoptosis inducer staurosporine also induced measurable cytoplasmic mislocalisation of endogenous FUS. Additionally, this technique was able to detect the subtler effect of mutation in a secondary gene (CYLD) on endogenous TDP-43 localisation.

ConclusionsThese findings validate this methodology as a novel in vitro technique for the quantification of TDP-43 or FUS mislocalisation that can be used to assess the pathogenicity of predicted FTD- or ALS-causative mutations.


title: A chloride efflux transporter OsBIRG1 regulates grain size and salt tolerance in rice

abstract: Grain size is determined by the number of cells and cell size of the grain. Regulation of grain size is crucial for improving crop yield. However, the genes and underlying molecular mechanisms controlling grain size remain elusive. Here we report a member of Detoxification efflux carrier (DTX)/Multidrug and Toxic Compound Extrusion (MATE) family transporter, BIG RICE GRAIN 1 (BIRG1), negatively regulates the grain size in rice. BIRG1 is highly expressed in reproductive organs and roots. In birg1 grain, the size of the outer parenchyma layer cells of spikelet hulls is noticeably larger but the cell number is not altered compared with that in the wild-type (WT) grain. When expressed in Xenopus oocytes, BIRG1 exhibits chloride efflux activity. In line with the role of BIRG1 in mediating chloride efflux, the birg1 mutant shows reduced tolerance to salt stress under which the chloride level is toxic. Moreover, the birg1 grains contain higher level of chloride compared to WT grains when grown under normal paddy field. The birg1 roots accumulate more chloride than those of WT under saline condition. Collectively, our findings suggest that BIRG1 functions as a chloride efflux transporter regulating grain size and salt tolerance via controlling chloride homeostasis in rice.


title: Dynamics of the auditory continuity illusion

abstract: Illusions give intriguing insights into perceptual and neural dynamics. In the auditory continuity illusion, two brief tones separated by a silent gap may be heard as one continuous tone if a noise burst with appropriate characteristics fills the gap. This illusion probes the conditions under which listeners link related sounds across time and maintain perceptual continuity in the face of sudden changes in sound mixtures. Conceptual explanations of this illusion have been proposed, but its neural basis is still being investigated. In this work we provide a dynamical systems framework, grounded in principles of neural dynamics, to explain the continuity illusion. We construct an idealized firing rate model of a neural population and analyze the conditions under which firing rate responses persist during the interruption between the two tones. First, we show that sustained inputs and hysteresis dynamics (a mismatch between tone levels needed to activate and inactivate the population) can produce continuous responses. Second, we show that transient inputs and bistable dynamics (coexistence of two stable firing rate levels) can also produce continuous responses. Finally, we combine these input types together to obtain neural dynamics consistent with two requirements for the continuity illusion as articulated in a well-known theory of auditory scene analysis: sustained responses occur if noise provides sufficient evidence that the tone continues and if there is no evidence of discontinuities between the tones and noise. By grounding these notions in a quantitative model that incorporates elements of neural circuits (recurrent excitation, and mutual inhibition, specifically), we identify plausible mechanisms for the continuity illusion. Our findings can help guide future studies of neural correlate of this illusion and inform development of more biophysically-based models of the auditory continuity illusion.


title: Parallel inference of hierarchical latent dynamics in two-photon calcium imaging of neuronal populations

abstract: Dynamic latent variable modelling has provided a powerful tool for understanding how populations of neurons compute. For spiking data, such latent variable modelling can treat the data as a set of point-processes, due to the fact that spiking dynamics occur on a much faster timescale than the computational dynamics being inferred. In contrast, for other experimental techniques, the slow dynamics governing the observed data are similar in timescale to the computational dynamics that researchers want to infer. An example of this is in calcium imaging data, where calcium dynamics can have timescales on the order of hundreds of milliseconds. As such, the successful application of dynamic latent variable modelling to modalities like calcium imaging data will rest on the ability to disentangle the deeper- and shallower-level dynamical systems contributions to the data. To-date, no techniques have been developed to directly achieve this. Here we solve this problem by extending recent advances using sequential variational autoencoders for dynamic latent variable modelling of neural data. Our system VaLPACa (Variational Ladders for Parallel Autoencoding of Calcium imaging data) solves the problem of disentangling deeper- and shallower-level dynamics by incorporating a ladder architecture that can infer a hierarchy of dynamical systems. Using some built-in inductive biases for calcium dynamics, we show that we can disentangle calcium flux from the underlying dynamics of neural computation. First, we demonstrate with synthetic calcium data that we can correctly disentangle an underlying Lorenz attractor from calcium dynamics. Next, we show that we can infer appropriate rotational dynamics in spiking data from macaque motor cortex after it has been converted into calcium fluorescence data via a calcium dynamics model. Finally, we show that our method applied to real calcium imaging data from primary visual cortex in mice allows us to infer latent factors that carry salient sensory information about unexpected stimuli. These results demonstrate that variational ladder autoencoders are a promising approach for inferring hierarchical dynamics in experimental settings where the measured variable has its own slow dynamics, such as calcium imaging data. Our new, open-source tool thereby provides the neuroscience community with the ability to apply dynamic latent variable modelling to a wider array of data modalities.


title: Neural responses to natural visual motion are spatially selective across the visual field, with selectivity differing across brain areas and task

abstract: It is well established that neural responses to visual stimuli are enhanced at select locations in the visual field. While spatial selectivity and the effects of spatial attention are well-understood for discrete tasks (e.g., visual cueing paradigms), little is known about neural response during a naturalistic visual experience that involves complex dynamic visual stimuli, for instance, driving. In this study, we assess the strength of neural responses across the visual space during a kart race video game. Specifically, we measure the correlation strength of scalp evoked potentials with optical flow magnitude at individual locations on the screen. We find the strongest neural responses for task-relevant locations in visual space, selectively extending to areas beyond the focus of overt attention: while the drivers gaze is directed upon the heading direction at the center of the screen, we observe robust neural evoked responses also to peripheral areas such as the road and surrounding buildings. Importantly, this spatial selectivity of neural responses differs across scalp locations. Moreover, during active gameplay, the strength of the spatially-selective neural responses are enhanced compared to passive viewing. Spatially selective neural gains have previously been interpreted as an attentional gain mechanism. In this view, the present data suggest that different brain areas focus attention on different task-relevant portions of the visual field, reaching beyond the focus of overt attention.


