bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arrayed CRISPRi library to suppress genes required forSchizosaccharomyces pombeviability
Authors: Ishikawa Ken , Soejima Saeko , Nishimura Takashi , Saitoh Shigeaki 
Published: March 2024

SummaryThe fission yeast,Schizosaccharomyces pombe,is an excellent eukaryote model organism to study essential biological processes. Its genome contains ∼1200 genes essential for cell viability, most of which are evolutionarily conserved. To study these essential genes, resources enabling conditional perturbation of target genes are required. Here, we constructed comprehensive arrayed libraries of plasmids and strains to knock down essential genes inS. pombe, using a dCas9-mediated CRISPRi. These libraries cover ∼98% of all essential genes in fission yeast. We estimate that in ∼60% of the strains in the library, transcription of a target gene was repressed so efficiently that cell proliferation was significantly inhibited. To demonstrate usefulness of these libraries, we performed metabolic analyses with knockdown strains and revealed a flexible interaction among metabolic pathways. Libraries established in this study enable comprehensive functional analyses of essential genes inS. pombeand will facilitate understanding of essential biological processes in eukaryotes.
The host genotype actively shapes its microbiome across generations in laboratory mice
Authors: Benga Laurentiu , Rehm Anna , Gougoula Christina , Westhoff Philipp , Wachtmeister Thorsten , Benten W. Peter M. , Engelhardt Eva , Weber Andreas P.M. , Köhrer Karl , Sager Martin , Janssen Stefan 
Published: March 2024

AbstractBackgroundThe microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.ResultsTo further dissect the influence of host genetics and maternal inheritance, we collected 2-cell stage embryos from two representative wildtypes, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.ConclusionsObserving the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate.graphical abstract
Comparison of Single-cell Long-read and Short-read Transcriptome Sequencing of Patient-derived Organoid Cells of ccRCC: Quality Evaluation of the MAS-ISO-seq Approach
Authors: Zajac Natalia , Zhang Qin , Bratus-Neuschwander Anna , Qi Weihong , Bolck Hella Anna , Karakulak Tülay , Oltra Tamara Carrasco , Moch Holger , Kahraman Abdullah , Rehrauer Hubert 
Published: March 2024

AbstractSingle-cell RNA sequencing is used in profiling gene expression differences between cells. Short-read sequencing platforms provide high throughput and high-quality information at the gene-level, but the technique is hindered by limited read length, failing in providing an understanding of the cell heterogeneity at the isoform level. This gap has recently been addressed by the long-read sequencing platforms that provide the opportunity to preserve full-length transcript information during sequencing. To objectively evaluate the information obtained from both methods, we sequenced four samples of patient-derived organoid cells of clear cell renal cell carcinoma and one healthy sample of kidney organoid cells on Illumina Novaseq 6000 and PacBio Sequel IIe. For both methods, for each sample, the cDNA was derived from the same 10x Genomics 3’ single-cell gene expression cDNA library. Here we present the technical characteristics of both datasets and compare cell metrics and gene-level information. We show that the two methods largely overlap in the results but we also identify sources of variability which present a set of advantages and disadvantages to both methods.
Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data
Authors: Haag Julia , Jordan Alexander I. , Stamatakis Alexandros 
Published: March 2024

AbstractMotivationGenotype datasets typically contain a large number of single nucleotide polymorphisms for a comparatively small number of individuals. To identify similarities between individuals and to infer an individual’s origin or membership to a population, dimensionality reduction techniques are routinely deployed. However, inherent (technical) difficulties such as missing or noisy data need to be accounted for when analyzing a lower dimensional representation of genotype data, and the intrinsic uncertainty of such analyses should be reported in all studies. However, to date, there exists no stability assessment technique for genotype data that can estimate this uncertainty.ResultHere, we present Pandora, a stability estimation framework for genotype data based on bootstrapping. Pandora computes an overall score to quantify the stability of the entire embedding, infers per-individual support values, and also deploys ak-means clustering approach to assess the uncertainty of assignments to potential cultural groups. Using published empirical and simulated datasets, we demonstrate the usage and utility of Pandora for studies that rely on dimensionality reduction techniques.Availability and ImplementationPandora is available on GitHubhttps://github.com/tschuelia/Pandora.Contactjulia.haag@h-its.orgSupplementary informationSupplementary data are available online.
Phylogeny-aware modeling uncovers molecular functional convergences associated with complex multicellularity in Eukarya
Authors: Pereira Lobo Francisco , Benjamim da Costa Dalbert , Martins da Silva Thieres Tayroni , de Oliveira Maycon Douglas 
Published: March 2024

