title: The Global Register of Introduced and Invasive Species: Country Compendium

abstract:
The Country Compendium of the Global Register of Introduced and Invasive Species (GRIIS) is a collation of data across 196 individual country checklists of alienspecies, along with a designation of those species with evidence of impact at a country level. The Compendium provides a baseline for monitoring the distribution and invasion status of all major taxonomic groups, and can be used for the purpose of global analyses of Introduced (alien, non-native, exotic) and Invasive species (invasive alien species), including regional, single and multi-species taxon assessments and comparisons. It enables exploration of gaps and inferred absences of species for countries, and provides a means for short to medium term refinement of GRIIS Checklists. The Country Compendium is, for example, instrumental, along with data on first records of introduction, for assessing and reporting on invasive alien species targets, including for the Convention on Biological Diversity and Sustainable Development Goals. The GRIIS Country Compendium provides a baseline and mechanism for tracking the spread of introduced and invasive alien species across countries globally.

O_TBL View this table:
org.highwire.dtl.DTLVardef@eb30fdorg.highwire.dtl.DTLVardef@dd338aorg.highwire.dtl.DTLVardef@62b8daorg.highwire.dtl.DTLVardef@1561763org.highwire.dtl.DTLVardef@119988e_HPS_FORMAT_FIGEXP  M_TBL C_TBL


title: DNA metabarcoding reveals the threat of rapidly expanding barred owl populations to native wildlife in western North America

abstract: Invasive predators can have detrimental impacts on native species and biological communities through direct consumptive effects and indirect effects on trophic interactions. As an invasive, apex predator achieving high densities, barred owls (Strix varia) may pose a substantial threat to native wildlife in western North American forests. Studies of the trophic ecology of barred owls in their invasive range, however, have involved morphological examinations of prey remains with limited taxonomic resolution. We conducted DNA metabarcoding using intestinal samples collected from barred owls at the leading edge of their range expansion in northeastern California. Using customized primers, we screened the intestinal contents of 124 barred owls and detected a broad diet of 78 unique prey types (48 vertebrates and 30 invertebrates), including many previously undetected prey types. Mammals were the most consumed vertebrate class (frequency of occurrence = 65%), followed by amphibians (32%), birds (22%), and reptiles (19%). Diets differed regionally but were similar among ages and sexes and exhibited limited variation in response to local environmental conditions. Our work highlights the generalist predatory strategy of invasive barred owls, indicates that they will not serve as ecological replacements for the congeneric spotted owls (S. occidentalis) they displace, and identifies numerous native species potentially threatened by their range expansion. Expanding currently limited barred owl removals could benefit native species and wildlife communities in western North America. More broadly, DNA metabarcoding provides a powerful tool for conducting detailed assessments of species consumed by invasive predators, potentially incentivizing conservation actions and improving outcomes.

category: ecology


title: Evaluating drivers of spatiotemporal individual condition of a bottom-associated marine fish

abstract: A fishs body condition is described by its weight given its length and is often positively associated with fitness. Atlantic cod (Gadus morhua) in the south-eastern Baltic Sea has experienced a drastic deterioration of its physiological status since the early 1990s to levels that compromise the growth or even survival of the population. Several hypotheses have been proposed (e.g., competition, hypoxia, lack of prey) and evaluated temporally using averages over large spatial scales (basin or population level). However, as these variables operate at local spatial scales and are heterogenous in space, it is important to evaluate the link between body condition and covariates on local scales as well. By applying a geostatistical model that includes spatially and spatiotemporally correlated random effects using Gaussian Markov random fields, we analyze the body condition of cod in the autumn (main feeding season) in relation to biotic and abiotic covariates at different spatial scales and their spatiotemporal dynamics. We find that body condition declined over the whole domain until 2008, after which a plateau was reached. Oxygen, sprat biomass (at the subdivision level), haul-level temperature, and the biomass of the benthic isopod Saduria entomon (to a lesser extent) where positively related to condition, whereas the haul-level density of cod and depth were negatively associated with condition. However, the effect sizes of these variables were small, such that even though cod are now found in deeper and less-oxygenated waters, this could not alone explain the steep decline that occurred between 1993-2008. In fact, latent spatial and spatiotemporal variation was several times larger in magnitude than any single covariates coefficient, and spatial and spatiotemporal random effects explained 6.5 times more variation than all fixed effects. However, body condition is a complicated trait to analyze as it builds up over a long time period. Hence, observational analysis of condition data should be complemented with e.g., tagging studies or otoliths analyses, before mechanistic links between condition and covariates can be determined. Understanding the drivers of spatiotemporal variation in body condition is critical for identifying impacts of environmental change and for the management of marine fish and fisheries.


title: Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure

abstract: Genome-wide association studies (GWAS) have mapped thousands of variants for numerous polygenic traits and diseases. However, with some exceptions, mechanistic understanding of which precise variants affect which genes in which tissues to modulate trait variation is still lacking. To this end, we introduce a novel class of genomic analyses applicable to any complex trait using GWAS together with gene expression and chromatin accessibility data from multiple tissues. Here we identify the transcription factors (TFs) and regulatory variants within active enhancers regulating specific genes in individual tissues to explain trait heritability of blood pressure (BP), a classical polygenic trait. We show that kidney-, adrenal-, heart-, and arterial-specific regulatory variants contribute to 2.5%, 5.3%, 7.7%, and 11.8% of variant heritability, respectively. Collectively, [~]500,000 predicted regulatory variants across these four tissues explain 33.4% of variant heritability. We demonstrate that these variants are enriched in enhancers binding specific TFs in each tissue. Our findings suggest that gene regulatory networks perturbed by common regulatory variants in a tissue relevant to a phenotype are the primary source of interindividual variation of BP. These studies provide an approach to scan each human tissue for its physiological contribution to a trait.

category: genetics


title: Commercial ChIP-Seq library preparation kits performed differently for different classes of protein targets

abstract:
BackgroundChIP-Seq is a powerful method commonly used to study global protein-DNA interactions including both transcription factors and histone modifications. We have found that the choice of ChIP-Seq library preparation protocol plays an important role in overall ChIP-Seq data quality. However, very few studies have compared ChIP-Seq libraries prepared by different protocols using multiple targets and a broad range of input DNA levels.

ResultsIn this study, we evaluated the performance of four ChIP-Seq library preparation protocols [NEB NEBNext Ultra II, Roche KAPA HyperPrep, Diagenode MicroPlex, and Bioo (now PerkinElmer) NEXTflex] on three target proteins, chosen to represent the three typical signal enrichment patterns in ChIP-Seq experiments: sharp peaks (H3K4me3), broad domains (H3K27me3) and punctate peaks with a protein binding motif (CTCF). We also tested a broad range of different input DNA levels from 0.10 to 10 ng for H3K4me3 and H3K27me3 experiments.

ConclusionsOur results suggest that the NEB protocol may be better for preparing H3K4me3 (and potentially other histone modifications with sharp peak enrichment) libraries; the Bioo protocol may be better for preparing H3K27me3 (and potentially other histone modifications with broad domain enrichment) libraries, and the Diagenode protocol may be better for preparing CTCF (and potentially other transcription factors with well-defined binding motifs) libraries. For ChIP-Seq experiments using novel targets without a known signal enrichment pattern, the NEB protocol might be the best choice as it performed well for each of the three targets we tested across a wide array of input DNA levels.

category: bioinformatics


title: moRphology - dEep Learning Imaging Cells (RELIC) - to Differentiate Between Normal and Pathological Kidney Exfoliated Cells

abstract: Chronic kidney disease (CKD) is characterised by progressive loss of kidney function leading to kidney failure. Significant kidney damage can occur before symptoms are detected. Currently, kidney tissue biopsy is the gold standard for evaluation of renal damage and CKD severity. This study explores how to precisely quantify morphology characteristics of kidney cells exfoliated into urine, with a view to establish a future urine-based non-invasive diagnostic for CKD. We report the development of a novel deep learning method, which was able to discover a RELIC (moRphology dEep Learning Imaging Cells) signature that can differentiate between kidney cells exfoliated in human urine of and CKD patients with varying degree of kidney damage and non-CKD controls. Exfoliated proximal tubule cells (PTCs) originating from kidneys were isolated from the urine of patients with different levels of kidney damage using previously published methods. An advanced combination of artificial intelligence techniques, deep learning, swarm intelligence, and discriminative analysis was used to discover a RELIC signature in brightfield microscopy images of exfoliated PTCs. Kidney damage in the study subjects was characterised by assessing kidney tissues obtained through a nephrectomy or kidney biopsy. A special deep learning algorithm was developed and trained to create a predictive tool. The algorithm was then used to analyse data from patients with normal and fibrotic kidneys. Data were then classified according to different groups (healthy or fibrosis) and clustering of the training and validation cells was determined for model validation. We developed a novel deep learning method, to obtain RELIC signatures and identify specific deep morphological features which can be used to differentiate urinary PTC cells shed by people with CKD (confirmed by tissue histology obtained from an invasive kidney biopsy) from those without CKD, with a discriminatory accuracy of 82%. We identified a RELIC signature which can be used on a collection of bright field images of exfoliated urinary PTCs to create a predictive tool and differentiate between normal and pathological kidney cells. This study, for the first time, provides a proof of concept that urinary exfoliated tubule cells in patients with kidney fibrosis and healthy controls differ in appearance (morphology) as observed under a basic brightfield microscope. The results suggest that morphological signatures of exfoliated PTCs have the potential to serve as a non-invasive marker of kidney fibrosis.