title: Implicit and explicit learning of Bayesian priors differently impacts bias during perceptual decision-making

abstract: Knowledge without awareness, or implicit knowledge, influences a variety of behaviors. It is unknown however, whether implicit knowledge of statistical structure informs visual perceptual decisions or whether explicit knowledge of statistical probabilities is required. Here, we measured visual decision-making performance using a novel task in which humans reported the orientation of two differently colored translational Glass patterns; each color associated with different orientation probabilities. The task design allowed us to assess participants ability to learn and use a general orientation prior as well as a color specific feature prior. Classifying decision-makers based on a questionnaire revealed that both implicit and explicit learners implemented a general orientation bias by adjusting the starting point of evidence accumulation in the drift diffusion model framework. Explicit learners additionally adjusted the drift rate offset. When subjects implemented a stimulus specific bias, they did so by adjusting primarily the drift rate offset. We conclude that humans can learn priors implicitly for perceptual decision-making and depending on awareness implement the priors using different mechanisms.


title: Accounting for dispersal improves the understanding of species abundance patterns

abstract: A long-standing question in ecology is how are species population distributed across space. The highest abundance has been hypothesized to be in the spatial or niche center, though mixed patterns from empirical studies has triggered a recent debate. Here we propose a conceptual framework based on environmental suitability and dispersal to interpret the mixed evidence. We demonstrate that the highest abundance could occur in the spatial center, in the niche center, or somewhere in-between the two centers, depending on the environmental setup and dispersal ability. We found that spatial and niche centers rarely overlap, suggesting the counteracting effect between the two factors, rather than reinforcement, is the norm in determining abundance patterns. The varied locations of highest abundance mirror the mixed evidence in literature, suggesting the "abundant-centre" and "abundant-niche centre" hypotheses are not mutually exclusive. This highlights the importance in understanding the biogeographic patterns through the lens of underlying mechanisms.

category: ecology


title: Disentangling effects of climate and land use on biodiversity and ecosystem services - a multi-scale experimental design

abstract:
O_LIClimate and land-use change are key drivers of environmental degradation in the Anthropocene, but too little is known about their interactive effects on biodiversity and ecosystem services. Long-term data on biodiversity trends are currently lacking. Furthermore, previous ecological studies have rarely considered climate and land use in a joint design, did not achieve variable independence or lost statistical power by not covering the full range of environmental gradients.
C_LIO_LIHere, we introduce a multi-scale space-for-time study design to disentangle effects of climate and land use on biodiversity and ecosystem services. The site selection approach coupled extensive GIS-based exploration and correlation heatmaps with a crossed and nested design covering regional, landscape and local scales. Its implementation in Bavaria (Germany) resulted in a set of study plots that maximizes the potential range and independence of environmental variables at different spatial scales.
C_LIO_LIStratifying the state of Bavaria into five climate zones and three prevailing land-use types, i.e. near-natural, agriculture and urban, resulted in 60 study regions covering a mean annual temperature gradient of 5.6-9.8 {degrees}C and a spatial extent of 380x360 km. Within these regions, we nested 180 study plots located in contrasting local land-use types, i.e. forests, grasslands, arable land or settlement (local climate gradient 4.5-10 {degrees}C). This approach achieved low correlations between climate and land-use (proportional cover) at the regional and landscape scale with |r [≤]0.33| and |r [≤]0.29|, respectively. Furthermore, using correlation heatmaps for local plot selection reduced potentially confounding relationships between landscape composition and configuration for plots located in forests, arable land and settlements.
C_LIO_LIThe suggested design expands upon previous research in covering a significant range of environmental gradients and including a diversity of dominant land-use types at different scales within different climatic contexts. It allows independent assessment of the relative contribution of multi-scale climate and land use on biodiversity and ecosystem services. Understanding potential interdependencies among global change drivers is essential to develop effective restoration and mitigation strategies against biodiversity decline, especially in expectation of future climatic changes. Importantly, this study also provides a baseline for long-term ecological monitoring programs.
C_LI


title: Moral Hazard Heterogeneity: Genes and Insurance Influence Smoking after a Health Shock

abstract:
Decision-making in the realm of health behaviors, such as smoking or drinking, is influenced both by biological factors, such as genetic predispositions, as well as environmental factors, such as financial liquidity and health insurance status. We show how the choice of smoking after a cardio-vascular health shock is jointly determined by the interaction between these biological and environmental constraints. Individuals who suffer a health shock when uninsured are 25.6 percentage points more likely to reduce smoking, but this is true only for those who have a low index of genetic predisposition to smoking. Individuals with a low index of genetic predisposition are more strategic and flexible in their behavioral response to an external shock. This differential elasticity of response depending on your genetic variants is evidence of individual-level heterogeneity in moral hazard. These results suggest that genetic heterogeneity is a factor that should be considered when evaluating the importance and fairness of health insurance policies.

JEL CODESI12, I13, D63, D91


title: Coordination of movement via complementary interactions of leaders and followers in termite mating pairs

abstract: Leadership of animal group movements depends on social feedback, hence leaders signals and followers responses should be attuned to each other. However, leader and follower roles are difficult to disentangle in species with high levels of coordination. To overcome this challenge, we investigated a simple case of movement coordination: termite pairs in which a female leads a male as they search for a nest site. To tease apart leader and follower roles, we created conspecific and heterospecific pairs of Coptotermes gestroi and C. formosanus, which share a pairing pheromone so that males follow females of either species. Conspecific pairs were stable for both species, even though C. gestroi females produce less pheromone than C. formosanus. Heterospecific pairs with C. gestroi males were also stable, but not those with C. formosanus males. We attributed this difference to the C. gestroi males unique capacity to follow females that release small amounts of pheromone; C. formosanus males cannot follow or reject C. gestroi females as unsuitable. This conclusion was supported by an information-theoretic analysis that detected information flow from C. formosanus females to C. gestroi males as in conspecific pairs, but not from C. gestroi females to C. formosanus males. Despite their following ability, C. gestroi males lost to C. formosanus males in competitions to follow C. formosanus females. Thus, partner selection has shaped the species-specific association of mating pairs. Our results demonstrate that a similar level of coordination can emerge from distinct sets of complementary sender-receiver interactions.

category: animal behavior and cognition


title: Evaluate effects of multiple users in collaborative Brain-Computer Interfaces: A SSVEP study

abstract: This study investigates the effects of collaboration on task performance in brain-computer interface (BCI) based on steady-state visually evoked potential (SSVEP). Navigation tasks were performed in a virtual environment under two conditions, e.g., individual performance and team performance. The results showed that average task completion time in the collaborative condition is decreased by 6 percent compared with that of individual performance, which is inline with other studies in collaborative BCI (cBCI) and joint decision-making. Our work is a step forward for the progress in BCI studies that include multi-user interactions.

