bluuebunny/crossref_metadata_2025 huggingface dataset:
scMoC: Single-Cell Multi-omics clustering
Authors: Eltager Mostafa , Abdelaal Tamim , Mahfouz Ahmed , Reinders Marcel J.T.
Published: February 2021

Motivation

Single-cell multi-omics assays simultaneously measure different molecular features from the same cell. A key question is how to benefit from the complementary data available and perform cross-modal clustering of cells.

Results

We proposeSingle-CellMulti-omicsClustering (scMoC), an approach to identify cell clusters from data with co-measurements of scRNA-seq and scATAC-seq from the same cell. We overcome the high sparsity of the scATAC-seq data by using an imputation strategy that exploits the less-sparse scRNA-seq data available from the same cell. Subsequently, scMoC identifies clusters of cells by merging clusterings derived from both data domains individually. We tested scMoC on datasets generated using different protocols with variable data sparsity levels. We show that, due to its imputation scheme, scMoC 1) is able to generate informative scATAC-seq data due to its RNA guided imputation strategy, and 2) results in integrated clusters based on both RNA and ATAC information that are biologically meaningful either from the RNA or from the ATAC perspective.

Availability

The code is freely available at:https://github.com/meltager/scmoc.

Supplementary information

Supplementary data are available online.
Effects of substrate stiffness and actin velocity onin silicofibronectin fibril morphometry and mechanics
Authors: Weinberg Seth H. , Saini Navpreet , Lemmon Christopher A.
Published: February 2021

Assembly of the extracellular matrix protein fibronectin (FN) into insoluble, viscoelastic fibrils is a critical step during embryonic development and wound healing; misregulation of FN fibril assembly has been implicated in many diseases, including fibrotic diseases and cancer. We have previously developed a computational model of FN fibril assembly that recapitulates the morphometry and mechanics of cell-derived FN fibrils. Here we use this model to probe two important questions: how is FN fibril formation affected by the contractile phenotype of the cell, and how is FN fibril formation affected by the stiffness of the surrounding tissue? We show that FN fibril formation depends strongly on the contractile phenotype of the cell, but only weakly on tissue stiffness. These results are consistent with previous experimental data and provide a better insight into conditions that promote FN fibril assembly. We have also used the model to look at two distinct phenotypes of FN fibrils that we have previously identified; we show that the ratio of the two phenotypes depends on both tissue stiffness and contractile phenotype, with intermediate contractility and high tissue stiffness creating an optimal condition for stably stretched fibrils. Finally, we have investigated how re-stretch of a fibril affects cellular response. We probed how the contractile phenotype of the re-stretching cell affects the mechanics of the fibril; results indicate that the number of myosin motors only weakly affects the cellular response, but increasing actin velocity results in a decrease in the apparent stiffness of the fibril and a decrease in the stably-applied force to the fibril. Taken together, these results give novel insights into the combinatorial effects of tissue stiffness and cell contractility on FN fibril assembly.
Fiber-associatedLachnospiraceaereduce colon tumorigenesis by modulation of the tumor-immune microenvironment
Authors: Almeida Ana S , Tran Tam T T , Ghosh Tarini S. , Ribiere Celine , Foley Cathriona , Azevedo Lisa A , Pellanda Paola , Frei Werner , Hueston Cara M , Kumar Raju , Flemer Burkhardt , Sequeira Inês , O’Riordain Micheal , Shanahan Fergus , O’Toole Paul W.
Published: February 2021

Patients with colorectal cancer (CRC) harbor gut microbiomes that differ in structure and function from those of healthy individuals, suggesting this altered microbiome could contribute to tumorigenesis. Despite increasing evidence implicating the gut microbiome in CRC, the collective role of different microbial consortia in CRC carcinogenesis is unclear. We have previously described these consortia as co-abundance groups that co-exist at different abundance levels in the same patient. Here, we report that tumor biopsy tissue from patients with a “high-risk” Pathogen-type microbiome had a different immune transcriptome and immune cell infiltrate from those with a “low-risk”Lachnospiraceae-type microbiome. Transplantation from patients of the two fecal microbiome types into mice with an orthotopic tumor differentially affected tumor growth and the systemic anti-tumor immune response. The differences in tumor volume and immunophenotype between mice receiving the high-risk and the low-risk microbiome correlated with differences in the engrafted human microbial species and predicted microbiome-encoded metabolites in the two groups. Of twelve taxa whose abundance in recipient mice led to increased tumor onset, seven corresponded with differentially abundant taxa in a global dataset of 325 CRC patients versus 310 healthy controls. These data suggest that the enrichment for aLachnospiraceae-type configuration of the gut microbiome may influence colon cancer progression and disease outcome by modulating the local and systemic anti-tumor immune response.