title: Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability

abstract: Neural activity in the cortex is highly variable in response to repeated stimuli. Population recordings across the cortex demonstrate that the variability of neuronal responses is shared among large groups of neurons and concentrates in a low dimensional space. However, the source of the populationwide shared variability is unknown. In this work, we analyzed the dynamical regimes of spatially distributed networks of excitatory and inhibitory neurons. We found chaotic spatiotemporal dynamics in networks with similar excitatory and inhibitory projection widths, an anatomical feature of the cortex. The chaotic solutions contain broadband frequency power in rate variability and have distancedependent and low-dimensional correlations, in agreement with experimental findings. In addition, rate chaos can be induced by globally correlated noisy inputs. These results suggest that spatiotemporal chaos in cortical networks can explain the shared variability observed in neuronal population responses.

category: neuroscience


title: Transmission of Cervid Prions to Humanized Mice Demonstrates the Zoonotic Potential of CWD

abstract: Prions cause infectious and fatal neurodegenerative diseases in mammals. Chronic wasting disease (CWD), a prion disease of cervids, spreads efficiently among wild and farmed animals. Potential transmission to humans of CWD is a growing concern due to its increasing prevalence. Here, we provide the strongest evidence to date supporting the zoonotic potential of CWD prions, and their probable materialization in humans using mice expressing human prion protein (PrP) as an infection model. Inoculation of these mice with deer CWD isolates resulted in atypical clinical manifestations, with prion seeding activity and efficient transmissible infectivity in the brain and, remarkably, in feces. Intriguingly, the protease-resistant PrP in the brain resembled that found in a familial human prion disease and was transmissible upon second passage. Our results are the first evidence that CWD can infect humans with a distinctive clinical presentation, signature, and tropism, and might be transmissible between humans while current diagnostic assays might fail to detect it. These findings have major implications for public health and CWD management.


title: Activation of IP10/CXCR3 signaling with highly coincidental with PrPSc deposit in the brains of scrapie infected mice

abstract: Activation of chemokine IP10, also named as CXCL10, and its receptor CXCR3 in CNS is described in some neurodegenerative diseases. Our previous study has also demonstrated an increased brain IP10 levels in several scrapie infected rodent models. However, the detailed alteration of IP10/CXCR3 signaling in CNS during prion infection remains unsettled. Here, we found the increased IP10 signals in the brains of scrapie infected mice mainly localized in the neurons and the activated microglia using various methodologies. The levels of CXCR3 were markedly increased in brains of the scrapie infected mice and in the prion infected cell line SMB-S15. The increased CXCR3 mainly distributed in neurons. Obviously morphological colocalizations of PrP/PrPSc with IP10 and CXCR3 in the brains of scrapie infected mice were observed in the assays of immunohistochemistry (IHC) and immunofluorescence. Additionally, IHC analysis with whole brain sections demonstrated that the increased IP10 and CXCR3 accumulated in the brain regions with more PrPSc deposits. Co-immunoprecipitation and biomolecular interaction assays identified the evidence for the molecular interactions of PrP with IP10 and CXCR3. Compared to the normal partner cell line SMB-PS, the more portion of IP10 accumulated insides of prion infected SMB-S15 cells. Removal of prion replication in SMB-S15 cells by resveratrol converted the pattern of the accumulation and secretion of cellular IP10. Our data here demonstrate an activation of IP10/CXCR3 signaling in the brain tissues of prion infection, highly coincidental with PrPSc deposit. Modulation of brain IP10/CXCR3 signaling is potential therapeutic target for reducing the progression of prion diseases.


title: Evolution of influenza A virus hemagglutinin H1 and H3 across host species

abstract:
The Influenza A virus (IAV) hemagglutinin protein (HA) has been studied extensively, but its evolution has not been thoroughly compared among major host species. We compared H3 and H1 evolutionary rates among 49 lineages differentiated by host (avian, canine, equine, human, swine), phylogeny, and geography. Rates of nonsynonymous evolution, relative to synonymous rates, were higher in mammalian than avian hosts. Human seasonal HA and classical swine H1 accumulated 11-13 glycosylation sites, primarily in the antigenically important head domain, whereas lower numbers were maintained in other hosts. Canines had the highest ratio of nonsynonymous to synonymous changes in the more conserved stalk domain. Amino acid changes in canine viruses occurred disproportionately at residues located at protein interfaces. This suggests that they were adaptations affecting the major structural rearrangement of HA, which is critical for cell entry. These findings invite further study of how host ecology and physiology affect natural selection.

AUTHOR SUMMARYInfluenza virus evolution is of practical importance to health in addition to being an excellent system for the study of parasite/host evolution. Our work explores a largely untapped aspect of influenza evolution: sequence evolution in non-human hosts. This is important in its own right, in terms of both science and domestic animal health. It also puts the evolution of human influenza in a larger, comparative context. Our results also provide evidence concerning the evolution of the hemagglutinin stem domain, which has not been a focus of study but has new importance due to the development of stem-based universal influenza vaccines.

category: evolutionary biology


title: A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset

abstract:
To identify operational taxonomy units (OTUs) signaling disease onset in an observational study, a powerful strategy was selecting participants by matched sets and profiling temporal metagenomes, followed by trajectory analysis. Existing trajectory analyses modeled individual OTU or microbial community without adjusting for the within-community correlation and matched-set-specific latent factors. We proposed a joint model with matching and regularization (JMR) to detect OTU-specific compositional trajectory predictive of host disease status, using nested random effects and covariate taxa pre-selected by Bray-Curtis distance and elastic net regression. We demonstrated that JMR effectively controlled the false discovery and pseudo biomarkers in a simulation study that generated temporal high-dimensional metagenomic counts with random intercept or slope. Application of the competing methods in the simulated data and the TEDDY cohort showed that JMR outperformed the other methods and identified important taxa in infants fecal samples with dynamics preceding host disease status.

IMPORTANCEWe proposed a framework to link taxon-specific compositional trajectory and the risk of host developing disease without transformation of the relative abundance. The heterogeneity between matched sets was considered in our model, with improved detection power and well-controlled false positive rate. The inherent negative correlation in microbiota composition due to sum-to-one constraint was adjusted by incorporating the top-correlated taxa as covariate. We designed a simulation pipeline to generate true biomarkers (i.e., causal OTUs and/or those interacting with causal OTUs) for disease onset and the pseudo biomarkers caused by sum-to-one or latent noises. Our method successfully reduced pseudo biomarker rate in simulation results, as well as identified more microbial trajectories signaling autoimmune status of young children enrolled in the TEDDY cohort.


title: From motif to function:Inferring the functions of long zinc finger proteins through combinatorial selection

abstract: C2H2 zinc finger proteins (ZFPs) comprise of the largest group of DNA-binding proteins in human genome, and many of them contain long, tandem array of fingers, making the motif discovery, prediction of in vivo cis-regulatory elements (CREs), and understanding their functions particularly challenging. Previous work established that due to the dependent recognition between sub-motifs, the simple, additive recognition model impedes motif discovery and compromises our understanding about how ZFPs work. This work uses ZFP3, a 13-finger long ZFP with no known function, as case example to address the reverse question---given the full-length motif learned through in vitro experiments, like Spec-seq and HT-SELEX, how to reliably identify its in vivo cis-regulatory elements (CREs) and further predict this genes functions. Through sorting of all possible sites within the ChIP-seq peaks with similar predicted binding energy into groups and comparing the aggregate ChIP-seq signals between groups, it is evident that either its full-length or individual sub-motif alone fails to correctly identify all high-affinity specific sites without false-positives, thus it is necessary to revise current algorithm, and use both the core and upstream motifs as separate components to improve the prediction accuracy. Furthermore, significant number of regulatory elements of ZFP3 are found to be proximal to genes associated with microtubules organization and ciliogenesis, which coincides with the fact that ZFP3 is specifically upregulated in multiple ciliated cells. At last, local chromatin accessibility and active chromatin marks like H3K27ac are found to positively associate with the differential binding of ZFP3 between tested cell lines. Overall, this work establishes a novel "From motif to function" strategy for long ZFPs, and the data analysis workflows are implemented through R package TFCookbook for reuse onto other ZFPs.


title: A neurocomputational theory of action regulation predicts motor behavior in neurotypical individuals and patients with Parkinsons disease

abstract:
Surviving in an uncertain environment requires not only the ability to select the best action, but also the flexibility to withhold inappropriate actions when the environmental conditions change. Although selecting and withholding actions have been extensively studied in both human and animals, there is still lack of consensus on the mechanism underlying these action regulation functions, and more importantly, how they inter-relate. A critical gap impeding progress is the lack of a computational theory that will integrate the mechanisms of action regulation into a unified framework. The current study aims to advance our understanding by developing a neurodynamical computational theory that models the mechanism of action regulation that involves suppressing responses, and predicts how disruption of this mechanism can lead to motor deficits in Parkinsons disease (PD) patients. We tested the model predictions in neurotypical individuals and PD patients in three behavioral tasks that involve free action selection between two opposed directions, action selection in the presence of conflicting information and abandoning an ongoing action when a stop signal is presented. Our results and theory suggest an integrated mechanism of action regulation that affects both action initiation and inhibition. When this mechanism is disrupted, motor behavior is affected, leading to longer reaction times and higher error rates in action inhibition.

