bluuebunny/crossref_metadata_2025 huggingface dataset:
Domestic dog lineages reveal genetic drivers of behavioral diversification
Authors: Dutrow Emily V. , Serpell James A. , Ostrander Elaine A.
Published: April 2022

Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing an innovative framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates, and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.
Elevated arginine levels in liver tumors promote metabolic reprogramming and tumor growth
Authors: Mossmann Dirk , Park Sujin , Ryback Brendan , Weißenberger Diana , Colombi Marco , Hindupur Sravanth K. , Dazert Eva , Coto-Llerena Mairene , Caner Ercan , Cenzano Veronica J. , Piscuoglio Salvatore , Bosch Fatima , Terracciano Luigi M. , Sauer Uwe , Hall Michael N.
Published: April 2022

Arginine auxotropy, due to reduced expression of urea cycle genes, is common in cancer. However, little is known about the levels of arginine in these cancers. Here, we report that arginine levels are elevated in hepatocellular carcinoma (HCC) despite reduced expression of urea cycle enzymes. Liver tumors accumulate high levels specifically of arginine via increased uptake and, more importantly, via suppression of arginine-to-polyamine conversion due to reduced arginase 1 (ARG1) and agmatinase (AGMAT) expression. Furthermore, the high levels of arginine are required for tumor growth. Mechanistically, high levels of arginine promote tumorigenesis via transcriptional regulation of metabolic genes, including upregulation of asparagine synthetase (ASNS). ASNS-derived asparagine further enhances arginine uptake, creating a positive feedback loop to sustain high arginine levels and oncogenic metabolism. Thus, arginine is a novel second messenger-like molecule that reprograms metabolism to promote tumor growth.
Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data
Authors: Wang Kaiwen , Yang Yuqiu , Wu Fangjiang , Song Bing , Wang Xinlei , Wang Tao
Published: April 2022

While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are dramatically different from scRNA-seq data in many aspects. This calls for the evaluation and development of computational methods specific for CyTOF data. Dimension reduction (DR) is one of the critical steps of single cell data analysis. Here, we benchmark the performances of 21 DR methods on 110 real and 425 synthetic CyTOF samples. We find that less well-known methods like SAUCIE, SQuaD-MDS, and scvis are the overall best performers. In particular, SAUCIE and scvis are well balanced, SQuaD-MDS excels at structure preservation, whereas UMAP has great downstream analysis performance. We also find that t- SNE (along with SQuad-MDS/t-SNE Hybrid) possesses the best local structure preservation. Nevertheless, there is a high level of complementarity between these tools, so the choice of method should depend on the underlying data structure and the analytical needs.
Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury
Authors: Malagola E. , Vasciaveo A. , Ochiai Y. , Kim W. , Middelhoff M. , Nienhüser H. , Deng L. , Belin B. , LaBella J. , Zamechek LB. , Wong M.H. , Li L. , Guha C. , Cheng CW. , Yan KS. , Califano A. , Wang T.C.
Published: April 2022

The currently accepted intestinal epithelial cell organization model proposes that crypt base columnar (CBC) cells marked by high levels ofLgr5expression represent the sole intestinal stem cell (ISC) compartment. However, previous studies have indicated that Lgr5+cells are dispensable for intestinal regeneration, leading to two major hypotheses: one favoring the presence of a quiescent reserve stem cell population, the other calling for differentiated cell plasticity. To investigate these possibilities, we studied crypt epithelial cell organization, during homeostasis and regeneration, in unbiased fashion, via high-resolution single-cell profiling. These studies, combined within vivolineage tracing, show thatLgr5is not a specific ISC marker and that stemness potential exists beyond the crypt base in the isthmus region, whose cells, contrary to differentiated cells, participate in tissue homeostasis and support intestinal regeneration. Our results provide a novel model of organization for the intestinal crypt epithelium in which stemness potential is not restricted to CBC cells and suggesting that neither de-differentiation nor reserve stem cell populations are drivers of intestinal regeneration.
Projecting clumped transcriptomes onto single cell atlases to achieve single cell resolution
Authors: Johansen Nelson , Quon Gerald
Published: April 2022

Multi-modal single cell RNA assays capture RNA content as well as other data modalities, such as spatial cell position or the electrophysiological properties of cells. Compared to dedicated scRNA-seq assays however, they may unintentionally capture RNA from multiple adjacent cells, exhibit lower RNA sequencing depth compared to scRNA-seq, or lack genome-wide RNA measurements. We present scProjection, a method for mapping individual multi-modal RNA measurements to deeply sequenced scRNA-seq atlases to extract cell type-specific, single cell gene expression profiles. We demonstrate several use cases of scProjection, including the identification of spatial motifs from spatial transcriptome assays, distinguishing RNA contributions from neighboring cells in both spatial and multi-modal single cell assays, and imputing expression measurements of un-measured genes from gene markers. scProjection therefore combines the advantages of both multi-modal and scRNA-seq assays to yield precise multi-modal measurements of single cells.
The global effects of alcohol consumption on Gross Domestic Product in high- and low-income countries: a systematic review and meta-analysis
Authors: Mahesarajah Swettha , Pazoki Raha
Published: April 2022

Aims and objectives

This study aims to measure the disease burden and the economic burden associated with alcohol consumption in both high- and low-income countries. To emphasise the necessity of making this issue a worldwide priority, the percentage of GDP attributable to alcohol-related costs will be stated.