AbstractA major trait of Eukarya is the independent evolution of complex multicellular lineages of animals and plants with specialized cell types organized in tissues, organs and systems. The number of cell types (NCT) has been commonly adopted as a proxy in comparative studies investigating the genomic evolution of biological complexity. Although expansions of homologous genes playing roles in extracellular processes, signal transduction pathways, and the immune system have been reported as associated with NCT variation in metazoans, the evolutionary patterns coordinating the genomic evolution of multicellularity throughout Eukarya remain poorly understood. We used Gene Ontology (GO) as a genome annotation scaffold to represent biological functions shared by genes regardless of their homology relationships to search for molecular functional convergences associated with NCT. For that we integrated phenotypic, genomic, annotation and phylogenetic data to build phylogeny-aware models and searched for expansions of homologous regions and of GO terms associated with NCT values across 49 eukaryotic species, including complex multicellular plants and metazoans. Virtually all homologous regions associated with NCT are metazoan- and vertebrate-specific expansions of paralogs with key roles in developmental pathways. The functional annotation, in contrast, detected previously unknown biological themes coded by non-homologous genes independently expanded in multicellular plants and metazoans, such as system and anatomical development, immunity, regulatory mechanisms of embryogenesis, response to external stimuli and detection of natural rhythmic processes. Our findings unveil functional molecular convergences shared by these contrasting groups due to common selective pressures in the lifestyle of complex multicellular lineages.
Lysine-Cysteine-Serine-Tryptophan Inserted into the DNA-Binding Domain of Human Mineralocorticoid Receptor Increases Transcriptional Activation by Aldosterone
Authors: Katsu Yoshinao , Zhang Jiawen , Baker Michael E. 
Published: March 2024

AbstractDue to alternative splicing in an ancestral DNA-binding domain (DBD) of the mineralocorticoid receptor (MR), humans contain two almost identical MR transcripts with either 984 amino acids (MR-984) or 988 amino acids (MR-988), in which their DBDs differ by only four amino acids, Lys,Cys,Ser,Trp (KCSW). Human MRs also contain mutations at two sites, codons 180 and 241, in the amino terminal domain (NTD). Together, there are five distinct full-length human MR genes in GenBank. Human MR-984, which was cloned in 1987, has been extensively studied. Human MR-988, cloned in 1995, contains KCSW in its DBD. Neither this human MR-988 nor the other human MR-988 genes have been studied for their response to aldosterone and other corticosteroids. Here, we report that transcriptional activation of human MR-988 by aldosterone is increased by about 50% compared to activation of human MR-984 in HEK293 cells transfected with the TAT3 promoter, while the half-maximal response (EC50) is similar for aldosterone activation of MR-984 and MR-988. Transcriptional activation of human MR also depends on the amino acids at codons 180 and 241. Interestingly, in HEK293 cells transfected with the MMTV promoter, transcriptional activation by aldosterone of human MR-988 is similar to activation of human MR-984, indicating that the promoter has a role in the regulation of the response of human MR-988 to aldosterone. The physiological responses to aldosterone and other corticosteroids in humans with MR genes containing KCSW and with differences at codons 180 and 241 in the NTD warrant investigation.
Transcription factor prediction using protein 3D secondary structures
Authors: Liebold Jeanine , Neuhaus Fabian , Geiser Janina , Kurtz Stefan , Baumbach Jan , Newaz Khalique 
Published: March 2024