Graphical Abstract

Proposed model of how the high-risk Pathogen and low-riskLachnospiraceaeCAGs differentially modulate the tumor immune response.
A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota
Authors: Sommer Alice J , Peters Annette , Rommel Martina , Cyrys Josef , Grallert Harald , Haller Dirk , Müller Christian L , Bind Marie-Abèle C
Published: February 2021

Statistical analysis of microbial genomic data within epidemiological cohort studies holds the promise to assess the influence of environmental exposures on both the host and the host-associated microbiome. The observational character of prospective cohort data and the intricate characteristics of microbiome data make it, however, challenging to discover causal associations between environment and microbiome. Here, we introduce a causal inference framework based on the Rubin Causal Model that can help scientists to investigate such environment-host microbiome relationships, to capitalize on existing, possibly powerful, test statistics, and test plausible sharp null hypotheses. Using data from the German KORA cohort study, we illustrate our framework by designing two hypothetical randomized experiments with interventions of (i) air pollution reduction and (ii) smoking prevention. We study the effects of these interventions on the human gut microbiome by testing shifts in microbial diversity, changes in individual microbial abundances, and microbial network wiring between groups of matched subjects via randomization-based inference. In the smoking prevention scenario, we identify a small interconnected group of taxa worth further scrutiny, including Christensenellaceae and Ruminococcaceae genera, that have been previously associated with blood metabolite changes. These findings demonstrate that our framework may uncover potentially causal links between environmental exposure and the gut microbiome from observational data. We anticipate the present statistical framework to be a good starting point for further discoveries on the role of the gut microbiome in environmental health.
An Adeno-Associated Viral vector encoding Neurotrophin 3 injected into affected forelimb muscles modestly improves sensorimotor function after contusive mid-cervical spinal cord injury
Authors: Sydney Smith Jared D. , Megaro Vanessa , Spejo Aline Barroso , Moon Lawrence D. F.
Published: February 2021

Traumatic spinal cord injury (SCI) in humans occurs most frequently in the cervical spine where it can cause substantial sensorimotor impairments to upper limb function. The altered input to spinal circuits below the lesion leads to maladaptive reorganisation which often leads to hyperreflexia in proprioceptive circuits. Neurotrophin 3 (NT3) is growth factor essential for the development of proprioceptive neurons. We have previously shown that following bilateral corticospinal tract axotomy, intramuscular delivery of an Adeno-Associated Viral vector encoding NT3 (AAV-NT3) induces proprioceptive circuit reorganisation linked to functional recovery. To assess its therapeutic effects following a clinically relevant bilateral C5-C6 contusion in rats, AAV-NT3 was injected intramuscularly into the dominant limb 24 hours after injury and forelimb function was assessed over 13 weeks. The injury generated hyperreflexia of a distal forelimb proprioceptive circuit. There was also loss of fine motor skills during reach-and-grasp and walking on a horizontal ladder. Ex vivo magnetic resonance imaging (MRI) revealed atrophy of the spinal cord and white matter disruption throughout the lesion site together with extensive loss of grey matter. Unexpectedly, animals treated with AAV-NT3 had a slightly smaller lesion in the regions close to the epicentre compared to PBS treated animals. Rats treated with AAV-NT3 showed subtly better performance on the horizontal ladder and transient benefits on reach-and-grasp. AAV-NT3 did not normalise hyperreflexia in a treated muscle. The treatment increased the amount of NT3 in treated muscles but, unexpectedly, serum levels were only elevated in a small subset of animals. These results show that this dose and delivery of AAV-NT3 may generate subtle improvements in locomotion but additional treatments will be required to overcome the widespread sensorimotor deficits caused by contusion injury.
Cytotoxic lymphocytes target HIV-1 Gag through granzyme M-mediated cleavage
Authors: Saccon Elisa , Mikaeloff Flora , Ivern Pol Figueras , Végvári Ákos , Sönnerborg Anders , Neogi Ujjwal , van Domselaar Robert
Published: February 2021

HIV-1 leads to progression to immunodeficiency and death of individuals who do not receive successful antiretroviral therapy. Initially, the host’s immune response controls the infection, but cannot eliminate the HIV-1 from the host. Cytotoxic lymphocytes are the key effector cells in this response and can mediate crucial antiviral responses through the release of a set of proteases called granzymes towards HIV-1-infected cells. However, little is known about the immunological molecular mechanisms by which granzymes could control HIV-1. Since we noted that HIV-1 subtype C (HIV-1C) Gag with the tetrapeptide insertion PYKE contains a putative granzyme M (GrM) cleavage site (KEPL) that overlaps with the PYKE insertion, we analyzed the proteolytic activity of GrM towards Gag. Immunoblot analysis showed that GrM could cleave Gag proteins from HIV-1B and variants from HIV-1C of which the Gag-PYKE variant was cleaved with extremely high efficiency. The main cleavage site was directly after the insertion after leucine residue 483. GrM-mediated cleavage of Gag was also observed in co-cultures using cytotoxic lymphocytes as effector cells and this cleavage could be inhibited by a GrM inhibitor peptide. Altogether, our data indicate towards a noncytotoxic immunological mechanism by which GrM-positive cytotoxic lymphocytes target the HIV-1 Gag protein within infected cells to potentially control HIV-1 infection. This mechanism could be exploited in new therapeutic strategies to treat HIV-1-infected patients to improve immunological control of the infection.
Pervasive effects ofWolbachiaon host activity
Authors: Hague Michael T.J. , Woods H. Arthur , Cooper Brandon S.
Published: February 2021