category: bioengineering


title: Predicting functional consequences of mutations using molecular interaction network features

abstract: Variant interpretation remains a central challenge for precision medicine. Missense variants are particularly difficult to understand as they change only a single amino acid in protein sequence yet can have large and varied effects on protein activity. Numerous tools have been developed to identify missense variants with putative disease consequences from protein sequence and structure. However, biological function arises through higher order interactions among proteins and molecules within cells. We therefore sought to capture information about the potential of missense mutations to perturb protein interaction networks by integrating protein structure and interaction data. We developed 16 network-based annotations for missense mutations that provide orthogonal information to features classically used to prioritize variants. We then evaluated them in the context of a proven machine-learning framework for variant effect prediction across multiple benchmark datasets to demonstrate their potential to improve variant classification. Interestingly, network features resulted in larger performance gains for classifying somatic mutations than for germline variants, possibly due to different constraints on what mutations are tolerated at the cellular versus organismal level. Our results suggest that modeling variant potential to perturb context-specific interactome networks is a fruitful strategy to advance in silico variant effect prediction.

category: bioinformatics


title: cinaR: A comprehensive R package for the dif-ferential analyses and functional interpretation of ATAC-seq data

abstract:
SummaryATAC-seq is a frequently used assay to study chromatin accessibility levels. Differential chromatin accessibility analyses between biological groups and functional interpretation of these differential regions are essential in ATAC-seq data analyses. Although distinct methods and analyses pipelines are developed for this purpose, a stand-alone R package that combines state-of-the art differential and functional enrichment analyses pipelines is missing. To fill this gap, we developed cinaR (Chromatin Analyses in R), which is a single wrapper function and provides users with various data analyses and visualization options, including functional enrichment analyses with gene sets curated from multiple sources.

Availability and implementationcinaR is an R/CRAN package which is under GPL-3 License and its source code is freely accessible at https://CRAN.R-project.org/package=cinaR.

Gene sets are available at https://CRAN.R-project.org/package=cinaRgenesets.

Bone marrow ATAC-seq data is available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165120

Contactonur.karakaslar@jax.org or duygu.ucar@jax.org


title: cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data


title: Network diffusion for scalable embedding of massive single-cell ATAC-seq data

abstract:
With the rapid development of single-cell ATAC-seq technology, it has become possible to profile the chromatin accessibility of massive individual cells. However, it remains challenging to characterize their regulatory heterogeneity due to the high-dimensional, sparse and near-binary nature of data. Most existing data representation methods were designed based on correlation, which may be ill-defined for sparse data. Moreover, these methods do not well address the issue of excessive zeros. Thus, a simple, fast and scalable approach is needed to analyze single-cell ATAC-seq data with massive cells, address the "missingness" and accurately categorize cell types. To this end, we developed a network diffusion method for scalable embedding of massive single-cell ATAC-seq data (named as scAND). Specifically, we considered the near-binary single-cell ATAC-seq data as a bipartite network that reflects the accessible relationship between cells and accessible regions, and further adopted a simple and scalable network diffusion method to embed it. scAND can take information from similar cells to alleviate the sparsity and improve cell type identification. Extensive tests and comparison with existing methods using synthetic and real data as benchmarks demonstrated its distinct superiorities in terms of clustering accuracy, robustness, scalability and data integration.

AvailabilityThe Python-based scAND tool is freely available at http://page.amss.ac.cn/shihua.zhang/software.html.


title: The dynamics of cell-free DNA from urine and blood after a full marathon

abstract:
PurposeCell-free DNA (cfDNA) has been investigated as a minimally invasive biomarker for many diseases, particularly cancer. An increase in cfDNA has been observed during exercise. Neutrophil extracellular traps (NETs) may be the origin of cfDNA in response to acute exercise, but the mechanisms of generation of cfDNA during exercise remain unclear. In this study we investigated the dynamics of serum and urinary cfDNA levels and determined the relevance of other biomarkers to serum and urinary cfDNA levels and fragment size after a full marathon.

MethodsSamples were collected from 23 healthy male subjects. Blood and urine samples were collected before and immediately, two hours, and one day after the full marathon. The measurements included serum and urinary cfDNA, creatine kinase, myoglobin, creatinine, white blood cells, platelets, and lactoferrin from blood, and amylase, albumin, and creatinine from urine.

ResultsSerum and urinary cfDNA levels increased after a full marathon. Creatine kinase, myoglobin, and creatinine in blood, and albumin and creatinine in urine also increased significantly after a full marathon. Serum cfDNA showed peak values about 180 bp after the full marathon. Values over 1000 bp were present at two hours post-marathon. Urinary cfDNA showed peak values from 35 bp to 50 bp after the full marathon. Values over 1000 bp appeared at Immediately and two hours post marathon.

ConclusionThis study revealed that both serum and urinary cfDNA levels transiently increased after a full marathon. In addition, these cfDNA fragment varied in size.

category: physiology


title: Conditional Stomatal Closure in a Fern Shares Molecular Features with Flowering Plant Active Stomatal Responses

abstract:
Stomata evolved as plants transitioned from water to land, enabling carbon dioxide uptake and water loss to be controlled. In flowering plants, the most recently divergent land plant lineage, stomatal pores actively close in response to drought. In this response, the phytohormone abscisic acid (ABA) triggers signalling cascades that lead to ion and water loss in the guard cells of the stomatal complex, causing a reduction in turgor and pore closure. Whether this stimulus-response coupling pathway acts in other major land plant lineages is unclear, with some investigations reporting that stomatal closure involves ABA but others concluding that closure is passive. Here we show that in the model fern Ceratopteris richardii active stomatal closure is conditional on sensitisation by pre-exposure to either low humidity or exogenous ABA and is promoted by ABA. RNA-seq analysis and de novo transcriptome assembly reconstructed the protein coding complement of the C. richardii genome with coverage comparable to other plant models, enabling transcriptional signatures of stomatal sensitisation and closure to be identified. In both cases, changes in abundance of homologs of ABA, Ca2+ and ROS-related signalling components were observed, suggesting that the closure response pathway is conserved in ferns and flowering plants. These signatures further suggested that sensitisation is achieved by lowering the threshold required for a subsequent closure-inducing signal to trigger a response. We conclude that the canonical signalling network for active stomatal closure functioned in at least a rudimentary form in the stomata of the last common ancestor of ferns and flowering plants.

Significance StatementStomata are valve-like pores that control the uptake of CO2 and the loss of water vapour in almost all land plants. In flowering plants, stomatal opening and closure is actively regulated by a stimulus-response coupling network. Whether active stomatal responses are present in other land plant lineages such as ferns has been hotly debated. Here we show that stomatal responses in the fern Ceratopteris richardii are active but depend on their past growth environment, and demonstrate that fern stomatal closure and sensitisation are associated with the altered expression of genes whose homologs function in the canonical stomatal regulatory network of flowering plants. Genetic pathways for active stomatal regulation therefore most likely evolved before the divergence of ferns and flowering plants.


title: Smartphone-assisted real-time estimation of chlorophyll and carotenoid contents in spinach following the inversion of red and green color features

abstract:
PurposeChlorophyll (Chl) content is a reliable indicator of leaf nitrogen content and plant health status. Currently available methods for image-based Chl estimation require complex mathematical derivations and high-throughput imaging set-up along with multiplex image-preprocessing steps. Further, the influence of carotenoid (CAR) content has been largely ignored in the process. The present study describes a smartphone-based leaf image analysis method for real-time estimation of Chl content and Chl/CAR ratio.