Author SummaryHumans can rapidly regulate actions according to updated demands of the environment. A key component of action regulation is action inhibition, the failure of which contributes to various neuropsychiatric disorders. When faced with multiple choices, dealing with conflicting information, or current actions become inappropriate or unwanted, we should be able to pause or completely abandon actions. Despite extensive efforts to understand how the brain selects, pauses, and abandons actions based on environmental demands, the mechanisms underlying these action regulation functions and, perhaps more importantly, how they inter-relate remain elusive. Part of this challenge lies in the fact that these mechanisms were rarely explored together, making it difficult to develop a unified theory that explains the computational aspects of action regulation functions. The current study introduces a large-scale model that better characterizes the computations of action regulation functions, how they are implemented within brain networks that involve frontal, motor and basal ganglia (BG) circuits, and how disruption of these circuits can lead to deficits in motor behavior seen in Parkinsons disease (PD).The model was developed by studying the motor behavior of healthy individuals and PD patients in three motor tasks that involve action inhibition. Overall, the model explains many key aspects on how the brain regulates actions that involve inhibitory processes, opening new avenues for improving and developing therapeutic interventions for diseases that may involve these circuits.


title: Listeria monocytogenes Infection Alters Extracellular Vesicles Produced by Trophoblast Stem Cells to Confer a Pro-Inflammatory State

abstract: Placental immunity is critical for fetal health during pregnancy, as invading pathogens can be transmitted from the maternal blood to the fetus through this organ. However, inflammatory responses in the placenta can adversely affect both the fetus and the pregnant mother, and the balance between protective placental immune response and detrimental inflammation is poorly understood. Extracellular vesicles (EVs) are membrane-enclosed vesicles that play a critical role in placental immunity. EVs produced by placental trophoblasts mediate immune tolerance to the fetus and to the placenta itself, but these EVs can also activate detrimental inflammatory responses. The regulation of these effects is not well-characterized, and the role of trophoblast EVs (tEVs) in the response to infection has yet to be defined. The Gram-positive bacterial pathogen Listeria monocytogenes (Lm) infects the placenta, serving as a model to study tEV function in this context. We investigated the effect of Lm infection on the production and function of tEVs, using a trophoblast stem cell (TSCs) model. We found that tEVs from infected TSCs were immunostimulatory, activating macrophages to a pro-inflammatory state. Surprisingly, this activation made RAW 264.7 macrophages more susceptible to subsequent Lm infection. Increased susceptibility to infection has not previously been reported as an effect of EVs. Proteomic analysis and RNA sequencing revealed that tEVs from infected TSCs had altered cargo compared to those from uninfected TSCs. Together, these results suggest an immunomodulatory role for tEVs during prenatal infection.

category: immunology


title: First detection of Leptospira santarosai in the reproductive track of a boar: a potential threat to swine production and public health

abstract:
BackgroundLeptospirosis causes significant economic losses and is an occupational risk in the swine industry, especially in developing tropical regions where social and geoclimatic conditions are favorable for the transmission of this disease. Although vaccination can reduce infection risk, efficacy is diminished if local genetic and antigenic variants of the pathogen are not accounted for in the vaccine. Identifying and characterizing strains that circulate in different populations is therefore critical for public health mitigation practices.

Methodology/Principal findingsOur study was conducted on a rural breeding farm in Ecuador, where we identified, for the first time, Leptospira santarosai in the kidneys, testicles, and ejaculate of a vaccinated boar. L. santarosai was detected with a PCR assay that targets lipL32, and identified by target MLST gene sequencing using an Oxford Nanopore MinION sequencer.

Conclusions/SignificanceAs L. santarosai is pathogenic in other livestock species and humans, our finding highlights the need to evaluate the prevalence and epidemiological significance of this pathogen in pigs. In addition, further studies are needed to identify and characterize local serovars that may impact diagnosis and vaccination programs to better control leptospirosis in pigs and spillover into the human population.

Author summaryLeptospirosis poses a significant threat to human and animal health. In tropical countries, leptospirosis is very common, and responsible of economic losses in the livestock industry. In peridomestic and rural farms, the spillover of leptospira to humans is particularly likely as humans live and work in close proximity to animals. Although animal vaccination can reduce risk of infection, efficacy is diminished when local variants are not included in the vaccine. This report describes, for the first time, the presence of Leptospira santarosai in the reproductive tract of a vaccinated domestic boar from a rural farm in Ecuador. We detected the pathogen in its semen and urine, and despite no tissue damage, was observed in the kidneys, testes or epididymis. The farm veterinarian reported reproductive problems in sows inseminated with the semen from this boar. Our results highlight the importance of recognizing locally circulating serovars and species so that they can be included in vaccines to prevent infection and disease. Effective control of leptospirosis in livestock not only reduces economic losses for breeders, but also reduces the risk of infection and disease in humans.

category: microbiology


title: Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates non-gradual expansion of the disease vector

abstract:
BackgroundDriven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion.

ResultsBy applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Ae. aegypti, sampled along an altitudinal temperature gradient in Nepal (200- 1300m), we identify adaptive traits and describe the species genomic footprint of climate adaptation to colder ecoregions. We found two clusters of differentiation with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300m) and all other lowland populations ([≤] 800 m). We revealed non-synonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern.

ConclusionOther than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. This finding either indicates a differential invasion history to Nepal or local high-altitude adaptation explaining the populations phenotypic cold tolerance. In any case, this highland population can be assumed to carry pre-adapted alleles relevant for the species invasion into colder ecoregions worldwide that way expanding their climate niche.

category: genomics


title: Functional characterization of TANGLED1 interaction with PHRAGMOPLAST ORIENTING KINESIN1 during mitosis in Arabidopsis

abstract:
Cell division plane orientation is critical for plant and animal development and growth. TANGLED1 (TAN1) and AUXIN-INDUCED-IN-ROOT-CULTURES9 (AIR9) are division-site localized microtubule-binding proteins required for division plane positioning. tan1 and air9 Arabidopsis thaliana single mutants have minor or no noticeable phenotypes but the tan1 air9 double mutant has synthetic phenotypes including stunted growth, misoriented divisions, and aberrant cell-file rotation in the root differentiation zone. These data suggest that TAN1 plays a role in nondividing cells. To determine whether TAN1 is required in elongating and differentiating cells in the tan1 air9 double mutant, we limited its expression to actively dividing cells using the G2/M-specific promoter of the syntaxin KNOLLE (pKN:TAN1-YFP). Unexpectedly, in addition to rescuing division plane defects, pKN:TAN1-YFP rescued root growth and the root differentiation zone cell file rotation defects in the tan1 air9 double mutant. This suggests that defects that occur in the meristematic zone later affect the organization of elongating and differentiating cells.

Summary StatementExpression of TAN1 in the root meristematic zone rescues cell file rotation defects in tan1 air9 mutants, suggesting defects that occur in mitosis may influence organization of nondividing cells.

category: plant biology


title: Action at a distance: Defects in division plane positioning in the root meristematic zone affect cell organization in the differentiation zone


title: Release of VAMP5-positive extracellular vesicles from specialized domains of retinal Müller cells in vivo

abstract: Cell-cell interactions in the central nervous system (CNS) are based on the release of molecules mediating signal exchange and providing structural and trophic support through vesicular exocytosis and the formation of extracellular vesicles (EVs). The specific mechanisms employed by each cell type in the brain are incompletely understood. Here, we explored the means of communication used by Muller cells, a type of glial cells in the retina, which forms part of the CNS. Using immunohistochemical, electron microscopic, and molecular analyses, we provide evidence for the release of distinct EVs from highly specialized domains of Muller cells in retinae from adult mice in vivo. We identify VAMP5 as a Muller cell-specific SNARE component that is part of EVs and responsive to ischemia, and we reveal differences between the secretomes of affinity-purified Muller cells and neurons in vitro. Our findings suggest EV-based communication as an important mediator of cellular interactions in the retina.


title: Two interdigitated fine-scale channels for encoding motion and stereopsis within the human magnocellular stream

abstract: In humans and non-human primates (NHPs), motion and stereopsis are processed within fine-scale cortical sites, including V2 thick stripes and their extensions into areas V3 and V3A that are believed to be under the influence of magnocellular stream. However, in both species, the functional organization (overlapping vs. interdigitated) of these sites remains unclear. Using high-resolution functional MRI (fMRI), we found evidence for two interdigitated channels within human extrastriate areas that contribute to processing motion and stereopsis. Across multiple experiments that included different stimuli (random dots, gratings, and natural scenes), the functional selectivity of these channels for motion vs. stereopsis remained consistent. Furthermore, an analysis of resting state functional connectivity revealed stronger functional connectivity within the two channels rather than between them. This finding provides a new perspective toward the mesoscale organization of the magnocellular stream within the human extrastriate visual cortex, beyond our previous understanding based on animal models.