Design

Systematic review and meta-analysis

Data sources

A systematic search concerning health and social costs was conducted primarily through PubMed and subsequent citation chaining of appropriate systematic reviews. Other electronic databases such as Google Scholar was also freely searched.

Eligibility criteria for selecting studies

Observational studies examining alcohol-related harm, alcohol-related disease, and alcohol-related expenditure with all studies measuring alcohol-related harm using the alcohol-attributable fraction (AAF).

Results

9 cross-sectional studies were obtained assessing the consequences of alcohol on the respective country’s economy with all studies utilising a prevalence-based approach. 5 studies were eligible for a meta-analysis in the statistically programming software, R. The pooled estimate of the economic burden of alcohol in 5 countries equated to be 0.01% of GDP. Though inconsistencies in cost estimations resulted in an underestimation, our results provide evidence to suggest that alcohol negatively affects both individuals and society. The available literature on the topic of the economic impact of alcohol is inadequate; especially when investigating concerns in poorer regions of the world.

Conclusion

Though the current estimate of global GDP attributable to alcohol use is low, the evidence suggesting the global increase of alcohol consumption is paramount to avoid future calamities. Cooperative leadership from the World Health Organisation (WHO), International Monetary Fund, and the World Bank are requisite to control the harmful patterns of alcohol consumption seen across the globe.

STRENGTHS AND LIMITATIONS OF THIS STUDY

This is the first systematic review assessing the detrimental consequences of alcohol on economic health with the inclusion of both lower-middle income and high-income countries.

This study provides a pooled estimate of the global estimate of the percentage of GDP attributable to alcohol related costs using statistical package, R which has not been done before.

The obtainment of research conducted in low-income countries proved to be difficult, and as a result no low-middle income countries were used when calculating the pooled estimate. Therefore, the accuracy of the provided estimate was decreased.
Different Routes for Direct Interspecies Electron Transfer with Diverse Electron-Accepting Partners
Authors: Holmes Dawn E. , Zhou Jinjie , Smith Jessica A. , Wang Caiqin , Liu Xinying , Lovley Derek R.
Published: April 2022

Direct interspecies electron transfer (DIET) may be most important in methanogenic environments, but studies to date that have examined the mechanisms for electron transfer from electron-donating partners have primarily focused on co-cultures in which fumarate was the terminal electron acceptor. To better understand DIET with methanogens, the transcriptome of Geobacter metallireducens during DIET-based growth with Geobacter sulfurreducens reducing fumarate was compared with the transcriptome of G. metallireducens grown in co-culture with diverse Methanosarcina species. The transcriptome of G. metallireducens co-cultured with G. sulfurreducens was significantly different from those with Methanosarcina. Furthermore, the transcriptome of G. metallireducens grown with Methanosarcina barkeri, which lacks outer-surface cytochromes, was different from the transcriptome of G. metallireducens co-cultured with Methanosarcina acetivorans or Methanosarcina subterranea, which have an outer-surface c-type cytochrome that serves as an electrical connect for DIET. Differences in G. metallireducens expression patterns for c-type cytochrome genes were particularly notable. The impact of deleting G. metallireducens c-type cytochrome genes depended upon the electron-accepting partner. Multiple cytochromes that G. metallireducens required for DIET with G. sulfurreducens and for Fe(III) oxide reduction were not required for DIET with the Methanosarcina species. Porin-cytochrome complexes and e-pili were required for optimal DIET with all partners. Shewanella oneidensis, another electroactive microbe with abundant outer-surface c-type cytochromes, did not grow via DIET. The results demonstrate that the presence of outer-surface cytochromes does not necessarily confer the capacity for DIET, and also emphasize the substantial impact of the physiology of the electron-accepting partner on the physiology of the electron-donating DIET partner.
The Image Data Explorer: interactive exploration of image-derived data
Authors: Muller Coralie , Serrano-Solano Beatriz , Sun Yi , Tischer Christian , Hériché Jean-Karim
Published: April 2022

Many bioimage analysis projects produce quantitative descriptors of regions of interest in images. Associating these descriptors with visual characteristics of the objects they describe is a key step in understanding the data at hand. However, as many bioimage data and their analysis workflows are moving to the cloud, addressing interactive data exploration in remote environments has become a pressing issue. To address it, we developed the Image Data Explorer (IDE) as a web application that integrates interactive linked visualization of images and derived data points with exploratory data analysis methods, annotation, classification and feature selection functionalities. The IDE is written in R using the shiny framework. It can be easily deployed on a remote server or on a local computer. The IDE is available at https://git.embl.de/heriche/image-data-explorer and a cloud deployment is accessible at https://shiny-portal.embl.de/shinyapps/app/01_image-data-explorer.
Characterizing dynamic neural representations of scene attractiveness
Authors: Kaiser Daniel
Published: April 2022

