bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and Genomic Analyses ofDrosophila melanogasterModels of Chromatin Modification Disorders
Authors: MacPherson Rebecca A. , Shankar Vijay , Anholt Robert R. H. , Mackay Trudy F. C. 
Published: April 2023

ABSTRACTSwitch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF(Brahma-Related Gene-1Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference inDrosophila melanogasterto reduce expression of six genes(brm, osa, Snrl, SMC1, SMC3, vtd)orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, includingBap60,which is orthologous toSMARCD1,a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genesbrm, osa,and/or Snrl recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
Protein language models can capture protein quaternary state
Authors: Avraham Orly , Tsaban Tomer , Ben-Aharon Ziv , Tsaban Linoy , Schueler-Furman Ora 
Published: April 2023

AbstractBackgroundDetermining a protein’s quaternary state,i.e. how many monomers assemble together to form the functioning unit, is a critical step in protein characterization, and deducing it is not trivial. Many proteins form multimers for their activity, and over 50% are estimated to naturally form homomultimers. Experimental quaternary state determination can be challenging and require extensive work. To complement these efforts, a number of computational tools have been developed for quaternary state prediction, often utilizing experimentally validated structural information. Recently, dramatic advances have been made in the field of deep learning for predicting protein structure and other characteristics. Protein language models that apply computational natural-language models to proteins successfully capture secondary structure, protein cell localization and other characteristics, from a single sequence. Here we hypothesize that information about the protein quaternary state may be contained within protein sequences as well, allowing us to benefit from these novel approaches in the context of quaternary state prediction.ResultsWe generated embeddings for a large dataset of quaternary state labels, extracted from the curated QSbio dataset. We then trained a model for quaternary state classification and assessed it on a non-overlapping set of distinct folds (ECOD family level). Our model, named QUEEN (QUaternary state prediction using dEEp learNing), performs worse than approaches that include information from solved crystal structures. However, we show that it successfully learned to distinguish multimers from monomers, and that the specific quaternary state is predicted with moderate success, better than a simple model that transfers annotation based on sequence similarity. Our results demonstrate that complex, quaternary state related information is included in these embeddings.ConclusionsQUEEN is the first to investigate the power of embeddings for the prediction of the quaternary state of proteins. As such, it lays out the strength as well as limitations of a sequence-based protein language model approach compared to structure-based approaches. Since it does not require any structural information and is fast, we anticipate that it will be of wide use both for in-depth investigation of specific systems, as well as for studies of large sets of protein sequences. A simple colab implementation is available at:https://colab.research.google.com/github/Orly-A/QUEEN_prediction/blob/main/QUEEN_prediction_notebook.ipynb.
FLUTE: a Python GUI for interactive phasor analysis of FLIM data
Authors: Gottlieb Dale , Asadipour Bahar , Ung Thi Phuong Lien , Stringari Chiara 
Published: April 2023

AbstractFluorescence lifetime imaging microscopy (FLIM) is a powerful technique used to probe the local environment of fluorophores. The phasor approach to FLIM data is a fit-free analysis and is increasingly used due to its ease of interpretation. To date, no open-source graphical user interface (GUI) for phasor analysis of FLIM data is available thus limiting the widespread use of phasor analysis in biomedical research. Here we present (F)luorescence (L)ifetime (U)l(t)imate (E)xplorer (FLUTE), a Python GUI that is designed to fill this gap. FLUTE simplifies and automates many aspects of FLIM analysis, such as calibrating the FLIM data, performing interactive exploration of the phasor plot with cursors, displaying the phasor plot and the FLIM images with different lifetime contrasts and calculating the relative concentration of molecular species. The final edited datasets after applying the desired filters and thresholds can be exported for further user specific analysis. FLUTE was tested using several FLIM datasets including autofluorescence of Zebrafish embryos, cells in vitro and intact live tissues. In summary, our user-friendly GUI extends the advantages of phasor plotting by making the data visualization and analysis easy and interactive, allows for analysis of large FLIM datasets and accelerates FLIM analysis for non-specialized labs.Impact statementThis work introduces the first open-source graphical user interface (GUI) for phasor analysis of Fluorescence Lifetime Microscopy (FLIM) data. Phasor analysis is increasingly used for FLIM data analysis in biomedical research as it reduces the complexity of the analysis and provides a powerful visualization of the data content and optimization of data handling with respect to multiexponential fitting. However, the development of quantitative FLIM applications in the life sciences has been until now hampered by the lack of an open source and user-friendly graphical user interface. Here we introduce FLUTE that expands some possibilities of phasor FLIM image processing, accelerates the whole FLIM analysis and simplifies the visualization and the analysis of FLIM data, thus making phasor analysis possible for a broader base of researchers. FLUTE will be of interest to researchers with interests ranging from physics to biology and will facilitate research in several biomedical fields.
An integrated map of genetic variation from 1,062 wheat genomes
Authors: Bi Aoyue , Xu Daxing , Kang Lipeng , Guo Yafei , Song Xinyue , Zhao Xuebo , Zhang Jijin , Zhang Zhiliang , Li Yiwen , Yin Changbin , Wang Jing , Lu Fei 
Published: April 2023