title: Functional Specialization of Parallel Distributed Networks Revealed by Analysis of Trial-to-Trial Variation in Processing Demands

abstract: Multiple large-scale networks populate human association cortex. Here we explored the functional properties of these networks by exploiting trial-to-trial variation in component processing demands. In two behavioral studies (N=136 and N=238), participants quantified strategies used to solve individual task trials that spanned remembering, imagining future scenarios, and various control trials. These trials were also all scanned in an independent sample of functional MRI participants (N=10), each with sufficient data to precisely define within-individual networks. Stable latent factors varied across trials and correlated with trial-level functional responses selectively across networks. One network linked to parahippocampal cortex, labeled Default Network A (DN-A), tracked scene construction, including for control trials that possessed minimal episodic memory demands. To the degree a trial encouraged participants to construct a mental scene with vivid imagery and awareness about spatial locations of objects or places, the response in DN-A increased. The juxtaposed Default Network B (DN-B) showed no such response but varied in relation to social processing demands. Another adjacent network, labeled Frontoparietal Network B (FPN-B), robustly correlated with trial difficulty. These results support that DN-A and DN-B are specialized networks differentially supporting information processing within spatial and social domains. Both networks are dissociable from a closely juxtaposed domain-general control network that tracks cognitive effort.


title: Gut microbiota analysis of the western honeybee (Apis mellifera L.) infested with the mite Varroa destructor reveals altered bacterial and archaeal community

abstract: The western honeybee, Apis mellifera L., is a crop pollinator that makes royal jelly and other hive products. However, widespread concerns arise about opportunistic diseases (e.g., bacteria, fungi, or mites) or chemicals that have an effect on the health and number of colonies, as well as their activity. The relationships between the gut microbiota and its host are currently being researched extensively. The effects of Varroa destructor infection on the gut microbial community, in particular, have received little investigation. This work utilized amplicon sequencing of the bacterial and archaeal 16S rRNA genes to assess the bacterial and archaeal communities of adult bee groups (healthy and affected by Varroa designed in NG and VG, respectively) and larvae from Varroa destructor-infected hives. Our results suggest that the genus Bombella was substantially dominant in larvae, while the genera Gillamella, unidentified Lactobacillaceae, and Snodgrassella were significantly dominant in adult bees. NG and VG, on the other hand, did not differ statistically significantly. The PICRUSt study revealed a significant difference in the KEGG classifications of larvae and adult bee groups. A greater number of genes involved in cofactor and vitamin production were identified in larvae. Additionally, despite the complexity of the honeybees bacterial community, all groups exhibited a straightforward archaeal community structure. Surprisingly, methanogen was detected in low abundance in the microbiota of honeybees. In summary, larvae and adult bees infected with Varroa destructor exhibit altered gut microbiota composition and function.


title: The structure and evolutionary diversity of the fungal E3-binding protein

abstract: The pyruvate dehydrogenase complex (PDC) is a central metabolic enzyme in all living cells composed majorly of E1, E2, and E3. Tight coupling of their reactions makes each component essential, so that loss impacts oxidative metabolism pathologically. E3 retention is mediated by the E3-binding protein (E3BP), which has not previously been clearly resolved within the PDC. Here, the structure of the fungal E3BP in complex with the PDC core from N.crassa is resolved to 3.2[A], showing its mode of binding. Fungal and mammalian E3BP are shown to be orthologs, arguing E3BP as a broadly eukaryotic gene. Fungal E3BP architectures predicted from sequence data and computational models further bridge the evolutionary distance between N. crassa and humans, and suggest discriminants for E3-specificity. This is confirmed by similarities in their respective E3-binding domains, where a novel interaction is also predicted that may affect the interaction of its lipoyl substrate with recruited E3.

category: molecular biology


title: BIN2 phosphorylates the Thr280 of CO to restrict its function in promoting Arabidopsis flowering

abstract:
CONSTANS (CO) is a central regulator of floral initiation in response to photoperiod. In this study, we show that the GSK3 kinase BIN2 physically interacts with CO and the gain-of-function mutant bin2-1 displays late flowering phenotype through down-regulation of FT transcription. Genetic analyses show that BIN2 genetically acts upstream of CO in regulating flowering time. Further, we illustrate that BIN2 phosphorylates the Thr280 residue of CO. Importantly, the BIN2 phosphorylation of Thr280 residue restricts the function of CO in promoting flowering. Moreover, we reveal that the N-terminal part of CO harboring the B-Box domain mediates the interaction of both CO-CO and BIN2-CO. We find that BIN2 inhibits the formation of CO dimer/oligomer. Taken together, this study reveals that BIN2 regulates flowering time through phosphorylating the Thr280 of CO and inhibiting the CO-CO interaction in Arabidopsis.

HighlightBIN2 regulates flowering time through phosphorylating the Thr280 of CO in Arabidopsis.


title: Environmental DNA persistence and fish detection in captive sponges

abstract: Large and hyper-diverse marine ecosystems pose significant challenges to biodiversity monitoring. While environmental DNA (eDNA) promises to meet many of these challenges, recent studies suggested that sponges, as  natural samplers of eDNA, could further streamline the workflow for detecting marine vertebrates. However, beyond pilot studies demonstrating the ability of sponges to capture eDNA, little is known about the journey of eDNA particles in the sponge tissues, and the effectiveness of the latter compared to water samples. Here, we present the results of a controlled aquarium experiment to examine the persistence and detectability of eDNA from three encrusting sponge species and how these compare with established water filtration techniques. Our results indicate that sponges and water samples have highly similar detectability for fish of different sizes and abundances, but different sponge species exhibit considerable variance in performance. Interestingly, one sponge appeared to mirror the eDNA degradation profile of water samples, while another sponge retained eDNA throughout the experiment. A third sponge yielded virtually no DNA sequences at all. Overall, our study suggests that some sponges will be suitable as natural samplers, while others will introduce significant problems for laboratory processing. We suggest that an initial optimization phase will be required in any future studies aiming to employ sponges for biodiversity assessment. With time, factoring in technical and natural accessibility, it is expected that specific sponge taxa may become the  chosen natural samplers in certain habitats and regions.


title: Speciation without gene-flow in hybridizing deer

abstract:
Hybridisation in nature is part of the continuum of speciation. Under the ecological speciation model, divergent selection acts on ecological differences between populations, gradually creating barriers to gene flow and ultimately leading to reproductive isolation. Here, we used white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) to investigate patterns of speciation in hybridising sister species. We quantified genome-wide introgression and performed genome scans to look for signatures of four different selection scenarios. Despite modern evidence of hybridization, we found no sign of introgression, no signature of divergence with gene flow, and localized patterns of allopatric and balancing selection in the genome. Of note, genes under balancing selection were related to immunity and MHC or sensory perception of smell, the latter of which is consistent with deer biology. The deficiency of patterns selection suggests that white-tailed and mule deer were spatially separated during the glaciation cycles of the Pleistocene where genome wide differentiation accrued via drift.

Absence of historical introgression signs could suggest Dobzhansky-Muller incompatibilities and selection against hybrids, and that both species are now far along the speciation continuum. Our results suggests that WTD & MD do not conform to a speciation with gene flow scenario, but that they evolved via drift in allopatry during the Quaternary and that both species are currently advanced along the speciation continuum.


title: TAF4b Transcriptional Regulation During Cellular Quiescence of Developing Prospermatogonia

abstract: Prospermatogonia (ProSpg) link the embryonic development of male primordial germ cells to the healthy establishment of postnatal spermatogonia and long-term mammalian spermatogenesis. While these spermatogenic precursor cells undergo the characteristic transitions of cycling and quiescence, the transcriptional events underlying these developmental hallmarks remain unknown. Here we investigated the expression and function of TAF4b in the timely development of mouse ProSpg using an integration of gene expression profiling and chromatin mapping. We find that Taf4b mRNA expression is elevated during the transition of M-to-T1 ProSpg and Taf4b-deficient ProSpg are delayed in their entry into quiescence. Gene ontology, protein network analysis, and chromatin mapping demonstrate that TAF4b is both a direct and indirect regulator of cell cycle-related gene expression programs during ProSpg quiescence. By comparing the transcriptome changes in male and female Taf4b-deficient embryonic germ cells, we revealed that TAF4b promotes sex-independent and -dependent gene expression pathways, highlighting its unique and critical role in the fertility of both sexes.


title: Supercoiling-mediated feedback rapidly couples and tunes transcription

abstract: Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. The resulting intergene coupling may provide a mechanism to control transcriptional variance in engineered gene networks and explain the behavior of co-localized native circuits. However, a theoretical framework is needed for integrating both biophysical and biochemical transcriptional regulation to investigate the role of supercoiling-mediated feedback within multi-gene systems. Here, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical intergene coupling and explore integration of this biophysical model with a set of canonical biochemical gene regulatory systems. We find that gene syntax--the relative ordering and orientation of genes--defines the expression profiles, variance, burst dynamics, and intergene correlation of two-gene systems. By applying our model to both a synthetic toggle switch and the endogenous zebrafish segmentation network, we find that supercoiling can enhance or weaken conventional biochemical regulatory strategies such as mRNA- and protein-mediated feedback loops. Together, our results suggest that supercoiling couples behavior between neighboring genes, representing a novel regulatory mechanism. Integrating biophysical regulation into the analysis and design of gene regulation provides a framework for enhanced understanding of native networks and engineering of synthetic gene circuits.

category: synthetic biology


title: Multistage and transmission-blocking tubulin targeting potent antimalarial discovered from the open access MMV Pathogen Box

abstract:
Development of resistance to current antimalarial therapies remains a significant source of concern. To address this risk, new drugs with novel targets in distinct developmental stages of Plasmodium parasites are required. In our current work, we have targeted P. falciparum Tubulin (PfTubulin) proteins which represent some of the potential drug targets for malaria chemotherapy. Plasmodial Microtubules play a crucial role during parasite proliferation, growth, and transmission, which render them highly desirable targets for the development of next-generation chemotherapeutics. Towards this, we have evaluated the antimalarial activity of Tubulin targeting compounds received from the Medicines for Malaria Venture (MMV) "Pathogen Box" against the human malaria parasite, P. falciparum (including 3D7, RKL-9 (Chloroquine resistant) and R539T (Artemisinin resistant) strains). At nanomolar concentrations, filtered out compounds exhibited pronounced multistage antimalarial effects across the parasite life cycle, including intra-erythrocytic blood stages, liver stage parasites, gametocytes and ookinetes. Concomitantly, these compounds were found to impede male gamete ex-flagellation, thus showing transmission-blocking potential of these compounds. Target mining of these potent compounds, by combining in silico, biochemical and biophysical assays, implicated PfTubulin as their molecular target, which may possibly act by disrupting microtubule assembly dynamics by binding at the interface of -{beta}Tubulin-dimer. Further, promising ADME profile of the parent scaffold supported its consideration as a lead compound for further development. Thus, our work highlights the potential of targeting PfTubulin proteins in discovering and developing next-generation, multistage antimalarial agents for treating Multi-Drug Resistant (MDR) malaria parasites.

