bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations
Authors: Bubnis Greg , Grubmüller Helmut
Published: June 2020

Membrane topology changes such as poration, stalk formation, and hemi-fusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our atomistic simulations, we developed a novel “gizmo” potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid head-groups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes.

STATEMENT OF SIGNIFICANCE

The primary steps and nucleation of lipid membrane pore formation are key to membrane fusion, viral infection, and vesicular cellular transport. Despite decades experimental and theoretical studies, the underlying mechanisms are still not fully understood at the atomic level. Using a committor-based reaction coordinate and atomistic simulations, we report new structural and energetics insight into the full poration process. We find that the pore nucleates via an elastic indentation rather than by forming a hydrophobic defect. Subsequently, water pierces the thinned slab as a prerequisite for the following axial merger of the first lipid headgroups from opposite monolayers, which precedes and best characterizes the transition state. We also identify a metastable prepore basin, thereby explaining previous indirect experimental evidence.
Structure of a dominant negative mutant reveals a stalled intermediate state of anthrax protective antigen pore maturation
Authors: Scott Harry , Huang Wei , Gonti Srinivas , Zhang Kaiming , Mehzabeen Nurjahan , Day Alexander , Battaile Kevin P. , Lovell Scott , Bann James G. , Taylor Derek J.
Published: June 2020

Anthrax is a severe bacterial infection caused byBacillus anthracis, which produces a tripartite toxin that includes protective antigen (PA), lethal factor (LF) and edema factor (EF). A series of dominant-negative mutations have been previously identified that prevent the heptameric PA prepore from forming the pH-induced, membrane spanning beta-barrel pore that is required for translocation of EF and LF to the cytoplasm of the infected cell. Here we show that the dominant negative D425A mutation stalls the formation of the pore at a reversible intermediate maturation state, which exhibits many of the structural aspects of the pore but fails to form the phi(ϕ)-clamp and beta-barrel structure needed for full pore maturation. Overall, this structure reveals that ϕ-clamp and beta-barrel pore formation are later steps in the pathway to pore formation, thereby providing a regulatory mechanism to prevent premature translocation of EF and LF.
Competitive hierarchies, antibiosis, and the distribution of bacterial life history traits in a microbiome*
Authors: Humphrey Parris T , Satterlee Trang T , Whiteman Noah K
Published: June 2020

Microbiome manipulation requires an understanding of how species interact within communities. Can outcomes of ecological interactions be predicted from microbial life history traits, the identity of the species, or both? We addressed these questions by studying the competitive interaction network in a community of 40 endophyticPseudomonasspp. bacterial isolates from a native plant. Pairwise competition experiments revealed competitive dominance ofP. fluorescensoverP. syringaestrains within this microbiome-derived community.P. syringaestrains with higher growth rates won more contests, whileP. fluorescensstrains with shorter lag times and lower growth rates won more contests. Adding to their competitive dominance,P. fluorescensstrains often produced antibiotics to which fewP. syringaestrains were resistant. Many competitive outcomes amongP. syringaestrains were predicted to be reversed byP. fluorescensinhibitors because indirect benefits accrued to less competitive strains.P. fluorescensstrains frequently changed competitive outcomes, suggesting a critical role of strains within this bacterial clade in structuring plant microbiome communities. Microbial traits also may provide a handle for directing the outcome of colonization processes within microbiomes.
Diet-regulated production of PDGFcc by macrophages controls energy storage
Authors: Cox Nehemiah , Crozet Lucile , Holtman Inge R. , Loyher Pierre-Louis , Lazarov Tomi , Mass Elvira , Stanley E. Richard , Glass Christopher K. , Geissmann Frederic
Published: June 2020

Macrophages control inflammation in obese animals, and may also directly or indirectly regulate energy storage. In a genetic screen we identify a PDGF-family growth factor,Pvf3, produced by macrophages and required for lipid storage inDrosophilalarvae’s fat body cells. We next demonstrate using genetic and pharmacological approaches thatPvf3ortholog PDGFcc, produced byCcr2-independent embryo-derived tissue macrophages, is also required for storage in mammalian white adipose tissue. PDGFcc production by resident macrophages is regulated by diet, acts on white adipocytes in a paracrine manner, and controls adipocyte hypertrophy in high-fat diet fed and genetically hyperphagic mice. Upon PDGFcc blockade, excess lipids are redirected at the organismal level toward thermogenesis and hepatic storage in adults. This process is altogether independent from inflammation and insulin resistance promoted byCcr2-dependent monocytes/macrophages. Our data identify a conserved macrophagedependent mechanism that controls energy storage, conducive to the design of pharmacological interventions.
Previous oil exposure alters oil avoidance behavior in a common marsh fish, the Gulf KillifishFundulus grandis
Authors: Martin Charles W. , McDonald Ashley M. , Rieucau Guillaume , Roberts Brian J.
Published: June 2020

