bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk stratification for multidrug-resistant bacteria in patients with skin and soft tissue infection
Authors: Barbier François , Timsit Jean-François
Published: February 2020

Purpose of review

This article summarizes the available evidence enabling a stratification of risk for multidrug-resistant bacteria (MDRB) in patients with skin and soft tissue infection (SSTI).

Recent findings

MDRB are increasingly reported in both healthcare-associated (HCA) and community-acquired (CA)-SSTI, including in patients with life-threatening presentations for whom early initiation of adequate antimicrobial therapy is pivotal to improve outcomes. Community-associated methicillin-resistant Staphylococcus aureus (MRSA) is now endemic in several geographical areas and may cause outbreaks in frail populations or other at-risk clusters. Pseudomonas aeruginosa and other nonfermenting Gram-negative pathogens are involved in CA-SSTI on an occasional basis, especially in patients with chronic wounds or recent antimicrobial exposure. The burden of HCA-SSTI because of MRSA, MR P. aeruginosa, MR Acinetobacter baumannii, extended-spectrum β-lactamase-producing Enterobacterales and vancomycin-resistant enterococci is amplifying in endemic settings. Severe comorbidities, prolonged hospitalization, invasive procedures, prior colonization or infection and antimicrobial exposure stand as the main risk factors for these conditions. Worryingly, carbapenemase-producing Enterobacterales are emerging as causative pathogens in HCA-SSTI.

The choice of empirical agents depends on the type and location of SSTI, place of onset, initial severity and whether the patient presents or not with risk factors for MDRB, with local epidemiology and prior antimicrobial use being among the main features to consider.
Managing urban flood resilience through the English planning system: insights from the ‘SuDS-face’
Authors: Potter Karen , Vilcan Tudor
Published: February 2020

In academic and professional circles, ‘resilience thinking’ has emerged as the dominant paradigm in flood risk management, which emphasizes the need to plan and design cities that can absorb water and replicate natural processes more closely. In this paper, we explore how planners in England are expected to respond to the resilience agenda against the realities in practice, zoning in on the delivery of sustainable (urban) drainage systems (SuDS). Our exploration highlights that, while SuDS are being implemented, they are largely characterized by a ‘bog standard’ design. We found that there are three main institutional factors that are constraining the implementation of SuDS: the lack of legislative backing, the power afforded to private commercial interests in the neoliberalized planning process, compounded by the severe lack of resources in local authorities. What is missing at the moment is SuDS process and design that is flexible, integrated, collaborative and innovative. There are clear implications that, without the necessary institutional support, resilience thinking will remain largely aspirational, and professionals will struggle to gain traction and translate the larger flood resilience policy agenda into England's future climate-resilient places.

This article is part of the theme issue ‘Urban flood resilience’.
Sensitivity of shotgun metagenomics to host DNA: abundance estimates depend on bioinformatic tools and contamination is the main issue
Authors: McArdle Andrew J. , Kaforou Myrsini
Published: February 2020

A recent study reported that increasing host DNA abundance and reducing read depth impairs the sensitivity of detection of low-abundance micro-organisms by shotgun metagenomics. The authors used DNA from a synthetic bacterial community with abundances varying across several orders of magnitude and added varying proportions of host DNA. However, the use of a marker-gene-based abundance estimation tool (MetaPhlAn2) requires considerable depth to detect marker genes from low-abundance organisms. Here, we reanalyse the deposited data, and place the study in the broader context of low microbial biomass metagenomics. We opted for a fast and sensitive read binning tool (Kraken 2) with abundance estimates from Bracken. With this approach all organisms are detected even when the sample comprises 99 % host DNA and similarly accurate abundance estimates are provided (mean squared error 0.45 vs. 0.3 in the original study). We show that off-target genera, whether contaminants or misidentified reads, come to represent over 10 % of reads when the sample is 99 % host DNA and exceed counts of many target genera. Therefore, we applied Decontam, a contaminant detection tool, which was able to remove 61 % of off-target species and 79 % of off-target reads. We conclude that read binning tools can remain sensitive to low-abundance organisms even with high host DNA content, but even low levels of contamination pose a significant problem due to low microbial biomass. Analytical mitigations are available, such as Decontam, although steps to reduce contamination are critical.
Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search
Authors: Wahba Lamia , Jain Nimit , Fire Andrew Z , Shoura Massa J , Artiles Karen L , McCoy Matthew J , Jeong Dae Eun
Published: February 2020

In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic datasets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic dataset can be readily queried using web-based tools, meta-searches through all such datasets are less accessible. In this brief communication, we demonstrate such a meta-meta-genomic approach, examining close matches to the Wuhan coronavirus 2019-nCoV in all high-throughput sequencing datasets in the NCBI Sequence Read Archive accessible with the keyword "virome". In addition to the homology to bat coronaviruses observed in descriptions of the 2019-nCoV sequence (F. Wu et al. 2020, Nature, doi.org/10.1038/s41586-020-2008-3; P. Zhou et al. 2020, Nature, doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in a metavirome dataset generated from the lungs of deceased Pangolins reported by Liu et al. (Viruses 11:11, 2019, http://doi.org/10.3390/v11110979). Our observations are relevant to discussions of the derivation of 2019-nCoV and illustrate the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.
Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma
Authors: Kim Soyeon , Forno Erick , Zhang Rong , Yan Qi , Boutaoui Nadia , Acosta-Pérez Edna , Canino Glorisa , Chen Wei , Celedón Juan C.
Published: February 2020