Aesthetic experiences during natural vision are varied: they can arise from viewing scenic landscapes, interesting architecture, or attractive people. Recent research in the field of neuroaesthetics has taught us a lot about where in the brain such aesthetic experiences are represented. Much less is known about when such experiences arise during the cortical processing cascade. Particularly, the dynamic neural representation of perceived attractiveness for rich natural scenes is not well understood. Here, I present data from an EEG experiment, in which participants provided attractiveness judgments for a set of diverse natural scenes. Using multivariate pattern analysis, I demonstrate that scene attractiveness is mirrored in early brain signals that arise within 200ms of vision, suggesting that the aesthetic appeal of scenes is first resolved during perceptual processing. In more detailed analyses, I show that even such early neural correlates of scene attractiveness are partly related to inter-individual variation in aesthetic preferences and that they generalize across scene contents. Together, these results characterize the time-resolved neural dynamics that give rise to aesthetic experiences in complex natural environments.
Novel trans-translation-associated gene regulation revealed by prophage excision-triggered switching of ribosome rescue pathway
Authors: Onodera Haruka , Niwa Tatsuya , Taguchi Hideki , Chadani Yuhei
Published: April 2022

Escherichia coli has multiple pathways to release a nonproductive ribosome complex stalled at the 3’ end of nonstop mRNAs: SsrA RNA-mediated trans-translation and stop codon-independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and thus its expression is repressed by trans-translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans-translation, but the situations in which ArfA is expressed to rescue the nonproductive complexes have not been elucidated. Here, we demonstrated that the excision of the CP4-57 prophage adjacent to the E. coli ssrA gene leads to the inactivation of SsrA RNA and switches the primary rescue pathway from trans-translation to the ArfA/RF2 pathway. A comparative quantitative proteomic analysis revealed that the switching of the rescue pathway rearranges not only the proteome landscape in E. coli cells but also the phenotype, such as motility. Among the proteins with significantly increased abundance in the ssrA-inactivated cells, we found ZntR, whose mRNA is transcribed together as the upstream part of the nonstop arfA mRNA. Further analysis revealed that the translation of the nonstop ORF of arfA triggered the repression of the upstream zntR ORF, via trans-translation-coupled exonucleolytic (RUTEX) degradation by a polynucleotide phosphorylase. These results provide a novel example of trans-translation-dependent regulation, and shed new light on the physiological roles of prophages in gene expression.
Neural dynamics and architecture of the heading direction circuit in a vertebrate brain
Authors: Petrucco Luigi , Lavian Hagar , Wu You Kure , Svara Fabian , Štih Vilim , Portugues Ruben
Published: April 2022

Animals can use different strategies to navigate. They may guide their movements by relying on external cues in their environment or, alternatively, by using an internal cognitive map of the space around them and their position within it. An essential part of this representation are heading cells, neurons whose activity depends on the heading direction of the animal. Although those cells have been found in vertebrates, the full network has never been observed and there is very little mechanistic understanding of how these cells acquire their response properties. In this study, we use volumetric functional imaging in larval zebrafish to observe, for the first time in a vertebrate, a full network that encodes allocentric heading direction. This network of approximately one hundred inhibitory neurons is arranged in an anatomical circle in the anterior hindbrain. Its activity is driven purely by the integration of internally generated signals, indicating that a simple vertebrate brain can encode maps of how an animal moves within its surroundings. Single cell reconstructions of electron micrographs allow us to uncover how the connectivity pattern of neurons within the network supports the implementation of a ring attractor network. The neurons we identify share features with neurons in the dorsal tegmentum nucleus of rodents and the fly central complex, showing that similar connectivity and mechanistic principles underlie the generation of cognitive maps of heading direction across the animal kingdom.
Biomolecular condensates govern PARP inhibitor trapping and present mechanisms of resistance
Authors: Gopal Angelica A. , Fernandez Bianca , Delano Justin , Weissleder Ralph , Dubach J. Matthew
Published: April 2022