Oil spills threaten the structure and function of ecological communities. In the northern Gulf of Mexico, the 2010 Deepwater Horizon spill was among the largest marine disasters in history. While many predicted catastrophic consequences for nearshore fishes, field studies indicate surprising resilience in populations and communities. One potential mechanism for this resilience is the recognition and behavioral avoidance at small spatial scales of the toxic chemical constituents found in oil. Previous research indicates many marsh fishes have the capacity to avoid oil contaminated areas. Here, we test whether prior oil exposure of a common marsh fish, the Gulf killifishFundulus grandis, alters this avoidance response. Using choice tests between unoiled and a range of oiled sediments, we found that, even at low levels of previous exposure, killifish lose recognition of oiled sediments. Preference for unoiled sediments was lost across the entire range of oil concentrations tested here after oil exposure, and some evidence for preference of oiled sediments was even demonstrated. These results provide evidence for lack of response to toxic environments in exposed individuals, suggesting sublethal impairment of sensory mechanisms on an individual level despite organism survival. Future research should highlight additional sublethal consequences that affect ecosystem and food web functioning.
Elongation Inhibitors do not Prevent the Release of Puromycylated Nascent Polypeptide Chains from Ribosomes
Authors: Hobson Benjamin D. , Kong Linghao , Hartwick Erik W. , Gonzalez Ruben L. , Sims Peter A.
Published: June 2020

Puromycin is an amino-acyl transfer RNA analog widely employed in studies of protein synthesis. Since puromycin is covalently incorporated into nascent polypeptide chains, anti-puromycin immunofluorescence enables visualization of nascent protein synthesis. A common assumption in studies of local messenger RNA translation is that the anti-puromycin staining of puromycylated nascent polypeptides in fixed cells accurately reports on their original site of translation, particularly when ribosomes are stalled with elongation inhibitors prior to puromycin treatment. However, when we attempted to implement a proximity ligation assay to detect ribosome-puromycin complexes, we found no evidence to support this assumption. We further demonstrated, using biochemical assays and live cell imaging of nascent polypeptides, that puromycylated nascent polypeptides rapidly dissociate from ribosomes even in the presence of elongation inhibitors. Our results suggest that attempts to define precise subcellular translation sites using anti-puromycin immunostaining may be confounded by release of puromycylated nascent polypeptide chains prior to fixation.
A learned map for places and concepts in the human MTL
Authors: Herweg Nora A. , Kunz Lukas , Schonhaut Daniel R. , Brandt Armin , Wanda Paul A. , Sharan Ashwini D. , Sperling Michael R. , Schulze-Bonhage Andreas , Kahana Michael J.
Published: June 2020

Distinct lines of research in both humans and animals point to a specific role of the hippocampus in both spatial and episodic memory function. The discovery of concept cells in the hippocampus and surrounding medial-temporal lobe (MTL) regions suggests that the MTL maps physical and semantic spaces with a similar neural architecture. Here, we studied the emergence of such maps using MTL micro-wire recordings from 20 patients navigating a virtual environment featuring salient landmarks with established semantic meaning. We present several key findings: The array of local field potentials in the MTL contains sufficient information to decode subjects’ instantaneous location in the environment. Closer examination revealed that the field potentials represent both the subjects’ locations in virtual space and in high-dimensional semantic space. We further show that both spatial and semantic representations strengthen over time. This learning effect appears as subjects increase their knowledge of the environment’s spatial and semantic layout. Similarly, we observe a learning effect on temporal sequence coding. Over time, field potentials come to represent future locations, even after controlling for spatial proximity. This predictive coding of future states, more so than the strength of spatial representations per se, explains variability in subjects’ navigation performance. Our results thus support the conceptualization of the MTL as a memory space, building semantic knowledge, spatial and non-spatial, from episodic experience to plan future actions and predict their outcomes.

Significance statement

Using rare micro-wire recordings, we studied the representation of spatial, semantic and temporal information in the human MTL. Our findings demonstrate that subjects acquire a cognitive map that simultaneously represents the spatial and semantic relations between landmarks. We further show that the same learned representation is used to predict future states, implicating MTL cell assemblies as the building blocks of prospective memory functions.
Changes in the functional connectome and behavior after exposure to chronic stress and increasing neurogenesis
Authors: Culig Luka , Steadman Patrick E. , Kenney Justin W. , Legendre Sandra , Minier Frédéric , Hen René , Frankland Paul W. , Belzung Catherine
Published: June 2020

Addition of new neurons to the dentate gyrus might change the activity of neural circuitry in the areas which the hippocampus projects to. The size of the hippocampus and the number of adult newborn granule cells are decreased by unpredictable chronic mild stress (UCMS). Additionally, one of the notable effects of chronic stress is the induction of ΔFosB, an unusually stable transcription factor which accumulates over time in several brain areas. This accumulation has been observed in many animal models of depression and it could have a protective role against stress, but no studies so far have explored how a specific increase in neurogenesis might regulate the induction and which brain networks might be predominately affected.

