bluuebunny/crossref_metadata_2025 huggingface dataset:
Giant Jurassic dragon lacewing larvae with lacustrine palaeoecology represent the oldest fossil record of larval neuropterans
Authors: Du Xuheng , Niu Kecheng , Bao Tong
Published: February 2023

Neuropterans seem to be less specious among holometabolans, while they are in fact the relicts of a diverse group from the Mesozoic era. Their early radiation resulted in great family level morphological heterogeneity of extant neuropterans, especially of their larvae. The earliest previously reported fossil larvae of this group were from the Early Cretaceous, where they already showed high taxonomic diversity and an extremely wide range of variations in morphotypes. In this work, the earliest record of the larva of the neuropteranPalaeoneurorthus baiigen. et sp. nov. from the Middle Jurassic Daohugou Beds of China is described. The larvae, which have large and elongated bodies, straight stylets with curved apices, an extremely elongated cervix and an extended anterior lobe of pronotum, are placed in Nevrorthidae. The elongated cervix is probably a specialized adaptation for hunting small organisms. The palaeoenvironment of these larvae indicates that larvae of Nevrorthidae have exhibited stable aquatic ecology since the Middle Jurassic, and underwent a possible shift from lakes to more lotic yet constricted modern mountain rivulet habitats over time.
Characterization of Shigella flexneri in Northern Vietnam in 2012 –2016
Authors: Nguyen Dong Tu , Morita Masatomo , Ngo Tuan Cuong , Le Thanh Huong , Le Dang Hai , Nguyen Hoai Thu , Akeda Yukihiro , Ohnishi Makoto , Izumiya Hidemasa
Published: February 2023

Introduction: Shigellosis remains a considerable public health concern in developing countries. Shigella flexneri and Shigella sonnei are prevalent worldwide and S. sonnei has been replacing S. flexneri.
Gap Statement: S. flexneri still causes outbreaks in Northern Vietnam and limited information is available on its genetic characteristics.
Aim: This study aimed to characterize the genetic characteristics of S. flexneri strains from Northern Vietnam.
Methodology: This study used 17 isolates from eight incidents, collected in Northern Vietnam between 2012 and 2016. The samples were subjected to whole genome sequencing (WGS), molecular serotyping, cluster analysis, and identification of antimicrobial resistance genes. Additionally, phylogenetic analysis was performed including isolates from previous studies.
Results: Clusters were identified according to spatiotemporal backgrounds. The results suggested that two incidents in Yen Bai province in 2015 and 2016 were derived from a very recent common ancestor. All isolates belonged to phylogroup (PG) 3, which was divided into two sub-lineages. Thirteen of 17 isolates, including those from the Yen Bai incidents, belonged to sub-lineage Sub-1 and were serotyped as 1a. The remaining four isolates belonged to sub-lineage Sub-2 and were the globally predominant serotype 2a. The Sub-1 S. flexneri isolates possessed the gtrI gene, which encodes the glycosyl transferase that determines serotype 1a, with bacteriophage elements in the vicinity.
Conclusion: This study revealed two PG3 sub-lineages of S. flexneri in Northern Vietnam, of which Sub-1 might be specific to the region.
Sphingobium lignivorans sp. nov., isolated from river sediment downstream of a paper mill
Authors: Allemann Marco N. , Presley Gerald N. , Elkins James G. , Michener Joshua K.
Published: February 2023

A bacterial isolate, B1D3AT, was isolated from river sediment collected from the Hiwassee River near Calhoun, TN, by enrichment culturing with a model 5–5′ lignin dimer, dehydrodivanillate, as its sole carbon source. B1D3AT was also shown to utilize several model lignin-derived monomers and dimers as sole carbon sources in a variety of minimal media. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed yellow/cream-coloured colonies on rich agar. Optimal growth occurred at 30 °C, pH 7–8, and in the absence of NaCl. The major fatty acids of B1D3AT were C18 : 1 ω7c and C17 : 1 ω6c. The predominant hydroxy fatty acids were C14 : 0 2-OH and C15 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and sphingoglycolipid. B1D3AT contained spermidine as the only major polyamine. The major isoprenoid quinone was Q-10 with minor amounts of Q-9 and Q-11. The genomic DNA G+C content of B1D3AT was 65.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 49 core, universal genes defined by Clusters of Orthologous Groups gene families indicated that B1D3AT was a member of the genus

Sphingobium

. B1D3AT was most closely related to

Sphingobium

sp. SYK-6, with a 100 % 16S rRNA gene sequence similarity. B1D3AT showed 78.1–89.9 % average nucleotide identity and 19.5–22.2% digital DNA–DNA hybridization identity with other type strains from the genus