AbstractMotivationTranscription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs. Recently proposed TF prediction methods do not rely on DBDs. Such methods use features of protein sequences to train a machine learning model, and then use the trained model to predict whether a protein is a TF or not. Because the 3-dimensional (3D) structure of a protein captures more information than its sequence, using 3D protein structures will likely allow for more accurate prediction of novel TFs.ResultsWe propose a deep learning-based TF prediction method(StrucTFactor), which is the first method to utilize 3D secondary structural information of proteins. We compare StrucTFactor with recent state-of-the-art TF prediction methods based on∼525 000 proteins across 12 datasets, capturing different aspects of data bias (including sequence redundancy) possibly influencing a method’s performance. We find that StrucTFactor significantly (p-value<0.001) outperforms the existing TF prediction methods, improving the performance over its closest competitor by up to 17% based on Matthews correlation coefficient.AvailabilityData and source code are available athttps://github.com/lieboldj/StrucTFactorand on our website athttps://apps.cosy.bio/StrucTFactor/Contactkhalique.newaz@uni-hamburg.deSupplementary informationIncluded
Optimizing Design of Genomics Studies for Clonal Evolution Analysis
Authors: Srivatsa Arjun , Schwartz Russell 
Published: March 2024

AbstractGenomic biotechnologies have seen rapid development over the past two decades, allowing for both the inference and modification of genetic and epigenetic information at the single cell level. While these tools present enormous potential for basic research, diagnostics, and treatment, they also raise difficult issues of how to design research studies to deploy these tools most effectively. In designing a study at the population or individual level, a researcher might combine several different sequencing modalities and sampling protocols, each with different utility, costs, and other tradeoffs. The central problem this paper attempts to address is then how one might create an optimal study design for a genomic analysis, with particular focus on studies involving somatic variation, typically for applications in cancer genomics. We pose the study design problem as a stochastic constrained nonlinear optimization problem and introduce a simulation-centered optimization procedure that iteratively optimizes the objective function using surrogate modeling combined with pattern and gradient search. Finally, we demonstrate the use of our procedure on diverse test cases to derive resource and study design allocations optimized for various objectives for the study of somatic cell populations.
Epidemiological, Serological, and Virological Analysis of an Outbreak of Elephant Hemorrhagic Disease in Switzerland
Authors: Ackermann Mathias , Kubacki Jakub , Heaggans-Ebbeson Sarah , Hayward Gary S. , Lechmann Julia 
Published: March 2024

AbstractElephant hemorrhagic disease (EHD), caused by several Elephant endotheliotropic herpesviruses (EEHV), represents a frequently lethal syndrome, affecting both captive and free-living elephants. In summer 2022, three young Asian elephants (Elephas maximus) succumbed to EHD in a zoo in Switzerland, despite of considerable preventive efforts and early detection of EEHV1A viremia. In this communication, we describe the extent of preventive measures in terms of prior virus detection, active survey of viremia, and antibody status. In the course of the outbreak, the causative virus was concomitantly analyzed and eventually fully sequenced and compared to other EEHV types and strains.The conclusions from these analyses may be summarized in three points: (1) A previously undetected EEHV1A strain had remained unrecognized among these elephants. Probably, the new virus re-emerged after almost 40 years of latency from one of the oldest elephants in the zoo. (2) While two of the three affected animals had prior immune responses against EEHV1, their strain-specific immunity proved insufficient to prevent EHD. (3) There is an urgent need to develop efficient antiviral drugs and protective vaccines. In particular, ways need to be found to circumvent the present unavailability of appropriate cell cultures and animal models.
Crosstalk of the MAP3K1 and EGFR pathways mediates gene-environment interactions that disrupt developmental tissue closure
Authors: Wang Jingjing , Xiao Bo , Kimura Eiki , Mongan Maureen , Hsu Wei-Wen , Medvedovic Mario , Puga Alvaro , Xia Ying 
Published: March 2024