MethodsColor features were obtained from RGB (red, green, blue) images of spinach leaves using a smartphone, and inverse R and G values were calculated. Correlation analysis of color indices and photosynthetic pigment (PP) contents was performed, followed by principal component analysis (PCA). Linear mathematical modeling was performed for describing regression equations for predicting PP contents.

Results1/R and 1/G showed strong positive linear correlation (0.93 < r2 < 0.96) with Chl and CAR contents, respectively. Furthermore, 1/R+1/G and [1/R]/[1/G] presented strong positive linear correlation with Chl + CAR (r2 = 0.95) and Chl/CAR (r2 = 0.88), respectively. PCA confirmed the association of color indices with the respective PP features, which were subsequently estimated using the correlation models. A smartphone-based companion application was developed using the linear models for non-invasive, real-time estimation of Chl content and Chl/CAR ratio.

ConclusionThe ratios 1/R and 1/G indicate the contents of Chl and CAR via linear models. The smartphone application developed using the linear models enables real-time estimation of Chl content and Chl/CAR ratio without complicated image preprocessing steps or mathematical derivations.


title: Minimal interplay between explicit knowledge, dynamics of learning and temporal expectations in different, complex uni- and multisensory contexts

abstract: While temporal expectations (TE) generally improve reactions to temporally predictable events, it remains unknown how temporal rule learning and explicit knowledge about temporal rules contribute to performance improvements and whether any contributions generalise across modalities. Here, participants discriminated the frequency of diverging auditory, visual or audiovisual targets embedded in auditory, visual or audiovisual distractor sequences. Temporal regularities were manipulated run-wise (early vs. late target within sequence). Behavioural performance (accuracy, RT) plus measures from a computational learning model all suggest that temporal rule learning occurred but did not generalise across modalities, that dynamics of learning (size of TE effect across runs) and explicit knowledge have little to no effect on the strength of TE, and that explicit knowledge affects performance - if at all - in a context dependent manner: only under complex task regimes (unknown target modality) might it partially help to resolve response conflict while it is lowering performance in less complex environments..


title: Context dependency of time-based event-related expectations for different modalities

abstract: Expectations about the temporal occurrence of events (when) are often tied with the expectations about certain event-related properties (what and where) happening at these time points. For instance, slowly waking up in the morning we expect our alarm clock to go off; however, the longer we do not hear it the more likely we already missed it. However, most current evidence for complex time-based event-related expectations (TBEEs) is based on the visual modality. Here we tested whether TBEEs can also act cross-modally. To this end, visual and auditory stimulus streams were presented which contained early and late targets embedded among distractors (to maximise temporal target uncertainty). Foreperiod-modality-contingencies were manipulated run-wise so that visual targets either occurred early in 80% of trials and auditory targets occurred late in 80 % of trials or vice versa. Participants showed increased sensitivity for expected auditory early/visual late targets which increased over time while the opposite pattern was observed for visual early/auditory late targets. A benefit in reaction times was only found for auditory early trials. Together, this pattern of results suggests that context-dependent TBEEs for auditory targets after short foreperiods (be they correct or not) dominated and determined which modality became more expected at the late position irrespective of the veridical statistical regularity. Hence, TBEEs in cross-modal and uncertain environments are context-dependent, shaped by the dominant modality in temporal tasks (i.e. auditory) and only boost performance cross-modally when expectations about the event after the short foreperiod match with the run-wise context (i.e. auditory early/visual late).


title: Lag structure of BOLD signals within white matter in resting-state fMRI

abstract:
PurposePrevious studies have demonstrated that BOLD signals in gray matter in resting-state functional MRI (RSfMRI) have variable time lags, representing apparent propagations of fMRI BOLD signals in gray matter. We complemented existing findings and explored the corresponding variations of signal latencies in white matter.

MethodsWe used data from the Brain Genomics Superstruct Project, consisting of 1412 subjects (both sexes included) and divided the dataset into ten equal groups to study both the patterns and reproducibility of latency estimates within white matter. We constructed latency matrices by computing cross-correlations between voxel pairs. We also applied a clustering analysis to identify functional networks within white matter, based on which latency analysis was also performed to investigate lead/lag relationship at network level. A dataset consisting of various sensory states (eyes closed, eyes open and eyes open with fixation) was also included to examine the relationship between latency structure and different states.

ResultsProjections of voxel latencies from the latency matrices were highly correlated (average Pearson correlation coefficient = 0.89) across the subgroups, confirming the reproducibility and structure of signal lags in white matter. Analysis of latencies within and between networks revealed a similar pattern of inter- and intra-network communication to that reported for gray matter. Moreover, a dominant direction, from inferior to superior regions, of BOLD signal propagation was revealed by higher resolution clustering. The variations of lag structure within white matter are associated with different sensory states.

ConclusionsThese findings provide additional insight into the character and roles of white matter BOLD signals in brain functions.


title: Latency structure of BOLD signals within white matter in resting-state fMRI


title: Inhibiting microglia proliferation after spinal cord injury improves recovery in mice and nonhuman primates

abstract:
No curative treatment is available for any deficits induced by spinal cord injury (SCI). Following injury, microglia undergo highly diverse activation processes, including proliferation, and play a critical role on functional recovery.

In a translational objective, we investigated whether a transient pharmacological reduction of microglia proliferation after injury is beneficial for functional recovery after SCI in mice and nonhuman primates. The colony stimulating factor-1 receptor (CSF1R) regulates proliferation, differentiation, and survival of microglia, we thus used an oral administration of GW2580, a CSF1R inhibitor.

First, transient post-injury GW2580 administration in mice improves motor function recovery, promotes tissues preservation and/or reorganization (identified by coherent anti-stokes Raman scattering microscopy), and modulates glial reactivity.

Second, post-injury GW2580-treatment in nonhuman primates reduces microglia proliferation, improves functional motor function recovery, and promotes tissue protection. Notably, three months after lesion microglia reactivity returned to baseline value.

Finally, to initiate the investigation on molecular mechanisms induced by a transient post-SCI GW2580-treatment, we used microglia-specific transcriptomic analysis in mice. Notably, we detected a downregulation in the expression of inflammatory-associated genes and we identified genes that were up-regulated by SCI and further downregulated by the treatment.