Sphingobium

. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain B1D3AT should be classified as representing a novel species of the genus

Sphingobium

, for which the name Sphingobium lignivorans sp. nov. is proposed. The type strain is strain B1D3AT (ATCC TSD-279T=DSM 111877T).
Characterization of a TatA/TatB binding site on the TatC component of the Escherichia coli twin arginine translocase
Authors: Severi Emmanuele , Bunoro Batista Mariana , Lannoy Adelie , Stansfeld Phillip J. , Palmer Tracy
Published: February 2023

The twin arginine transport (Tat) pathway exports folded proteins across the cytoplasmic membranes of prokaryotes and the thylakoid membranes of chloroplasts. In

Escherichia coli

and other Gram-negative bacteria, the Tat machinery comprises TatA, TatB and TatC components. A Tat receptor complex, formed from all three proteins, binds Tat substrates, which triggers receptor organization and recruitment of further TatA molecules to form the active Tat translocon. The polytopic membrane protein TatC forms the core of the Tat receptor and harbours two binding sites for the sequence-related TatA and TatB proteins. A ‘polar’ cluster binding site, formed by TatC transmembrane helices (TMH) 5 and 6 is occupied by TatB in the resting receptor and exchanges for TatA during receptor activation. The second binding site, lying further along TMH6, is occupied by TatA in the resting state, but its functional relevance is unclear. Here we have probed the role of this second binding site through a programme of random and targeted mutagenesis. Characterization of three stably produced TatC variants, P221R, M222R and L225P, each of which is inactive for protein transport, demonstrated that the substitutions did not affect assembly of the Tat receptor. Moreover, the substitutions that we analysed did not abolish TatA or TatB binding to either binding site. Using targeted mutagenesis we introduced bulky substitutions into the TatA binding site. Molecular dynamics simulations and crosslinking analysis indicated that TatA binding at this site was substantially reduced by these amino acid changes, but TatC retained function. While it is not clear whether TatA binding at the TMH6 site is essential for Tat activity, the isolation of inactivating substitutions indicates that this region of the protein has a critical function.
Spatial Patterns of White Matter Hyperintensities: A Systematic Review
Authors: Botz Jonas , Lohner Valerie , Schirmer Markus D.
Published: February 2023

Background

White matter hyperintensities are an important marker of cerebral small vessel disease. This disease burden is commonly described as hyperintense areas in the cerebral white matter, as seen on T2-weighted fluid attenuated inversion recovery magnetic resonance imaging data. Studies have demonstrated associations with various cognitive impairments, neurological diseases, and neuropathologies, as well as clinical and risk factors, such as age, sex, and hypertension. Due to their heterogeneous appearance in location and size, studies have started to investigate spatial distributions and patterns, beyond summarizing this cerebrovascular disease burden in a single metric - its volume. Here, we review the evidence of association of white matter hyperintensity spatial patterns with its risk factors and clinical diagnoses.

Design/Methods

We performed a systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) Statement. We used the standards for reporting vascular changes on neuroimaging criteria to construct a search string for literature search on PubMed. Studies written in English from the earliest records available until January 31st, 2023, were eligible for inclusion if they reported on spatial patterns of white matter hyperintensities of presumed vascular origin.

Results

A total of 380 studies were identified by the initial literature search, of which 41 studies satisfied the inclusion criteria. These studies included cohorts based on mild cognitive impairment (15/41), Alzheimer’s Disease (14/41), Dementia (5/41), Parkinson’s Disease (3/41), and subjective cognitive decline (2/41). Additionally, 6 of 41 studies investigated cognitively normal, older cohorts, two of which were population-based, or other clinical findings such as acute ischemic stroke or reduced cardiac output. Cohorts ranged from 32 to 882 patients/participants (median cohort size 191.5 and 51.6 % female (range: 17.9 - 81.3 %)). The studies included in this review have identified spatial heterogeneity of WMHs with various impairments, diseases, and pathologies as well as with sex and (cerebro)vascular risk factors.

