bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale
Authors: Saunders Lauren M. , Srivatsan Sanjay R. , Duran Madeleine , Dorrity Michael W. , Ewing Brent , Linbo Tor , Shendure Jay , Raible David W. , Moens Cecilia B. , Kimelman David , Trapnell Cole
Published: August 2022

The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data, however, has been collected from wild type embryos without an appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos, encompassing 19 time points, 23 genetic perturbations, and totaling 3.2M cells. The high degree of replication in our study (8 or more embryos per condition) allows us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types, resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons, a cell population that comprises less than 1% of the embryo. Additionally, time-series profiling of individual mutants identified a group of brachyury-independent cells with strikingly similar transcriptomes to notochord sheath cells, leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high-resolution, organism-scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types, while also addressing long-standing challenges in developmental genetics, including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals.
Choice of climate data influences current and future global invasion risks for twoPhelsumageckos
Authors: Dubos Nicolas , Fieldsend Thomas W. , Roesch Markus A. , Augros Stéphane , Besnard Aurélien , Choeur Arthur , Ineich Ivan , Krysko Kenneth , Leroy Boris , Malone Sparkle L. , Probst Jean-Michel , Raxworthy Christopher , Crottini Angelica
Published: August 2022

Invasion risks may be influenced either negatively or positively by climate change, depending on the species. These can be predicted with species distribution models, but projections can be strongly affected by input environmental data (climate data source, Global Circulation Models and Shared Socio-economic Pathways SSP). We modelled the distribution ofPhelsuma grandisandP. laticauda, two Malagasy reptiles that are spreading globally. We accounted for drivers of spread and establishment using socio-economic factors (e.g., distance from ports) and two climate data sources, i.e., Climatologies at High Resolution for the Earth’s and Land Surface Areas (CHELSA) and Worldclim. We further quantified the degree of agreement in invasion risk models that utilised CHELSA and Worldclim data for current and future conditions. Most areas identified as highly exposed to invasion risks were consistently identified (e.g. in Caribbean and Pacific Islands). However, projected risks differed locally. We also found notable differences in quantitative invasion risk (3% difference in suitability scores forP. laticaudaand up to 14% forP. grandis) under current conditions. Despite both species native distributions overlap substantially, climate change will drive opposite responses on invasion risks by 2070 (decrease forP. grandis, increase forP. laticauda). Overall, projections of future invasion risks were the most affected by climate data source, followed by SSP. Our results highlight that assessments of current and future invasion risks are sensitive to the climate data source, especially in Islands. We stress the need to account for multiple climatologies when assessing invasion risks.
Re-inventing pathogen passage for social microbes
Authors: Dimitriu Tatiana , Souissi Wided , Morwool Peter , Darby Alistair , Crickmore Neil , Raymond Ben
Published: August 2022

Passage experiments that sequentially infect hosts with parasites have long been used to manipulate virulence. However, in many invertebrate pathogens passage has been applied naively without a full theoretical understanding of how best to select for increased virulence. This has led to very mixed results. Understanding the evolution of virulence is complex because selection on parasites occurs across multiple spatial scales with potentially different conflicts operating on parasites with different life-histories. For example, in social microbes, strong selection on replication rate within hosts can lead to cheating and loss of virulence, because investment in public goods virulence reduces replication rate. In contrast, selection acting at a between host scale maintains virulence by selecting on parasite population size. In this study we tested how different scales of selection and varying mutation supply affect evolution of virulence against resistant hosts in the specialist insect pathogen Bacillus thuringiensis., aiming to optimize methods for strain improvement against a difficult to kill insect target. We show that selection for infectivity using competition between sub-populations in a metapopulation prevents social cheating, acts to retain key virulence plasmids and facilitates increased virulence. Increased virulence was associated with reduced efficiency of sporulation, and loss of function in putative regulatory genes but not with altered expression of known virulence factors. Selection in a metapopulation provides a broadly applicable tool for improving the efficacy of biocontrol agents. Moreover, a structured host population can facilitate artificial selection on infectivity, while selection on life history traits such as faster replication or larger population sizes can reduce virulence can reduce virulence in social microbes.
Improved memory CD8 T cell response to delayed vaccine boost is associated with a distinct molecular signature
Authors: Natalini Ambra , Simonetti Sonia , Favaretto Gabriele , Lucantonio Lorenzo , Peruzzi Giovanna , Muñoz-Ruiz Miguel , Kelly Gavin , Contino Alessandra Maria , Sbrocchi Roberta , Battella Simone , Capone Stefania , Folgori Antonella , Nicosia Alfredo , Santoni Angela , Hayday Adrian C. , Di Rosa Francesca
Published: August 2022