Nasal airway epithelial methylation profiles have been associated with asthma, but the effects of such profiles on expression of distant cis-genes are largely unknown. We identified 16,867 significant methylation-gene expression pairs in nasal epithelium from Puerto Rican children and adolescents (with and without asthma) in an expression quantitative trait methylation (eQTM) analysis of cis-genes located within 1 Mb of the methylation probes tested. Most eQTM methylation probes were distant from their target genes, and more likely located in enhancer regions of their target genes in lung tissue than control probes. The top 500 eQTM genes were enriched in pathways for immune processes and epithelial integrity, and also more likely to be differentially expressed in atopic asthma. Moreover, we identified 5,934 paths through which methylation probes could affect atopic asthma through gene expression. Our findings suggest that distant epigenetic regulation of gene expression in airway epithelium plays a role in atopic asthma.
Long-term single-cell imaging and simulations of microtubules reveal driving forces for wall pattering during proto-xylem development
Authors: Schneider René , van ’t Klooster Kris , Picard Kelsey , van der Gucht Jasper , Demura Taku , Janson Marcel , Sampathkumar Arun , Deinum Eva E. , Ketelaar Tijs , Persson Staffan
Published: February 2020

Plants are the tallest organisms on Earth; a feature sustained by solute-transporting xylem vessels in the plant vasculature. The xylem vessels are supported by strong cell walls that are assembled in intricate patterns. Cortical microtubules direct wall deposition and need to rapidly re-organize during xylem cell development. We established long-term live-cell imaging of singleArabidopsiscells undergoing proto-xylem trans-differentiation, resulting in spiral wall patterns, to investigate the microtubule re-organization. The initial disperse microtubule array rapidly readjusted into well-defined microtubule bands, which required local de-stabilization of individual microtubules in band-interspersing gap regions. Using extensive microtubule simulations, we could recapitulate the processin silicoand found that local recruitment of microtubule-bound nucleation is critical for pattern formation, which we confirmedin vivo. Our simulations further indicated that the initial microtubule alignment impact microtubule band patterning. We confirmed this prediction usingkataninmutants, which have microtubule organization defects, and uncovered active KATANIN recruitment to the forming microtubule bands. Our combination of quantitative microscopy and modelling outlines a framework towards a comprehensive understanding of microtubule re-organization during wall pattern formation.
Autophagic degradation of the Cucumber mosaic virus virulence factor 2b balances antiviral RNA silencing with proviral plant fitness and virus seed transmission
Authors: Shukla Aayushi , Hoffmann Gesa , López-González Silvia , Hofius Daniel , Hafrén Anders
Published: February 2020

Autophagy is a conserved intracellular degradation pathway that has recently emerged as an integral part of plant responses to virus infection. The elucidated mechanisms of autophagy range from the selective degradation of viral components to a more general attenuation of disease symptoms. In addition, several viruses are able to manipulate the autophagy machinery and counteract autophagy-dependent resistance. Despite these findings, the complex interplay of autophagy activities, viral pathogenicity factors, and host defence pathways in disease development remains poorly understood. In the current study, we analysed the interaction between autophagy and Cucumber mosaic virus (CMV) inArabidopsis thaliana. We show that autophagy is induced during CMV infection and promotes the turnover of the major CMV virulence protein and RNA silencing suppressor 2b. Intriguingly, 2b itself dampens plant autophagy. In accordance with 2b degradation, we found that autophagy provides resistance against CMV by reducing viral RNA accumulation in an RNA silencing-dependent manner. Moreover, autophagy and RNA silencing pathways contribute to plant longevity and fecundity of CMV infected plants in an additive manner, uncoupling it from resistance. In addition to reduced fecundity, autophagy-deficient plants also failed to support seed transmission of the virus. We propose that autophagy attenuates CMV virulence via 2b degradation and thereby increases both plant and virus fitness with a trade-off penalty arising from increased RNA silencing-mediated resistance.