AbstractAberrant signal transduction pathways can adversely derail developmental processes. One such process is embryonic eyelid closure that requires MAP3K1.Map3k1knockout mice have defective eyelid closure and an autosomal recessive eye-open at birth phenotype.In uteroexposure to dioxin, a persistent environmental toxicant, causes the same eye defect inMap3k1+/-hemizygous but not wild type pups. Here we explore the mechanisms ofMap3k1(gene) and dioxin (environment) interactions (GxE) in the tissue closure defect. We show that, acting through the AHR, dioxin activates EGFR signaling, which in turn depresses MAP3K1-dependent JNK activity. This effect of dioxin is exacerbated byMap3k1heterozygosity. Therefore, dioxin exposedMap3k1+/-embryonic eyelids have a marked reduction of JNK activity, accelerated differentiation and impeded polarization in the epithelial cells. Knocking outAhrorEgfrin eyelid epithelium attenuates the open-eye defects in dioxin-treatedMap3k1+/-pups, whereas knockout ofJnk1andS1pr, encoding the S1P receptors upstream of the MAP3K1-JNK pathway, potentiates dioxin toxicity. Our novel findings suggest that dioxin and genes of the AHR, EGFR and S1P-MAP3K1-JNK pathways constitute a multifactorial mechanism underlying tissue closure abnormalities.Summary statementThe crosstalk between a global environmental pollutant and the pre-existing genetic conditions is mediated through interactive signaling pathways, resulting in anatomical tissue closure abnormalities in development.
BAK knockdown delays bleaching and alleviates oxidative DNA damage in a reef-building coral
Authors: Majerová Eva , Steinle Camryn , Drury Crawford 
Published: March 2024

AbstractClimate change is rapidly pushing coral reefs towards extinction. Efforts to restore and protect these ecosystems using resilient corals are increasing, but our understanding of cellular mechanisms of thermal resilience and trade-offs remains limited. Here, we demonstrate downregulation of pa-BAK slows bleaching and stabilizes the symbiosis during acute heat stress inPocillopora acuta. Counterintuitively, oxidative DNA damage – a hallmark of the thermal stress response in corals – was prevented in corals with such “forced” symbiosis stability, possibly through alterations in mitochondrial ROS release. Using expression data of genes representing various stress-response pathways, we propose a model that coral heat stress response is mediated via the AMPK/Foxo3/Nrf2 signaling network. Developing our understanding of heat-stress defense mechanisms promoting stability in the coral-algal symbiosis is fundamental for effective modern coral reef restoration practices based on improving system resilience.
Interventions for the management of post COVID-19 condition (long COVID): Protocol for a living systematic review & network meta-analysis
Authors: Zeraatkar Dena , Ling Michael , Kirsh Sarah , Jassal Tanvir , Pitre Tyler , Chakraborty Samantha , Turner Tari , Turkstra Lyn , McIntyre Roger S. , Izcovich Ariel , Mbuagbaw Lawrence , Agoritsas Thomas , Flottorp Signe A. , Garner Paul , Couban Rachel , Busse Jason W. 
Published: March 2024