Conclusions

The results show that studying white matter hyperintensities on a more granular level might give a deeper understanding of the underlying neuropathology and their effects. This motivates further studies examining the spatial patterns of white matter hyperintensities.
Measurement of Accumulation of Antibiotics toStaphylococcus aureusin Phagosomes of Live Macrophages
Authors: Kelly Joey J. , Dalesandro Brianna E. , Liu Zichen , Chordia Mahendra D. , Ongwae George M. , Pires Marcos M.
Published: February 2023

Staphylococcus aureus(S. aureus) has evolved the ability to persist after uptake into host immune cells. This intracellular niche enablesS. aureusto potentially escape host immune responses and survive the lethal actions of antibiotics. While the elevated tolerance ofS. aureusto small-molecule antibiotics is likely to be multifactorial, we pose that there may be contributions related to permeation of antibiotics into phagocytic vacuoles, which would require translocation across two mammalian bilayers. To empirically test this, we adapted our recently developed permeability assay to determine the accumulation of FDA-approved antibiotics into phagocytic vacuoles of live macrophages. Bioorthogonal reactive handles were metabolically anchored within the surface ofS. aureus,and complementary tags were chemically added to antibiotics. Following phagocytosis of taggedS. aureuscells, we were able to specifically analyze the arrival of antibiotics within the phagosomes of infected macrophages. Our findings enabled the determination of permeability differences between extra- and intracellularS. aureus, thus providing a roadmap to dissect the contribution of antibiotic permeability to intracellular pathogens.
Environmental context, parameter sensitivity and structural sensitivity impact predictions of annual-plant coexistence
Authors: Cervantes-Loreto Alba , Pastore Abigail I. , Brown Christopher R.P. , Maraffini Michelle L. , Aldebert Clement , Mayfield Margaret M. , Stouffer Daniel B.
Published: February 2023

Predicting the outcome of interactions between species is central to our current understanding of diversity maintenance. However, we have limited information about the robustness of many model-based predictions of species coexistence. This limitation is partly because several sources of uncertainty are often ignored when making predictions. Here, we introduce a framework to simultaneously explore how different mathematical models, different environmental contexts, and parameter uncertainty impact the probability of predicting species coexistence. Using a set of pairwise competition experiments on annual plants, we provide direct evidence that subtle differences between models lead to contrasting predictions of both coexistence and competitive exclusion. We also show that the effects of environmental context-dependency and parameter uncertainty on predictions of species coexistence are not independent of the model used to describe population dynamics. Our work suggests that predictions of species coexistence and extrapolations thereof may be particularly vulnerable to these underappreciated founts of uncertainty.
Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities
Authors: Vlaanderen Eric J. , Ghaly Timothy M. , Moore Lisa R. , Focardi Amaranta , Paulsen Ian T. , Tetu Sasha G.
Published: February 2023

Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.
Improvedin situCharacterization of Proteome-wide Protein Complex Dynamics with Thermal Proximity Co-Aggregation
Authors: Sun Siyuan , Zheng Zhenxiang , Wang Jun , Li Fengming , He An , Tian Ruijun , Tan Chris Soon Heng
Published: February 2023

Vast majority of cellular activities are carried out by protein complexes that assembled dynamically in response to cellular needs and environmental cues. Large scale efforts had uncovered a large repertoire of functionally uncharacterized protein complexes which necessitate new strategies to delineate their roles in various cellular activities and diseases. Thermal proximity co-aggregation profiling could be readily deployed to simultaneously characterize the dynamics for hundreds to thousands of protein complexesin situacross different cellular conditions. Toward this goal, we had optimized the original method both experimentally and computationally. In this new iteration termed Slim-TPCA, fewer temperatures are used which increase throughputs by over 3X, while coupled with new scoring metrics and statistical evaluation resulted in minimal compromise in coverage and the detection of more relevant protein complexes. Overall, less samples are needed, false positives from batch effects are minimized and statistical evaluation time is reduced by two orders of magnitude. We applied Slim-TPCA to profile state of protein complexes in K562 cells under different duration of glucose deprivation. More protein complexes are found dissociated based on TPCA signature in accordance with expected downregulation of most cellular activities. These complexes include 55S ribosome and various respiratory complexes in mitochondria revealing the utility of TPCA to study protein complexes in organelles. On other hand, protein complexes involved in protein transport and degradation are found increasingly associated revealing their involvement in metabolic reprogramming during glucose deprivation. In summary. Slim-TPCA is an efficient strategy for proteome-wide characterization of protein complexes. The various algorithmic improvement of Slim-TPCA is available as Python package athttps://pypi.org/project/Slim-TPCA/
High-fidelity Database-free Deep Learning Reconstruction for Real-time Cine Cardiac MRI
Authors: Demirel Ömer Burak , Zhang Chi , Yaman Burhaneddin , Gulle Merve , Shenoy Chetan , Leiner Tim , Kellman Peter , Akçakaya Mehmet
Published: February 2023