Heritable symbionts have diverse effects on the physiology, reproduction, and fitness of their hosts. Maternally transmittedWolbachiaare one of the most common endosymbionts in nature, infecting about half of all insect species. We test the hypothesis thatWolbachiaalter host behavior by assessing the effects of 14 differentWolbachiastrains on the locomotor activity of nineDrosophilahost species. We find thatWolbachiaalter the activity of six different host genotypes, including all hosts in our assay infected withwRi-likeWolbachiastrains (wRi,wSuz,wAur), which have rapidly spread amongDrosophilaspecies in only the last 13,000 years. WhileWolbachiaeffects on host activity were common, the direction of these effects varied unpredictability and sometimes depended on host sex. We hypothesize that the prominent effects ofwRi-likeWolbachiamay be explained by patterns ofWolbachiatiter and localization within host somatic tissues, particularly in the central nervous system. Our findings support the view thatWolbachiahave wide-ranging effects on host behavior. The fitness consequences of these behavioral modifications are important for understanding the evolution of host-symbiont interactions, including howWolbachiaspread within host populations.
Pathogen and endophyte assemblages co-vary with beech bark disease progression, tree decline, and regional climate
Authors: Morrison Eric W. , Kasson Matt T. , Heath Jeremy J. , Garnas Jeff R.
Published: February 2021

Plant-pathogen interactions are often considered in a pairwise manner with minimal consideration of the impacts of the broader endophytic community on disease progression and/or outcomes for disease agents and hosts. Community interactions may be especially relevant in the context of disease complexes (i.e, interacting or functionally redundant causal agents) and decline diseases (where saprobes and weak pathogens synergize the effects of primary infections and hasten host mortality). Here we describe the bark endophyte communities associated with a widespread decline disease of American beech, beech bark disease (BBD), caused by an invasive scale insect (Cryptococcus fagisuga) and two fungal pathogens,Neonectria faginataandN. ditissima. We show that the two primary fungal disease agents co-occur more broadly than previously understood (35.5% of infected trees), including within the same 1-cm diameter phloem samples. The two species appear to have contrasting associations with climate and stages of tree decline, whereinN. faginatawas associated with warmer andN. ditissimawith cooler temperatures.Neonectria ditissimashowed a positive association with tree crown dieback – no such association was observed forN. faginata. Further, we identify fungal endophytes that may modulate disease progression as entomopathogens, mycoparasites, saprotrophs and/or additional pathogens, includingClonostachys roseaandFusarium babinda. These fungi may alter the trajectory of disease via feedbacks with the primary disease agents or by altering symptom expression or rates of tree decline across the range of BBD.
A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duckAythya fuligula(Tufted Duck)
Authors: Mueller Ralf C , Ellström Patrik , Howe Kerstin , Uliano-Silva Marcela , Kuo Richard I , Miedzinska Katarzyna , Warr Amanda , Fedrigo Olivier , Haase Bettina , Mountcastle Jacquelyn , Chow William , Torrance James , Wood Jonathan , Järhult Josef D , Naguib Mahmoud M , Olsen Björn , Jarvis Erich D , Smith Jacqueline , Eöry Lél , Kraus Robert HS
Published: February 2021

Background

The tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza out-breaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.

Results

This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (cDNA) from brain, ileum, lung, ovary, spleen and testis using Illumina short-read and PacBio long-read sequencing platforms, which was used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies an average of 7.9 isoforms per gene. We also identified 246 small RNA families.

Conclusions

This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to the avian influenza virus.
Permeant Fluorescent Probes Visualize the Activation of SARM1 and Uncover an Anti-neurodegenerative Drug Candidate
Authors: Li Wan Hua , Huang Ke , Cai Yang , Wang Qian Wen , Zhu Wen Jie , Hou Yun Nan , Wang Sujing , Cao Sheng , Zhao Zhi Ying , Xie Xu Jie , Du Yang , Lee Chi-Sing , Lee Hon Cheung , Zhang Hongmin , Zhao Yong Juan
Published: February 2021