We attempted to investigate the role of increasing adult hippocampal neurogenesis on stress-related behavior and the functional brain circuitry involved in mice exposed to UCMS. We usediBaxmice, in which the pro-apoptotic geneBaxcan be selectively ablated in neural stem cells, therefore inducibly enhancing survival of newborn neurons after tamoxifen administration. The animals were exposed to UCMS for 9 weeks and treated with tamoxifen in week 3 after the beginning of UCMS. In week 8, they were submitted to a battery of behavioral tests to assess depressive-like and anxiety-like behavior. In week 9, blood was collected to assess basal corticosterone levels, and the animals were sacrificed and their brain collected for ΔFosB immunohistochemistry. Brain-wide maps of ΔFosB expression were constructed and graph theoretical analyses were used to study the changes in brain networks after stress.

UCMS induced negative correlations between the lateral entorhinal cortex and both the hippocampal structures and the nucleus accumbens in the VEH-treated mice, which were not present in other groups. Ranking nodes by degree reveals a strong thalamic-cortical signature in both non-stress (NS) groups. Exposure to UCMS seems to induce activity in thalamic areas and cerebral nuclei, with a different signature in the UCMS TAM group, which seems to completely “disengage” the neocortex and has most of its nodes with the most connections in the thalamic areas.
Contributions and competition of Mg2+and K+in folding and stabilization of the Twister Ribozyme
Authors: Kognole Abhishek A. , MacKerell Alexander D.
Published: June 2020

Native folded and compact intermediate states of RNA typically involve tertiary structures in the presence of divalent ions such as Mg2+in a background of monovalent ions. In a recent study we showed how the presence of Mg2+impacts the transition from partially unfolded to folded states through a “push-pull” mechanism where the ion both favors and disfavors the sampling of specific phosphate-phosphate interactions. To better understand the ion atmosphere of RNA in folded and partially folded states results from atomistic Umbrella Sampling and oscillating chemical potential Grand Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) simulations are used to obtain atomic-level details of the distributions of Mg2+and K+ions around Twister RNA. Results show the presence of 100 mM Mg2+to lead to increased charge neutralization over that predicted by counterion condensation theory. Upon going from partially unfolded to folded states overall charge neutralization increases at all studied ion concentrations that, while associated with an increase in the number of direct ion-phosphate interactions, is fully accounted for by the monovalent K+ions. Furthermore, K+preferentially interacts with purine N7 atoms of helical regions in partially unfolded states thereby potentially stabilizing them. Thus, both secondary helical structures and formation of tertiary structures leads to increased counterion condensation, thereby stabilizing those structural features of Twister. Notably, it is shown that K+can act as a surrogate for Mg2+by participating in specific interactions with non-sequential phosphate pairs that occur in the folded state, explaining the ability of Twister to self-cleave at sub-millimolar Mg2+concentrations.
Evolutionary transcriptomics implicatesHAND2in the origins of implantation and regulation of gestation length
Authors: Marinić Mirna , Mika Katelyn , Chigurupati Sravanthi , Lynch Vincent J.
Published: June 2020

The developmental origins and evolutionary histories of cell types, tissues and organ systems contribute to the ways in which their dysfunction leads to disease. In mammals for example, the nature and extent of maternal-fetal interactions, how those interactions develop, and their evolutionary history likely influence diseases of pregnancy such as infertility and preterm birth. Here we show genes that evolved to be expressed at the maternal-fetal interface in Eutherian (‘Placental’) mammals play essential roles in the evolution of pregnancy and are associated with immune system disorders and preterm birth. Among these genes is the transcription factorHAND2, which suppresses estrogen signaling, an innovation of Eutherians, thereby allowing blastocyst implantation. We found thatHAND2is dynamically expressed in the decidua throughout the menstrual cycle and pregnancy, gradually decreasing to reach a low at term. HAND2 regulates a small but distinct set of target genes in endometrial stromal fibroblasts including the cytokineIL15, which was also dynamically expressed throughout the menstrual cycle and gestation, and promoted the migration of natural killer cells and extravillous cytotrophoblasts. Remarkably, we found that theHAND2promoter loops to a distal enhancer containing SNPs implicated in the regulation of gestation length and birth weight. Collectively, these data connectHAND2expression at the maternal-fetal interface with the evolution of implantation and gestation length regulation, and preterm birth.
Role of TLR4 in persistentLeptospira interrogansinfection: a comparativein vivostudy in mice
Authors: Nair Nisha , Guedes Mariana Soares , Hajjar Adeline , Werts Catherine , Gomes-Solecki Maria
Published: June 2020