Real-time cine cardiac MRI provides an ECG-free free-breathing alternative to clinical gold-standard ECG-gated breath-hold segmented cine MRI for evaluation of heart function. Real-time cine MRI data acquisition during free breathing snapshot imaging enables imaging of patient cohorts that cannot be imaged with segmented or breath-hold acquisitions, but requires rapid imaging to achieve sufficient spatial-temporal resolutions. However, at high acceleration rates, conventional reconstruction techniques suffer from residual aliasing and temporal blurring, including advanced methods such as compressed sensing with radial trajectories. Recently, deep learning (DL) reconstruction has emerged as a powerful tool in MRI. However, its utility for free-breathing real-time cine MRI has been limited, as database-learning of spatio-temporal correlations with varying breathing and cardiac motion patterns across subjects has been challenging. Zero-shot self-supervised physics-guided deep learning (PG-DL) reconstruction has been proposed to overcome such challenges of database training by enabling subject-specific training. In this work, we adapt zeroshot PG-DL for real-time cine MRI with a spatio-temporal regularization. We compare our method to TGRAPPA, locally low-rank (LLR) regularized reconstruction and database-trained PG-DL reconstruction, both for retrospectively and prospectively accelerated datasets. Results on highly accelerated real-time Cartesian cine MRI show that the proposed method outperforms other reconstruction methods, both visibly in terms of noise and aliasing, and quantitatively.
A Photoactivated Protein Degrader for Optical Control of Synaptic Function
Authors: Ko T. , Jou C. , Grau-Perales A.B. , Reynders M. , Fenton A.A. , Trauner D.
Published: February 2023

Hundreds of proteins determine the function of synapses, and synapses define the neuronal circuits that subserve myriad brain, cognitive, and behavioral functions. It is thus necessary to precisely manipulate specific proteins at specific sub-cellular locations and times to elucidate the roles of particular proteins and synapses in brain function. We developed PHOtochemically TArgeting Chimeras (PHOTACs) as a strategy to optically degrade specific proteins with high spatial and temporal precision. PHOTACs are small molecules that, upon wavelength-selective illumination, catalyze ubiquitylation and degradation of target proteins through endogenous proteasomes. Here we describe the design and chemical properties of a PHOTAC that targets Ca2+/calmodulin-dependent protein kinase II alpha (CaMKIIα), which is abundant and crucial for baseline synaptic function of excitatory neurons. We validate the PHOTAC strategy, showing that theCaMKIIα-PHOTACis effective in mouse brain tissue. Light activation ofCaMKIIα-PHOTACremoved CaMKIIα from regions of the mouse hippocampus only within 25 μm of the illuminated brain surface. The optically-controlled degradation decreases synaptic function within minutes of light activation, measured by the light-initiated attenuation of evoked field excitatory postsynaptic potential (fEPSP) responses to physiological stimulation. The PHOTACs methodology should be broadly applicable to other key proteins implicated in synaptic function, especially for evaluating their precise roles in the maintenance of long-term potentiation and memory within subcellular dendritic domains.
When is warmer better? Disentangling within- and between-generation effects of thermal history on survival
Authors: Rebolledo Adriana P. , Sgrò Carla M. , Monro Keyne
Published: February 2023

Understanding the fitness consequences of thermal history is necessary to predict organismal responses to global warming. This is especially challenging for ectotherms with complex life cycles, since distinct life stages can differ in thermal sensitivity, acclimate to different thermal environments, and accrue responses to acclimation within and between generations.

Although acclimation is widely hypothesized to benefit organisms by helping them (or their offspring) to compensate for negative impacts of environmental change, equivocal support for this hypothesis highlights the need to assess alternatives. However, assessments that do so in ways that explicitly dissect responses across life stages and generations remain limited.

We assess alternative hypotheses for acclimation responses (none, beneficial, colder-is-better, and warmer-is-better) within and between generations of an externally-fertilizing marine tubeworm whose vulnerability to warming rests on survival at early planktonic stages (gametes, embryos, and larvae). We start by acclimating parents, gametes, and embryos to ambient and projected warmer temperatures (17 °C and 22 °C) factorially by life stage. We then rear individuals with differing acclimation histories to the end of larval development at test temperatures from 10 °C to 28 °C (upper and lower survival limits) to estimate thermal survival curves for development, and compare curves among acclimation histories.

We show that survival curves are most responsive to parental acclimation followed by acclimation at embryogenesis, but are buffered against acclimation at fertilization. Moreover, curves respond independently to acclimation within and between generations, and respond largely as predicted by the warmer-is-better hypothesis, despite the semblance of beneficial acclimation after successive acclimations to warmer temperature.