SARM1 regulates axonal degeneration through its NAD-metabolizing activity and is a drug target for neurodegenerative disorders. We designed and synthesized fluorescent conjugates of styryl derivative with pyridine to serve as substrates of SARM1, which exhibited large red-shifts after conversion. With the conjugates, SARM1 activation was visualized in live cells following elevation of endogenous NMN or treatment with a cell-permeant NMN-analog. In neurons, imaging documented SARM1 activation preceded vincristine-induced axonal degeneration by hours. Library screening identified a derivative of nisoldipine as a covalent inhibitor of SARM1 that reacted with Cys311 in its Armadillo-domain and blocked its NMN-activation, protecting axons from degeneration. CryoEM showed that SARM1 was locked into an inactive conformation by the inhibitor, uncovering an unsuspected neuroprotective mechanism of dihydropyridines.
Dichotomous regulation of lysosomes by MYC and TFEB controls hematopoietic stem cell fate
Authors: García-Prat Laura , Kaufmann Kerstin B. , Schneiter Florin , Voisin Veronique , Murison Alex , Chen Jocelyn , Chan-Seng-Yue Michelle , Gan Olga I. , McLeod Jessica L. , Smith Sabrina A. , Shoong Michelle C. , Paris Darrien , Pan Kristele , Zeng Andy G.X. , Krivdova Gabriela , Gupta Kinam , Takayanagi Shin-Ichiro , Wagenblast Elvin , Wang Weijia , Lupien Mathieu , Schroeder Timm , Xie Stephanie Z. , Dick John E.
Published: February 2021

It is critical to understand how quiescent long-term hematopoietic stem cells (LT-HSC) sense demand from daily and stress-mediated cues and transition into bioenergetically active progeny to differentiate and meet these cellular needs. Here, we show that lysosomes, which are sophisticated nutrient sensing and signaling centers, are dichotomously regulated by the Transcription Factor EB (TFEB) and MYC to balance catabolic and anabolic processes required for activating LT-HSC and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway causes membrane receptor degradation, limiting LT-HSC metabolic and mitogenic activation, which promotes quiescence, self-renewal and governs erythroid-myeloid commitment. By contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism to drive LT-HSC activation. Collectively, our study identifies lysosomes as a central regulatory hub for proper and coordinated stem cell fate determination.
Towns and Trails Drive Carnivore Connectivity using a Step Selection Approach
Authors: Whittington Jesse , Baron Robin , Hebblewhite Mark , Ford Adam T. , Paczkowski John
Published: February 2021

Global increases in human activity threaten connectivity of animal populations. Protection and restoration of animal movement corridors requires robust models to forecast the effects of human activity on connectivity. Recent advances in the field of animal movement ecology and step selection functions offer new approaches for estimating connectivity. We show how a combination of hidden Markov movement models and step selection functions can be used to simulate realistic movement paths with multiple behavioral states. Simulated paths can be used to generate utilization distributions and estimate changes in connectivity for multiple land use scenarios. We applied movement models to 20 years of grizzly bear (Ursus arctos) and gray wolf (Canis lupus) data collected in and around Banff National Park, Canada. These carnivores avoided areas near towns in all seasons, avoided areas of high trail density in most seasons, and campgrounds during summer and fall. We simulated movement paths for three landscape scenarios: reference conditions with no anthropogenic development, current conditions, and future conditions with expanded town footprints and trail networks. We counted the number of paths that crossed valley-wide, digital transects through mountain tourist towns of Banff and Canmore, Alberta. We divided current and future crossing rates by the reference crossing rates to estimate connectivity. Current connectivity rates ranged between 7 and 45% of reference values with an average of 21% for grizzly bears and 25% for wolves. Potential town expansion and increased development of trails further decreased connectivity an average of 6% in future scenarios. Anthropogenic developments reduced the amount of available high quality large carnivore habitat in the Bow Valley by an average of 14% under current conditions and 16% under future conditions. Our approach for estimating connectivity provides a robust and flexible method for combining movement models with step selection analyses to estimate connectivity for a variety of species.
Natural Selection as the Sum over all Histories
Authors: Neal-Sturgess C E
Published: February 2021

As evolution can be connected to the principle of least action, and if it is depicted in evolution-space versus time then it corresponds to the direction of ultimate causation. As an organism evolves and follows a path of proximate causation, if the vector is closely parallel to that of the Ultimate Causation then the changes will confer desirable attributes which will lead to further development. If, however, the variations do not occur in a direction close to that of the ultimate causation vector the evolved organism will quickly die out. Therefore Natural Selection may be viewed as similar to Feynman’s “sum over all histories”. This approach is compatible with both Neutral Theory and Selection, as it includes both positive and negative mutations and selection. Therefore, the principle of least action gives a direction, but not a purpose, to evolution.
Extracellular S100B alters spontaneous Ca2+fluxes in dopaminergic neurons via L-type voltage gated calcium channels: Implications for Parkinson’s disease
Authors: Bancroft Eric A. , Pandey Gauri , Zarate Sara M. , Srinivasan Rahul
Published: February 2021