Toll-Like Receptor (TLR) 4, the LPS receptor, plays a central role in the control of leptospirosis and absence of TLR4 results in lethal infection in mice. Because human TLR4 does not sense the atypical leptospiral-LPS, we hypothesized that TLR4/MD-2 humanized transgenic mice (huTLR4) may be more susceptible to leptospirosis than wild-type mice, and thus may constitute a model of acute human leptospirosis. Therefore, we infected huTLR4 mice, which express human TLR4 but not murine TLR4, with a high but sublethal dose ofL. interrogansserovar Copenhageni FioCruz (Leptospira) in comparison to C57BL/6J wildtype (WT) and, as a control, a congenic strain in which thetlr4coding sequences are deleted (muTLR4Lps-del). We show that the huTLR4 gene is fully functional in the murine background. We found that dissemination ofLeptospirain blood, shedding in urine, colonization of the kidney and overall kinetics of leptospirosis progression is equivalent between WT and huTLR4 C57BL/6J mice. Furthermore, inflammation of the kidney appeared to be subdued in huTLR4 compared to WT mice in that we observed less infiltrates of mononuclear lymphocytes, less innate immune markers and no relevant differences in fibrosis markers. Contrary to our hypothesis, huTLR4 mice showed less inflammation and kidney pathology, and are not more susceptible to leptospirosis than WT mice. This study is significant as it indicates that one intact TLR4 gene, be it mouse or human, is necessary to control acute leptospirosis.

Contribution to the field

Differences of recognition exist between mouse and human TLR4, in that the anchor of LPS in the outer membrane ofLeptospira(LipidA) activates murine, but not human TLR4. We hypothesized that if human TLR4 does not sense leptospiral-LPS, then transgenic mice in which murine TLR4 was replaced with human TLR4, should be more susceptible toLeptospiradissemination as compared to congenic wild-type mice, which could result in a more robust inflammatory response and pathology in the kidney. However, we found that impaired sensing of leptospiral-LPS in huTLR4 mice did not affect overall infection in comparison to wild-type mice and does not result in increased pathology of the kidney. Our study indicates that rather than leptospiral-LPS sensing, the presence of a fully functional TLR4 receptor is necessary to control acute leptospirosis.
Divergent impact of grazing on plant communities of created wetlands with varying hydrology and antecedent land use
Authors: Lodge Kimberly A. , Tyler Anna Christina
Published: June 2020

Destruction of natural wetlands has warranted the creation of wetlands to mitigate the reduction of valuable ecosystem functions and services. However, the complex interactions between key drivers of wetland community structure – hydrology, nutrient availability and herbivory – makes creation of functional wetland replacements challenging. We examined interactions among these drivers, and their impacts on plant communities and soil characteristics in two created wetlands with different hydrology and land use histories: a shallow emergent marsh on a previous gravel depository and a seasonally flooded marsh on a former cattle pasture. In paired plots open to or protected from large wetland grazers we observed seasonal variation in grazing impacts on plant communities and an increase in effect size over time. At the permanently flooded marsh with high grazing waterfowl densities and low nutrients, open plots had significantly reduced plant growth and diversity, and an increase in submerged vegetation. In contrast, grazer density was lower and nutrients were higher in the seasonally flooded marsh, where grazer access enhanced plant diversity and reduced invasive plant cover. These results suggest the possibility of long-term grazer-induced shifts in community composition and delivery of key ecosystem services in young, vulnerable created wetlands. To improve created wetland design and function, we suggest that in addition to hydrologic conditions, the impact of prior land use on present nutrient availability be considered. Further, enhanced heterogeneity of spatial and bathymetric structure can provide conditions for diverse plant communities and balanced habitat use by wetland grazers.
A visual atlas of meiotic protein dynamics in living fission yeast
Authors: Escorcia Wilber , Tripathi Vishnu P. , Yuan Ji-Ping , Forsburg Susan L.
Published: June 2020

Meiosis is a carefully choreographed dynamic process that re-purposes proteins from somatic/vegetative cell division, as well as meiosis-specific factors, to carry out the differentiation and recombination pathway common to sexually reproducing eukaryotes. Studies of individual proteins from a variety of different experimental protocols can make it difficult to compare details between them. Using a consistent protocol in otherwise wild type fission yeast cells, this report provides an atlas of dynamic protein behavior of representative proteins at different stages during normal zygotic meiosis in fission yeast. This establishes common landmarks to facilitate comparison of different proteins and shows that initiation of S phase likely occurs prior to nuclear fusion/karyogamy.