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a class of cancer drugs that enzymatically inhibit PARP activity at sites of DNA damage. In the context of BRCA mutations, PARPi can be synthetically lethal, presenting ideal genetic targeting. Yet, PARPi function primarily by trapping PARP1 onto sites of DNA damage. How PARPi trap and why some are better trappers remain unknown. Here, we show trapping occurs primarily through a kinetic phenomenon within biomolecular condensates that correlates with PARPi koff. Our results suggest PARP trapping is not the physical stalling of PARP1 on DNA, rather the high probability of PARP re-binding damaged DNA in the absence of other DNA binding protein recruitment. Furthermore, we found recruitment of the DNA binding protein RPA1 correlates to cell line PARPi sensitivity independent of RPA1 expression, demonstrating that condensate recruitment alone can impact efficacy. These results shed new light on how PARPi function, describe how PARPi properties correlate to trapping potency, and suggest previously unknown mechanisms of PARPi resistance.
Variable paralog expression underlies phenotype variation
Authors: Bailon-Zambrano Raisa , Sucharov Juliana , Mumme-Monheit Abigail , Murry Matthew , Stenzel Amanda , Pulvino Anthony T. , Mitchell Jennyfer M. , Colborn Kathryn L. , Nichols James T.
Published: April 2022

Human faces are variable; we look different from one another. Craniofacial disorders further increase this variability. Here we used the zebrafish mef2ca mutant, which produces variable phenotypes, to understand craniofacial variation. Comparing different mef2ca alleles demonstrated that severity, measured by penetrance and expressivity, correlates with variation. Years of selective breeding for low and high penetrance produced strains that are either resilient, or sensitive, to the mef2ca mutation. Comparing these strains further demonstrates that severity correlates with variation. Gene expression studies indicated that selective breeding upregulated and downregulated mef2ca paralog expression in the low- and high-penetrance strains, respectively. We hypothesized that heritable paralog expression variation underlies mutant phenotype variation. In support, mutagenizing all mef2ca paralogs in the low-penetrance strain demonstrated modular buffering by paralogs. Specifically, some paralogs buffer severity while others buffer variability. We present a novel, mechanistic model for phenotypic variation where cryptic vestigial paralog expression modularly buffers development and contributes to evolution. These studies are a major step forward in understanding of the mechanisms of facial variation, including how some genetically resilient individuals can overcome a deleterious mutation.
The single-cell atlas of the murine reproductive tissues during preterm labor
Authors: Garcia-Flores Valeria , Romero Roberto , Peyvandipour Azam , Galaz Jose , Pusod Errile , Panaitescu Bogdan , Miller Derek , Xu Yi , Tao Li , Liu Zhenjie , Tarca Adi L. , Pique-Regi Roger , Gomez-Lopez Nardhy
Published: April 2022

Preterm birth, the leading cause of perinatal morbidity and mortality worldwide, frequently results from the syndrome of preterm labor. Intra-amniotic infection is the best-established causal link to preterm labor, and involves premature activation of the parturition cascade in the reproductive tissues. Herein, we utilized single-cell RNA-sequencing (scRNA-seq) to generate a single-cell atlas of the murine uterus, decidua, and cervix in a model of infection-induced preterm labor. We show that preterm labor affects the transcriptomic profiles of specific immune and non-immune cell subsets. Shared and tissue-specific gene expression signatures were identified among affected cells. Importantly, determination of intercellular communications implicates specific cell types preterm labor-associated signaling pathways across tissues. Last,in silicocomparison of murine and human uterine cell-cell interactions reveals conserved signaling pathways implicated in labor. Thus, scRNA-seq provides new insights into the preterm labor-driven cellular landscape and communications in the reproductive tissues.
Environment as a limiting factor of the historical global spread of mungbean
Authors: Ong Pei-Wen , Lin Ya-Ping , Chen Hung-Wei , Lo Cheng-Yu , Burlyaeva Marina , Noble Thomas , Nair Ramakrishnan , Schafleitner Roland , Vishnyakova Margarita , Bishop-von-Wettberg Eric , Samsonova Maria , Nuzhdin Sergey , Ting Chau-Ti , Lee Cheng-Ruei
Published: April 2022

While the domestication history has been investigated in many crops, the process of cultivation range expansion and factors governing this process received relatively little attention. Here using mungbean (Vigna radiatavar.radiata) as a test case, we investigated the genomes of more than one thousand accessions to illustrate climatic adaptation’s role in dictating the unique routes of cultivation range expansion. Despite the geographical proximity between South and Central Asia, genetic evidence suggests mungbean cultivation first spread from South Asia to Southeast, East, and finally reached Central Asia. Combining evidence from demographic inference, climatic niche modeling, plant morphology, and records from ancient Chinese sources, we showed that the specific route was shaped by the unique combinations of climatic constraints and farmer practices across Asia, which imposed divergent selection favoring higher yield in the south but short-season and more drought-tolerant accessions in the north. Our results suggest that mungbean did not radiate from the domestication center as expected purely under human activity, but instead the spread of mungbean cultivation is highly constrained by climatic adaptation, echoing the idea that human commensals are more difficult to spread through the south-north axis of continents.
Impact of freeze-thaw-induced pit aspiration on stem water transport in a subalpine conifer (Abies veitchii)
Authors: Taneda Haruhiko , Ogasa Mayumi Y. , Yazaki Kenichi , Funayama-Noguchi Sachiko , Miyazawa Yoshiyuki , Mayr Stefan , Maruta Emiko
Published: April 2022