Author summary

The capacity of plants to fight pathogenic viruses in order to survive and minimize damage relies on profound cellular reprogramming events. These include the synthesis of new as well as the degradation of pre-existing cellular components, together shifting cellular homeostasis towards a better tolerance of disease and fortification of antiviral defence mechanisms. Autophagy is a prominent and highly conserved cellular degradation pathway that supports plant stress resilience. Autophagy functions vary broadly and range from rather unspecific renewal of cytoplasm to highly selective degradation of a wide collection of specific substrates. Autophagy is well established to be involved during virus infections in animals, and its importance has also recently emerged in virus diseases of plants. However, we are still far from a comprehensive understanding of the complexity of autophagy activities in host-virus interactions and how autophagy pathway engineering could be applied against viruses. Here, we have analyzed one of the traditional model plant viruses, Cucumber mosaic virus (CMV), and its interactions with autophagy. Our study revealed that autophagy is tightly integrated into CMV disease, influencing processes from plant health to CMV epidemiology.
Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation
Authors: Chen Lin-Xing , Méheust Raphaël , Crits-Christoph Alexander , McMahon Katherine D. , Nelson Tara Colenbrander , Warren Lesley A. , Banfield Jillian F.
Published: February 2020

There is growing evidence that phages with unusually large genomes are common across various natural and human microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. Here, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Twenty-two manually curated genomes (18 are complete) ranging from 159 to 527 kbp in length were found to encode thepmoCgene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC show high similarity (> 90%) and affiliate phylogenetically with those of coexisting bacterial methanotrophs, and their abundance patterns correlate with the abundances of these bacteria, supporting host-phage relationships. We suggest that phage PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contribute to growth on methane. Transcriptomics data from one system showed that the phage-associatedpmoCgenes are actively expressedin situ. Augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this powerful greenhouse gas into the environment.
Cognitive performance in children and adolescents at high-risk for obsessive-compulsive disorder
Authors: Bernardes Elisa Teixeira , Cappi Carolina , de Marco e Souza Marina , Hoexter Marcelo Queiroz , Chacon Priscila , Requena Guaraci , Miguel Euripedes Constantino , Shavitt Roseli Gedanke , Polanczyk Guilherme Vanoni , Batistuzzo Marcelo Camargo
Published: February 2020

Background

Cognitive performance has been studied in subclinical obsessive-compulsive (OC) adults and in adults relatives of OCD patients. Meanwhile, no study has been conducted with children under the same conditions. Across a sample with 49 participants, we investigated whether children and adolescents at high-risk (HR) for OCD (n=18) would present an impaired performance on neurocognitive domains compared to healthy controls (HC, n=31), especially in visuoconstructive ability, executive functions, and intellectual efficiency, functions previously associated with OCD.

Methods

For the HR group, we considered the first-degree children relatives of patients with OCD that present obsessive-compulsive symptoms (OCS), but do not meet diagnostic criteria for OCD. Child psychiatric diagnoses were assessed by the Kiddie Schedule for Affective Disorders and Schizophrenia (K-SADS-PL) by experienced and trained psychologists and OCS were measured by Yale-Brown Obsessive-Compulsive Scale (Y-BOCS).

Results

Although we did not find differences in the domains previously hypothesized, a Multivariate Analysis of Variance (MANOVA) revealed impairments in processing speed in HR group (p=0.019; F=3.115), and at-test identified a higher IQ discrepancy in HR group when compared to HC (p=0.030;t=-2.239), and a discrepancy in verbal and non-verbal abilities as in the memory and working memory tasks.

Conclusions

Our results suggest that differences in motor and processing speed and in IQ discrepancy are already present and were identified in a non-clinical sample of HR subjects. Further studies should investigate neurocognitive domains as possible predictors of pediatric OCD.
Environmental Exposures Influence Nasal Microbiome Composition in a Longitudinal Study of Division I Collegiate Athletes
Authors: Kask Oliver , Kyman Shari , Conn Kathryn A. , Gormley Jenny , Gardner Julia , Johns Robert A. , Caporaso J. Gregory , Bycura Dierdra , Sutliffe Jay T. , Cope Emily K.
Published: February 2020

Background

The anterior nares host a complex microbial community that contributes to upper airway health. Although the bacterial composition of the nasal passages have been well characterized in healthy and diseased cohorts, the role of prolonged environmental exposures and exercise in shaping the nasal microbiome in healthy adults is poorly understood. In this study, we longitudinally sampled female collegiate Division I athletes from two teams experiencing a similar athletic season and exercise regimen but vastly different environmental exposures (Swim/Dive and Basketball). Using 16S rRNA gene sequencing, we evaluated the longitudinal dynamics of the nasal microbiome pre-, during-, and at the end of the athletic season.

Results

The nasal microbiota of the Swim/Dive and Basketball teams were distinct from each other at each time point sampled, driven by either low abundance (Jaccard, PERMANOVA p<0.05) or high-abundance changes in composition (Bray-Curtis, PERMANOVA p<0.05). The rate of change of microbial communities were greater in the Swim/Dive team compared to the Basketball team characterized by an increase inStaphylococcusin Swim/Dive and a decrease inCorynebacteriumin both teams over time.