Although the prime/boost interval can impact vaccine responses, the criteria for deciding its time length are poorly defined. To address this, we examined CD8 T cell responsiveness to boost in a BALB/c mouse model of intramuscular (i.m.) vaccination by priming with HIV-1 gag-encoding Chimpanzee adenovector, and boosting with HIV-1 gag-encoding Modified Vaccinia virus Ankara. We found that boost was more effective at day(d)100 than at d30 post-prime, as evaluated at d45 post-boost by multi-lymphoid organ assessment of gag-specific CD8 T cell frequency, CD62L-expression (as a guide to memory status) andin vivokilling. RNA-sequencing of splenic gag-primed CD8 T cells at d100 revealed a quiescent, but highly responsive signature, that trended toward a central memory (CD62L+) phenotype. Interestingly, gag-specific CD8 T cell frequency selectively diminished in the blood at d100, relative to the spleen, lymph nodes and bone marrow. These results move forward the rational design of prime/boost intervals.
Esearch3D: Propagating gene expression in chromatin networks to illuminate active enhancers
Authors: Heer Maninder , Giudice Luca , Mengoni Claudia , Giugno Rosalba , Rico Daniel
Published: August 2022

Most cell type-specific genes are regulated by the interaction of enhancers with their promoters. The identification of enhancers is not trivial as enhancers are diverse in their characteristics and dynamic in their interaction partners. Currently, enhancer-associated features such as histone modifications, co-activators or bi-directional transcription are used in lieu of any definitive and universal enhancer feature. We present Esearch3D, a new approach that leverages network theory approaches to identify active enhancers. Our work is based on the fact that enhancers act as a source of regulatory information to increase the rate of transcription of their target genes and that the flow of this information is mediated by the folding of chromatin in the three-dimensional (3D) nuclear space between the enhancer and the target gene promoter. Esearch3D reverse engineers this flow of information to calculate the likelihood of enhancer activity in intergenic regions by propagating the transcription levels of genes across 3D-genome networks. Regions predicted to have high enhancer activity are shown to be enriched in annotations indicative of enhancer activity. These include: enhancer-associated histone marks, bi-directional CAGE-seq, STARR-seq, P300 and RNA polymerase II ChIP-seq, and expression quantitative trait loci (eQTL). Esearch3D successfully leverages the relationship between chromatin architecture and global transcription and represents a novel approach to predict active enhancers and understand the complex underpinnings of regulatory networks. The method is available at:https://github.com/InfOmics/Esearch3D.
Silent transcription intervals and translational bursting lead to diverse phenotypic switching
Authors: Yang Xiyan , Luo Songhao , Zhang Zhenquan , Wang Zihao , Zhou Tianshou , Zhang Jiajun
Published: August 2022

Bimodality of gene expression, as a mechanism generating phenotypic diversity, enhances the survival of cells in a fluctuating environment. Growing experimental evidence suggests that silent transcription intervals and translational bursting play important roles in regulating phenotypic switching. Characterizing these kinetics is challenging. Here, we develop an interpretable and tractable model, the generalized telegraph model (GTM), which considers silent transcription intervals described by a general waiting-time distribution and translational bursting characterized by an arbitrary distribution. Using methods of queuing theory, we derive analytical expressions of all moment statistics and distribution of protein counts. We show that non-exponential inactive times and translational bursting can lead to two nonzero bimodalities that cannot be captured in the classical telegraph model (CTM). In addition, we find that both silent-intervals noise and translational burst-size noise can amplify gene expression noise, as well as induce diverse dynamic expressions. Our results not only provide an alternative mechanism for phenotypic switching driven by silent transcription intervals and translational bursting, but also can be used to infer complex promoter structures based on experimental data.

SIGNIFICANCE

Understanding how phenotypic diversity arises among isogenic cell populations is a fundamental problem in biology. Previous studies have shown that the bimodality of gene expression contributing to phenotypic variations is mostly caused by the intrinsic or extrinsic regulations of underlying systems. It is unclear whether bimodality occurs in the absence of these regulations. The CTM has made great success in interpreting many experimental phenomena, but it cannot capture the bimodal distributions with two nonzero peaks that have been demonstrated in experiments. In particular, recent single-cell studies have shown non-exponential inactive periods and non-geometric translational bursting in gene expression. How to model these kinetics is challenging. We develop a stochastic gene model, namely the GTM, to model the silent transcription intervals by a general waiting-time distribution and translational bursting by an arbitrary distribution. By mapping the GTM into a queuing model, we derive the steady-state distribution of gene products that can be used for analyzing phenotypic switching. We find that non-exponential inactive times and translational bursting can lead to two nonzero bimodalities that cannot be captured in the CTM. These results indicate that both silent transcription intervals and translational bursting have important roles in controlling cell phenotypic variations in fluctuating environments.
Relaxed targeting rules allow PIWI-clade Argonaute proteins to silence ever-mutating transposons
Authors: Gainetdinov Ildar , Cecchini Katharine , Vega-Badillo Joel , Bagci Ayca , Colpan Cansu , Arif Amena , Wu Pei-Hsuan , Zamore Phillip D.
Published: August 2022