Parkinson’s disease (PD) is associated with an abnormal increase in S100B within the midbrain and cerebrospinal fluid. In addition, overexpression of S100B in mice accelerates the loss of substantia nigra pars compacta (SNc) dopaminergic (DA) neurons, suggesting a role for this protein in PD pathogenesis. We found that in the mouse SNc, S100B labeled astrocytic processes completely envelop the somata of tyrosine hydroxylase (TH) positive DA neurons. Based on this finding, we rationalized that abnormal increases in extracellularly secreted S100B by astrocytic processes in the SNc could alter DA neuron activity, thereby causing dysregulated midbrain function. To test this hypothesis, we measured the effect of bath perfused S100B peptide on the frequency and amplitude of spontaneous calcium fluxes in identified TH+and TH−midbrain neurons from 3-week old mouse primary midbrain cultures. Acute exposure to 50 pM S100B caused a 2-fold increase in calcium flux frequency only in TH+DA neurons. The L-type voltage gated calcium channel (VGCC) inhibitor, diltiazem eliminated S100B-mediated increases in DA neuron calcium flux frequency, while the T-type specific VGCC blocker mibefradil failed to inhibit the stimulatory effect of S100B. Chronic exposure to S100B caused a 3-fold reduction in calcium flux frequencies of TH+neurons and also reduced calcium flux amplitudes in TH−neurons by ∼4-fold. Together, our results suggest that exposure to S100B pathologically alters spontaneous calcium activity in midbrain neurons via an extracellular mechanism involving L-type VGCCs expressed in DA neurons. These findings are relevant to understanding mechanisms underlying DA neuron loss during PD.

Table of Contents Image

Main Points

Extracellular S100B increases Ca2+fluxes in dopaminergic neurons

L-type VGCCs in dopaminergic neurons are required for S100B-mediated increases in Ca2+fluxes

Chronic S100B alters Ca2+fluxes in dopaminergic and non-dopaminergic neurons
Myo-inositol Oxygenase Overexpression Rescues Vitamin C Deficient Arabidopsis (vtc) Mutants
Authors: Acosta-Gamboa Lucia M. , Nirman Nepal , Karina Medina-Jimenez , Campbell Zachary C. , Cunningham Shannon S. , Ae Lee Jung , Argelia Lorence
Published: February 2021

Biosynthesis ofl-ascorbate (AsA) in plants is carried out by a complex metabolic network, which involvesd-mannose/l-galactose,d-galacturonate,l-gulose, andmyo-inositol as main precursors. Arabidopsis lines over-expressing enzymes in themyo-inositol pathway have elevated AsA, accumulate more biomass of both aerial and root tissues, and are tolerant to abiotic stresses as shown by manual and digital phenotyping. We crossedmyo-inositol oxygenase (MIOX4) over-expressers with two low-vitamin C mutants (vtc1-1 andvtc2-1) encoding enzymes involved ind-mannose/l-galactose route. The purpose of developing these crosses was to test MIOX4’s ability to restore the low AsA phenotype in mutants, and to assess the contribution of individual biosynthetic pathways to abiotic stress tolerance. We used a powerful high-throughput phenotyping platform for detailed phenotypic characterization of the Arabidopsis crosses with visible, fluorescence, near-infrared and infrared sensors. We combined digital phenotyping with photosynthetic parameters and soil water potential measurements. Our results show thatMIOX4is able to restore the AsA content of the mutants and the restored lines (vtc+MIOX4) show high AsA, enhanced growth rate, accumulate more biomass, and display healthier chlorophyll fluorescence and water content profiles compared to controls.

Highlights

Constitutive expression of amyo-inositol oxygenase restored vitamin C deficient (vtcmutants). The restored lines have elevated ascorbate content and are tolerant to abiotic stresses. Under normal and abiotic stress conditions, the restored lines have enhanced biomass and increased water retention.
Comparative biofilm assays usingEnterococcus faecalisOG1RF identify new determinants of biofilm formation
Authors: Willett Julia L. E. , Dale Jennifer L. , Kwiatkowski Lucy M. , Powers Jennifer L. , Korir Michelle L. , Kohli Rhea , Barnes Aaron M. T. , Dunny Gary M.
Published: February 2021

Enterococcus faecalisis a common commensal organism and a prolific nosocomial pathogen that causes biofilm-associated infections. NumerousE. faecalisOG1RF genes required for biofilm formation have been identified, but few studies have compared genetic determinants of biofilm formation and biofilm morphology across multiple conditions. Here, we cultured transposon (Tn) libraries in CDC biofilm reactors in two different media and used Tn sequencing (TnSeq) to identify core and accessory biofilm determinants, including many genes that are poorly characterized or annotated as hypothetical. Multiple secondary assays (96-well plates, submerged Aclar, and MultiRep biofilm reactors) were used to validate phenotypes of new biofilm determinants. We quantified biofilm cells and used fluorescence microscopy to visualize biofilms formed by 6 Tn mutants identified using TnSeq and found that disrupting these genes (OG1RF_10350,prsA,tig, OG1RF_10576, OG1RF_11288, and OG1RF_11456) leads to significant time- and medium-dependent changes in biofilm architecture. Structural predictions revealed potential roles in cell wall homeostasis for OG1RF_10350 and OG1RF_11288 and signaling for OG1RF_11456. Additionally, we identified growth medium-specific hallmarks of OG1RF biofilm morphology. This study demonstrates howE. faecalisbiofilm architecture is modulated by growth medium and experimental conditions, and identifies multiple new genetic determinants of biofilm formation.