Conclusions

This is the first study that has evaluated the nasal microbiome in athletes. We obtained longitudinal nasal swabs from two gender-matched teams with similar age distributions (18-22 years old) over a 6 month period. Differences in the microbiota between teams and over time indicate that chlorine exposure, and potentially athletic training, induced changes in the nasal microbiome.
Targeted attenuation of elevated histone marks atSNCAalleviates α-synuclein in Parkinson’s disease
Authors: Guhathakurta Subhrangshu , Kim Jinil , Basu Sambuddha , Adler Evan , Je Goun , Fiadeiro Mariana Bernardo , Kim Yoon-Seong
Published: February 2020

Epigenetic de-regulation of α-synuclein plays a key role in Parkinson’s disease (PD). Analysis of theSNCApromoter using the ENCODE database revealed the presence of important histone posttranslational modifications (PTMs) including transcription-promoting marks, H3K4me3 and H3K27ac, and repressive mark, H3K27me3. We investigated these histone marks in postmortem brains of controls and PD patients and observed that only H3K4me3 was significantly elevated at theSNCApromoter of the substantia nigra (SN) of PD patients both in punch biopsy as well as in NeuN positive neuronal nuclei samples. To understand the importance of H3K4me3 in regulation of α-synuclein, we developed CRISPR/dCas9-based locus-specific H3K4me3 demethylating system where the catalytic domain of JARID1A was recruited to theSNCApromoter. This CRISPR/dCas9 SunTag-JARID1A significantly reduced H3K4me3 atSNCApromoter and concomitantly decreased α-synuclein both in the neuronal cell line SH-SY5Y and idiopathic PD-iPSC derived dopaminergic neurons. In sum, this study indicates that α-synuclein expression in PD is controlled bySNCA’shistone PTMs and modulation of the histone landscape ofSNCAcan reduce α-synuclein expression.
Structure-based identification and functional characterization of an essential lipocalin in the malaria parasitePlasmodium falciparum
Authors: Burda Paul-Christian , Crosskey Thomas , Lauk Katharina , Zurborg Aimo , Söhnchen Christoph , Liffner Benjamin , Wilcke Louisa , Strauss Jan , Jeffries Cy , Svergun Dmitri I. , Wilson Danny W. , Wilmanns Matthias , Gilberger Tim-Wolf
Published: February 2020

Proteins of the lipocalin family are known to bind small hydrophobic ligands and are involved in various physiological processes ranging from lipid transport to oxidative stress responses. The genome of the malaria parasitePlasmodium falciparumcontains a single protein PF3D7_0925900 with a lipocalin signature. Using crystallography and small-angle X-ray scattering, we show that the protein has a tetrameric structure of typical lipocalin monomers, hence we name itP. falciparumlipocalin (PfLCN), the first lipocalin structurally and functionally characterized in a single-celled eukaryote. We show thatPfLCN is expressed in the intraerythrocytic stages of the parasite and localizes to the parasitophorous and food vacuoles. Conditional knockdown ofPfLCN impairs parasite development, which can be rescued by treatment with the radical scavenger Trolox or by temporal inhibition of hemoglobin digestion. This suggests a key function ofPfLCN in counteracting oxidative stress induced cell damage during multiplication of parasites within red blood cells.
Revisiting the links-species scaling relationship in food webs
Authors: MacDonald Andrew , Banville Francis , Poisot Timothée
Published: February 2020

Predicting the number of interactions that species in a food web will establish is an important task. These trophic interactions underlie many ecological and evolutionary processes, ranging from biomass fluxes, ecosystem stability, resilience to extinction, and resistance against novel species. We investigate and compare several ways to predict the number of interactions in food webs. We conclude that a simple beta-binomial model outperforms other models, with the added desirable property of respecting biological constraints. We show how this simple relationship gives rise to a predicted distribution of several quantities related to link number in food webs, including the scaling of network structure with space, and the probability that a network will be stable.
Neonatal levels of acute phase proteins and risk of autism spectrum disorders
Authors: Gardner Renee M. , Lee Brian K. , Brynge Martin , Sjöqvist Hugo , Dalman Christina , Karlsson Håkan
Published: February 2020

Background

Immune signaling pathways influence neurodevelopment and are hypothesized to contribute to the etiology of autism spectrum disorders (ASD). We aimed to assess risk of ASD in relation to levels of neonatal acute phase proteins, key components of innate immune function, measured in neonatal dried blood spots.

Method

We included 924 ASD cases, 1092 unaffected population-based controls, and 203 unaffected siblings to ASD cases in this case-control study nested within the register-based Stockholm Youth Cohort. Concentrations of nine different acute phase proteins were measured in eluates from neonatal dried blood spots from cases, controls, and siblings using a bead-based multiplex assay.

Results

C reactive protein was consistently associated with odds of ASD in case-control comparisons, with higher odds associated with the highest quintile compared to the middle quintile (OR 1.50, 95% CI 1.10 – 2.04) in adjusted analyses. In contrast, the lowest quintiles of alpha-2-macroglobulin (3.71, 1.21 – 11.33), ferritin (4.20, 1.40 – 12.65), and Serum Amyloid P (3.05, 1.16 – 8.01) were associated with odds of ASD in the matched sibling comparison. Neonatal acute phase proteins varied with perinatal environmental factors and maternal/fetal phenotypes. Significant interactions in terms of risk for ASD were observed between neonatal acute phase proteins and maternal infection in late pregnancy, maternal anemia, and maternal psychiatric history.