Our study demonstrates the varied nature of thermal acclimation, and the importance of considering how acclimation responses aggregate across complex life cycles when predicting vulnerability to warming.
Vulture: Cloud-enabled scalable mining of microbial reads in public scRNA-seq data
Authors: Chen Junyi , Yin Danqing , Wong Harris Y.H. , Duan Xin , Yu Ken H.O. , Ho Joshua W. K.
Published: February 2023

The rapidly growing collection of public single-cell sequencing data have become a valuable resource for molecular, cellular and microbial discovery. Previous studies mostly overlooked detecting pathogens in human single-cell sequencing data. Moreover, existing bioinformatics tools lack the scalability to deal with big public data. We introduce Vulture, a scalable cloud-based pipeline that performs microbial calling for single-cell RNA sequencing (scRNA-seq) data, enabling meta-analysis of host-microbial studies from the public domain. In our scalability benchmarking experiments, Vulture can outperform the state-of-the-art cloud-based pipeline Cumulus with a 40% and 80% reduction of runtime and cost, respectively. Furthermore, Vulture is 2-10 times faster than PathogenTrack and Venus, while generating comparable results. We applied Vulture to two COVID-19, three hepatocellular carcinoma (HCC), and two gastric cancer human patient cohorts with public sequencing reads data from scRNA-seq experiments and discovered cell-type specific enrichment of SARS-CoV2, hepatitis B virus (HBV), andH. pyloripositive cells, respectively. In the HCC analysis, all cohorts showed hepatocyte-only enrichment of HBV, with cell subtype-associated HBV enrichment based on inferred copy number variations. In summary, Vulture presents a scalable and economical framework to mine unknown host-microbial interactions from large-scale public scRNA-seq data. Vulture is available via an open-source license athttps://github.com/holab-hku/Vulture.
Goal-Directed Learning is Multidimensional and Accompanied by Diverse and Widespread Changes in Neocortical Signaling
Authors: Marrero Krista , Aruljothi Krithiga , Delgadillo Christian , Kabbara Sarah , Swatch Lovleen , Zagha Edward
Published: February 2023

New tasks are often learned in stages with each stage reflecting a different learning challenge. Accordingly, each learning stage is likely mediated by distinct neuronal processes. And yet, most rodent studies of the neuronal correlates of goal-directed learning focus on individual outcome measures and individual brain regions. Here, we longitudinally studied mice from naïve to expert performance in a head-fixed, operant conditioning whisker discrimination task. In addition to tracking the primary behavioral outcome of stimulus discrimination, we tracked and compared an array of object-based and temporal-based behavioral measures. These behavioral analyses identify multiple, partially overlapping learning stages in this task, consistent with initial response implementation, early stimulus-response generalization, and late response inhibition. To begin to understand the neuronal foundations of these learning processes, we performed widefield Ca2+imaging of dorsal neocortex throughout learning and correlated behavioral measures with neuronal activity. We found distinct and widespread correlations between neocortical activation patterns and various behavioral measures. For example, improvements in sensory discrimination correlated with target stimulus evoked activations of licking-related cortices along with distractor stimulus evoked global cortical suppression. Our study reveals multidimensional learning for a simple goal-directed learning task and generates hypotheses for the neuronal modulations underlying these various learning processes.
Viral proteogenomic and expression profiling during fully productive replication of a skin-tropic herpesvirus in the natural host
Authors: Volkening Jeremy , Spatz Stephen J. , Ponnuraj Nagendraprabhu , Akbar Haji , Arrington Justine V. , Jarosinski Keith W.
Published: February 2023

Efficient transmission of herpesviruses is essential for dissemination in host populations; however, little is known about the viral genes that mediate transmission, mostly due to their close relationship to their natural host. Marek’s disease is a devastating herpesviral disease of chickens caused by Marek’s disease virus (MDV) and an excellent natural model to study skin- tropic herpesviruses and transmission. Similar to varicella zoster virus that causes chicken pox in humans, the only site where fully productive replication occurs is in epithelial skin cells and this is required for host to host transmission. Here, we enriched for actively replicating virus in feather follicle epithelial skin cells of live chickens to measure both viral transcription and protein expression using combined RNA sequencing and LC/MS-MS bottom-up proteomics. Enrichment produced a previously unseen breadth and depth of viral peptide sequencing. We confirmed protein translation for 84 viral genes at high confidence (1% FDR) and correlated relative protein abundance with RNA expression levels. Using a proteogenomic approach, we confirmed translation of most well-characterized spliced viral transcripts and identified a novel, abundant isoform of the 14 kDa transcript family via both intron-spanning sequencing reads as well as a high-quality junction-spanning peptide identification. We identified peptides representing alternative start codon usage in several genes and putative novel microORFs at the 5’ ends of two core herpesviral genes, pUL47 and ICP4, along with evidence of transcription and translation of the capsid scaffold protein pUL26.5. Using a natural animal host model system to examine viral gene expression provides a robust, efficient, and meaningful way of validating results gathered from cell culture systems.