Importance

E. faecalisis an opportunistic pathogen and a leading cause of hospital-acquired infections, in part due to its ability to form biofilms. A complete understanding of the genes required forE. faecalisbiofilm formation as well as specific features of biofilm morphology related to nutrient availability and growth conditions is crucial for understanding howE. faecalisbiofilm-associated infections develop and resist treatment in patients. We employed a comprehensive approach to analysis of biofilm determinants by combining TnSeq primary screens with secondary phenotypic validation using diverse biofilm assays. This enabled identification of numerous core (important under many conditions) and accessory (important under specific conditions) biofilm determinants inE. faecalisOG1RF. We found multiple genes whose disruption results in drastic changes to OG1RF biofilm morphology. These results expand our understanding of the genetic requirements for biofilm formation inE. faecalisthat affect the time course of biofilm development as well as the response to specific nutritional conditions.
Targeting an anchored phosphatase-deacetylase unit restores renal ciliary homeostasis
Authors: Gopalan Janani , Omar Mitch , Roy Ankita , Cruz Nelly M. , Falcone Jerome , Forbush Katherine , Himmelfarb Jonathan , Freedman Benjamin S. , Scott John D.
Published: February 2021

Pathophysiological defects in water homeostasis can lead to renal failure. Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic disorder associated with abnormal cytoskeletal dynamics in the kidney collecting ducts and perturbed calcium and cAMP signaling in the ciliary compartment. We show that collecting ducts in mice lacking the A-Kinase anchoring protein AKAP220 exhibit enhanced development of primary cilia. Mechanistic studies reveal that AKAP220-associated protein phosphatase 1 (PP1) mediates this phenotype by promoting changes in the stability of histone deacetylase 6 (HDAC6) with concomitant defects in actin dynamics. This proceeds through a previously unrecognized adaptor function for PP1 as all ciliogenesis and cytoskeletal phenotypes are recapitulated in mIMCD3 knock-in cells expressing a phosphatase-targeting defective AKAP220-ΔPP1 mutant. Pharmacological blocking of local HDAC6 activity alters cilia development and reduces cystogenesis in kidney-on-chip and organoid models of ADPKD. These findings identify the AKAP220-PPI-HDAC6 pathway as a key effector in primary cilia development.
De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure
Authors: Martinson John , Bencic David C. , Toth Gregory P. , Kostich Mitchell S. , Flick Robert W. , See Mary J. , Lattier David , Biales Adam D. , Huang Weichun
Published: February 2021

The Fathead Minnow (FHM) is one of the most important and widely used model organisms in aquatic toxicology. The lack of a high-quality and well-annotated FHM reference genome, however, has severely hampered the efforts using modem ‘omics approaches with FHM for environmental toxicogenomics studies. We present here a de novo assembled and nearly complete reference of the fathead minnow genome. Compared to the current fragmented and sparsely annotated FHM genome assembly (FHM1), the new highly contiguous and well-annotated FHM reference genome (FHM2) represents a major improvement, having 95.1% of the complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) and a scaffold N50 of 12.0 Mbps. The completeness of gene annotation for the FHM2 reference genome was demonstrated to be comparable to that of the zebrafish (ZF) GRCz11 reference genome. In addition, our comparative genomics analyses between FHM and ZF revealed highly conserved coding regions between two species while discovering much more compact gene structure in FHM than ZF. This study not only provides insights for assembling a highly repetitive AT-rich genome, but also delivers a critical genomic resource essential for toxicogenomics studies in environmental toxicology.
The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes
Authors: Carter Stephen D. , Tran Ngoc-Han , De Mazière Ann , Ashkenazi Avi , Klumperman Judith , Jensen Grant J. , Walter Peter
Published: February 2021

The signaling network of the unfolded protein response (UPR) adjusts the protein folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1α, spans the ER membrane and activates through oligomerization. IRE1α oligomers accumulate in dynamic foci. We determined thein-situstructure of IRE1α foci by cryogenic correlated light and electron microscopy (cryo-CLEM), combined with electron cryo-tomography (cryo-ET) and complementary immuno-electron microscopy. IRE1α oligomers localize to a network of narrow anastomosing ER tubes (diameter ~28 nm) with complex branching. The lumen of the tubes contains protein filaments, likely composed of linear arrays of IRE1α lumenal domain dimers, arranged in two intertwined, left-handed helices. Our findings define a previously unrecognized ER subdomain and suggest positive feedback in IRE1 signaling.
Larvae and adults exhibit contrasting patterns of immune gene expression and infection resistance in wild flour beetle populations
Authors: Tate Ann T. , Perry Abby , Jent Derrick G.
Published: February 2021