During winter, subalpine conifers experience frequent freeze-thaw cycles in stem xylem, which may cause embolism and pit aspiration due to increased water volume during the sap to ice transition. This study examined the occurrence and ecological impacts of a combination of freeze-thaw-induced pit aspiration and embolism. In subalpine Abies veitchii trees, the fraction of closed pits and embolized tracheids as well as conductivity losses were measured to examine pit aspiration and its effects, triggered by natural and artificial stem freezing. When trees incurred mild drought stress in February and early March, 70% to 80% of stem conductivity was lost. Cryo-scanning electron microscopy indicated <20% embolized tracheids but ∼90% closed pits. Severe drought stress in late March caused 96 ± 1.2% (mean ± SE) loss of stem conductivity, while the fraction of embolized tracheids increased to 64 ± 6.6%, and aspirated pit fraction decreased to 23 ± 5.6%. Experimental freeze-thaw cycles also induced from 7.1 ± 0.89% to 49 ± 10% pit aspiration, and the fraction of closed pits was positively correlated to the percent loss of stem hydraulic conductivity. Results indicated that freezing-induced pit aspiration is an important factor for stem xylem dysfunction under mild drought. Upon severe drought in winter, stem water transport is predominantly inhibited by xylem embolism.
Drosophila Keap1 oxidative/xenobiotic response factor interacts with B-type lamin to regulate nuclear lamina and heterochromatin
Authors: Carlson Jennifer , Neidviecky Emma , Cook Isabel , Deng Huai
Published: April 2022

The essential function of the Keap1-Nrf2 pathway in mediating transcriptional response to xenobiotic and oxidative stimuli has been well established. However, the mechanisms whereby Keap1 and Nrf2 regulate developmental genes remains unclear. We hypothesized that Drosophila Keap1 (dKeap1) and Nrf2 (CncC) proteins regulate transcription through controlling high-order chromatin structure. Here, we describe evidence supporting that dKeap1 can regulate chromatin through interaction with lamin, the intermediate filament proteins that form nuclear lamina and organize the overall chromatin architecture. dKeap1 and lamin Dm0, the B-type lamin in Drosophila, interact with each other and form complexes in the nucleus. Overexpression of dKeap1 resulted in a redistribution of lamin Dm0 to the intra-nuclear area and consistently, caused a spreading of the heterochromatin marker H3K9me2 from the pericentromeric region to chromosome arms. Overexpression of dKeap1 fusion proteins in the dKeap1 null background significantly disrupted the nuclear lamina morphology, indicating that dKeap1 is required for the maintenance of a normal nuclear lamina. Knock down of dKeap1 partially rescued the lethality caused by lamin Dm0 overexpression, suggesting that dKeap1 and lamin Dm0 function in the same pathway during development. Taken together, these results support a model where dKeap1 regulates chromatin structure and developmental transcription through interaction with lamin proteins, revealing a novel epigenetic function of the Keap1 oxidative/xenobiotic response factor.
A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage
Authors: Lau Rebecca K. , Enustun Eray , Gu Yajie , Nguyen Justin V. , Corbett Kevin D.
Published: April 2022

To protect themselves from the constant threat of bacteriophage (phage) infection, bacteria have evolved diverse immune systems including restriction/modification, CRISPR/Cas, and many others. Here we describe the discovery of a two-protein transcriptional regulator module associated with hundreds of CBASS (Cyclic oligonucleotide Based Anti-phage Signaling System) immune systems, and demonstrate that this module drives expression of its associated CBASS system in response to DNA damage. We show that the helix-turn-helix transcriptional repressor CapH binds the promoter region of its associated CBASS system to repress transcription until it is cleaved by the metallopeptidase CapP. CapP is inactive except in the presence of single-stranded DNA, and CapP activity in cells is stimulated by DNA-damaging drugs. Together, CapH and CapP drive increased expression of their associated CBASS system in response to DNA damage. In both their structures and mechanisms, CapH and CapP resemble regulators that drive increased expression of DNA damage response genes in radiation-resistant Deinococcus, and control the mobilization of prophages and mobile elements in response to DNA damage. We also identify CapH and CapP-related proteins associated with diverse known and putative bacterial immune systems, including DISARM and two uncharacterized operons encoding proteins related to eukaryotic ubiquitin signaling pathways. Overall, our data highlight a mechanism by which bacterial immune systems can sense and respond to a universal stress signal, potentially enabling multiple immune systems to mount a coordinated defensive effort against an invading pathogen.
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
Authors: Wright Robyn J. , Comeau André M. , Langille Morgan G.I.
Published: April 2022

In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are “best”, there are two tools that have been used the most to-date: Kraken (k-mer based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool-parameter-database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all “best” choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool-parameter-database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.
Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics
Authors: Frankenfield Ashley M. , Ni Jiawei , Ahmed Mustafa , Hao Ling
Published: April 2022