Conclusions

Indicators of the neonatal innate immune response are associated with risk for ASD, though the nature of these associations varies considerably with factors in the perinatal environment and the genetic background of the comparison group.
A Critical Role for Perivascular Cells in Amplifying Viral Haemorrhage Induced by Dengue Virus Non-Structural Protein 1
Authors: Cheung Yin P. , Mastrullo Valeria , Maselli Davide , Butsabong Teemapron , Madeddu Paolo , Maringer Kevin , Campagnolo Paola
Published: February 2020

Dengue is the most prevalent arthropod-borne viral disease affecting humans, with severe dengue typified by potentially fatal microvascular leakage and hypovolaemic shock. Blood vessels of the microvasculature are composed of a tubular structure of endothelial cells ensheathed by perivascular cells (pericytes). Pericytes support endothelial cell barrier formation and maintenance through paracrine and contact-mediated signalling, and are critical to microvascular integrity. Pericyte dysfunction has been linked to vascular leakage in noncommunicable pathologies such as diabetic retinopathy, but has never been linked to infection-related vascular leakage. Dengue vascular leakage has been shown to result in part from the direct action of the secreted dengue virus (DENV) non-structural protein NS1 on endothelial cells. Using primary human vascular cells, we show here that NS1 also causes pericyte dysfunction, and that NS1-induced endothelial hyperpermeability is more pronounced in the presence of pericytes. Notably, NS1 specifically disrupted the ability of pericytes to support endothelial cell function in a 3D microvascular assay, with no effect on pericyte viability or physiology. These effects are mediated at least in part through contact-independent paracrine signals involved in endothelial barrier maintenance by pericytes. We therefore identify a role for pericytes in amplifying NS1-induced microvascular hyperpermeability in severe dengue, and thus show that pericytes can play a critical role in the aetiology of an infectious vascular leakage syndrome. These findings open new avenues of research for the development of drugs and diagnostic assays for combating infection-induced vascular leakage, such as severe dengue.

SIGNIFICANCE STATEMENT

The World Health Organisation considers dengue one of the top ten global public health problems. There is no specific antiviral therapy to treat dengue virus and no way of predicting which patients will develop potentially fatal severe dengue, typified by vascular leakage and circulatory shock. We show here that perivascular cells (pericytes) amplify the vascular leakage-inducing effects of the dengue viral protein NS1 through contact-independent signalling to endothelial cells. While pericytes are known to contribute to noncommunicable vascular leakage, this is the first time these cells have been implicated in the vascular effects of an infectious disease. Our findings could pave the way for new therapies and diagnostics to combat dengue, and potentially other infectious vascular leakage syndromes.
β-L-1-[5-(E-2-Bromovinyl)-2-(Hydroxymethyl)-1,3-Dioxolan-4-yl)] Uracil (L-BHDU) Inhibits Varicella Zoster Virus Replication by Depleting the Cellular dTTP Pool
Authors: De Chandrav , Liu Dongmei , Singh Uma S. , Chu Chung K. , Moffat Jennifer F.
Published: February 2020

ß-L-1-[5-(E-2-bromovinyl)-2-(hydroxymethyl)-1,3-(dioxolan-4-yl)] uracil (L-BHDU) inhibits varicella zoster virus (VZV) replication in cultured cells, human skin, and in SCID-Hu mice with skin xenografts. VZV thymidine kinase converts L-BHDU to monophosphate (MP) and diphosphate (DP) forms, but the triphosphate form was not detected in infected cells and the antiviral mechanism was unknown. Given its similar structure to uridine, we asked if L-BHDU interfered with viral DNA replication via inhibition of the purine and/or pyrimidine biosynthesis pathways. Addition of purines to the medium was unable to restore VZV replication in the presence of L-BHDU. In contrast, excess thymidine and uridine in proportion to L-BHDU restored VZV replication, suggesting that the active form of L-BHDU interfered with pyrimidine biosynthesis. However, addition of thymidine and uridine failed to restore VZV replication in non-dividing cells treated with L-BHDU. Like other herpesviruses, VZV infection increased thymidine triphosphate (dTTP) in confluent cells while L-BHDU treatment decreased the dTTP pool by nearly 4-fold. The active form(s) of L-BHDU did not interfere with cellular metabolism, suggesting viral target(s).
Optical Control of Cytokine Signaling via Bioinspired, Polymer-Induced Latency
Authors: Perdue Lacey A , Do Priscilla , David Camille , Chyong Andrew , Kellner Anna , Ruggieri Amanda , Kim Hye Ryong , Salaita Khalid , Lesinski Gregory B , Porter Christopher C , Dreaden Erik C
Published: February 2020