In nature, hosts face shifting patterns of parasite exposure and life history trade-offs as they develop from birth to old age. As a result, the net fitness benefit of immunological investment can change dramatically from one life stage to the next. Previous work has revealed a puzzling diversity of relative immune investment patterns among juvenile and adult stages, and it is not clear whether lessons learned from one particular population or species can be generalized to wild populations, after accounting for local adaptation and other variance-generating processes. In this study, we quantify larval and adult immune gene expression and resistance to bacterial infection in two flour beetle species (Tribolium castaneumandT. confusum) from two lab-adapted and five wild-derived populations. Our results provide a clear signal of higher infection-induced immunological investment and resistance in adults relative to larvae, despite variation among species in immune gene regulation. Better characterization of stage-specific investment in infection resistance in natural populations can inform our understanding of life history evolution and improve predictions of disease dynamics in the wild.
Visualization of SARS-CoV-2 Infection Scenes by ‘Zero-Shot’ Enhancements of Electron Microscopy Images
Authors: Drefs Jakob , Salwig Sebastian , Lücke Jörg
Published: February 2021

Electron microscopy (EM) recordings of infected tissues serve to diagnose a disease, and they can contribute to our understanding of infection processes. Consequently, a large number of EM images of the interaction of SARS-CoV-2 viruses with cells have been made available by numerous labs. However, due to EM recording techniques at high resolution, images of infection scenes are very noisy and they appear two dimensional (‘flat’). Current research consequently aims (A) at methods that can remove noise, and (B) at techniques that allow for recovering a 3D impression of the virus or its parts. Here we discuss a novel method which can recover a spatial impression of a whole infection scene at high resolution. In contrast to previous approaches which aim at the reconstruction of single spike proteins or a single virus, the here used method can be applied to a single noisy EM image of an infection scene. As one example image, we show a high resolution image of SARS-CoV-2 viruses in Vero cell cultures (Fig. 1). The method we use is based on probabilistic machine learning algorithms which can operate in a ‘zero-shot’ setting, i.e., in a setting when just one noisy image (and no large and clean image corpus) is available. The probabilistic method we apply can estimate non-noisy images by inferring first order statistics (pixel means) across image patches using a previously learned probabilistic image representation. Estimating higher order statistics and appropriately chosen probabilistic models then allow for the generation of images that enhance details and give a spatial impression of a full nanoscopic scene.
Toroidal topology of population activity in grid cells
Authors: Gardner Richard J. , Hermansen Erik , Pachitariu Marius , Burak Yoram , Baas Nils A. , Dunn Benjamin A. , Moser May-Britt , Moser Edvard I.
Published: February 2021

The medial entorhinal cortex (MEC) is part of a neural system for mapping a subject’s position within a physical environment1,2. Grid cells, a key component of this system, fire in a characteristic hexagonal pattern of locations3, and are organized in modules4,5which collectively form a population code for the animal’s allocentric position1,6–8. The invariance of the correlation structure of this population code across environments9,10and behavioural states11,12, independently of specific sensory inputs, has pointed to intrinsic, recurrently connected continuous attractor networks (CANs) as a possible substrate of the grid pattern1,2,13–16. However, whether grid cell networks show continuous attractor dynamics, and how they interface with inputs from the environment, has remained elusive due to the small samples of cells obtained to date. Here we show, with simultaneous recordings from many hundreds of grid cells, and subsequent topological data analysis, that the joint activity of grid cells from an individual module resides on a toroidal manifold, as expected in a two-dimensional CAN. Positions on the torus correspond to the moving animal’s position in the environment. Individual cells are preferentially active at singular positions on the torus. Their positions are maintained, with minimal distortion, between environments and from wakefulness to sleep, as predicted by CAN models for grid cells but not by alternative feed-forward models where grid patterns are created from external inputs by Hebbian plasticity17–22. This demonstration of network dynamics on a toroidal manifold provides the first population-level visualization of CAN dynamics in grid cells.
Feasibility of X-ray beam nanofocusing with compound refractive lenses
Authors: Kohn V. G. , Folomeshkin M. S.
Published: February 2021

A more general analytical theory of X-ray beam propagation through compound refractive lenses (CRLs) than the earlier study by Kohn [(2003). JETP, 97, 204–215] is presented. The problem of nanofocusing with CRLs is examined in detail. For a CRL with a relatively large aperture the focusing efficiency is limited by the radiation absorption in the lens material. The aperture does not affect the focusing process and it is replaced by the effective aperture. The X-ray transverse beam size at the focus is then by a factor of γ = β/δ times smaller than the transverse beam size just behind the CRL. Here, δ and β are the real and imaginary parts of the CRL material refractive index n = 1 − δ + iβ. In this instance, to improve focusing efficiency, it is advantageous to decrease the CRL aperture and increase the photon energy E. However, with increasing photon energy, the material absorption decreases, which results in the CRL aperture impact on the transverse beam size. The latter leads to the fact that with a proper CRL length the beam size is independent of both the aperture and photon energy but depends only on the CRL material electron density and is approximately equal to w

c
= λ/(8δ)1/2, where λ denotes the radiation wavelength, as predicted by Bergemann et al. [(2003). Phys. Rev. Lett, 91, 204801].
Side-bounce beamlines using single-reflection diamond monochromators at Cornell High Energy Synchrotron Source
Authors: Stoupin Stanislav , Krawczyk Thomas , Sagan David , Temnykh Alexander , Smieska Louisa , Woll Arthur , Ruff Jacob , Lyndaker Aaron , Pauling Alan , Croom Brendan P. , Trigg Edward B.
Published: February 2021