Mass spectrometry-based proteomics is constantly challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are often abundant and almost impossible to avoid. For data-dependent acquisition (DDA) proteomics, exclusion list can be used to reduce the influence of protein contaminants. However, protein contamination has not been evaluated and is rarely addressed in data-independent acquisition (DIA). How protein contaminants influence proteomics data is also unclear. In this study, we established protein contaminant FASTA and spectral libraries that are applicable to all proteomic workflows and evaluated the impact of protein contaminants on both DDA and DIA proteomics. We demonstrated that including our contaminant libraries can reduce false discoveries and increase protein identifications, without influencing the quantification accuracy in various proteomic software platforms. With the pressing need to standardize proteomic workflow in the research community, we highly recommend including our contaminant FASTA and spectral libraries in all bottom-up proteomics workflow. Our contaminant libraries and a step-by-step tutorial to incorporate these libraries in different DDA and DIA data analysis platforms can be valuable resources for proteomics researchers, which are freely accessible at https://github.com/HaoGroup-ProtContLib.
The conserved histone chaperone Spt6 facilitates DNA replication and mediates genome instability
Authors: Miller Catherine LW , Winston Fred
Published: April 2022

Histone chaperones are an important class of proteins that regulate chromatin accessibility for DNA-templated processes. Spt6 is a conserved histone chaperone and key regulator of transcription and chromatin structure. However, its functions outside of these roles have been little explored. In this work, we demonstrate a role for S. cerevisiae Spt6 in DNA replication and more broadly as a regulator of genome stability. Spt6 binds the replication machinery and depletion or mutation of Spt6 impairs DNA replication in vivo. Additionally, spt6 mutants are sensitive to DNA replication stress inducing agents, with increased sensitivity when combined with loss of DNA replication associated factors. Furthermore, spt6 mutants have elevated levels of DNA double strand breaks and recombination. These effects appear to be independent of R-loops, which are not elevated in spt6 mutants. Our results identify Spt6 as a regulator of genome stability, at least in part through a role in DNA replication.
RISKS OF NEONATAL MORTALITY IN NEONATES WITH NEONATAL ENCEPHALOPATHY IN A TERTIARY NEWBORN CARE UNIT IN ZIMBABWE OVER A 12-MONTH PERIOD
Authors: Gannon Hannah , Chimhini Gwen , Cortina-Borja Mario , Chiyaka Tarisai , Mangiza Marcia , Fitzgerald Felicity , Heys Michelle , Neal Sam , Chimhuya Simbarashe
Published: April 2022

Background

Neonatal encephalopathy (NE) accounts for ∼23% of the 2.4 million annual global neonatal deaths. Most of these deaths occur in sub-Saharan Africa. However, data from low resource settings are scarce. We reviewed risk factors of neonatal mortality in neonates admitted with NE from a tertiary neonatal unit in Zimbabwe.

Methods

A retrospective review of risk factors of short-term NE mortality was conducted at Sally Mugabe Central Hospital (SMCH) (November 2018 – October 2019). Data were gathered using a tablet-based data capture and quality improvement newborn care application (Neotree). Analyses were performed on data from all admitted neonates with a diagnosis of NE, incorporating maternal, intrapartum and neonatal risk predictors of the primary outcome, mortality.

Results

494/2894 neonates had NE on admission and were included. Of these, 94 died giving a NE-case fatality rate (CFR) of 190 per 1000 admitted neonates. Caesarean section (odds ratio (OR) 2.95(95% confidence intervals (CI) 1.39-6.25), convulsions (OR 7.13 (1.41-36.1)), lethargy (OR 3.13 (1.24-7.91)), Thompson score “11-14” (OR 2.98 (1.08-8.22)) or “15-22” (OR 17.61 (1.74-178.0)) were significantly associated with neonatal death. No maternal risk factors were associated with mortality.

Conclusion

Nearly 1 in 5 neonates diagnosed with NE died before discharge, similar to other low-resource setting but more than in typical high resource centres. The Thompson score, a validated, sensitive and specific tool for diagnosing neonates with NE was a good predictor of worse outcomes in this setting. On univariable analysis time-period, specifically a period of staff shortages due to industrial action, had a significant impact on NE mortality. Emergency caesarean section was associated with increased mortality, suggesting perinatal care is likely to be a key moment for future interventions
Updating mortality risk estimation in intensive care units from high-dimensional electronic health records with incomplete data
Authors: Bouvarel Bertrand , Carrat Fabrice , Lapidus Nathanael
Published: April 2022

Context

Intensive care units (ICU) are subject to a high mortality rate, currently addressed by the implementation of scores (SAPS II, SOFA, APACHE II) assessing the risk of in-hospital mortality from admission data. Their performances are satisfactory to predict death when complications occur early after admission; however, they may become irrelevant in the case of long hospital stays.