In animals, piRNAs direct PIWI-clade Argonaute proteins to slice complementary transposon transcripts. Transposons can evade silencing through target site mutations. We report that PIWIs efficiently cleave transcripts only partially paired to their piRNA guide. Measurements of mouse PIWI protein affinity and cleavage rates for thousands of RNAs in vitro and in vivo show that PIWI slicing tolerates mismatches to any target nucleotide, including those flanking the scissile phosphate. Although piRNA 5’ terminal nucleotides accelerate target finding, they are dispensable for binding or catalysis—unlike AGO-clade Argonautes, which require uninterrupted siRNA:target pairing from the seed to the nucleotides past the scissile bond. PIWIs are thus better equipped than AGOs to target newly acquired or rapidly diverging endogenous transposons without recourse to novel small RNA guides.
Robust replication initiation from coupled homeostatic mechanisms
Authors: Berger Mareike , ten Wolde Pieter Rein
Published: August 2022

The bacteriumEscherichia coliinitiates replication once per cell cycle at a precise volume per origin and adds an on average constant volume between successive initiation events, independent of the initiation size. Yet, a molecular model that can explain these observations has been lacking. Experiments indicate thatE. colicontrols replication initiation via titration and activation of the initiator protein DnaA. Here, we study by mathematical modelling how these two mechanisms interact to generate robust replication-initiation cycles. We first show that a mechanism solely based on titration generates stable replication cycles at low growth rates, but inevitably causes premature reinitiation events at higher growth rates. In this regime, the DnaA activation switch becomes essential for stable replication initiation. Conversely, while the activation switch alone yields robust rhythms at high growth rates, titration can strongly enhance the stability of the switch at low growth rates. Our analysis thus predicts that both mechanisms together drive robust replication cycles at all growth rates. In addition, it reveals how an origin-density sensor yields adder correlations.
A cryptic transactivation domain of EZH2 binds AR and AR’s splice variant promoting oncogene activation and tumorous transformation
Authors: Wang Jun , Park Kwang-Su , Yu Xufen , Gong Weida , Earp H. Shelton , Wang Gang Greg , Jin Jian , Cai Ling
Published: August 2022

Enhancer of Zeste Homolog 2 (EZH2) and androgen receptor (AR) are crucial chromatin regulators involved in the development and/or progression of prostate tumor, including advanced castration-resistant prostate cancer (CRPC). To sustain prostate tumorigenicity, EZH2 establishes noncanonical biochemical interaction with AR for mediating oncogene activation, in addition to its canonical role as a transcriptional repressor and enzymatic subunit of Polycomb Repressive Complex 2 (PRC2). However, the molecular basis underlying non-canonical activities of EZH2 in prostate cancer remains elusive and therapeutic strategies for targeting EZH2:AR-mediated oncogene activation activities are also lacking. Here, we report that a cryptic transactivation domain of EZH2 (EZH2TAD) binds both AR and AR spliced variant 7 (AR-V7, an AR variant enriched in CRPC), mediating assembly and/or recruitment of transactivation-related machineries at genomic sites that lack PRC2 binding. Such noncanonical targets of EZH2:AR/AR-V7:(co)activators are enriched for the clinically-relevant oncogenes. We also show that EZH2TADis required for the chromatin recruitment of EZH2, for EZH2-mediated oncogene activation, and for CRPC growth in vitro and in vivo. To completely block EZH2’s multifaceted oncogenic activities in prostate cancer, we employed MS177, a recently developed proteolysis targeting chimera (PROTAC) of EZH2. Strikingly, MS177 achieved on-target depletion of both EZH2’s canonical (EZH2:PRC2) and noncanonical (EZH2TAD:AR/AR-V7:coactivators) complexes in prostate tumor, eliciting much more potent antitumor effects than the catalytic inhibitors of EZH2. Overall, this study reports previously unappreciated requirements of EZH2TADfor mediating EZH2’s noncanonical (co)activator recruitment and gene-activation functions in prostate tumor and suggests EZH2-targeting PROTACs as potentially attractive therapeutics for the treatment of aggressive prostate tumors that rely on the circuits wired by EZH2 and AR.
An investigation of the sex-specific genetic architecture of fitness inDrosophila melanogaster
Authors: Singh Amardeep , Hasan Asad , Agrawal Aneil F.
Published: August 2022

In dioecious populations, the sexes employ divergent reproductive strategies to maximize fitness and, as a result, genetic variants can affect fitness differently in males and females. Moreover, recent studies have highlighted an important role of the mating environment in shaping the strength and direction of sex-specific selection. Here, we measure adult fitness for each sex of 357 lines from theDrosophilaSynthetic Population Resource (DSPR) in two different mating environments. We analyze the data using three different approaches to gain insight into the sex-specific genetic architecture for fitness: classical quantitative genetics, genomic associations, and a mutational burden approach. The quantitative genetics analysis finds that, on average segregating genetic variation in this population has concordant fitness effects both across the sexes and across mating environments. We do not find specific genomic regions with strong associations with either sexually antagonistic (SA) or sexually concordant (SC) fitness effects, yet there is modest evidence of an excess of genomic regions with weak associations, both with SA and SC fitness effects. Our examination of mutational burden indicates stronger selection against indels and loss-of-function variants in females than males.
Parallel evolution of reduced cancer risk and tumor suppressor duplications in Xenarthra
Authors: Vazquez Juan Manuel , Pena Maria T. , Muhammad Baaqeyah , Kraft Morgan , Adams Linda B. , Lynch Vincent J.
Published: August 2022