Cytokine signaling is challenging to study and therapeutically exploit as the effects of these protein are often pleiotropic. A subset of cytokines can, however, exert signal specificity via association with latency-inducing proteins which cage the cytokine until disrupted by discreet biological stimuli. Inspired by this precision, here we describe a strategy for synthetic induction of cytokine latency via modification with photo-labile polymers that mimic latency while attached, then restore protein activity in response to light, thus controlling the magnitude, duration, and location of cytokine signals. We characterize the high dynamic range of latent cytokine activity modulation and find that polymer-induced latency, alone, can prolongin vivocirculation and bias receptor subunit binding. We further show that protein de-repression can be achieved with near single-cell resolution and demonstrate the feasibility of transcutaneous photoactivation. Future extensions of this approach could enable multicolor, optical reprogramming of cytokine signaling networks and more precise immunotherapies.
Co-expression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders
Authors: Pang Kaifang , Wang Li , Wang Wei , Zhou Jian , Cheng Chao , Han Kihoon , Zoghbi Huda Y. , Liu Zhandong
Published: February 2020

Recent large-scale sequencing studies have identified a great number of genes whose disruptions cause neurodevelopmental disorders (NDDs). However, cell-type-specific functions of NDD genes and their contributions to NDD pathology are unclear. Here, we integrated NDD genetics with single-cell RNA sequencing data to identify cell-type and temporal convergence of genes involved in different NDDs. By assessing the co-expression enrichment pattern of various NDD gene sets, we identified mid-fetal cortical neural progenitor cell development—more specifically, ventricular radial glia-to-intermediate progenitor cell transition at gestational week 10—as a key convergent point in autism spectrum disorder (ASD) and epilepsy. Integrated gene ontology-based analyses further revealed that ASD genes function as upstream regulators to activate neural differentiation and inhibit cell cycle during the transition, whereas epilepsy genes function as downstream effectors in the same processes, offering a potential explanation for the high comorbidity rate of the two disorders. Together, our study provides a framework for investigating the cell-type-specific pathophysiology of NDDs.
A GT-seq panel for walleye (Sander vitreus) provides a generalized workflow for efficient development and implementation of amplicon panels in non-model organisms
Authors: Bootsma Matthew L. , Gruenthal Kristen M. , McKinney Garrett J. , Simmons Levi , Miller Loren , Sass Greg G. , Larson Wesley A.
Published: February 2020

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals, but studies describing detailed workflows of GTseq panel development are rare. Here, we develop a dual-purpose GT-seq panel for walleye (Sander vitreus) and discuss trade-offs associated with different development and genotyping approaches. Our GT-seq panel was developed using restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We then conducted simulations to test the utility of loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We conducted three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. Optimization focused on reducing variation in amplification rate among loci and minimizing the proportion of off-target sequence, both of which are important considerations for developing large GT-seq panels. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (1) inexpensive Chelex extractions performed well for genotyping, (2) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was likely unnecessary, and (3) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings should aid in their construction in myriad taxa.
Neuronal lipolysis participates in PUFA-mediated neural function and neurodegeneration
Authors: Yang Leilei , Liang Jingjing , Lam Sin Man , Yavuz Ahmet , Wang Meng C. , Shui Guanghou , Ding Mei , Huang Xun
Published: February 2020

Lipid droplets (LDs) are dynamic cytoplasmic organelles present in most eukaryotic cells. The appearance of LDs in neurons is not usually observed under physiological conditions, but is associated with neural diseases. It remains unclear how LD dynamics is regulated in neurons and how the appearance of LDs affects neuronal functions. We discovered that mutations of two key lipolysis genesatgl-1andlid-1lead to LD appearance in neurons ofCaenorhabditis elegans. This neuronal lipid accumulation protects neurons from hyperactivation-triggered neurodegeneration, with a mild decrease in touch sensation. We also discovered that reduced biosynthesis of polyunsaturated fatty acids (PUFAs) causes similar effects, synergistically with decreased lipolysis. Furthermore, we demonstrated that these changes in lipolysis and PUFA biosynthesis increase PUFA partitioning toward triacylglycerol, and reduced incorporation of PUFAs into phospholipids increases neuronal protection. Together, these results suggest the crucial role of neuronal lipolysis in regulating neural functions and neurodegeneration cell-autonomously.

Highlights

Neuronal lipolysis prevents LD accumulation in neurons.

Defective neuronal lipolysis leads to touch sensation defect.

Blocking neuronal lipolysis alleviates neurodegeneration.

Neuronal lipolysis andde novoPUFA biosynthesis have a synergistic effect in neurodegeneration.

The incorporation of PUFAs into phospholipids promotes neurodegeneration.
Slow oscillation-spindle coupling predicts sequence-based language learning
Authors: Cross Zachariah R. , Helfrich Randolph F. , Corcoran Andrew W. , Dede Adam J. O. , Kohler Mark J. , Coussens Scott W. , Zou-Williams Lena , Schlesewsky Matthias , Gaskell M. Gareth , Knight Robert T. , Bornkessel-Schlesewsky Ina
Published: February 2020