Author Summary

In the natural host, the transcriptome and proteome of many herpesviruses are poorly defined. Here, we evaluated the viral transcriptome and proteome in feather follicle epithelial skin cells of chickens infected with Marek’s disease virus (MDV), an important poultry pathogen as well as an excellent model for skin-tropic human alphaherpesvirus replication in skin cells. Using fluorescently tagged virus, we significantly enriched the number of infected cells sampled from live chickens, greatly enhancing the detection of viral transcripts and proteins within a host background. Based on this, we could confirm the translation of most transcripts using deep MS/MS-based proteomics and identify novel expressed peptides supportive of an increasingly complex translational and regulatory viral landscape. The demonstrated deep peptide sequencing capability can serve as a template for future work in herpesviral proteomics.
Delirium, Confusion, or Altered mental status as a risk for abnormal head computed tomogram findings in older adults in the emergency department: A systematic review and meta-analysis
Authors: Lee Sangil , Cavalier Faithe R. , Hayes Jane M. , Doering Michelle , Lo Alexander X. , Khoujah Danya , Howard Matthew A. , de Wit Kerstin , Liu Shan W.
Published: February 2023

Background

Delirium, confusion, and altered mental status are common presentations among older adults to the emergency department (ED). We aimed to report the association between delirium, confusion or altered mental status in older ED patients and acute abnormal findings on head computed tomogram (CT).

Methods

A systematic review was conducted using Ovid Medline, Embase,Clinicaltrials.gov, Web of Science, and Cochrane Central from conception to April 8th, 2021. We included citations if they described patients aged 65 years or older who received head imaging at the time of ED assessment, and reported whether or not patients had delirium, confusion, or altered mental status. Screening, data extraction, and bias assessment were performed in duplicate. We estimated the odds ratios (OR) for abnormal neuroimaging in patients with altered mental status.

Results

The search strategy identified 3,014 unique citations, of which two studies reporting on 909 patients with delirium, confusion or altered mental status were included. No study formally assessed for delirium. The OR for abnormal head CT findings in patients with delirium, confusion or altered mental status was 0.35 (95% CI 0.031 to 3.97) compared to patients without delirium, confusion or altered mental status.

Conclusion

We did not find a statistically significant association between delirium, confusion or altered mental status and abnormal CT findings in older ED patients.
Types of Arrhythmias and the risk of sudden cardiac death in dialysis patients: A Systematic Review and Meta-analysis
Authors: Chander Subhash , Lohana Sindhu , Sadarat FNU , Kumari Roopa
Published: February 2023

Background

Patients on long-term dialysis therapy due to ESRD tend to have a high mortality rate, predominantly due to cardiovascular complications, which is associated with an increased risk of arrhythmias compared to the general population. Arrhythmia has been firmly identified as the primary cause of sudden death during dialysis, as studies have shown a correlation between the timing of dialysis sessions and episodes of sudden death, as well as relationships with serum or dialysate electrotype concentrations. It also associated with a six-fold increased risk of developing ventricular fibrillation following a first myocardial infarction.

Methods

This systematic review and meta-analysis followed the guidelines provided by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The reviewers searched the Cochrane Library, MEDLINE, Europe PMC, and Google Scholar Databases for relevant data sources. We included only randomized controlled trials and cohort studies published in English. A quantitative analysis (meta-analysis) was conducted using Review Manager version 5.4 (RevMan 5.4; The Nordic Cochrane Center, The Cochrane Collaboration, 2014).

Results

The initial database search yielded 547 studies, of which 213 duplicates were excluded. The title, abstract, and full-text screening excluded 247 studies, and the final total included 13 studies reporting the incidence of SCD mortality in this meta-analysis.

Conclusion

SCD remains a major public health concern, particularly in patients undergoing dialysis. Meta-analysis results show that bradyarrhythmia emerges as a common type of arrhythmia leading to SCD; however, other types of arrhythmias should also be considered.
Mortality and Mode of Dialysis
Authors: Chander Subhash , Lohana Sindhu , Sadarat FNU , Kumari Roopa
Published: February 2023

Background

Dialysis is an intervention used chiefly to cover poorly functioning kidneys’ ultrafiltration and diffusion functions. Dialysis can be performed using three major approaches: peritoneal dialysis, hemodialysis, and continuous renal replacement therapy, which have varying degrees of efficiency. We sought to compare the mortality rates among patients receiving different dialysis modalities.

Study Design

Statistical Review and Meta-Analysis.

Setting & Population

The investigation was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Data sources were drawn from Google Scholar, ResearchGate, PubMed (MEDLINE), Cochrane Library, and Embase databases. Eligible patients had to be ones presenting with acute or chronic kidney failure who required assistance with kidney function.