The risk of developing cancer is correlated with body size and lifespan within species, but there is no correlation between cancer and either body size or lifespan between species indicating that large, long-lived species have evolved enhanced cancer protection mechanisms. Previously we showed that several large bodied Afrotherian lineages evolved reduced intrinsic cancer risk, particularly elephants and their extinct relatives (Proboscideans), coincident with pervasive duplication of tumor suppressor genes (Vazquez and Lynch 2021). Unexpectedly, we also found that Xenarthrans (sloths, armadillos, and anteaters) evolved very low intrinsic cancer risk. Here, we show that: 1) several Xenarthran lineages that independently evolved large bodies, long lifespans, and reduced intrinsic cancer risk; 2) reduced cancer risk in the stem lineages of Xenarthra and Pilosa occurred coincident with bursts of tumor suppressor gene duplications; 3) cells from sloths proliferate extremely slowly while Xenarthran cells induce apoptosis are very low levels of DNA damage; and 4) the prevalence of cancer is extremely low Xenarthrans, and cancer is nearly absent from armadillos. These data implicate the duplication of tumor suppressor genes in the evolution of remarkably large body sizes and decreased cancer risk in Xenarthrans and suggest they are a remarkably cancer resistant group of mammals.

Abstract Figure
Improved detection and classification of plasmids from circularized and fragmented assemblies
Authors: Giménez Matías , Ferrés Ignacio , Iraola Gregorio
Published: August 2022

Plasmids are mobile genetic elements important for bacterial adaptation. The study of plasmids from sequencing data is challenging because short reads produce fragmented assemblies, requiring of subsequent discrimination between chromosome and plasmid sequences. Although circularized assemblies are now possible using long-read data, there is still a need to differentiate plasmids from other circular elements. Here, we present plaSquid, a dockerized tool developed in Nextflow that expands plasmid detection and improves replicon typing and mobility groups classification schemes, outperforming previously available methods in both precision and sensitivity. When applied to ∼10.5 million metagenomic contigs, plaSquid revealed a 2.7-fold increase in plasmid phylogenetic diversity. Also, we used plaSquid to uncover a significant role of plasmids in the widespread distribution of clinically-relevant antimicrobial resistance genes in the built environment, from cities to spacecraft. Together, we present an improved approach to study plasmid biology from fragmented or circularized genomic and metagenomic assemblies.
mRNA vaccines and hybrid immunity use different B cell germlines to neutralize Omicron BA.4 and BA.5
Authors: Andreano Emanuele , Paciello Ida , Pierleoni Giulio , Maccari Giuseppe , Antonelli Giada , Abbiento Valentina , Pileri Piero , Benincasa Linda , Giglioli Ginevra , Piccini Giulia , De Santi Concetta , Sala Claudia , Medini Duccio , Montomoli Emanuele , Maes Piet , Rappuoli Rino
Published: August 2022

SARS-CoV-2 omicron BA.4 and BA.5, characterized by high transmissibility and ability to escape natural and vaccine induced immunity, are rampaging worldwide. To understand the escape mechanisms, we tested the neutralizing activity against omicron BA.4 and BA.5 of a panel of 482 human monoclonal antibodies that had been isolated from people who received two or three mRNA vaccine doses or from people that had been vaccinated after infection. None of the antibodies isolated after two vaccine doses neutralized omicron BA.4 and BA.5, while these variants were neutralized by approximately 15% of antibodies obtained from people that received three doses or had been vaccinated after infection. Remarkably, the antibodies isolated after three vaccine doses targeted mainly the receptor binding domain (RBD) Class 1/2 epitope region and were encoded by the IGHV1-69 and IGHV3-66 B cell germlines, while the antibodies isolated after infection recognized mostly the RBD Class 3 epitope region and the NTD, and were encoded by the IGHV2-5;IGHJ4-1 and IGHV1-24;IGHJ4-1 germlines. The observation that mRNA vaccination and hybrid immunity elicit a different immunity against the same antigen is intriguing and its understanding may help to design the next generation of therapeutics and vaccines against COVID-19.
Oncogenic IDH mutations increase heterochromatin-related replication stress without impacting tumor mutation burden
Authors: Schvartzman Juan-Manuel , Forsyth Grace , Walch Henry , Chatila Walid , Santella Anthony , Menghrajani Kamal , Sánchez-Vega Francisco , Koche Richard , Thompson Craig B.
Published: August 2022