The design and implementation of new beamlines featuring side-bounce (single-reflection) diamond monochromators at Cornell High Energy Synchrotron Source (CHESS) are described. Undulator radiation is monochromated using an interchangeable set of diamond crystal plates reflecting radiation in the horizontal (synchrotron) plane, where each crystal plate is set to one of the low-index Bragg reflections (111, 220, 311 and 400) in either Bragg or Laue reflection geometries. At the nominal Bragg angle of 18° these reflections deliver monochromated X-rays with photon energies of 9.7, 15.9, 18.65 and 22.5 keV, respectively. An X-ray mirror downstream of the diamond monochromator is used for rejection of higher radiation harmonics and for initial focusing of the monochromated beam. The characteristics of the X-ray beam entering the experimental station were measured experimentally and compared with the results of simulations. A reasonable agreement is demonstrated. It is shown that the use of selected high-dislocation-density `mosaic' diamond single-crystal plates produced using the chemical vapor deposition method yields a few-fold enhancement in the flux density of the monochromated beam in comparison with that delivered by perfect crystals under the same conditions. At present, the Functional Materials Beamline at CHESS, which is used for time-resolved in situ characterization of soft materials during processing, has been outfitted with the described setup.
1-2-3-4! Measuring the values of live music: methods, models and motivations
Authors: van der Hoeven Arno , Behr Adam , Hamilton Craig , Mulder Martijn , Rozbicka Patrycja
Published: February 2021

Purpose

This paper sets out to compare different methodologies for measuring the value(s) of live popular music and to explore the different motivations amongst a range of organisations engaged in that work.

Design/methodology/approach

The authors analyse how the values of live music are measured, who does it and why. Based on this analysis the authors present a model that visualises the myriad of organisations, methods, aims and objectives involved.

Findings

The authors identify three approaches to measuring the impact of live music (economic impact studies, mapping and censuses and social sciences and humanities) and three types of actors (industry, policy and academia). The analysis of these demonstrates that measuring live music is not a neutral activity, but itself constructs a vision on how live music ecologies function

Practical implications

For cultural organisations, demonstrating the outcomes of their work is important in acquiring various forms of support. The model presented in this paper helps them to select adequate methodologies and to reflect on the consequences of particular approaches to measuring live music activities.

Originality/value

While the number of studies measuring live music's impact is growing, theoretical and methodological reflection on these activities is missing. The authors compare the different methodologies by discussing strengths and weaknesses. This results in a model that identifies gaps in existing studies and explores new directions for future live music research. It enhances understanding of how different ways of measuring live music affect policymaking and conceptions of what live music is and should be.
Impact of social and technical lean management on operational performance in manufacturing SMEs: the roles of process and management innovations
Authors: Abdallah Ayman Bahjat , Alkhaldi Rasha Zuhair , Aljuaid Majed M.
Published: February 2021

Purpose

The purpose of the current study is to address a debatable issue in the extant literature regarding lean management (LM), innovation and operational performance (OP) relationships in the manufacturing SMEs. It conceptualizes LM in terms of social and technical aspects and investigates their effects on process innovation, management innovation and OP. The mediating roles of process and management innovations on social/technical-OP relationships are also explored.

Design/methodology/approach

The study analyzes survey data gathered from 268 manufacturing SMEs belonging to different industry types in Jordan. Validity and reliability tests of the first and second order constructs were performed. Structural equation modeling (SEM) was used to test the study hypotheses.

Findings

Both social and technical LM were found to positively affect OP. Social LM positively affected both process and management innovations. However, the effect of technical LM on both types of innovation was not significant. In addition, process and management innovations positively mediated social LM-OP relationship. Nonetheless, neither type of innovation showed mediating effects on technical LM-OP relationship.

Originality/value

This study is one of the first to highlight the proposed relationships, in general, and in the context of SMEs in a developing country context, in particular. It offers important implications for the managers of SMEs to benefit from LM implementation and avoid its failure, enhance innovation efforts by focusing on social LM practices and subsequently achieve higher levels of OP.
Prime Broking Default at the National Stock Exchange
Authors: Varma Jayanth R , Agarwalla Sobhesh Kumar
Published: February 2021

When Prime Broking defaulted on its equity derivative positions at the National Stock Exchange, the central counterparty (CCP) suffered substantial losses, although there was no significant movement in the relevant market prices. This revealed hidden risks arising from collateral, liquidity and concentration, wrong-way risks and operational risks in the default management process, even when the market risk environment is benign. The CCP ends up with risks it is not designed to handle and similar to those faced by a bank. The CCP suffered massive losses, even though its market risk models functioned flawlessly.