Selection Criteria for Studies

The eligibility criteria included studies with participants requiring dialysis and comparing two of the three dialysis modalities that provided outcomes on mortality rates. Inclusion criteria (underlying disease, chronic or acute kidney disease, presenting signs, age categories, subject consent, etc.), the type of dialysis modalities under investigation, and the mortality rates (% per modality group).

Index Texts

‘mortalities, fatalities, dialysis, hemodialysis, continuous renal replacement therapy (CRRT), Peritoneal dialysis, and comparative.’

Outcomes

We sought to explore the studies’ findings by comparing the mortality rates among the three broad categories of dialysis. Therefore, we aimed to compare mortality rates in CRRT vs. Hemodialysis, mortality Rates in CRRT vs. PD, and mortality rates in patients with PD vs. HD.

Results

Fifteen studies were narrowed down from the study search and were placed into three categories: PD vs. CRRT (4), PD vs. HD (5), and CRRT vs. HD (6). For the three outcomes, none recorded statistically significant differences in mortality rates between the patient categories (p= 0.92, 0.009, 0.22).

Conclusion

Like other interventions for patients with chronic kidney disease, dialysis is associated with detrimental effects caused by the inflammatory response and worsening progression of the condition. Mortality is a common complication among dialysis patients, independent of modality, based on the lack of statistically significant differences between the three groups.
Taste matters: Mapping expectancy-based appetitive placebo effects onto the brain
Authors: Khalid Iraj , Rodrigues Belina , Dreyfus Hippolyte , Frileux Solène , Meissner Karin , Fossati Philippe , Hare Todd Anthony , Schmidt Liane
Published: February 2023

Expectancies, which are higher order prognostic beliefs, can have powerful effects on experiences, behavior and brain. However, it is unknown where, how, and when, in the brain, prognostic beliefs influence appetitive interoceptive experiences and related economic behavior. This study combined a placebo intervention on hunger with computational modelling and functional magnetic resonance imaging of value-based decision-making. The results show that prognostic beliefs about hunger shape hunger experiences, how much participants value food and food-value encoding in the prefrontal cortex. Computational modelling further revealed that these placebo effects were underpinned by how much and when during the decision process taste and health information are integrated into the accumulation of evidence toward a food choice. The drift weights of both sources of information further moderated ventromedial and dorsolateral prefrontal cortex interactions during choice formation. These findings provide novel insights into the neurocognitive mechanisms that translate higher order prognostic beliefs into non-aversive interoceptive sensitivity and shape decision-making.
Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype
Authors: Simonin Marie , Préveaux Anne , Marais Coralie , Garin Tiffany , Arnault Gontran , Sarniguet Alain , Barret Matthieu
Published: February 2023

Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) underin vitroconditions. The SynComs were composed of highly abundant and prevalent, sub-dominant or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities usinggyrBgene amplicon sequencing and assessed their impacts on germination and seedling phenotype.

All strains and SynComs successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings.Stenotrophomonas rhizophilabecame dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness.

Most individual strains had no effect on seedling phenotypes, at the exception ofPseudomonas viridiflavaandPaenibacillus sp. thathad detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina)were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa.

Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.
Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complex through fuzzy interaction and mesoscale condensation
Authors: Xie Shangqiang , Yue Congran , Ye Sheng , Li Zhenlu
Published: February 2023

Nuclear transition protein TNP1 is a crucial player mediating histone-protamine exchange in condensing spermatids. A unique combination of intrinsic disorder and multivalent properties turns TNP1 into an ideal agent for orchestrating the formation of versatile TNP-DNA assembly and endows the protein with potent value for vaccine design. Despite its significance, the physicochemical property and the molecular mechanism taken by TNP1 for histone replacement and DNA condensation are still poorly understood. In this study, for the first time, we expressed and purified in vitro human TNP1. We investigated the hierarchical dynamics of TNP1: DNA interaction by combing computational simulations, biochemical assay, fluorescence imaging, and atomic force microscopy. We analyzed fuzzy interactions between TNP1 and DNA at the atomistic level and assessed the influence of TNP1 association on the electrostatic and mechanical properties of DNA. Furthermore, the alteration of the physicochemical properties of the TNP1-DNA complex modulates its molecular assembly and phase separation. Our study sets the foundation for understanding TNP1-mediated histone replacement and sheds light on the encapsulation of genetic material by TNP1 for vaccine development.
Structural landscape of the Respiratory Syncytial Virus nucleocapsids
Authors: Gonnin Lorène , Desfosses Ambroise , Bacia-Verloop Maria , Chevret Didier , Galloux Marie , Éléouët Jean-François , Gutsche Irina
Published: February 2023