Meiosis is an important process for sexually reproducing organisms. Unique dynamics of recombination and chromosome segregation are required for this differentiation process. Fission yeast is an excellent model to study meiotic progression and chromosome dynamics. Historically, different methodologies have been used to examine protein dynamics in fixed or live cells, which makes comparisons more difficult. In this report, we use fluorescently tagged proteins and live-cell microscopy under uniform conditions to compare meiotic signposts that define dynamic behavior of proteins during meiotic DNA synthesis, nuclear fusion, chromosome alignment, genetic recombination, metaphase, and meiosis. This establishes a reference atlas of protein behavior during meiotic differentiation.
Predicting tumour mutational burden from histopathological images using multiscale deep learning
Authors: Jain Mika S , Massoud Tarik F
Published: June 2020

Tumour mutational burden (TMB) is an important biomarker for predicting response to immunotherapy in cancer patients. Gold-standard measurement of TMB is performed using whole exome sequencing (WES), which is not available at most hospitals owing to its high cost, operational complexity, and long turnover times. We developed a machine learning algorithm, Image2TMB, which can predict TMB from readily available lung adenocarcinoma histopathological images. Image2TMB integrates the predictions of three deep learning models that operate at different resolution scales (5X, 10X, and 20X magnification) to determine if the TMB of a cancer is high or low. On a held-out set of patients, Image2TMB achieves an area under the precision recall curve of 0.92, an average precision of 0.89, and has the predictive power of a targeted sequencing panel of approximately 100 genes. This study demonstrates that it is possible to infer genomic features from histopathology images, and potentially opens avenues for exploring genotype-phenotype relationships.
Differences in movement and dynamic resource selection between breeders and floaters revealed with an Ornstein-Uhlenbeck space use model
Authors: Eisaguirre Joseph M. , Booms Travis L. , Barger Christopher P. , Lewis Stephen B. , Breed Greg A.
Published: June 2020

In populations of many taxa, a large fraction of sexually mature individuals do not breed but are attempting to enter the breeding population. Such individuals, often referred to as “floaters” play critical roles in determining dynamics and stability of these populations. Floaters are difficult to study, however, so we lack data on the roles they play in population ecology and conservation status of many species. Here, we paired satellite telemetry and a new mechanistic space use model based on an Ornstein-Uhlenbeck process to study the differential habitat selection and space use of floater and territorial golden eaglesAquila chrysaetos. Our sample consisted of 49 individuals tracked over complete breeding seasons across four years, totalling 104 eagle breeding seasons. Modeling these data with the new mechanistic approach was required to parse key differences in movement and separate aspects of resource selection from central place behavior. We found that floaters generally had more expansive space use patterns and larger home ranges, partitioning space with territorial individuals seemingly on fine scales through differential habitat and resource selection. Floater and territorial eagle home ranges overlapped markedly, suggesting floaters use the interstices between territories. Further, floater and territorial eagles differed in how they selected for uplift variables, key components of soaring birds’ energy landscape, with territorial eagles apparently better able to find and use thermal uplift. We also found relatively low individual heterogeneity in resource selection, especially among territorial individuals, suggesting a narrow realized niche for breeding individuals. This work furthers our understanding of floaters’ potential roles in population ecology of territorial species, as well as suggests that conserving landscapes occupied by territorial eagles also protects floaters.
Protective Antibodies Against Human Parainfluenza Virus Type 3 (HPIV3) Infection
Authors: Boonyaratanakornkit Jim , Singh Suruchi , Weidle Connor , Rodarte Justas , Bakthavatsalam Ramasamy , Perkins Jonathan , Stewart-Jones Guillaume B.E. , Kwong Peter D. , McGuire Andrew T. , Pancera Marie , Taylor Justin J.
Published: June 2020

Human parainfluenza virus type III (HPIV3) is a common respiratory pathogen that afflicts children and can be fatal in vulnerable populations, including the immunocompromised. Unfortunately, an effective vaccine or therapeutic is not currently available, resulting in tens of thousands of hospitalizations per year. In an effort to discover a protective antibody against HPIV3, we screened the B cell repertoires from peripheral blood, tonsils, or spleen from healthy children and adults. These analyses yielded five monoclonal antibodies that potently neutralized HPIV3in vitro. These HPIV3 neutralizing antibodies targeted two non-overlapping epitopes of the HPIV3 F protein, with most targeting the apex. Importantly, prophylactic administration of one of these antibodies, named PI3-E12, resulted in potent protection against HPIV3 infection in cotton rats. Additionally, PI3-E12 could also be used therapeutically to suppress HPIV3 in immunocompromised animals. These results demonstrate the potential clinical utility of PI3-E12 for the prevention or treatment of HPIV3 in both immunocompetent and immunocompromised individuals.
Red fox viromes across an urban-rural gradient
Authors: Campbell Sarah J , Ashley Wilbur , Gil-Fernandez Margarita , Newsome Thomas M. , Di Giallonardo Francesca , Ortiz-Baez Ayda Susana , Mahar Jackie E , Towerton Alison L , Gillings Michael , Holmes Edward C , Carthey Alexandra JR , Geoghegan Jemma L
Published: June 2020