Thus, a transient oral GW2580 treatment post-injury may provide a promising therapeutic strategy for SCI patients and may also be extended to other central nervous system disorders displaying microglia activation.


title: Limb apparent motion perception: modification by tDCS, and clinically or experimentally altered bodily states

abstract: Limb apparent motion perception (LAMP) refers to the illusory visual perception of a moving limb upon observing two rapidly alternating photographs depicting the same limb in two different postures. Fast stimulus onset asynchronies (SOAs) induce the more visually guided perception of physically impossible movements. Slow SOAs induce the perception of physically possible movements. According to the motor theory of LAMP, the latter perception depends upon the observers sensorimotor representations. Here, we tested this theory in two independent studies by performing a central (study 1) and peripheral (study 2) manipulation of the bodys sensorimotor states during two LAMP tasks. In the first sham-controlled transcranial direct current stimulation between-subject designed study, we observed that the dampening of left sensorimotor cortex activity through cathodal stimulation biased LAMP towards the more visually guided perception of physically impossible movements for stimulus pairs at slow SOAs. In the second, online within-subject designed study, we tested three participant groups twice: (1) individuals with an acquired lower limb amputation, either while wearing or not wearing their prosthesis; (2) individuals with body integrity dysphoria (i.e., with a desire for amputation of a healthy leg) while sitting in a regular position or binding up the undesired leg (to simulate the desired amputation); (3) able-bodied individuals while sitting in a normal position or sitting on one of their legs. We found that the momentary sensorimotor state crucially impacted LAMP in individuals with an amputation and able-bodied participants, but not in BID individuals. Taken together, the results of these two studies substantiate the motor theory of LAMP.


title: Sleep deprivation exacerbates seizures and diminishes GABAergic tonic inhibition

abstract: Patients with epilepsy report that sleep deprivation is a common trigger for breakthrough seizures. The basic mechanism of this phenomenon is unknown. In the Kv1.1-/- mouse model of epilepsy, daily sleep deprivation indeed exacerbated seizures though these effects were lost after the 3rd day. Sleep deprivation also accelerated mortality in ~52% of Kv1.1-/- mice, not observed in controls. Voltage-clamp experiments on the day after recovery from sleep deprivation showed reductions in GABAergic tonic inhibition in dentate granule cells both in Kv1.1-/- and wild-type mice. Our results suggest that sleep deprivation is detrimental to seizures and survival, possibly due to reductions in GABAergic tonic inhibition.


title: Cross-modal perceptual enhancement of unisensory targets is uni-directional and does not affect temporal expectations

abstract: Previous studies demonstrated that redundant target stimuli can enhance performance due to multisensory interplay and interactively facilitate performance enhancements due to temporal expectations (TE; faster and accurate reactions to temporally expected targets). Here we tested whether other types of multisensory interactions - i.e. interactions evoked by temporally flanking irrelevant stimuli - can result in similar performance patterns and boost not only unisensory target perception (multi-vs. unisensory sequences) but also unisensory temporal expectations (expected vs. unexpected). To test our hypothesis, we presented sequences of 12 stimuli (10 Hz) which either consisted of auditory (A), visual (V) or alternating auditory-visual stimuli (e.g. A-V-A-V-...) with either auditory (AV(A)) or visual (AV(V)) targets. Participants had to discriminate target frequency which was unpredictable by temporal regularities (expected vs. unexpected target positions) and by stimulation sequence (A, V, AV(A), AV(V)). Moreover, we ran two experiments in which we presented redundant multisensory targets and manipulated the speed of the stimulation sequence (10 vs. 15 Hz stimulus trains) to control whether the results of Experiment 1 depended on sequence speed. Performance for unisensory targets was affected by temporally flanking distractors, with multisensory interactions selectively improving unisensory visual target perception. Yet, only redundant multisensory targets reliably affected TEs. Together, these results indicate that cross-modal facilitation of unisensory target perception in fast stimulus streams is uni-directional, but also differs from multisensory interactions evoked by redundant targets; more specifically, it appears to be context-dependent (task, design etc.) whether unisensory stimulation (unlike redundant target stimulation) allows for the generation of temporal expectations.


title: Odor-evoked Increases in Spiking Variability in the Olfactory Bulb

abstract:
At the onset of sensory stimulation, the variability and co-variability of spiking activity is widely reported to decrease, especially in cortex. Considering the potential benefits of such decreased variability for coding, it has been suggested that this could be a general principle governing all sensory systems. Here we show that this is not so. We recorded mitral cells in olfactory bulb (OB) of anesthetized rats and found increased variability and co-variability of spiking at the onset of olfactory stimulation. Using models and analysis, we predicted that these increases arise due to network interactions within OB, without increasing variability of input from the nose. We tested and confirmed this prediction in awake animals with direct optogenetic stimulation of OB to circumvent the pathway through the nose. Our results establish increases in spiking variability at stimulus onset as a viable alternative coding strategy to the more commonly observed decreases in variability in many cortical systems.

SummaryThe spiking variability of neural networks has important implications for how information is encoded to higher brain regions. It has been well documented by numerous labs in many cortical and motor regions that spiking variability decreases with stimulus onset, yet whether this principle holds in the olfactory bulb has not been tested. In stark contrast to this common view, we demonstrate that the onset of sensory input can cause an increase in the variability of neural activity in the mammalian olfactory bulb. We show this in both anesthetized and awake rodents. Furthermore, we use computational models to describe the mechanisms of this phenomenon. Our finding establish sensory evoked increases in spiking variability as a viable alternative.


title: Odor-evoked Increases in Olfactory Bulb Mitral Cell Spiking Variability


title: Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases

abstract: Elevated N-linked glycosylation of immunoglobulin G variable regions (IgG-VN-Glyc) is an emerging molecular phenotype associated with autoimmune disorders. To test the broader specificity of elevated IgG-VN-Glyc, we studied patients with distinct subtypes of myasthenia gravis (MG), a B cell-mediated autoimmune disease. Our experimental design included adaptive immune receptor repertoire sequencing to quantify and characterize N-glycosylation sites in the global B cell receptor repertoire, proteomics to examine glycosylation patterns of the circulating IgG, and production of human-derived recombinant autoantibodies, which were studied with mass spectrometry and antigen binding assays to confirm occupation of glycosylation sites and determine whether they alter binding. We found that the frequency of IgG-VN-Glyc motifs was increased in the B cell repertoire of MG patients when compared to healthy donors. Motifs were introduced by both biased V gene segment usage and somatic hypermutation. IgG-VN-Glyc could be observed in the circulating IgG in a subset of MG patients. Autoantigen binding, by patient-derived MG autoantigen-specific monoclonal antibodies with experimentally confirmed presence of IgG-VN-Glyc, was not altered by the glycosylation. Our findings extend prior work on patterns of variable region N-linked glycosylation in autoimmunity to MG subtypes. Although occupied IgG-VN-Glyc motifs are found on MG autoantigen-specific monoclonal antibodies, they are not required for binding to the autoantigen in this disease.


title: An Automated Radio-Telemetry System (ARTS) for Monitoring Small Mammals

abstract:
Point 1: The study of animals in nature is essential for developing an ecologically valid understanding of behavior. Small mammals, however, are often fossorial and exceedingly difficult to monitor in the wild. This limits both the taxonomic scope of field observation, and excludes species that are powerful models for the study of behavioral mechanisms.