Sentence comprehension involves the rapid decoding of both semantic and grammatical information, a process fundamental to communication. As with other complex cognitive processes, language comprehension relies, in part, on long-term memory. However, the electrophysiological mechanisms underpinning the initial encoding and generalisation of higher-order linguistic knowledge remain elusive, particularly from a sleep-based consolidation perspective. One candidate mechanism that may support the consolidation of higher-order language is the temporal coordination of slow oscillations (SO) and sleep spindles during non-rapid eye movement sleep (NREM). To examine this hypothesis, we analysed electroencephalographic (EEG) data recorded from 35 participants (Mage= 25.4, SD = 7.10; 16 males) during an artificial language learning task, contrasting performance between individuals who were given an 8hr nocturnal sleep period or an equivalent period of wake. We found that sleep relative to wake was associated with superior performance for rules that followed a sequence-based word order. Post-sleep sequence-based word order processing was further associated with less task-related theta desynchronisation, an electrophysiological signature of successful memory consolidation, as well as cognitive control and working memory. Frontal NREM SO-spindle coupling was also positively associated with behavioural sensitivity to sequence-based word order rules, as well as with task-related theta power. As such, theta activity during retrieval of previously learned information correlates with SO-spindle coupling, thus linking neural activity in the sleeping and waking brain. Taken together, this study presents converging behavioral and neurophysiological evidence for a role of NREM SO-spindle coupling and task-related theta activity as signatures of successful memory consolidation and retrieval in the context of higher-order language learning.

SIGNIFICANCE STATEMENT

The endogenous temporal coordination of neural oscillations supports information processing during both wake and sleep states. Here we demonstrate that slow oscillation-spindle coupling during non-rapid eye movement sleep predicts the consolidation of complex grammatical rules and modulates task-related oscillatory dynamics previously implicated in sentence processing. We show that increases in theta power predict enhanced sensitivity to grammatical violations after a period of sleep and strong slow oscillation-spindle coupling modulates subsequent task-related theta activity to influence behaviour. Our findings reveal a complex interaction between both wake- and sleep-related oscillatory dynamics during the early stages of language learning beyond the single word level.
CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity
Authors: Patel Manthan , Patel Divyesh , Datta Subhamoy , Singh Umashankar
Published: February 2020

The human CGGBP1 is implicated in a variety of cellular functions. It regulates genomic integrity, cell cycle, gene expression and cellular response to growth signals. Evidence suggests that these functions of CGGBP1 manifest through binding to GC-rich regions in the genome and regulation of interspersed repeats. Recent works show that CGGBP1 is needed for cytosine methylation homeostasis and genome-wide occupancy patterns of the epigenome regulator protein CTCF. It has remained unknown if cytosine methylation regulation and CTCF occupancy regulation by CGGBP1 are independent or interdependent processes. By sequencing immunoprecipitated methylated DNA, we have found that some transcription factor-binding sites resist stochastic changes in cytosine methylation. Of these, we have analyzed the CTCF-binding sites thoroughly and show that cytosine methylation regulation at CTCF-binding DNA sequence motifs by CGGBP1 is deterministic. These CTCF-binding sites are positioned at locations where the spread of cytosine methylationin cisdepends on the levels of CGGBP1. Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.
Fenbendazole controlsin vitrogrowth, virulence potential and animal infection in theCryptococcusmodel
Authors: de Oliveira Haroldo C. , Joffe Luna S. , Simon Karina S. , Castelli Rafael F. , Reis Flavia C. G. , Bryan Arielle M. , Borges Beatriz S. , Medeiros Lia C. Soares , Bocca Anamelia L. , Del Poeta Maurizio , Rodrigues Marcio L.
Published: February 2020

The human diseases caused by the fungal pathogensCryptococcus neoformansandC. gattiiare associated with high indices of mortality, and toxic and/or cost-prohibitive therapeutic protocols. The need for affordable antifungals to combat cryptococcal disease is unquestionable. Previous studies suggested benzimidazoles as promising anti-cryptococcal agents combining low cost and high antifungal efficacy, but their therapeutic potential has not been demonstrated so far. In this study, we investigated the antifungal potential of fenbendazole, the most effective anti-cryptococcal benzimidazole. Fenbendazole was inhibitory against 30 different isolates ofC. neoformansandC. gattiiat a low concentration. The mechanism of anti-cryptococcal activity of fenbendazole involved microtubule disorganization, as previously described for human parasites. In combination with fenbendazole, the concentrations of the standard antifungal amphotericin B required to control cryptococcal growth were lower than those required when this antifungal was used alone. Fenbendazole was not toxic to mammalian cells. During macrophage infection, the anti-cryptococcal effects of fenbendazole included inhibition of intracellular proliferation rates and reduced phagocytic escape through vomocytosis. Fenbendazole deeply affected the cryptococcal capsule. In a mice model of cryptococcosis, the efficacy of fenbendazole to control animal mortality was similar to that observed for amphotericin B. These results indicate that fenbendazole is a promising candidate for the future development of an efficient and affordable therapeutic tool to combat cryptococcosis.
TraCurate: efficiently curating cell tracks
Authors: Wagner S. , Thierbach K. , Zerjatke T. , Glauche I. , Roeder I. , Scherf N.
Published: February 2020