The Red fox (Vulpes vulpes) has established large populations in Australia’s urban and rural areas since its introduction following European settlement. Foxes’ cryptic and highly adaptable nature allows them to invade cities and live among humans while remaining largely unnoticed. Urban living and access to anthropogenic food resources also influences fox ecology. Urban foxes grow larger, live at higher densities and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To assess this possibility, we used a meta-transcriptomic approach to characterise the viromes of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. In contrast, urban fox viromes comprised a greater diversity of viruses compared to rural foxes. We identified nine potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of theAstroviridae, Picobirnaviridae, HepeviridaeandPicornaviridaeas well as rabbit haemorrhagic disease virus-2 (RHDV2). This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human-wildlife interface.

Importance

Urbanisation of wild environments is increasing as human populations continue to expand. Remnant pockets of natural environments and other green spaces in urban landscapes provide invasive wildlife such as red foxes with refuges within urban areas, where they thrive on the food resources provisioned by humans. Close contact between humans, domestic species and foxes likely increases the risk of novel pathogen emergence. Indeed, the vast majority of emerging infectious diseases in humans originate in wild animals. Here, we explored potential differences in viromes between urban fox invaders and their rural counterparts. Viromes of foxes and their ectoparasites comprise a diversity of viruses including those from theAstroviridae, Picobirnaviridae, Hepeviridae, CaliciviridaeandPicornaviridae. Microbial surveillance in foxes and other urban wildlife is vital for monitoring viral emergence and for the prevention of infectious diseases.
An integrated gene catalog of the zebrafish gut microbiome reveals significant homology with mammalian microbiomes
Authors: Gaulke Christopher A. , Beaver Laura M. , Armour Courtney R. , Humphreys Ian R. , Barton Carrie L. , Tanguay Robyn L. , Ho Emily , Sharpton Thomas J.
Published: June 2020

Gut microbiome research increasingly utilizes zebrafish (Danio rerio) given their amenability to high-throughput experimental designs. However, the utility of zebrafish for discerning translationally relevant host-microbiome interactions is constrained by a paucity of knowledge about the biological functions that zebrafish gut microbiota can execute, how these functions associate with zebrafish physiology, and the degree of homology between the genes encoded by the zebrafish and human gut microbiomes. To address this knowledge gap, we generated a foundational catalog of zebrafish gut microbiome genomic diversity consisting of 1,569,102 non-redundant genes from twenty-nine individual fish. We identified hundreds of novel microbial genes as well as dozens of biosynthetic gene clusters of potential clinical interest. The genomic diversity of the zebrafish gut microbiome varied significantly across diets and this variance associated with altered expression of intestinal genes involved in inflammation and immune activation. Zebrafish, mouse, and human fecal microbiomes shared > 50% of their total genomic diversity and the vast majority of gene family abundance for each individual metagenome (∼99%) was accounted for by genes that comprised this shared fraction. These results indicate that the zebrafish gut houses a functionally diverse microbial community that manifests extensive homology to that of humans and mice despite substantial disparities in taxonomic composition. We anticipate that the gene catalog developed here will enable future mechanistic study of host-microbiome interactions using the zebrafish model.

Importance

Zebrafish have emerged as an important model system for defining host-microbiome interactions. However, the utility of this model is blunted by limited insight into the functions that are carried by zebrafish gut microbiota, their relationship with zebrafish physiology, and their consistency with the functions carried by human gut microbiota. To address these limitations, we constructed the first genomic database of zebrafish gut microbiome diversity. We use this novel resource to demonstrate that the genomic diversity of the zebrafish gut microbiome varies with diet and this variance links with altered intestinal gene expression. We also identify substantial homology between zebrafish, human, and mouse metagenomic diversity, indicating that these microbiomes may operate similarly.
The role of hippocampal theta oscillations in working memory impairment in multiple sclerosis
Authors: Costers Lars , Van Schependom Jeroen , Laton Jorne , Baijot Johan , Sjøgård Martin , Wens Vincent , De Tiège Xavier , Goldman Serge , D’Haeseleer Miguel , D’hooghe Marie Beatrice , Woolrich Mark , Nagels Guy
Published: June 2020