Point 2: Here, we implement an automated radio telemetry system (ARTS) designed to track small fossorial mammals. Our ARTS uses an isotropic antenna array coupled with broadband receivers. We characterized transmission at our study site and tested the ARTS ability to track 48 prairie voles.

Point 3: We compared position estimates from nonlinear least squares, nonparameteric, and Bayesian trilateration methods and found Bayesian trilateration to have the smallest error. To examine the ability of the system to track biologically significant behavior we used ARTS data to investigate circadian rhythms of freely behaving prairie voles. We used Lomb-Scargle analysis to estimate periodic patterns from irregularly sampled time series of speed. Prairie voles demonstrated ultradian movement at periods of approximately 45 and 90 min, observations on a time scale not possible using data from traditional methods.

Point 4: This ARTS offers a new tool to observe rodent field behavior at time scales and in environments which have not been previously possible, such as investigating social and spatial behaviors on the scale of minutes, hours, and days in natural environments.


title: Temperature-dependent use of daily torpor attenuates the energetic consequences of habitat selection for a widespread bat

abstract: Homeothermy requires increased metabolic rates as temperatures decline below the thermoneutral zone, so homeotherms typically select microhabitats within or near their thermoneutral zones during periods of inactivity. However, many mammals and birds are heterotherms that relax internal controls on body temperature when maintaining a high, stable body temperature is energetically costly. Such heterotherms should be less tied to microhabitats near their thermoneutral zones, and because heterotherms spend more time in torpor and expend less energy at colder temperatures, heterotherms may even select microhabitats in which temperatures are well below their thermoneutral zones. We studied how temperature and daily torpor influence selection of diurnal roosts by a heterothermic bat (Myotis thysanodes). We (1) quantified the relationship between ambient temperature and daily duration of torpor, (2) simulated daily energy expenditure over a range of microhabitat (roost) temperatures, and (3) quantified the influence of roost temperature on roost selection. While warm roosts substantially reduced energy expenditure of simulated homeothermic bats, heterothermic bats modulated their use of torpor to maintain a constant level of energy expenditure over the course of a day. Daily torpor expanded the range of energetically economical microhabitats, such that roost selection was independent of roost temperature. Our work adds to a growing literature documenting functions of torpor beyond its historical conceptualization as a last-resort measure to save energy during extended or acute energetic stress.


title: Daily torpor reduces the energetic consequences of habitat selection for a widespread bat


title: Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions

abstract: The quest to map the genetic foundations of phenotypes has been empowered by the modern diversity, quality, and availability of genomic resources. Despite these expanding resources, the abundance of variation within lineages makes the association of genetic change to specific phenotypes improbable. Drawing such connections requires an a priori means of isolating the associated changes from background genomic variation. Evolution may provide these means via convergence; i.e., the shared variation that may result from replicate evolutionary experiments across independent trait occurrences. To leverage these opportunities, we developed TRACCER: Topologically Ranked Analysis of Convergence via Comparative Evolutionary Rates. As compared to current methods, this software empowers rate convergence analysis by factoring in topological relationships, because variation between phylogenetically proximate trait changes is more likely to be facilitating the trait. Pairwise comparisons are performed not with singular branches, but in reference to their most recent common ancestors. This ensures that comparisons represent identical genetic contexts and timeframes while obviating the problematic requirement of assigning ancestral states. We applied TRACCER to two case studies: marine mammal transitions, an unambiguous trait which has independently evolved three times, as well as the evolution of mammalian longevity, a less delineated trait but with more instances to compare. TRACCER, by factoring in topology, identifies highly significant, convergent genetic signals in these test cases, with important incongruities and statistical resolution when compared to existing convergence approaches. These improvements in sensitivity and specificity generate refined targets for downstream analysis of convergent evolution and identification of genotype-phenotype relationships.


title: Spontaneously Hypertensive Rat substrains show differences in premorbid addiction vulnerability traits and cocaine self-administration: Implications for a novel rat reduced complexity cross

abstract:
Forward genetic mapping of F2 crosses between closely related substrains of inbred rodents - referred to as a reduced complexity cross (RCC) - is a relatively new strategy for accelerating the pace of gene discovery for complex traits, such as drug addiction. RCCs to date were generated in mice, but rats are thought to be optimal for addiction genetic studies. Based on past literature, one inbred Spontaneously Hypertensive Rat substrain, SHR/NCrl, is predicted to exhibit a distinct behavioral profile as it relates to cocaine vulnerability traits relative to another substrain, SHR/NHsd. Direct substrain comparisons are a necessary first step before implementing an RCC. We evaluated a number of premorbid addiction vulnerability traits and cocaine self-administration behaviors using a longitudinal within-subjects design. Trait impulsivity and compulsivity were greater in SHR/NCrl than SHR/NHsd, as were reactivity to sucrose reward, sensitivity to acute psychostimulant effects of cocaine, and cocaine abuse liability studied under fixed-ratio and chained schedules of cocaine self-administration. Trait compulsivity correlated with the acute psychostimulant effects of cocaine, which in turn correlated with cocaine taking under the chained schedule. Trait compulsivity also was the best predictor of cocaine seeking responses. Heritability estimates indicated that 22%-40% of the variances for the above phenotypes can be explained by additive genetic factors, providing sufficient genetic variance to conduct genetic mapping in F2 crosses of SHR/NCrl and SHR/NHsd. These results provide compelling support for using an RCC approach in SHR substrains to uncover candidate genes and variants that are of relevance to cocaine use disorders.

HighlightsO_LIClosely related SHR substrains have distinct cocaine vulnerability traits
C_LIO_LIInhibitory control was poorer in SHR/NCrl than SHR/NHsd
C_LIO_LISHR/NCrl were more sucrose reactive and sensitive to acute cocaine than SHR/NHsd
C_LIO_LICocaine abuse liability was greater in SHR/NCrl than SHR/NHsd
C_LIO_LISHR substrains can be used in an RCC to uncover cocaine vulnerability genes & variants
C_LI


title: A Kiosk Station for the Assessment of Multiple Cognitive Domains and Enrichment of Monkeys

abstract:
BackgroundNonhuman primates (NHPs) are self-motivated to perform cognitive tasks on touchscreens in their animal housing setting. To leverage this ability, fully integrated hardware and software solutions are needed, that work within housing and husbandry routines while also spanning cognitive task constructs of the Research Domain Criteria (RDoC).

New MethodWe describe a Kiosk Station (KS-1) that provides robust hardware and software solutions for running cognitive tasks in cage-housed NHPs. KS-1 consists of a frame for mounting flexibly on housing cages, a touchscreen animal interface with mounts for receptables, reward pumps and cameras, and a compact computer cabinet with an interface for controlling behavior. Behavioral control is achieved with a unity3D program that is virtual-reality capable, allowing semi-naturalistic visual tasks to assess multiple cognitive domains.