Oncogenic mutations in the metabolic enzyme isocitrate dehydrogenase 1 and 2 (IDH1/2) have been found in a number of liquid and solid tumors. Their pathogenic mechanism of action involves production of 2-hydroxyglutarate (2HG), an oncometabolite that acts in part by inhibiting members of a family of dioxygenases that modulate chromatin dynamics. Recent work has suggested that mutant IDH (mIDH) and 2HG also impact sensitivity to inhibitors of poly-ADP ribose polymerases (PARP) but the molecular basis for this sensitivity is unclear. Unlike PARP inhibitor-sensitive BRCA1/2 tumors which exhibit impaired homologous recombination, IDH-mutant tumors have a silent mutational profile and lack mutational signatures associated with impaired homologous recombination. Instead, 2HG-producing IDH mutations lead to heterochromatin-dependent slowing of DNA replication and increased replication stress, resulting in DNA double strand breaks. This replicative stress manifests as replication fork slowing but the breaks are repaired without a significant increase in the cellular mutation burden. Faithful resolution of replicative stress in IDH-mutant cells is dependent on poly-ADP ribosylation. Treatment with PARP inhibitors restores replication fork speed but results in incomplete repair of DNA breaks. These findings provide evidence of a requirement for PARP in the replication of heterochromatin and further validate PARP as a potential therapeutic target in IDH-mutant tumors.
Dynamic remodeling of fiber networks with stiff inclusions under compressive loading
Authors: Carroll Bobby , Thanh Minh-Tri Ho , Patteson Alison
Published: August 2022

The ability of tissues to sustain and withstand mechanical stress is critical to tissue development and healthy tissue maintenance. The mechanical properties of tissues are typically considered to be dominated by the fibrous extracellular matrix (ECM) component of tissues. Fiber network mechanics can capture certain mechanical features of tissues, such as shear strain stiffening, but is insufficient in describing the compressive response of certain tissues and blood clots that are rich in extracellular matrix. To understand the mechanical response of tissues, we employ a contemporary mechanical model, a fibrous network of fibrin embedded with inert bead inclusions that preserve the volume-conserving constraints of cells in tissues. Combining bulk mechanical rheology and a custom imaging device, we show that the presence of inclusions alters the local dynamic remodeling of the networks undergoing uniaxial compressive strains and demonstrate non-affine correlated motion within a fiber-bead network, predicted to stretch fibers in the network and lead to the ability of the network to stiffen under compression, a key feature of real tissues. These findings have important implications for understanding how local structural properties of cells and ECM fibers impact the bulk mechanical response of real tissues.
Intrinsically disordered regions that drive phase separation form a robustly distinct protein class
Authors: Ibrahim Ayyam Y. , Khaodeuanepheng Nathan P. , Amarasekara Dhanush L. , Correia John J. , Lewis Karen A. , Fitzkee Nicholas C. , Hough Loren E. , Whitten Steven T.
Published: August 2022

Liquid-liquid phase separation (LLPS) of proteins is thought to be a primary driving force for the formation of membraneless organelles, which control a wide range of biological functions from stress response to ribosome biogenesis. LLPS of proteins in cells is primarily, though not exclusively, driven by intrinsically disordered (ID) domains. Accurate identification of ID regions (IDRs) that drive phase separation is important for testing the underlying mechanisms of phase separation, identifying biological processes that rely on phase separation, and designing sequences that modulate phase separation. To identify IDRs that drive phase separation, we first curated datasets of folded, ID, and phase-separating (PS) ID sequences. We then used these sequence sets to examine how broadly existing amino acids scales can be used to distinguish between the three classes of protein regions. We found that there are robust property differences between the classes and, consequently, that numerous combinations of amino acid property scales can be used to make robust predictions of LLPS. This result indicates that multiple, redundant mechanisms contribute to the formation of phase-separated droplets from IDRs. The top-performing scales were used to further optimize our previously developed predictor of PS IDRs, ParSe. We then modified ParSe to account for interactions between amino acids and obtained reasonable predictive power for mutations that have been designed to test the role of amino acid interactions in driving LLPS.
Urinary proteome changes during pregnancy in rats
Authors: Tang Shuxuan , Gao Youhe
Published: August 2022

Pregnancy involves a significant amount of physiological changes. A normal pregnancy is essential to ensure healthy maternal and fetal development. We sought to explore whether the urinary proteome could reflect the pregnancy process. Urine samples were collected from pregnant rats on gestational day 1, 4, 7, 11, 14, 16, 18, 20 (GD 1 d, GD 4 d, GD 7 d, GD 11 d, GD 14 d, GD 16 d, GD 18 d, GD 20 d), and control rats on days 0, 4, 7, 11, 14, 16, 18 and 20. The urinary proteome was profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), and differential proteins were obtained by comparing the 0 d (GD 1 d) of the same group at each time point within the two groups. Through the analysis of the enriched pathways of differentially expressed proteins in the pregnant group, during the period from fertilization to implantation, many pathways related to embryo implantation and trophoblast differentiation were enriched on GD 1 d, GD 4 d and GD 7 d. In addition, the developmental process of the fetal rat heart such as heart looping and endocardial cushion formation, are consistent with the timing of previous studies; the developmental process of the lung and the development of the rat embryo alveoli before birth are consistent with the reported timing; and the developmental time of the rat embryo pancreas is also during the period of pancreatic cell proliferation and differentiation. These processes were enriched only in the pregnancy group and not in the control group. Furthermore, coagulation-associated pathways were found to be increasingly prominent before labor, which is consistent with the previously reported trend of increasing coagulation function during pregnancy. Our results indicated urinary proteome can reflect some embryonic developmental and maternal changes in rat pregnancy.
ICAN: interpretable cross-attention network for identifying drug and target protein interactions
Authors: Kurata Hiroyuki , Tsukiyama Sho
Published: August 2022