TraCurate is an open-source software tool to curate and manually annotate cell tracking data from time-lapse microscopy. Although many studies of cellular behavior require high-quality, long-term observations across generations of cells, automated cell tracking is often imperfect and typically yields fragmented results that still contain many errors. TraCurate provides the functionality for the curation and correction of cell tracking data with minimal user interaction and expenditure of time and supports the extraction of complete cell tracks and cellular genealogies from experimental data. Source code and binary packages for Linux, macOS and Windows are available athttps://tracurate.gitlab.io/, as well as all other complementary tools described herein.
Network analysis identifies regulators of lineage-specific phenotypes inMycobacterium tuberculosis
Authors: Banaei-Esfahani Amir , Trauner Andrej , Borrell Sonia , Gygli Sebastian M. , Rustad Tige R. , Feldmann Julia , Gillet Ludovic C. , Schubert Olga T. , Sherman David R. , Beisel Christian , Gagneux Sebastien , Aebersold Ruedi , Collins Ben C.
Published: February 2020

TheMycobacterium tuberculosis(Mtb) complex comprises seven phylogenetically distinct human-adapted lineages exhibiting different geographical distribution and degrees of pathogenicity. Among these, Lineage 1 (L1) has been associated with low virulence whereas Lineage 2 (L2) has been linked to hyper-virulence, enhanced transmission and drug resistance. Here, we conducted multi-layer comparative analyses using whole genome sequencing data combined with quantitative transcriptomic and proteomic profiling of a set of L1 and L2 clinical strains, each grown under two different conditionsin vitro. Our data revealed different degrees of correlation between transcript and protein abundances across clinical strains and functional gene categories, indicating variable levels of post-transcriptional regulation in the tested lineages. Contrasting genomic and gene expression data showed that the magnitude of the transcriptional and translational changes was proportional to the phylogenetic distance between strains, with one out of three single nucleotide polymorphisms leading to a transcriptional and/or translational change on average. We devised a new genome-scale transcriptional regulatory model and identified several master transcription factors, strongly linked to the sigma factor network, whose targets were differentially regulated between the two lineages. These differences resulted in a higher basal expression of DosR proteins and a stronger response to nitric oxide (NO) exposure in L2 compared to L1. These patterns are most likely responsible for the shorter NO-induced growth arrest in L2 observed. Given the limited genetic variation between strains, it appears that phenotypic differences in Mtb are substantially driven by differences in the regulation of biochemical networks through master transcriptional regulators.

Highlights

Proteomic and transcriptomic characterization of fully sequenced diverse L1 and L2 clinical isolates of Mtb.

Post-transcriptional control mechanisms for regulatory and virulence genes are mitigated in Mtb L2.

By applying a genome-scale transcriptional framework, DosR, Rv1985c, Lsr2 and Rv0691c are identified as master transcription factors responsible for differential target gene expression in L2 strains compared to L1.

L1 and L2 DosR proteins respond differently to nitric oxide stress, thus determining a relevant phenotype.
The Clinical Kinase Index: Prioritizing Understudied Kinases as Targets for the Treatment of Cancer
Authors: Essegian Derek , Khurana Rimpi , Stathias Vasileios , Schürer Stephan C.
Published: February 2020

The approval of the first kinase inhibitor, Gleevec, in 2001, ushered in a paradigm shift for oncological treatment—the use of genomic data for targeted, efficacious therapies. Since then, over 48 additional small molecule kinase inhibitors have been approved, solidifying the case for kinases as a highly druggable and attractive target class. Despite the established role deregulated kinase activity plays in cancer, only 8% of the entire kinome has been effectively “drugged”. Moreover, a quarter of the 634 human kinases are vastly understudied. We have developed a comprehensive scoring system which utilizes differential gene expression, clinical and pathological parameters, overall survival and mutational hotspot analysis to rank and prioritize clinically-relevant kinase targets across 17 solid tumor cancers from The Cancer Genome Atlas (TCGA). Collectively, we report that dark kinases have potential clinical value as biomarkers or as new drug targets that warrant further study.
Temperature regulation as a tool to program synthetic microbial community composition
Authors: Krieger Adam , Zhang Jiahao , Lin Xiaoxia Nina
Published: February 2020

Engineering of synthetic microbial communities is emerging as a powerful new paradigm for performing various industrially, medically, and environmentally important processes. To reach the fullest potential, however, this approach requires further development in many aspects, a key one being regulating the community composition. Here we leverage well established mechanisms in ecology which govern the relative abundance of multi-species ecosystems and develop a new tool for programming the composition of synthetic microbial communities. Using a simple model system consisting of two microorganismsEscherichia coliandPseudomonas putida, which occupy different but partially overlapping thermal niches, we demonstrate that temperature regulation can be used to enable coexistence and program the community composition. We first investigate a constant temperature regime and show that different temperatures lead to different community compositions. Next, we invent a new cycling temperature regime and show that it can dynamically tune the microbial community, achieving a wide range of compositions depending on parameters that are readily manipulatable. Our work provides conclusive proof of concept that temperature regulation is a versatile and powerful tool capable of programming compositions of synthetic microbial communities.