GRAPHICAL ABSTRACT

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title: Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

abstract:
BackgroundExpression quantitative trait loci (eQTL) studies have shown how genetic variants affect downstream gene expression. To identify the upstream regulatory processes, single-cell data can be used. Single-cell data also offers the unique opportunity to reconstruct personalized co-expression networks--by exploiting the large number of cells per individual, we can identify SNPs that alter co-expression patterns (co-expression QTLs, co-eQTLs) using a limited number of individuals.

ResultsTo tackle the large multiple testing burden associated with a genome-wide analysis (i.e. the need to assess all combinations of SNPs and gene pairs), we conducted a co-eQTL meta-analysis across four scRNA-seq peripheral blood mononuclear cell datasets from three studies (reflecting 173 unique participants and 1 million cells) using a novel filtering strategy followed by a permutation-based approach. Before analysis, we evaluated the co-expression patterns to be used for co-eQTL identification using different external resources. The subsequent analysis identified a robust set of cell-type-specific co-eQTLs for 72 independent SNPs that affect 946 gene pairs, which we then replicated in a large bulk cohort. These co-eQTLs provide novel insights into how disease-associated variants alter regulatory networks. For instance, one co-eQTL SNP, rs1131017, that is associated with several autoimmune diseases affects the co-expression of RPS26 with other ribosomal genes. Interestingly, specifically in T cells, the SNP additionally affects co-expression of RPS26 and a group of genes associated with T cell-activation and autoimmune disease. Among these genes, we identified enrichment for targets of five T-cell-activation-related transcriptional factors whose binding sites harbor rs1131017. This reveals a previously overlooked process and pinpoints potential regulators that could explain the association of rs1131017 with autoimmune diseases.

ConclusionOur co-eQTL results highlight the importance of studying gene regulation at the context-specific level to understand the biological implications of genetic variation. With the expected growth of sc-eQTL datasets, our strategy--combined with our technical guidelines--will soon identify many more co-eQTLs, further helping to elucidate unknown disease mechanisms.


title: Broadly neutralizing antibodies against Omicron variants of SARS-CoV-2 derived from mRNA-lipid nanoparticle-immunized mice

abstract: The COVID-19 pandemic continues to threaten human health worldwide, as new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged. Currently, the predominant circulating strains around the world are Omicron variants, which can evade many therapeutic antibodies. Thus, the development of new broadly neutralizing antibodies remains an urgent need. In this work, we address this need by using the mRNA-lipid nanoparticle immunization method to generate a set of Omicron-targeting monoclonal antibodies. Five of our novel K-RBD-mAbs show strong binding and neutralizing activities toward all SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta and Omicron). Notably, the epitopes of these five K-RBD-mAbs are overlapping and localized around K417 and F486 of the spike protein receptor binding domain (RBD). Chimeric derivatives of the five antibodies (K-RBD-chAbs) neutralize Omicron sublineages BA.1 and BA.2 with low IC50 values that range from 5.7 to 12.9 ng/mL. Additionally, we performed antibody humanization on a broadly neutralizing chimeric antibody to create K-RBD-hAb-62, which still retains excellent neutralizing activity against Omicron. Our results collectively suggest that these five therapeutic antibodies may effectively combat current and emerging SARS-CoV-2 variants, including Omicron BA.1 and BA.2. Therefore, the antibodies can potentially be used as universal neutralizing antibodies against SARS-CoV-2.


title: Low-dose bivalent mRNA vaccine is highly effective against different SARS-CoV-2 variants in a transgenic mouse model

abstract: Combining optimized spike (S) protein-encoding mRNA vaccines to target multiple SARS-CoV-2 variants could improve COVID-19 control. We compared monovalent and bivalent mRNA vaccines encoding B.1.351 (Beta) and/or B.1.617.2 (Delta) SARS-CoV-2 S-protein, primarily in a transgenic mouse model and a Wistar rat model. The low-dose bivalent mRNA vaccine contained half the mRNA of each respective monovalent vaccine, but induced comparable neutralizing antibody titres, enrichment of lung-resident memory CD8+ T cells, specific CD4+ and CD8+ responses, and fully protected transgenic mice from SARS-CoV-2 lethality. The bivalent mRNA vaccine significantly reduced viral replication in both Beta- and Delta-challenged mice. Sera from bivalent mRNA vaccine immunized Wistar rats also contained neutralizing antibodies against the B.1.1.529 (Omicron BA.1) variant. These data suggest that low-dose and fit-for-purpose multivalent mRNA vaccines encoding distinct S-proteins is a feasible approach for increasing the potency of vaccines against emerging and co-circulating SARS-CoV-2 variants.


title: Compellingly high SARS-CoV-2 susceptibility of Golden Syrian hamsters suggests multiple zoonotic infections of pet hamsters during the COVID-19 pandemic

abstract: Golden Syrian hamsters (Mesocricetus auratus) are used as a research model for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Millions of Golden Syrian hamsters are also kept as pets in close contact to humans. To determine the minimum infective dose (MID) for assessing the zoonotic transmission risk, and to define the optimal infection dose for experimental studies, we orotracheally inoculated hamsters with SARS-CoV-2 doses from 1*105 to 1*10-4 tissue culture infectious dose 50 (TCID50). Body weight and virus shedding were monitored daily. 1*10-3 TCID50 was defined as the MID, and this was still sufficient to induce virus shedding at levels up to 102.75 TCID50/ml, equaling the estimated MID for humans. Virological and histological data revealed 1*102 TCID50 as the optimal dose for experimental infections. This compellingly high susceptibility resulting in productive infections in Golden Syrian hamsters needs to be considered also as a source of SARS-CoV-2 infections in humans.


title: Emergence of new subgenomic mRNAs in SARS-CoV-2

abstract: Two mutations occurred in SARS-CoV-2 early during the COVID-19 pandemic that have come to define circulating virus lineages1: first a change in the spike protein (D614G) that defines the B.1 lineage and second, a double substitution in the nucleocapsid protein (R203K, G204R) that defines the B.1.1 lineage, which has subsequently given rise to three Variants of Concern: Alpha, Gamma and Omicron. While the latter mutations appear unremarkable at the protein level, there are dramatic implications at the nucleotide level: the GGG[->]AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. We find that N.iORF3 also emerged independently within the Iota variant, and further show that additional TRS motifs have convergently evolved to express novel sgmRNAs; notably upstream of Spike within the nsp16 coding region of ORF1b, which is expressed during human infection. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. Greater attention to this aspect in the assessment of emerging strains of SARS-CoV-2 is warranted.


title: Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants

abstract: The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.

category: biochemistry


title: Matrix stiffness regulates Notch signaling activity in endothelial cells

abstract: The Notch signaling pathway plays a critical role in many developmental and disease related processes. It is widely accepted that Notch has a mechano-transduction module that regulates cleavage of the receptor. However, the role of biomechanical properties of the cellular environment on this module and on Notch signaling in general is still poorly understood. During angiogenesis, differentiation into tip and stalk cells is regulated by Notch. The endothelial cells in this process respond to biochemical and mechanical cues triggered by local stiffening of the ECM. Here, we investigated the influence of substrate stiffness on the Notch signaling pathway in endothelial cells. Using stiffness tuned PDMS substrates we show that Notch signaling pathway activity inversely correlates with the physiologically relevant substrate stiffness, with increased Notch activity on softer substrates. We show that trans-endocytosis of the Notch extracellular domain, but not the overall endocytosis, is regulated by substrate stiffness. Furthermore, we could show that integrin cell-matrix connections are both stiffness-dependent and influenced by Notch. Cadherin mediated cell-cell adhesion and Notch, however, influence each other in that basal Notch signaling is cell-cell contact dependent, but inhibition of the Notch signaling pathway also results in a reduction of VE-cadherin levels. We conclude that mechano-transduction of Notch activation depends on substrate stiffness highlighting the role of substrate rigidity as a modulator of Notch signaling. This may have important implications in pathological situations, such as tumor growth, associated with stiffening of the extracellular matrix.

category: cell biology


title: Src42A is required for E-cadherin dynamics at cell junctions during Drosophila axis elongation

abstract: Src kinases are important regulators of cell adhesion. Here we explored the function of Src42A in junction remodelling during Drosophila gastrulation. Src42A is required for tyrosine phosphorylation at bicellular and tricellular junctions in germband cells and localizes to hotspots of mechanical tension. The role of Src42A was investigated using maternal RNAi and by CRISPR-Cas9-induced germline mosaics. We find that during cell intercalations, Src42A is required for the contraction of junctions at anterior-posterior cell interfaces. The planar polarity of E-cadherin is compromised and E-cadherin accumulates at tricellular junctions after Src42A knock down. Furthermore, we provide evidence that Src42A acts in parallel to Abl, which has also been implicated in cell intercalations. Our data suggest that Src42A is involved in two related processes, one affecting tension generated by the planar polarity of MyoII and secondly, it can act as a signalling factor at tAJs in controlling E-cadherin residence time.

category: developmental biology


title: A benchmark of Hi-C scaffolders using reference genomes and de novo assemblies

abstract:
BackgroundStudying a new species using high-throughput sequencing requires a high-quality reference genome. However, assembling chromosome length sequences remains challenging. Recent advances in chromatin conformation capture (Hi-C) have provided a new approach to scaffolding genome assemblies, and the last ten years have seen a proliferation of such methods. However, to our knowledge no comprehensive benchmarking of Hi-C scaffolders has been conducted to date.