Drug–target protein interaction (DTI) identification is fundamental for drug discovery and drug repositioning, because therapeutic drugs act on disease-causing proteins. However, the DTI identification process often requires expensive and time-consuming tasks, including biological experiments involving large numbers of candidate compounds. Thus, a variety of computation approaches have been developed. Of the many approaches available, chemo-genomics feature-based methods have attracted considerable attention. These methods compute the feature descriptors of drugs and proteins as the input data to train machine and deep learning models to enable accurate prediction of unknown DTIs. In addition, attention-based learning methods have been proposed to identify and interpret DTI mechanisms. However, improvements are needed for enhancing prediction performance and DTI mechanism elucidation. To address these problems, we developed an attention-based method designated the interpretable cross-attention network (ICAN), which predicts DTIs using the Simplified Molecular Input Line Entry System of drugs and amino acid sequences of target proteins. We optimized the attention mechanism architecture by exploring the cross-attention or self-attention, attention layer depth, and selection of the context matrixes from the attention mechanism. We found that a plain attention mechanism that decodes drug-related protein context features without any protein-related drug context features effectively achieved high performance. The ICAN outperformed state-of-the-art methods in several respects and revealed with statistical significance that some weighted sites in the cross-attention weight represent experimental binding sites, thus demonstrating the high interpretability of the results.

Key points

We created the interpretable cross-attention network (ICAN), which is composed of nn.Embedding of FCS label-encoding vectors of SMILES of drugs and AA sequences of target proteins, cross-attention mechanisms, and a CNN output layer.

ICAN decoded drug-related protein context features without any protein-related drug context features, achieving high prediction performance despite the plain attention mechanism.

In comparison with seven state-of-the-art methods, ICAN provided the highest PRAUC for the imbalanced datasets (DAVIS and BindingDB).

Statistical analysis of attention-weight matrixes revealed that some weighted attention sites corresponded to experimental binding sites, demonstrating the high interpretability achievable with ICAN.
Single-cell Spatial Explorer: Easy exploration of spatial and multimodal transcriptomics
Authors: Pont Frédéric , Cerapio Juan Pablo , Gravelle Pauline , Ligat Laetitia , Valle Carine , Sarot Emeline , Perrier Marion , Lopez Frédéric , Laurent Camille , Fournié Jean Jacques , Tosolini Marie
Published: August 2022

The development of single cell technologies yields large datasets of informations as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ‘spatial transcriptomics’. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 6 human and murine tissues datasets.
Application of the fluorescence-activating and absorption-shifting tag (FAST) for flow cytometry in methanogenic archaea
Authors: Adlung Norman , Scheller Silvan
Published: August 2022

Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans are biochemically characterized and can be genetically engineered using a variety of molecular tools. Methanogens’ anaerobic lifestyle and autofluorescence, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives) which require oxygen for chromophore maturation. Here, we employ the tandem activation and absorption-shifting tag protein 2 (tdFAST2) which is fluorescent when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. tdFAST2 expression in M. acetivorans and M. maripaludis is not cytotoxic and tdFAST2:HBR-3,5DOM fluorescence can be clearly distinguished from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be clearly distinguished which allows high-throughput investigations of dynamics within single and mixed cultures.

Importance

Methane-producing archaea play an essential role in the global carbon cycle and have a high potential for biotechnological applications such as biofuel production, carbon dioxide capture, and in electrochemical systems. The oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins to study methanogens. By using the tdFAST2:HBR-3,5DOM fluorescence, which is functional also under anaerobic conditions and distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of dynamics within (mixed) cultures via flow cytometry are possible. This will accelerate the exploitation of the methanogens’ biotechnological potential.
Super-resolution imaging pinpoints ultrastructural changes at the node of Ranvier in patients with polyneuropathy
Authors: Appeltshauser Luise , Linke Janis , Heil Hannah S. , Karus Christine , Schenk Joachim , Hemmen Katherina , Sommer Claudia , Doppler Kathrin , Heinze Katrin G.
Published: August 2022