ResultsKS-1 is fully integrated into the regular housing routines of monkeys. A single person can operate multiple KS-1s. Monkeys engage with KS-1 at high motivation and cognitive performance levels at high intra-individual consistency.

Comparison with Existing MethodsKS-1 is optimized for flexible mounting onto standard apartment cage systems. KS-1 has a robust animal interface with options for gaze/reach monitoring. It has an integrated user interface for controlling multiple cognitive task using a common naturalistic object space designed to enhance task engagement. All custom KS-1 components are open-sourced.

ConclusionsKS-1 is a versatile tool for cognitive profiling and enrichment of cage-housed monkeys. It reliably measures multiple cognitive domains which promises to advance our understanding of animal cognition, inter-individual differences and underlying neurobiology in refined, ethologically meaningful behavioral foraging contexts.


title: In vivo co-registered hybrid-contrast imaging by successive photoacoustic tomography and magnetic resonance imaging

abstract: Magnetic resonance imaging (MRI) and photoacoustic tomography (PAT) are two advanced imaging modalities that offer two distinct image contrasts: MRI has a multi-parameter contrast mechanism that provides excellent anatomical soft tissue contrast, whereas PAT is capable of mapping tissue physiological metabolism and exogenous contrast agents with optical specificity. Attempts have been made to integrate these two modalities, but rigid and reliable registration of the images for in vivo imaging is still challenging. In this paper, we present a complete hardware-software solution for the successive acquisition and co-registration of PAT and MRI images in in vivo animal studies. Based on commercial PAT and MRI scanners, our solution includes a 3D-printed dual-modality animal imaging bed, a 3-D spatial image co-registration algorithm with bi-model markers, and a robust modality switching protocol for in vivo imaging studies. Using the proposed solution, we successfully demonstrated co-registered hybrid-contrast PAT-MRI imaging that simultaneously display multi-scale anatomical, functional and molecular characteristics on healthy and cancerous living mice. Week-long longitudinal dual-modality imaging of tumor development reveals information on size, border, vascular pattern, blood oxygenation, and molecular probe metabolism of the tumor micro-environment at the same time. Additionally, by incorporating soft-tissue information in the co-registered MRI image, we further show that PAT image quality could be enhanced by MRI-guided light fluence correction. The proposed methodology holds the promise for a wide range of pre-clinical research applications that benefit from the PAT-MRI dual-modality image contrast.


title: Multiplexed Ion Beam Imaging Readout of Single-Cell Immunoblotting

abstract: Improvements in single-cell protein analysis are required to study the cell-to-cell variation inherent to diseases, including cancer. Single-cell immunoblotting (scIB) offers proteoform detection specificity, but often relies on fluorescence-based readout and is therefore limited in multiplexing capability. Among rising multiplexed imaging methods is multiplexed ion beam imaging by time of flight (MIBI-TOF), a mass spectrometry imaging technology. MIBI-TOF employs metal-tagged antibodies that do not suffer from spectra overlap to the same degree as fluorophore-tagged antibodies. We report for the first-time MIBI-TOF of single-cell immunoblotting (scIB-MIBI-TOF). The scIB assay subjects single-cell lysate to protein immunoblotting on a microscale device consisting of a 50- to 75-m thick hydrated polyacrylamide (PA) gel matrix for protein immobilization prior to in-gel immunoprobing. We confirm antibody-protein binding in the PA gel with indirect fluorescence readout of metal-tagged antibodies. Since MIBI-TOF is a layer-by-layer imaging technique, and our protein target is immobilized within a 3D PA gel layer, we characterize the protein distribution throughout the PA gel depth by fluorescence confocal microscopy and find that the highest signal-to-noise ratio is achieved by imaging the entirety of the PA gel depth. Accordingly, we report the required MIBI-TOF ion dose strength needed to image varying PA gel depths. Lastly, by imaging ~42% of PA gel depth with MIBI-TOF, we detect two isoelectrically separated TurboGFP (tGFP) proteoforms from individual glioblastoma cells, demonstrating that highly multiplexed mass spectrometry-based readout is compatible with scIB.


title: Single-cell RNA-seq revealed the role of Alkbh5 in reproduction

abstract: This manuscript has been withdrawn by the authors as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author


title: BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models

abstract:
As the reconstruction of Genome-Scale Metabolic Models becomes standard practice in systems biology, the number of organisms having at least one metabolic model at the genome-scale is peaking at an unprecedented scale. The automation of several laborious tasks, such as gap-finding and gap-filling, allowed to develop GSMMs for poorly described organisms. However, such models quality can be compromised by the automation of several steps, which may lead to erroneous phenotype simulations.

The Biological networks constraint-based In Silico Optimization (BioISO) is a computational tool aimed at accelerating the reconstruction of Genome-Scale Metabolic Models. This tool facilitates the manual curation steps by reducing the large search spaces often met when debugging in silico biological models. BioISO uses a recursive relation-like algorithm and Flux Balance Analysis to evaluate and guide debugging of in silico phenotype simulations. The potential of BioISO to guide the debugging of model reconstructions was showcased using GSMMs available in literature and compared with the results of two other state-of-the-art gap-filling tools (Meneco and fastGapFill). Furthermore, BioISO was used as Menecos gap-finding algorithm to reduce the number of proposed solutions (reaction sets) for filling the gaps.

BioISO was implemented as a webserver available at https://bioiso.bio.di.uminho.pt; and integrated into merlin as a plugin. BioISOs implementation as a Python package can also be retrieved from https://github.com/BioSystemsUM/BioISO.

category: systems biology


title: Multiple bouts of high-intensity interval exercise reverse age-related functional connectivity disruptions without affecting motor learning in older adults

abstract:
Exercise has emerged as an intervention that may mitigate age-related resting state functional connectivity and sensorimotor declines. Here, 42 healthy older adults rested or completed 3 sets of high-intensity interval exercise for a total of 23 minutes, then immediately practiced an implicit motor task with their non-dominant hand across five separate sessions. Participants completed resting stage functional MRI before the first and after the fifth day of practice; they also returned 24-hours and 35-days later to complete short- and long-term retention. Independent component analysis of resting state functional MRI revealed increased connectivity in the frontoparietal, the dorsal attentional, and cerebellar networks and group. seed-based analysis showed strengthened connectivity between the limbic system and right cerebellum, and between the right cerebellum and bilateral middle temporal gyri in the exercise group. There was no motor learning advantage for the exercise group. Our data suggest that exercise paired with an implicit motor learning task in older adults can augment resting state functional connectivity without enhancing behaviour beyond that stimulated by skilled motor practice.