ResultsThrough a literature review we identified the most popular Hi-C scaffolders - Lachesis, HiRise, 3d-dna, SALSA, and AllHiC. We tested their ability to scaffold four well studied genomes - S. cerevisiae, L. tarentolae, A. thaliana, and H. sapiens. Scaffolders were tasked with both scaffolding fragmented versions of the reference genome as well as de novo assemblies derived from long read datasets. We found that all scaffolders can exceed 80% accuracy under ideal circumstances but that their performance quickly deteriorates under more challenging conditions. Surprisingly, many scaffolders also showed poor performance on the best assemblies, where contigs are near chromosome length. Overall, we found that HiRise and Lachesis offer the best performance on average across all conditions.

ConclusionsWe compare the performance of five Hi-C scaffolders using multiple reference species under both ideal and real-life conditions, thereby illuminating their strengths and weaknesses.


title: G6PD Inhibition Sensitizes Ovarian Cancer Cells to Oxidative Stress in the Metastatic Omental Microenvironment

abstract:
Ovarian cancer (OC) is the most lethal gynecological malignancy, with aggressive metastatic disease responsible for the majority of ovarian cancer related deaths. In particular, OC tumors preferentially metastasize to and proliferate rapidly in the omentum. Here, we show metastatic OC cells experience increased oxidative stress in the omental microenvironment. Metabolic reprogramming, including upregulation of the pentose phosphate pathway (PPP), a key cellular redox homeostasis mechanism, allows OC cells to compensate for this challenge. Inhibition of G6PD, the rate-limiting enzyme of the PPP, reduces tumor burden in pre-clinical models of OC, suggesting this adaptive metabolic dependency is important for OC omental metastasis.

HighlightsO_LIThe omental microenvironment poses a high oxidative stress metastatic niche for ovarian cancer cells.
C_LIO_LIG6PD, a key enzyme involved in redox homeostasis and the rate-limiting enzyme of the pentose phosphate pathway (PPP) is upregulated in omental metastasis.
C_LIO_LIInhibition of G6PD increases oxidative stress and cytotoxicity in the omental microenvironment.
C_LIO_LIPharmacological G6PD inhibition reduces omental metastases in vivo.
C_LI

category: cancer biology


title: Hybridization In The Late Pleistocene: Merging Morphological And Genetic Evidence

abstract: This is an exciting time for our understanding of the origin of our species. Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive one. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent paleogenomic work shows that gene flow between distinct lineages (e.g. Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the Late Pleistocene, likely contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of Late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridisation signals differentially. We urge further studies of the phenotype in order to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.

category: paleontology


title: Spatiotemporal Profiling of Seed-Associated Microbes of an Aquatic, Intermediate Recalcitrant Species, Zizania palustris L. and the Impact of Anti-Microbial Seed Treatments

abstract: Northern wild rice (NWR; Zizania palustris var. interior) (NWR) is an ecologically important, annual, aquatic species native to North America, that is also cultivated in irrigated paddies in Minnesota and California. NWR seeds are desiccation-sensitive and must be kept in hydrated conditions, in which viability can decline rapidly within the first two years of storage. During this period, microbial growth is rampant and the relationship between these communities and the viability of NWR seed is unclear. In this study, we cultured and identified bacteria and fungi found in 27 NWR seed stocks, collected over a five-year period from three locations and four NWR genotypes. Results revealed that microbial communities were heavily dependent on seed viability and communities began shifting after one year of seed storage. Fungi became more prominent as years in storage increased suggesting that fungi begin to outcompete bacteria. Spatial analysis of locations and genotypes revealed a core set of microbes found across locations and genotypes. Penicillium and Pseudomonas were ubiquitous in NWR hydrated seed storage. We also evaluated the efficacy of four antimicrobial treatments at reducing microbial growth in hydrated NWR seed storage. These treatments did not reduce or drastically change microbial growth or seed viability. However, previously undetected microbes were identified after treatments, which suggested a disruption to the major constituents of the microbiome. Overall, this study identified common microbial constituents found in an aquatic, recalcitrant species, adapted for a cold climate, during seed storage and provides a foundation for future studies to evaluate the effect of microbial communities on NWR seed viability during hydrated storage.


title: Vision-dependent and -independent molecular maturation of mouse retinal ganglion cells

abstract: The development and connectivity of retinal ganglion cells (RGCs), the retinas sole output neurons, are patterned by activity-independent transcriptional programs and activity-dependent remodeling. To inventory the molecular correlates of these influences, we applied high-throughput single-cell RNA sequencing (scRNA-seq) to mouse RGCs at six embryonic and postnatal ages. We identified temporally regulated modules of genes that correlate with, and likely regulate, multiple phases of RGC development, ranging from differentiation and axon guidance to synaptic recognition and refinement. Some of these genes are expressed broadly while others, including key transcription factors and recognition molecules, are selectively expressed by one or a few of the 45 transcriptomically distinct types defined previously in adult mice. Next, we used these results as a foundation to analyze the transcriptomes of RGCs in mice lacking visual experience due to dark rearing from birth or to mutations that ablate either bipolar or photoreceptor cells. 98.5% of visually deprived (VD) RGCs could be unequivocally assigned to a single RGC type based on their transcriptional profiles, demonstrating that visual activity is dispensable for acquisition and maintenance of RGC type identity. However, visual deprivation significantly reduced the transcriptomic distinctions among RGC types, implying that activity is required for complete RGC maturation or maintenance. Consistent with this notion, transcriptomic alternations in VD RGCs significantly overlapped with gene modules found in developing RGCs. Our results provide a resource for mechanistic analyses of RGC differentiation and maturation, and for investigating the role of activity in these processes.


title: Glutamatergic projections from ventral hippocampus to nucleus accumbens cholinergic neurons are altered in a mouse model of depression

abstract: The cholinergic interneurons (ChATs) of the nucleus accumbens (NAc) have a critical role in the activity of this region, specifically in the context of major depressive disorder. To understand the circuitry regulating this behavior we sought to determine the areas that directly project to these cells/interneurons by utilizing the monosynaptic cell-specific tracing technique. Mapping showed monosynaptic projections that are exclusive to NAc ChATs. To determine if some of these projections are altered in a depression mouse model, we used mice that do not express the calcium binding protein p11 specifically in ChATs (ChAT-p11 cKO) and display a depressive-like phenotype. Our data demonstrated that while the overall projection areas remain similar between wild type and in ChAT-p11 cKO mice, the number of projections coming from the ventral hippocampus (vHIP) is significantly reduced in the ChAT-p11 cKO mice. Furthermore, using optogenetics and electrophysiology we showed that glutamatergic projections from vHIP to NAc ChATs are severely altered in mutant mice. These results show that specific alterations in the circuitry of the accumbal ChAT interneurons could play an important role in the regulation of depressive-like behavior, reward seeking behavior in addictions, or psychiatric symptoms in neurodegenerative diseases.


title: Myeloid-Derived Suppressor Cells are relevant factors to predict the severity of multiple sclerosis

abstract:
Multiple Sclerosis (MS) is a highly heterogeneous demyelinating disease of the central nervous system (CNS) that needs for reliable biomarkers to foresee disease severity. Previous retrospective investigations in the MS model, experimental autoimmune encephalomyelitis (EAE), highlighted the important relationship between monocytic-myeloid-derived suppressor cells (M-MDSCs) and the experimented severity of the clinical course. In this work, we show for the first time cells resembling M-MDSCs associated to MS lesions, whose abundance was related to milder MS clinical courses. Moreover, Ly-6Chi cells (which are indistinguishable from circulating M-MDSCs in mice) are useful biomarkers to predict a milder severity of the EAE disease course and a lesser tissue damage extent. Finally, the abundance of M-MDSCs in blood from untreated MS patients at their first relapse was inversely correlated with EDSS at baseline and relapse recovery one-year later. In summary, our data point to M-MDSC load as a promising biomarker of patients clinical course severity.