Methods

Using the MIMIC-III database, we developed predictive models of short-term mortality in ICU from longitudinal data collected throughout patients’ stays of at least 48 hours. Several statistical learning approaches were compared, including deep neural networks and penalized regression. Missing data were handled using either complete case analysis or multiple imputation. Models’ performances were evaluated via repeated 5-fold cross-validation.

Results

Predictions relying on longitudinal data were more accurate than those relying solely on admission data. Complete case analyses from 19 predictors showed good discrimination (area under the ROC curve [AUC] > 0.77 for several statistical learning approaches) to predict death between 12 and 24 hours onwards, while keeping only 25% of patients in the sample. Multiple imputation allowed to include 70 predictors and keep 95% of patients, with similar performances, hence allowing predictions in patients with incomplete data. Calibration was satisfactory for all models.

Discussion

This proof of concept supports that automated analysis of electronic health records can be of great interest throughout patients’ stays, as a surveillance tool likely to detect lethal complications in ICU soon enough to take corrective measures. Though this framework relies on a large set of predictors, it is robust to data imputation and may be effective early after admission, as data is still scarce.
Cross-sectional association of skeletal muscle mass and strength with dietary habits and physical activity among first-year university students in Japan: Results from KEIJI-U study
Authors: Kusakabe Toru , Arai Hiroshi , Yamamoto Yuji , Nakao Kazuwa , Akamatsu Yasunori , Ishihara Yuki , Tagami Tetsuya , Yasoda Akihiro , Satoh-Asahara Noriko
Published: April 2022

Background

Recently, the high prevalence of young Japanese people who are underweight has received attention because of its potential impact on healthy life expectancy. Sarcopenia, defined as the presence of low muscle mass and function, is often observed in the underweight. However, few reports have described the prevalence and characteristics of sarcopenia in youth.

Methods

In this cross-sectional study, we measured skeletal muscle mass using a multifrequency bioelectrical impedance analysis device and handgrip strength (HGS) and administered questionnaires on dietary habits and physical activity to 1,264 first-year university students aged 18-20 years (838 males and 426 females). Sarcopenia was diagnosed based on the presence of both low skeletal muscle mass (SMI) and weak HGS according to the Asian Working Group for Sarcopenia.

Results

A total of 145 males (17.3%) and 69 females (16.2%) were diagnosed as underweight. Low SMI was diagnosed in 75 males (8.9%) and 18 females (4.2%), and weak HGS was diagnosed in 28 males (3.3%) and 10 females (2.3%). Then, sarcopenia was diagnosed in 8 males (1.0%) and 5 females (1.2%). There was a significantly higher prevalence of low SMI and/or weak HGS in underweight individuals compared with individuals in the other BMI ranges. The multivariate analyses indicated that SMI and HGS were significantly associated with BMI in both sexes. Furthermore, after adjusting for BMI, both SMI and HGS were significantly associated with physical activity in males, and SMI was significantly associated with energy intake and frequency of breakfast intake in females.

Conclusions

First-year university students showed a high incidence of being underweight with low SMI and/or weak HGS, but the prevalence of sarcopenia was low in both sexes. BMI, energy intake, frequency of breakfast intake, and physical activity were independently associated with skeletal muscle mass and strength in youth.
The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype
Authors: Barut Tuba , Halwe Nico Joel , Taddeo Adriano , Kelly Jenna N. , Schön Jacob , Ebert Nadine , Ulrich Lorenz , Devisme Christelle , Steiner Silvio , Trüeb Bettina Salome , Hoffmann Bernd , Veiga Inês Berenguer , Leborgne Nathan Georges François , Moreira Etori Aguiar , Breithaupt Angele , Wylezich Claudia , Höper Dirk , Wernike Kerstin , Godel Aurélie , Thomann Lisa , Flück Vera , Stalder Hanspeter , Brügger Melanie , Esteves Blandina I. Oliveira , Zumkehr Beatrice , Beilleau Guillaume , Kratzel Annika , Schmied Kimberly , Ochsenbein Sarah , Lang Reto M. , Wider Manon , Machahua Carlos , Dorn Patrick , Marti Thomas M. , Funke-Chambour Manuela , Rauch Andri , Widera Marek , Ciesek Sandra , Dijkman Ronald , Hoffmann Donata , Alves Marco P. , Benarafa Charaf , Beer Martin , Thiel Volker
Published: April 2022