Impact statementFive separate bouts of exercise paired with skilled motor practice strengthens resting state networks in brain regions that are susceptible to declines in older adults without affecting motor acquisition or learning.


title: Genetic inactivation of SARM1 axon degeneration pathway improves outcome trajectory after experimental traumatic brain injury based on pathological, radiological, and functional measures

abstract: Traumatic brain injury (TBI) causes chronic symptoms and increased risk of neurodegeneration. Axons in white matter tracts, such as the corpus callosum (CC), are critical components of neural circuits and particularly vulnerable to TBI. Treatments are needed to protect axons from traumatic injury and mitigate post-traumatic neurodegeneration. The Sarm1 gene is a central driver of axon degeneration through a conserved molecular pathway. Sarm1-/- mice with knockout (KO) of the Sarm1 gene enable genetic proof-of-concept testing of Sarm1 inactivation as a therapeutic target. We evaluated Sarm1 deletion effects after TBI using a concussive model that causes traumatic axonal injury and progresses to CC atrophy at 10 weeks, indicating post-traumatic neurodegeneration. Sarm1 wild-type (WT) mice developed significant CC atrophy that was reduced in Sarm1 KO mice. Using electron microscopy to quantify individual axons demonstrated that Sarm1 KO preserved more intact axons and reduced damaged or demyelinated axons. MRI in live mice identified significantly reduced CC volume after TBI in Sarm1 WT mice that was attenuated in Sarm1 KO mice. MR diffusion tensor imaging detected reduced fractional anisotropy in both genotypes while axial diffusivity remained higher in Sarm1 KO mice. Immunohistochemistry revealed significant attenuation of CC atrophy, myelin loss, and neuroinflammation in Sarm1 KO mice after TBI. Functionally, TBI resulted in late-stage motor learning and sleep deficits that were ameliorated in Sarm1 KO mice. Based on these findings, Sarm1 inactivation can protect axons and white matter tracts to improve translational outcomes associated with CC atrophy and post-traumatic neurodegeneration.


title: Increased disease burden in Interleukin-3 deficient mice after Mycobacterium tuberculosis and herpes simplex virus infections

abstract: Interleukin-3 (IL-3) is produced during infections caused by parasites, bacteria and viruses, but its contribution to immunity in this context remains largely unknown. In mouse models of parasitic infections, in which the effects of IL-3 have been most extensively studied, IL-3 has been variously reported as protective, detrimental or inconsequential. Similarly, mixed results have been reported in viral and bacterial infection models. Here, we investigated the effects of IL-3 in mouse models of Mycobacterium tuberculosis and herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2) infections by assessing the pathogen burden, disease manifestations and survival following infection. After infection with M. tuberculosis, IL-3 deficient mice showed higher bacillary burden, increased lung pathology and reduced survival compared to wild type mice. After infection with HSV-1 through cutaneous route and HSV-2 through vaginal route, IL-3 deficient mice showed higher viral burden, increased disease manifestations and reduced survival compared to wild type mice. Our results show that IL-3 makes a subtle but significant contribution to protective immunity in these mouse models of bacterial and viral infections.


title: Nitric oxide synthases from photosynthetic organisms improve growth and confer nitrosative stress tolerance in E. coli. Insights on the pterin cofactor

abstract:
Nitric oxide synthase (NOS) synthesizes NO from the substrate L-arginine (Arg). NOS with distinct biochemical properties were characterized from two photosynthetic microorganisms, the unicellular algae Ostreococcus tauri (OtNOS) and the cyanobacteria Synechococcus PCC 7335 (SyNOS). In this work we studied OtNOS and SyNOS recombinantly expressed in E. coli and analyzed bacterial growth and tolerance to nitrosative stress. Results show that the expression of OtNOS and SyNOS promotes bacterial growth and allows metabolizing Arg as N source. In accordance to a high NO producing activity, OtNOS expression induces the hmp flavohemoglobin in E. coli, suggesting that this strain is sensing nitrosative stress. The addition of 1 mM of the NO donor sodium nitroprusside (SNP) is toxic and generates a strong nitrosative stress. The expression of OtNOS or SyNOS reduced SNP toxicity restoring bacterial growth. Finally, using bioinformatic tools and ligand docking analyses, we propose tetrahydromonapterin (MH4), an endogenous pterin found in E. coli, as potential cofactor required for NOS catalytic activity. Our findings could be useful for the development of biotechnological applications using NOS expression to improve growth in bacteria.

Key points- The NO synthase (NOS) from photosynthetic microorganisms were expressed in E. coli
- Expression of NOS increases bacterial growth and tolerance to nitrosative stress.
- Ligand docking analyses indicate tetrahydromonapterin (MH4) as potential NOS cofactor in E. coli.


title: Fluidics System for Resolving Concentration-Dependent Effects of Dissolved Gases on Tissue Metabolism

abstract: Oxygen (O2) and other dissolved gases such as the gasotransmitters H2S, CO and NO affect cell metabolism and function. To evaluate effects of dissolved gases on processes in tissue, we developed a fluidics system that controls dissolved gases while simultaneously measuring parameters of electron transport, metabolism and secretory function. We use pancreatic islets, retina and liver to highlight its ability to assess effects of O2 and H2S. Protocols aimed at emulating hypoxia-reperfusion conditions resolved a previously unrecognized transient spike in O2 consumption rate (OCR) following replenishment of O2, and tissue-specific recovery of OCR following hypoxia. The system revealed both inhibitory and stimulatory effects of H2S on insulin secretion rate from isolated islets. The unique ability of this new system to quantify metabolic state and cell function in response to precise changes in dissolved gases provides a powerful platform for cell physiologists to study a wide range of disease states.

category: cell biology


title: A feedback mechanism mediated by myosin II-dependent apical targeting of Rab11 vesicles reinforces apical constriction

abstract: During tissue morphogenesis, cell shape changes resulting from cell-generated forces often require active regulation of intracellular trafficking. How mechanical stimuli influence intracellular trafficking and how such regulation impacts tissue mechanics are not fully understood. In this study, we identify an actomyosin dependent mechanism involving Rab11- mediated trafficking in regulating apical constriction in the Drosophila embryo. During Drosophila mesoderm invagination, apical actin and Myosin II (actomyosin) contractility induces apical accumulation of Rab11-marked vesicle-like structures ("Rab11 vesicles") by promoting a directional bias in dynein mediated vesicle transport. At the apical domain, Rab11 vesicles are enriched near the adherens junctions (AJs). The apical accumulation of Rab11 vesicles is essential to prevent fragmented apical AJs, breaks in the supracellular actomyosin network and a reduction in the apical constriction rate. This Rab11 function is separate from its role in promoting apical Myosin II accumulation. These findings suggest a feedback mechanism between actomyosin activity and Rab11-mediated intracellular trafficking that regulates the force generation machinery during tissue folding.


title: Actomyosin activity-dependent apical targeting of Rab11 vesicles reinforces apical constriction