Working memory (WM) problems are frequent in persons with multiple sclerosis (MS). Even though hippocampal damage has been repeatedly shown to play an important role, the underlying neurophysiological mechanisms remain unclear. This study aimed to investigate the neurophysiological underpinnings of WM impairment in MS using magnetoencephalography (MEG) data from a verbal n-back task. We analysed MEG recordings of 79 MS patients and 38 healthy subjects through event-related fields (ERFs) and theta (4-8 Hz) and alpha (8-13 Hz) oscillatory processes. Data was source reconstructed and parcellated based on previous findings in the healthy subject sample. MS patients showed a smaller maximum theta power increase in the right hippocampus between 0 and 400 ms than healthy subjects (p = 0.014). This theta power increase value correlated strongly and negatively with reaction time on the task in MS (r = −0.32, p = 0.029). Evidence was provided that this relationship could not be explained by a confounding relationship with MS-related neuronal damage. This study provides the first neurophysiological evidence of the influence of hippocampal dysfunction on WM performance in MS.
Variations in the Circle of Willis in a large population sample using 3D TOF angiography: The Tromsø Study
Authors: Hindenes Lars B. , Håberg Asta K. , Johnsen Liv Hege , Mathiesen Ellisiv B. , Robben David , Vangberg Torgil R.
Published: June 2020

The main arteries that supply blood to the brain originate from the Circle of Willis (CoW). The CoW exhibit considerable anatomical variations which may have clinical importance, but the variability is insufficiently characterised in the general population. We assessed the anatomical variability of CoW variants in a community-dwelling sample (N = 1,864, 874 men, mean age = 65.4, range 40 – 87 years), and independent and conditional frequencies of the CoW’s artery segments. CoW segments were classified as present or missing/hypoplastic (w/1mm diameter threshold) on 3T time-of-flight magnetic resonance angiography images. We also examined whether age and sex were associated with CoW variants. We identified 47 unique CoW variants, of which five variants constituted 68.5% of the sample. The complete variant was found in 11.9% of the subjects, and the most common variant (27.8%) was missing both posterior communicating arteries. Conditional frequencies showed patterns of interdependence across most missing segments in the CoW. CoW variants were associated with mean-split age (P = .0147), and there was a trend showing more missing segments with increasing age. We found no association with sex (P = .0526). Our population study reinforced age as associated with CoW variants, suggesting reduced collateral supply with older age.
BingleSeq: A user-friendly R package for Bulk and Single-cell RNA-Seq Data Analysis
Authors: Dimitrov Daniel , Gu Quan
Published: June 2020

RNA sequencing is a high-throughput sequencing technique considered as an indispensable research tool used in a broad range of transcriptome analysis studies. The most common application of RNA Sequencing is Differential Expression analysis and it is used to determine genetic loci with distinct expression across different conditions. On the other hand, an emerging field called single-cell RNA sequencing is used for transcriptome profiling at the individual cell level. The standard protocols for both these types of analyses include the processing of sequencing libraries and result in the generation of count matrices. An obstacle to these analyses and the acquisition of meaningful results is that both require programming expertise.

BingleSeq was developed as an intuitive application that provides a user-friendly solution for the analysis of count matrices produced by both Bulk and Single-cell RNA-Seq experiments. This was achieved by building an interactive dashboard-like user interface and incorporating three state-of-the-art software packages for each type of the aforementioned analyses, alongside additional features such as key visualisation techniques, functional gene annotation analysis and rank-based consensus for differential gene analysis results, among others. As a result, BingleSeq puts the best and most widely used packages and tools for RNA-Seq analyses at the fingertips of biologists with no programming experience.
Quantitative comparison ofDrosophilabehavior annotations by human observers and a machine learning algorithm
Authors: Leng Xubo , Wohl Margot , Ishii Kenichi , Nayak Pavan , Asahina Kenta
Published: June 2020

Automated quantification of behavior is increasingly prevalent in neuroscience research. Human judgments can influence machine-learning-based behavior classification at multiple steps in the process, for both supervised and unsupervised approaches. Such steps include the design of the algorithm for machine learning, the methods used for animal tracking, the choice of training images, and the benchmarking of classification outcomes. However, how these design choices contribute to the interpretation of automated behavioral classifications has not been extensively characterized. Here, we quantify the effects of experimenter choices on the outputs of automated classifiers ofDrosophilasocial behaviors.Drosophilabehaviors contain a considerable degree of variability, which was reflected in the confidence levels associated with both human and computer classifications. We found that a diversity of sex combinations and tracking features was important for robust performance of the automated classifiers. In particular, features concerning the relative position of flies contained useful information for training a machine-learning algorithm. These observations shed light on the importance of human influence on tracking algorithms, the selection of training images, and the quality of annotated sample images used to benchmark the performance of a classifier (the ‘ground truth’). Evaluation of these factors is necessary for researchers to accurately interpret behavioral data quantified by a machine-learning algorithm and to further improve automated classifications.