Variant of concern (VOC) Omicron-BA1 has achieved global predominance in early 2022. Therefore, surveillance and comprehensive characterization of Omicron-BA.1 in advanced primary cell culture systems and multiple animal models is urgently needed. Here, we characterized Omicron-BA.1 and recombinant Omicron-BA.1 spike gene mutants in comparison with VOC Delta in well-differentiated primary human nasal and bronchial epithelial cells in vitro, followed by in vivo fitness characterization in naïve hamsters, ferrets and hACE2-expressing mice, and in immunized hACE2-mice. We demonstrate a spike-mediated enhancement of early replication of Omicron-BA.1 in nasal epithelial cultures, but limited replication in bronchial epithelial cultures. In Syrian hamsters, Delta showed dominance over Omicron-BA.1 and in ferrets, Omicron-BA.1 infection was abortive. In mice expressing the authentic hACE2-receptor, Delta and a Delta spike clone also showed dominance over Omicron-BA.1 and an Omicron-BA.1 spike clone, respectively. Interestingly, in naïve K18-hACE2 mice, we observed Delta spike-mediated increased replication and pathogenicity and Omicron-BA.1 spike-mediated reduced replication and pathogenicity, suggesting that the spike gene is a major determinant of both Delta and Omicron-BA.1 replication and pathogenicity. Finally, the Omicron-BA.1 spike clone was less well controlled by mRNA-vaccination in K18-hACE2-mice and became more competitive compared to the progenitor and Delta spike clones, suggesting that spike gene-mediated immune evasion is another important factor that led to Omicron-BA.1 dominance.
ST6GAL1 sialyltransferase promotes acinar to ductal metaplasia and pancreatic cancer progression
Authors: Chakraborty Asmi , Bhalerao Nikita , Marciel Michael P. , Hwang Jihye , Britain Colleen M. , Eltoum Isam E. , Jones Robert B. , Alexander Katie L. , Smythies Lesley E. , Smith Phillip D. , Crossman David K. , Crowley Michael R. , Shin Boyoung , Harrington Laurie E. , Yan Zhaoqi , Bethea Maigen M. , Hunter Chad S. , Klug Christopher A. , Buchsbaum Donald J. , Bellis Susan L.
Published: April 2022

The role of aberrant glycosylation in pancreatic ductal adenocarcinoma (PDAC) remains an under-investigated area of research. In this study, we determined that the ST6GAL1 sialyltransferase, which adds α2,6-linked sialic acids to N-glycosylated proteins, is upregulated in patients with early-stage PDAC, and further increased in advanced disease. A tumor-promoting function for ST6GAL1 was elucidated using tumor xenograft models with human PDAC cells. Additionally, we developed a genetically-engineered mouse (GEM) with transgenic expression of ST6GAL1 in the pancreas, and found that mice with dual expression of ST6GAL1 and oncogenic KRASG12D have greatly accelerated PDAC progression and mortality compared with mice expressing KRASG12D alone. As ST6GAL1 imparts progenitor-like characteristics, we interrogated ST6GAL1’s role in acinar to ductal metaplasia (ADM), a process that fosters neoplasia by reprogramming acinar cells into ductal, progenitor-like cells. We confirmed that ST6GAL1 promotes ADM using multiple models including the 266-6 cell line, GEM-derived organoids and tissues, and an in vivo model of inflammation-induced ADM. EGFR is a key driver of ADM and is known to be activated by ST6GAL1-mediated sialylation. Importantly, EGFR activation was dramatically increased in acinar cells and organoids from mice with transgenic ST6GAL1 expression. These collective results highlight a novel glycosylation-dependent mechanism involved in early stages of pancreatic neoplasia.
Sensory regulation of absence seizures in a mouse model of Gnb1 encephalopathy
Authors: Teng Sasa , Zhen Fenghua , McRae Briana R. , Zhu Elaine , Frankel Wayne N. , Peng Yueqing
Published: April 2022

Absence seizures, a type of non-convulsive epilepsy manifested by spike-wave discharges (SWD) in the electroencephalogram (EEG), display synchronous reciprocal excitation between the neocortex and thalamus. Recent studies have revealed that inhibitory neurons in the reticular thalamic (RT) nucleus and excitatory thalamocortical (TC) neurons are two key subcortical players in generating SWD. However, the signals that drive SWD-related thalamic activity remain elusive. Here, we show that SWD predominately occurs during wakefulness in several mouse models of absence epilepsy. In more focused studies of Gnb1 mutant mice, we found that sensory input regulates SWD. Using in vivo recording, we demonstrate that TC cells are activated prior to the onset of SWD and then inhibited during SWD. On the contrary, RT cells are slightly inhibited prior to SWD, but are strongly activated during SWD. Furthermore, chemogenetic activation of TC cells leads to the enhancement of SWD in Gnb1 mice. Together, our results indicate that sensory input in the periphery can regulate SWD by activating the thalamocortical pathway.
An auto-inhibited state of protein kinase G and implications for selective activation
Authors: Sharma Rajesh , Kim Jeong Joo , Qin Liying , Henning Philipp , Akimoto Madoka , VanSchouwen Bryan , Kaur Gundeep , Sankaran Banumathi , MacKenzie Kevin R. , Melacini Giuseppe , Casteel Darren E. , Herberg Friedrich W. , Kim Choel
Published: April 2022

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cGMP signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Campaigns targeting nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis suggest that understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is still not well understood. Here we present a crystal structure of PKG Iβ in which the auto-inhibitory sequence and the cyclic nucleotide binding domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ auto-inhibitory sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I cyclic nucleotide binding domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wild type cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and activation of PKGs.