Human Respiratory Syncytial Virus (RSV) is a prevalent cause of severe respiratory infections in children and the elderly. The viral genome, enwrapped by the nucleoprotein N into a helical nucleocapsid (NC), is a template for the viral RNA synthesis and a scaffold for the virion assembly. Although the structures of NC filaments representative of the other major families of theMononegaviralesorder have been solved, a detailed understanding of the RSV NCs is missing. This cryo-electron microscopy (cryo-EM) analysis highlights the polymorphism of the RSV nucleocapsid-like assemblies. We reveal in particular the non-canonical arrangement of the RSV NC helix, composed of 16 N per asymmetric unit, and the resulting systematic variations in the RNA accessibility. We demonstrate that this unique helical symmetry originates from recurring longitudinal interactions by the C-terminal arm of the RSV N, whose truncation abrogates the inter-turn contacts. We report the cryo-EM structures of the full-length helical NC filaments, double-headed NCs, ring-capped NCs and double-decameric N-RNA rings, as well as those of the alternative assemblies formed by a C-terminally truncated N mutant. In addition, we demonstrate the functional importance of the interface involved in the formation of the double-headed and the ring-capped interactions. We put all these findings in the context of the RSV RNA synthesis machinery and delineate the structural basis for its further investigation.
Computational Mesoscale Framework for Biological Clustering and Fractal Aggregation
Authors: Zohravi Elnaz , Moreno Nicolas , Ellero Marco
Published: February 2023

Complex hierarchical clustering mediated by diffusion and reaction is ubiquitous to many naturally occurring phenomena. The aggregates typically exhibit a fractal behavior or non-integer size scaling compared to their intrinsic dimensionality (2 – 3 dimensions). Such fractal aggregates have attracted attention in studying biological (i.e. bronchi and nervous system morphogenesis, blood clotting) and synthetic (i.e. colloids, polymers, catalysts, nano-dendrites, multicellular organisms) systems. In general, biological clustering can occur on a wide range of spatial/temporal scales, and depending on the type of interactions, multiple mechanisms (or stages) can be involved. As a consequence, the modeling of biological clustering is typically a challenging task, requiring the use of a variety of methods to capture the characteristic behavior of specific biological systems. Herein, we proposed a generalized-mesoscale-clustering (GMC) framework that incorporates hydrodynamic interactions, bonding, and surface tension effects. This framework allows for studying both static and dynamic states of cluster development. We showcase the framework using a variety of biological clustering mechanisms, and further illustrate its versatility to model different scales, focusing on blood-related clustering ranging from fibrin network formation to platelet aggregation. Besides the introduction of the mesoscale clustering framework, we show that a single biomarker (such as fractal dimension) is insufficient to fully characterize and distinguish different cluster structures (morphologies). To overcome this limitation, we propose a comprehensive characterization that relates the structural properties of the cluster using four key parameters, namely the fractal dimension, pore-scale diffusion, as well as the characteristic times for initiation and consolidation of the cluster. Additionally, we show that the GMC framework allows tracking of bond density providing another biomarker for cluster temporal evolution and final steady-state. Furthermore, this feature and built-in hydrodynamics interactions offer the potential to investigate cluster mechanical properties in a variety of biological systems.
The evolution of democratic peace in animal societies
Authors: Hunt KL , Patel M , Croft DP , Franks DW , Green PA , Thompson FJ , Johnstone RA , Cant MA , Sankey DWE
Published: February 2023

A major goal in evolutionary biology is to elucidate common principles that drive human and other animal societies to adopt either a warlike or peaceful nature. One proposed explanation for the variation in aggression between human societies is the ‘democratic peace’ hypothesis. According to this theory, autocracies are more warlike than democracies because autocratic leaders can pursue fights for private gain. However, autocratic and democratic decision-making processes are not unique to humans and are widely observed across a diverse range of non-human animal societies. We use evolutionary game theory to evaluate whether the logic of democratic peace may apply across taxa; specifically adapting the classic Hawk-Dove model to consider conflict decisions made by groups rather than individuals. We find support for the democratic peace hypothesis without mechanisms involving complex human institutions and discuss how these findings might be relevant to non-human animal societies. We suggest that the degree to which collective decisions are shared may explain variation in the intensity of intergroup conflict in nature.
Uncovering the BIN1-SH3 interactome underpinning centronuclear myopathy
Authors: Zambo Boglarka , Edelweiss Evelina , Morlet Bastien , Negroni Luc , Pajkos Mátyás , Dosztányi Zsuzsanna , Ostergaard Soren , Trave Gilles , Laporte Jocelyn , Gogl Gergo
Published: February 2023

Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventionalin vitroand cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so-far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.