Significance Statement

Accurate quantification of animal behaviors is fundamental to neuroscience. Here, we quantitatively assess how human choices influence the performance of automated classifiers trained by a machine-learning algorithm. We found that human decisions about the computational tracking method, the training images, and the images used for performance evaluation impact both the classifier outputs and how human observers interpret the results. These factors are sometimes overlooked but are critical, especially because animal behavior is itself inherently variable. Automated quantification of animal behavior is becoming increasingly prevalent: our results provide a model for bridging the gap between traditional human annotations and computer-based annotations. Systematic assessment of human choices is important for developing behavior classifiers that perform robustly in a variety of experimental conditions.
Robust framework and software implementation for fast speciation mapping
Authors: Cohen Serge X. , Webb Samuel M. , Gueriau Pierre , Curis Emmanuel , Bertrand Loïc
Published: June 2020

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. Several authors have used different multivariate data processing strategies to establish speciation maps. In this manuscript, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. The algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.
First high-pressure XAFS results at the bending-magnet-based energy-dispersive XAFS beamline BL-8 at the Indus-2 synchrotron facility
Authors: Lahiri Debdutta , Dwivedi Ashutosh , Vasanthi R. , Jha S. N. , Garg Nandini
Published: June 2020

The static focusing optics of the existing energy-dispersive XAFS beamline BL-8 have been advantageously exploited to initiate diamond anvil cell based high-pressure XANES experiments at the Indus-2 synchrotron facility, India. In the framework of the limited photon statistics with the 2.5 GeV bending-magnet source, limited focusing optics and 4 mm-thick diamond windows of the sample cell, a (non-trivial) beamline alignment method for maximizing photon statistics at the sample position has been designed. Key strategies include the selection of a high X-ray energy edge, the truncation of the smallest achievable focal spot size to target size with a slit and optimization of the horizontal slit position for transmission of the desired energy band. A motor-scanning program for precise sample centering has been developed. These details are presented with rationalization for every step. With these strategies, NbK-edge XANES spectra for Nb2O5under high pressure (0–16.9 GPa) have been generated, reproducing the reported spectra for Nb2O5under ambient conditions and high pressure. These first HPXANES results are reported in this paper. The scope of extending good data quality to the EXAFS range in the future is addressed. This work should inspire and guide future high-pressure XAFS experiments with comparable infrastructure.
A new approach for numerical-diffusion control of flux-vector-splitting schemes for viscous-compressible flows
Authors: Kalita Paragmoni , Dass Anoop K. , Hazarika Jongki
Published: June 2020

Purpose

The flux vector splitting (FVS) schemes are known for their higher resistance to shock instabilities and carbuncle phenomena in high-speed flow computations, which are generally accompanied by relatively large numerical diffusion. However, it is desirable to control the numerical diffusion of FVS schemes inside the boundary layer for improved accuracy in viscous flow computations. This study aims to develop a new methodology for controlling the numerical diffusion of FVS schemes for viscous flow computations with the help of a recently developed boundary layer sensor.

Design/methodology/approach

The governing equations are solved using a cell-centered finite volume approach and Euler time integration. The gradients in the viscous fluxes are evaluated by applying the Green’s theorem. For the inviscid fluxes, a new approach is introduced, where the original upwind formulation of an FVS scheme is first cast into an equivalent central discretization along with a numerical diffusion term. Subsequently, the numerical diffusion is scaled down by using a novel scaling function that operates based on a boundary layer sensor. The effectiveness of the approach is demonstrated by applying the same on van Leer’s FVS and AUSM schemes. The resulting schemes are named as Diffusion-Regulated van Leer’s FVS-Viscous (DRvLFV) and Diffusion-Regulated AUSM-Viscous (DRAUSMV) schemes.

Findings

The numerical tests show that the DRvLFV scheme shows significant improvement over its parent scheme in resolving the skin friction and wall heat flux profiles. The DRAUSMV scheme is also found marginally more accurate than its parent scheme. However, stability requirements limit the scaling down of only the numerical diffusion term corresponding to the acoustic part of the AUSM scheme.

Originality/value

To the best of the authors’ knowledge, this is the first successful attempt to regulate the numerical diffusion of FVS schemes inside boundary layers by applying a novel scaling function to their artificial viscosity forms. The new methodology can reduce the erroneous smearing of boundary layers by FVS schemes in high-speed flow applications.