To shed light on nanoscale pathologies in patients with polyneuropathy, we assessed human nerve biopsies by super-resolution fluorescence microscopy. We focused on both physiological protein arrangement and pathological ultrastructural changes at the node of Ranvier, a crucial region of the peripheral myelinated axon. Direct stochastic optical reconstruction microscopy (dSTORM) revealed a ∼190 nm periodic protein arrangement of cytoskeletal proteins and axoglial cell adhesion molecules. Periodic distances increased at the paranodal region of the node of Ranvier in patients with polyneuropathy, both at the axonal cytoskeleton and at the axoglial junction. In-depth image analysis of human nerve biopsies revealed a partial loss of proteins of the axoglial complex (Caspr-1, neurofascin-155) in combination with detachment from the cytoskeletal anchor protein ß2-spectrin. Super-resolution dual-color colocalization data was supported by high-content confocal imaging combined with deep learning-based analysis, indicating that paranodal elongation occurs especially in acute and severe axonal neuropathy, as a possible correlate of Wallerian degeneration and related cytoskeletal damage. Our findings show that super-resolution imaging can identify, quantify and map elongated periodic protein distances in peripheral nerve biopsies for pathophysiological studies and direct implications for diagnostic assessment.

Graphical abstract

Pathological alterations of ultrastructural protein arrangement at the paranodal region of the node of Ranvier in polyneuropathy.Super-resolution microscopy allows for assessing ultrastructural protein arrangement and pathological alterations in patients with polyneuropathy. In human healthy nodes, axoglial and axoskeletal proteins follow a 190 nm periodic arrangement (left). In pathologically altered nodes (right), periodic protein distances of axonal ß2-spectrin elongate, in combination with elongation and partial loss of the axoglial complex of Caspr-1 and neurofascin-155. The axoglial complex itself colocalizes closely even in pathologically altered nodes. A complete loss of the axoglial complex could be the ultrastructural correlate of the detachment of paranodal myelin loops. Scale bar 2 μm.
Inferring time-varying generation time, serial interval and incubation period distributions for COVID-19
Authors: Chen Dongxuan , Lau Yiu Chung , Xu Xiao-Ke , Wang Lin , Du Zhanwei , Tsang Tim K. , Wu Peng , Lau Eric H. Y. , Wallinga Jacco , Cowling Benjamin J. , Ali Sheikh Taslim
Published: August 2022

Background

The generation time distribution, reflecting the time between successive infections in transmission chains, is one of the fundamental epidemiological parameters for describing COVID-19 transmission dynamics. However, because exact infection times are rarely known, it is often approximated by the serial interval distribution, reflecting the time between illness onsets of infector and infectee. This approximation holds under the assumption that infectors and infectees share the same incubation period distribution, which may not always be true.

Methods

We analyzed data on observed incubation period and serial interval distributions in China, during January and February 2020, under different sampling approaches, and developed an inferential framework to estimate the generation time distribution that accounts for variation over time due to changes in epidemiology, sampling biases and public health and social measures.

Results

We analyzed data on a total of 2989 confirmed cases for COVID-19 during January 1 to February 29, 2020 in Mainland China. During the study period, the empirical forward serial interval decreased from a mean of 8.90 days to 2.68 days. The estimated mean backward incubation period of infectors increased from 3.77 days to 9.61 days, and the mean forward incubation period of infectees also increased from 5.39 days to 7.21 days. The estimated mean forward generation time decreased from 7.27 days (95% confidence interval: 6.42, 8.07) to 4.21 days (95% confidence interval: 3.70, 4.74) days by January 29. We used simulations to examine the sensitivity of our modelling approach to a number of assumptions and alternative dynamics.

Conclusions

The proposed method can provide more reliable estimation of the temporal variation in the generation time distribution, enabling proper assessment of transmission dynamics.
Ethnic inequalities in age-related patterns of multiple long-term conditions in England: analysis of primary care and nationally representative survey data
Authors: Hayanga Brenda , Stafford Mai , Saunders Catherine L. , Bécares Laia
Published: August 2022

Background

Having multiple long-term conditions has been associated with a higher treatment burden, reduced quality of life and a higher risk of mortality. Epidemiological evidence suggests that people from minoritised ethnic groups have a higher prevalence of multiple long-term conditions (MLTCs) but questions remain regarding the patterning of MLTCs by age, how this varies for different ethnic group populations, and across conceptualisations of MLTCs (for example, MLTCs with and without mental health conditions). The aim of this study is to examine ethnic inequalities in age-related patterns of MLTCs, and combinations of physical and mental health conditions.

Methods

We analysed data from the English GP Patient Survey (GPPS) 2015-2017, and Clinical Practice Research Datalink (CPRD) Aurum from 2016, to give us insight into self-reported and primary care recorded long-term conditions in people aged 18 years and above. We described the association between two or more long-term conditions and age using multilevel regression models adjusting for sex and area-level deprivation with patients nested within GP practices. Similar analyses were repeated for MLTCs that included a mental health condition.