TeaserThe abundance of myeloid-derived suppressor cells is related to a milder clinical course in multiple sclerosis patients.


title: Macrophages undergo necroptosis during severe influenza A infection and contribute to virus-associated cytokine storm

abstract:
Influenza A virus (IAV) causes a major public health concern, because it is one of the leading causes of respiratory tract infections and hospitalization. Severe influenza has been associated with the cytokine storm, and IAV productive infection cell death in airway epithelial cells may contribute to the exacerbation of this proinflammatory event. On the other hand, IAV replication in macrophages is non-permissive and whether this immune cell may contribute to severe influenza physiopathology requires more details. Here, we investigated IAV-induced macrophage death, along with potential therapeutic intervention. We found that IAV or simply its surface glycoprotein hemagglutinin (HA) triggers necroptosis in human and murine macrophages in a Toll-like receptor-4 (TLR4) and TNF-dependent manner. Anti-TNF treatment, with the clinically approved drug etanercept, prevented the engagement of the necroptotic loop and mice mortality. impaired IAV-induced pro-inflammatory cytokine storm and lung injury. Our results implicate macrophage necroptosis with severe influenza in experimental models and potentially repurpose a clinically available therapy.

Author SummaryVarious fates of cell death have an integral role in the influenza A virus (IAV) pathogenesis and lung/respiratory dysfunction. IAV physiopathology is not restricted to airway epithelial cells, where this virus actively replicated. Macrophages should support both viral clearance and priming of adaptative immune response in patients that adequately control influenza. However, during severe IAV infection, macrophages - which are unable to support a permissive viral replication - undergo disruptive cell death and contribute to the exacerbated production of proinflammatory cytokines/chemokines. We characterized this process by showing that IAV or just its surface glycoprotein hemagglutinin (HA) trigger necroptosis, a disruptive and TNF-dependent cells death. Since TNF is a hallmark of pro-inflammatory cell death, we blocked this mediator with a repurposed biomedicine etanercept, which prevented the severe IAV infection in the experimental model. The present work improves the knowledge of influenza pathophysiology by highlighting the importance of macrophage cell death during severe infection.


title: lsaBGC provides a comprehensive framework for evolutionary analysis of biosynthetic gene clusters within focal taxa

abstract: Bacterial secondary metabolites, encoded by biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and be developed into high-value commercialized products, which have historically been mined from a select group of taxa. Despite this, dedicated bioinformatics tools for comparative analysis of BGCs are limited. We have thus developed lsaBGC to aid exploration of microdiversity and evolutionary trends across BGCs in any bacterial taxa of interest through calculation of population genetic statistics and metagenomic exploration. As a proof of concept, we applied lsaBGC to four genera commonly found in skin microbiomes to reveal novel insights on both well and less studied taxa and their secondary metabolites. We find evidence of horizontal gene transfer (HGT) within multiple genera. The BGC encoding for the carotenoid staphyloxanthin, a virulence factor in S. aureus, is ubiquitous across the genus of Staphylococcus and exhibits signatures of inter-species HGT, including mobilization onto plasmids. We also identified a non-ribosomal peptide synthetase (NRPS) BGC flanked by transposable elements, encoding for a predicted siderophore, which is highly conserved across several divergent Corynebacterium species commonly isolated from skin such as C. kefirresidentii. From strain-resolution metagenomics, we further determined that the C. kefirresidentii species complex is the most prevalent clade of Corynebacterium in skin metagenomes and is found in the skin microbiome of every participant surveyed. While ubiquitous across skin, the number of publicly-available genomes for this species complex is currently limited. Using lsaBGCs framework for metagenomic mining, we identified 34,545 novel single nucleotide variants (SNVs) in predicted BGCs of the species complex, including several novel, non-synonymous SNVs within highly conserved sites of enzymes. Ultimately, we envision that application of lsaBGC can highlight important, yet poorly studied, secondary metabolites as well as aid in the discovery and design of more efficacious commercialized metabolites.


title: Phylogenetic and phenotypic analysis of five subgroups of Ralstonia solanacearum phylotype IIB sequevar 4 reveals that the "not pathogenic to banana (NPB)" ecotype is polyphyletic.

abstract: The bacterial wilt pathogens in the Ralstonia solanacearum species complex (RSSC) have broad but finite host ranges. Population genetic surveys of RSSC pathogens show that many sequevars (subspecies groups) are predominantly recovered from wilting solanaceous plants. In contrast, strains in the IIB-4 sequevar have been isolated from plants in over a dozen families. We characterized the natural variation in host range of nineteen IIB-4 strains to explore the molecular determinants of host range within the RSSC. We used Illumina sequencing to assemble draft genomes of 12 strains. Based on whole genome phylogenetic analysis, these IIB-4 strains cluster into five subclades. We quantified virulence of each strain on tomato cv. Moneymaker (Solanaceae), banana cv. Dwarf Cavendish (Musaceae), melon cv. Sweet Granite (Cucurbitaceae), and impatiens cv. Beacon Orange (Balsaminaceae). To enable future meta-analyses that identify genetic factors that drive host-range, the raw virulence data is included as a supplemental table. Overall, the virulence patterns correlated with phylogeny. Strains from Martinique, Dominican Republic, Brazil, as well as multiple strains imported into Florida were highly virulent on tomato, melon, and impatiens. Several strains from Peru were highly virulent on tomato and had moderate-to-low virulence on banana, melon, and impatiens. One strain from Colombia was highly virulent on all hosts. Our findings reinforce the phenotypic plasticity within the Ralstonia solanacearum species complex.


title: A remarkable expansion of oligopeptide transporter genes in rust fungi (Pucciniales) suggests a specialization in nutrients acquisition for obligate biotrophy

abstract: Nutrients acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database (TCDB) focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared to a vast majority of fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Noteworthy, three metal transport-related families involved in the import, export and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family with 25 genes in average compared to seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.


title: Vegetation formation in Staphylococcus aureus endocarditis inversely correlates with RNAIII and sarA expression in invasive clonal complex 5 (CC5) isolates

abstract: Infective endocarditis (IE) is one of the most feared and lethal diseases caused by Staphylococcus aureus. Once established, the infection is fast-progressing and tissue destructive. S. aureus of the clonal complex 5 (CC5) commonly cause IE yet are severely understudied. IE results from bacterial colonization and formation of tissue biofilms (known as vegetations) on injured or inflamed cardiac endothelium. S. aureus IE is promoted by adhesins, coagulases, and superantigens, with the exotoxins and exoenzymes likely contributing to tissue destruction and dissemination. Expression of the large repertoire of virulence factors required for IE and sequelae is controlled by complex regulatory networks. We investigated the temporal expression of the global regulators agr (RNAIII), rot, sarS, sarA, sigB, and mgrA in 8 invasive CC5 isolates and established intrinsic expression patterns associated with IE outcomes. We show that vegetation formation, as tested in the rabbit model of IE, inversely correlates with RNAIII and sarA expression during growth in Todd-Hewitt broth (TH). Large vegetations with severe sequelae arise from strains with high-level expression of colonization factors but slower transition towards expression of the exotoxins. Overall, strains proficient in vegetation formation, a hallmark of IE, exhibit lower expression of RNAIII and sarA. Simultaneous high expression of RNAIII, sarA, sigB, and mgrA is the one phenotype assessed in this study that fails to promote IE. Thus, RNAIII and sarA expression that provides for rheostat control of colonization and virulence genes, rather than an on and off switch, promote both vegetation formation and lethal sepsis.


title: The association of ubiquitin-associated protein 2-like and Ras-GTP-activating protein SH3 domain binding protein 1 mediated by small nucleolar RNA is essential for stress granule formation

abstract: Stress granules (SGs) are dynamic, non-membranous structures composed of non-translating mRNAs and various proteins and play critical roles in cell survival under stressed conditions. Extensive proteomics analyses have been performed to identify proteins in SGs; however, the molecular functions of these components in SG formation remain unclear. In this report, we show that ubiquitin-associated protein 2-like (UBAP2L) is a novel component of SGs. UBAP2L localized to SGs in response to various stresses, and its depletion significantly suppressed SG organization. Proteomics and RNA sequencing analyses found that UBAP2L formed a protein-RNA complex with Ras-GTP-activating protein SH3 domain binding protein 1 (G3BP1) and small nucleolar RNAs (snoRNAs). In vitro binding analysis demonstrated that snoRNAs were required for UBAP2L association with G3BP1. In addition, decreased expression of snoRNAs reduced the interaction between UBAP2L and G3BP1 and suppressed SG formation. Our results reveal a critical role of a novel SG component, the UBAP2L/snoRNA/G3BP1 protein-RNA complex, and provide new insights into the regulation of SG assembly.


title: JiangShi: a widely distributed Mucin-like protein essential for Drosophila development

abstract: Epithelia exposed to elements of the environment are protected by a mucus barrier in mammals. This barrier also serves to lubricate during organ movements and to mediate substance exchanges between the environmental milieu and internal organs. A major component of the mucus barrier is a class of glycosylated proteins called Mucin. Mucin and mucin-related proteins are widely present in the animal kingdom. Mucin mis-regulation has been reported in many diseases such as cancers and ones involving the digestive and respiratory tracts. Although the biophysical properties of isolated Mucins have been extensively studied, in vivo models remain scarce for the study of their functions and regulations. Here we characterize the Mucin-like JiangShi (JS) protein and its mutations in the fruit fly Drosophila. JS is an extracellular glycoprotein with domain features reminiscent of mammalian non-membranous Mucins, and one of the most widely distributed Mucin-like proteins studied in Drosophila. Both loss and over-production of JS lead to terminal defects in adult structures and organismal death. Although the physiological function of JS remains poorly defined, we present a genetically tractable model system for the in vivo studies of Mucin-like molecules.