AbstractBackgroundUp to 15% of survivors of COVID-19 infection experience long-term health effects, including fatigue, myalgia, and impaired cognitive function, termed post COVID-19 condition or long COVID. Several trials that study the benefits and harms of various interventions to manage long COVID have been published and hundreds more are planned or are ongoing. Trustworthy systematic reviews that clarify the benefits and harms of interventions are critical to promote evidence-based practice.ObjectiveTo create and maintain a living systematic review and network meta-analysis addressing the benefits and harms of pharmacologic and non-pharmacologic interventions for the treatment and management of long COVID.MethodsEligible trials will randomize adults with long COVID, to pharmacologic or non-pharmacologic interventions, placebo, sham, or usual care. We will identify eligible studies by searches of MEDLINE, EMBASE, CINAHL, PsycInfo, AMED, and CENTRAL, from inception, without language restrictions.Reviewers will work independently and in duplicate to screen search records, collect data from eligible trials, including trial and patient characteristics and outcomes of interest, and assess risk of bias. Our outcomes of interest will include fatigue, pain, post-exertional malaise, changes in education or employment status, cognitive function, mental health, dyspnea, quality of life, patient-reported physical function, recovery, and serious adverse events.For each outcome, when possible, we will perform a frequentist random-effects network meta-analysis. When there are compelling reasons to suspect that certain interventions are only applicable or effective for a subtype of long COVID, we will perform separate network meta-analyses. The GRADE approach will guide our assessment of the certainty of evidence.We will update our living review biannually, upon the publication of a seminal trial, or when new evidence emerges that may change clinical practice.ConclusionThis living systematic review and network meta-analysis will provide comprehensive, trustworthy, and up-to-date summaries of the evidence addressing the benefits and harms of interventions for the treatment and management of long COVID. We will make our findings available publicly and work with guideline producing organizations to inform their recommendations.
Genetic variation inHIF1Ais associated with smoldering inflammation and disease progression in Multiple Sclerosis
Authors: Giordano Antonino , Stridh Pernilla , Preziosa Paolo , Pisa Marco , Sorosina Melissa , Mascia Elisabetta , Santoro Silvia , Misra Kaalindi , Clarelli Ferdinando , Ferrè Laura , Needhamsen Maria , Manouchehrinia Ali , Cannizzaro Miryam , Moridi Thomas , Shchetynsky Klementy , Ouellette Russell , Harroud Adil , Sandberg Elisabeth , Kuttikkatte Subita Balaram , Piehl Fredrik , Alfredsson Lars , Hillert Jan , Olsson Tomas , Fugger Lars , Attfield Kate , Granberg Tobias , Jagodic Maja , DeLuca Gabriele Carmine , Rocca Mara , Filippi Massimo , Kockum Ingrid , Esposito Federica 
Published: March 2024

ABSTRACTBackgroundUnderstanding the mechanisms underlying disease progression in Multiple Sclerosis (MS) is fundamental to pave the way to treatment advances. Smoldering demyelinating inflammation characterized by iron deposition is observed at the edges of chronic active lesions and represents a relevant substrate of disease progression in MS. However, the influence of genetic factors on these mechanisms is not known. Leveraging the importance of iron deposition in smoldering inflammation, we assessed whether variants in genes belonging to iron-related pathways affect disease progression in MS.MethodsWe investigated the association between Single Nucleotide Polymorphisms (SNPs) mapping to 334 genes in iron-related pathways and the risk of disease progression, studying 2,817 MS patients from Italy (n=755) and Sweden (n=2,062), and comparing relapsing-remitting (RR-MS) with secondary progressive (SP-MS) disease course. To better understand the link of the identified variant with smoldering inflammation, we applied a multilayered approach using independent cohorts from Italy, Sweden and the United Kingdom and encompassing gene expression, PRL analysis, neurofilament levels, post-mortem spinal cord pathology and pharmacogenomics.ResultsWe found an association between a locus in the Hypoxia-Inducible Factor 1-alpha (HIF1A) gene and the odds of SP-MS transition in the Italian cohort (rs11621525; SP-MS OR 0.57, 95% CI 0.44-0.72; P=3.30×10-6), which was replicated in the Swedish dataset (rs1951795; OR 0.79, 95% CI 0.67-0.95; P=0.0079). Additional analyses showed that patients carrying the protective allele exhibited reducedHIF1Aexpression in the immune cells, lower PRL volume, lower plasma/cerebrospinal fluid neurofilament levels, and lower inflammation and acute axonal injury in the post-mortem spinal cord. Moreover, the variant influenced the response to dimethyl fumarate, an approved MS drug with effect on mechanisms shared withHIF1Apathway.ConclusionA novel locus in theHIF1Agene, a crucial hub for iron-binding capacity, inflammation, and hypoxia response, is associated with the risk of disease progression in MS. Converging lines of evidence support the role of this locus in smoldering inflammation, prompting future studies to explore the potential ofHIF1Aas a therapeutic target in progressive MS.