Findings

For both self-reported and primary care recorded LTCs, people from most minoritised ethnic groups had a lower prevalence of MLTCs at younger ages compared to their white counterparts. We observed ethnic inequalities from middle age onwards such that in later life, Pakistani, Indian, Black Caribbean and people of Other ethnicity were at an increased risk of having MLTCs compared to white British people. These trends remained after adjusting for area-level deprivation. Compared to white British people, Gypsy and Irish Travellers had higher levels of MLTCs across the age groups, and Chinese people had lower levels. Pakistani and Bangladeshi people aged 50-74 years were more likely than white British people to report two or more LTCs that included a mental health condition. People from other minoritised ethnic groups were less likely to report this compared to white British people.

Conclusion

We find clear evidence of ethnic inequalities in MLTCs. It is imperative for health systems to recognise and respond to the higher prevalence of MLTCs that develop by middle age for many minoritised ethnic group people. The lower prevalence of MLTCs that include a mental health condition among some minoritised ethnic group people may be an underestimation due to underdiagnosis and/or inadequate care in primary care and requires further scrutiny.
The distribution of antimicrobial resistance genes across phylogroup, host species and geography in 16,000 publicly-availableE. coligenomes
Authors: Pursey Elizabeth , Dimitriu Tatiana , Gaze William H. , Westra Edze R. , van Houte Stineke
Published: August 2022

E. coliis a highly diverse bacterial species that generates a huge global burden of antimicrobial-resistant infections. A wealth of whole genome sequence data is available on public databases for this species, presenting new opportunities to analyse the distribution of antimicrobial resistance (AMR) genes across its genetic and ecological diversity. We extracted and categorised metadata on host species and geographic location and combined this within silicophylogrouping to describe the characteristics of ∼16,000 assembledE. coligenomes from the NCBI RefSeq database. We estimated AMR carriage using various metrics: counts of overall genes, multidrug- and extensively drug-resistant categories, and selected β-lactamases of current global concern –blaCTX-Mand carbapenemase genes. We present estimates of AMR carriage for these metrics by species type (human, agricultural/domestic animal, wild birds and other wild animals), geographic subregion, and across phylogroups. In addition, we describe the distribution of phylogroups within host types and geographic subregions. Our findings show high AMR carriage in commensal-associated phylogroups, agricultural and wild animal hosts and in many subregions. However, we also quantify large biases in sequencing data, the substantial gaps in our knowledge of AMR in many hosts, regions and environmental settings, and the need for systematic sampling to gain a more accurate picture.
Performance of Rapid Antigen Tests to Detect Symptomatic and Asymptomatic SARS-CoV-2 Infection
Authors: Soni Apurv , Herbert Carly , Lin Honghuang , Yan Yi , Pretz Caitlin , Stamegna Pamela , Wang Biqi , Orwig Taylor , Wright Colton , Tarrant Seanan , Behar Stephanie , Suvarna Thejas , Schrader Summer , Harman Emma , Nowak Chris , Kheterpal Vik , Rao Lokinendi V , Cashman Lisa , Orvek Elizabeth , Ayturk Didem , Gibson Laura , Zai Adrian , Wong Steven , Lazar Peter , Wang Ziyue , Filippaios Andreas , Barton Bruce , Achenbach Chad J. , Murphy Robert L. , Robinson Matthew , Manabe Yukari C. , Pandey Shishir , Colubri Andres , O’Connor Laurel , Lemon Stephenie C. , Fahey Nisha , Luzuriaga Katherine L , Hafer Nathaniel , Roth Kristian , Lowe Toby , Stenzel Timothy , Heetderks William , Broach John , McManus David D
Published: August 2022

Background

Performance of rapid antigen tests for SARS-CoV-2 (Ag-RDT) varies over the course of an infection, and their performance in screening for SARS-CoV-2 is not well established. We aimed to evaluate performance of Ag-RDT for detection of SARS-CoV-2 for symptomatic and asymptomatic participants.

Methods

Participants >2 years old across the United States enrolled in the study between October 2021 and February 2022. Participants completed Ag-RDT and molecular testing (RT-PCR) for SARS-CoV-2 every 48 hours for 15 days. This analysis was limited to participants who were asymptomatic and tested negative on their first day of study participation. Onset of infection was defined as the day of first positive RT-PCR result. Sensitivity of Ag-RDT was measured based on testing once, twice (after 48-hours), and thrice (after 96 hours). Analysis was repeated for different Days Post Index PCR Positivity (DPIPP) and stratified based on symptom-status.

Results

In total, 5,609 of 7,361 participants were eligible for this analysis. Among 154 participants who tested positive for SARS-CoV-2, 97 were asymptomatic and 57 had symptoms at infection onset. Serial testing with Ag-RDT twice 48-hours apart resulted in an aggregated sensitivity of 93.4% (95% CI: 89.1-96.1%) among symptomatic participants on DPIPP 0-6. Excluding singleton positives, aggregated sensitivity on DPIPP 0-6 for two-time serial-testing among asymptomatic participants was lower at 62.7% (54.7-70.0%) but improved to 79.0% (71.0-85.3%) with testing three times at 48-hour intervals.

Discussion

Performance of Ag-RDT was optimized when asymptomatic participants tested three-times at 48-hour intervals and when symptomatic participants tested two-times separated by 48-hours.