title: Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

abstract: The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is considered vulnerable due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts focused on both wild and ex-situ populations. A high-quality genome would also open avenues to investigate the genetic basis of the exceptionally long lifespan. Here, we produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture (Hi-C). We produced a 2.37 Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNAseq-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. We also performed a low-coverage re-sequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. The high-quality chromosome-level reference genome for A. gigantea is one of the most complete turtle genomes available. It is a powerful tool to assess the population structure in the wild population and reveal the geographic origins of ex-situ individuals relevant for genetic diversity management and rewilding efforts.


title: Single-cell mapping of tumor heterogeneity in pediatric rhabdomyosarcoma reveals developmental signatures with therapeutic relevance

abstract:
Rhabdomyosarcoma (RMS) is an aggressive human pediatric cancer. Despite robust expression of myogenic regulatory factors, RMS cells are blocked in a proliferative state and do not terminally differentiate. The extent to which the skeletal muscle lineage is represented in RMS tumors and the mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing (scRNAseq), mass cytometry (CyTOF) and high-content imaging to resolve RMS heterogeneity. ScRNAseq and CyTOF analysis of a total of 17 patient-derived primary cultures and three cell lines uncovered plastic myogenic subpopulations that delineate a branched trajectory. The less aggressive embryonal RMS (eRMS) harbor primarily muscle stem cell (MuSC)-like cells and exhibit sparse commitment to differentiation. The more aggressive alveolar RMS (aRMS) comprise primarily actively cycling committed progenitors with a paucity of differentiated cells. The oncogenic fusion protein PAX3:FOXO1 sustains aRMS cells in the cycling trajectory loop, which we show can re-wired towards differentiation upon its downregulation or by dual pharmacological RAF and MEK inhibition. Our findings provide insights into the developmental states and trajectories underlying RMS progression and identify the RAS pathway as a promising target of differentiation therapy for human aRMS.

STATEMENT OF SIGNIFICANCEWe present the first comprehensive single-cell transcriptomic and proteomic atlas of pediatric rhabdomyosarcoma (RMS), in which we identify impaired myogenic trajectories with prognostic value. We demonstrate that RAS pathway inhibitors disrupt the oncogenic trajectory and induce terminal differentiation, revealing novel therapeutic targets for the aggressive alveolar RMS subtype.


title: Evaluation of sex differences in laser-induced choroidal neovascularization severity, phenotype and disease progression

abstract: Age-related macular degeneration (AMD) progresses through two phases: a non-exudative "dry" stage that compromises vision but does not involve angiogenesis, and an angiogenic "wet" phase characterized by choroidal neovascularization (CNV), in which neovessels from the choroid break through the Bruchs membrane to form neovascular lesions in the macula. If left untreated, CNV leads to permanent central blindness, which the current standard of care (anti-VEGF therapy) arrests but does not reverse. In laser-induced CNV, a laser is used to rupture the Bruchs membrane, prompting the outgrowth of choroidal blood vessels in a wound healing response. This model was used to develop currently available CNV therapeutics, such as intravitreal injection of anti-VEGF and corticosteroid therapies and is considered a gold standard model for CNV. Laser-induced CNV thus remains a highly clinically relevant model of CNV secondary to AMD and other pathologies, such as myopia. A rapidly growing body of research suggests that the pathogenesis of myriad diseases is highly dependent on biological sex, yet most studies use only male animals. This highlights the importance of determining whether the severity and pathogenesis of commonly used models of disease, for example laser-induced CNV, differ between sexes. In the present study, we tracked longitudinal progression and pathogenesis of laser-induced CNV in male and female animals, and found that CNV severity did not differ between sexes. This lack of difference recapitulates findings in human patients with CNV, which have also identified that both sexes are at equal risk of CNV development in the contexts of both age-related macular degeneration induced CNV and myopic CNV.


title: Investigating the antioxidant effects of Aloe vera: Possible role in regulating lipid profile and liver function in high fat and fructose diet (HFFD) fed mice.

abstract: Fat rich diets are believed to induce obesity and contributes to the development of diabetes and cardiovascular disease while high fructose diet was reported to increase gut surface area and enhance nutrient uptake resulting in weight gain. The study investigate the role of Aloe vera supplementation on lipid profiles, oxidative stress as well as liver and hear histology in high fat and fructose diet fed mice. Twenty mice were distributed into four groups (n=5). The groups received regular diet, high fat and fructose died (HFFD), HFFD plus 10% Aloe vera (HFFD+AV1) and HFFD plus 20% Aloe vera (HFFD+AV2) respectively for 10 weeks. The cholesterol level of HFFD+AV treated mice were significantly lower compared to HFFD treated mice. The ALT level was significantly increased in HFFD treated mice relative to the control. Aloe vera significantly improve albumin level as well as Catalase and superoxide dismutase activities of HFFD treated mice. The liver tissues of control and HFFD+AV2 treated mice showed normal hepatocytes. The study suggest that Aloe vera supplementation could protect against HFFD induced oxidative stress and hyperlipidemia. These findings might be used for further research on food supplementation for the control of metabolic disorders.


title: Endogenous production of hyaluronan, PRG4, and cytokines is sensitive to cyclic loading in synoviocytes

abstract: Synovial fluid is composed of hyaluronan and proteoglycan-4 (PRG4 or lubricin), which work synergistically to maintain joint lubrication. In diseases like osteoarthritis, hyaluronan and PRG4 concentrations can be altered, resulting in lowered synovial fluid viscosity, and pro-inflammatory cytokine concentrations within the synovial fluid increase. Synovial fibroblasts within the synovium are responsible for contributing to synovial fluid and can be targeted to improve endogenous production of hyaluronan and PRG4 and to alter the cytokine profile. We cyclically loaded SW982 synoviocytes to 0%, 5%, 10%, or 20% strain for three hours at 1 Hz. To assess the impact of substrate stiffness, we compared the 0% strain group to cells grown on tissue culture plastic. We measured the expression of hyaluronan turnover genes, hyaluronan localization within the cell layer, hyaluronan concentration, PRG4 concentration, and the cytokine profile within the media. Our results show that the addition of cyclic loading increased HAS3 expression, but not in a magnitude-dependent response. Hyaluronidase expression was impacted by strain magnitude, which is exemplified by the decrease in hyaluronan concentration due to cyclic loading. We also show that PRG4 concentration is increased at 5% strain, while higher strain magnitude decreases overall PRG4 concentration. Finally, 10% and 20% strain show a distinct, more pro-inflammatory cytokine profile when compared to the unloaded group. Multivariate analysis showed distinct separation between certain strain groups in being able to predict strain group, hyaluronan concentration, and PRG4 concentration from gene expression or cytokine concentration data, highlighting the complexity of the system. Overall, this study shows that cyclic loading can be used tool to modulate the endogenous production of hyaluronan, PRG4, and cytokines from synovial fibroblasts.

category: bioengineering


title: Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans

abstract:
Given the risk of Candida albicans overgrowth in the gut, novel complementary therapies should be developed to reduce fungal dominancy. This study highlights the antifungal characteristics of a Bacillus subtilis-derived secondary metabolite, surfactin with high potential against C. albicans. Surfactin inhibited the growth of C. albicans following a 1-hour exposure, in addition to reduced adhesion and morphogenesis. Specifically, surfactin did not affect the level of reactive oxygen species but increased the level of reduced glutathione. Surprisingly, ethanol production enhanced following 2 hours of surfactin exposure. Surfactin treatment caused a significant reduction in intracellular iron, manganese and zinc content compared to control cells, whereas the level of copper was not affected. Alongside these physiological properties, surfactin also enhanced fluconazole efficacy. To gain detailed insights into the surfactin-related effects on C. albicans, genome-wide gene transcription analysis was performed. Surfactin treatment resulted in 1390 differentially expressed genes according to total transcriptome sequencing (RNA-Seq). Of these, 773 and 617 genes with at least a 1.5-fold increase or decrease in transcription, respectively, were selected for detailed investigation. Several genes involved in morphogenesis or related to metabolism (e.g., glycolysis, fermentation, fatty acid biosynthesis) were down-regulated. Moreover, surfactin decreased the expression of ERG1, ERG3, ERG9, ERG10 and ERG11 involved in ergosterol synthesis, whereas genes associated with ribosome biogenesis and iron metabolism and drug transport-related genes were up-regulated. Our data demonstrate that surfactin significantly influences the physiology and gene transcription of C. albicans, and could contribute to the development of a novel innovative complementary therapy.

ImportanceAlthough gut colonization by Candida albicans can be considered normal, it may be associated with intestinal diseases. Furthermore, Candida dominance in the gut may pose a potent risk for systemic candidiasis, especially for immunocompromised individuals. In recent years, interest has been growing for the use of Bacillus subtilis as a safe and effective probiotic for human healthcare. Surfactin is a B. subtilis-derived lipopeptide with potential antifungal activity; however, the mechanism underlying this remains unknown. In this study, surfactin negatively affected the adherence, morphogenesis and metabolism of C. albicans and increased ethanol production. These were associated with a reduction in intracellular iron, manganese and zinc while the copper content was not affected. Alongside these physiological modulations, surfactin also had a potent synergistic effect on fluconazole. Our results provide a definitive explanation for the surfactin-related antifungal effect of B. subtilis; furthermore, these data provide a good basis for future probiotic development.