AbstractThe construction of a high-quality wheat genome variation map is important to wheat genetic studies and breeding. In this study, we developed the second-generation whole-genome genetic variation map of wheat (VMap 2.0) by integrating whole-genome sequencing data of 1,062 diverse wheat accessions from 20 species/subspecies. VMap 2.0 contains 195.96 million single nucleotide polymorphisms (SNPs), 2.22 million insertions, and 4.72 million deletions, achieving a high density of variation map in which one variant exists in every 73 base pairs on average. By systematically analyzing the phylogenetic relationships and genetic diversity of tetraploid wheat, hexaploid wheat, and diploid goatgrass (Aegilops tauschii), we found that the genetic diversity of wild emmer wheat was 2.4 times higher than that of common wheat. In contrast, the genetic diversity of diploid goatgrass is 7.8 times higher than the D subgenome of hexaploid wheat. With the high-density genetic variations, VMap 2.0 is anticipated to facilitate high-resolution trait dissection and expedite prediction-based breeding of wheat.
Automated Integration of Multi-Slice Spatial Transcriptomics Data in 2D and 3D
Authors: Bienroth Denis , Charitakis Natalie , Wong Dillon , Jaeger-Honz Sabrina , Garkov Dimitar , Watt Kevin I. , Stolper Julian , Chambers-Smith Hazel , MacGregor Duncan , Christiansen Bronwyn , Piers Adam T. , Porrello Enzo R. , Elliott David A. , Klein Karsten , Nim Hieu T. , Schreiber Falk , Ramialison Mirana 
Published: April 2023

ABSTRACTThe field of spatial transcriptomics is rapidly evolving, with increasing sample complexity, resolution, and tissue size. Yet the field lacks comprehensive solutions for automated integration and analysis of multi-slice data in either stacked (3D) or co-planar (2D) formation. To address this, we developed VR-Omics, a free, platform-agnostic software that distinctively provides end-to-end automated processing of multi-slice data through a biologist-friendly interface. Benchmarking against existing methods demonstrates VR-Omics’ unique strengths to perform comprehensive end-to-end analysis of multi-slice stacked data. Applied to rare paediatric cardiac rhabdomyomas, VR-Omics uncovered previously undetected dysregulated metabolic networks through co-planar slice analysis, demonstrating its potential for biological discoveries.
Advancing Understanding of DNA-BfiI Restriction Endonuclease Cis and Trans Interactions through smFRET Technology
Authors: Ivanovaitė Šarūnė , Paksaitė Justė , Kopūstas Aurimas , Karzaitė Giedrė , Rutkauskas Danielis , Silanskas Arunas , Sasnauskas Giedrius , Zaremba Mindaugas , Jones Stephen K. , Tutkus Marijonas 
Published: April 2023

AbstractMonitoring of DNA-protein interactions is essential in understanding many biological processes. Proteins must find their target site on a DNA molecule to perform their function, and the mechanisms for target search differ across proteins. Revealing temporal interactions with two target sites, both inCisand inTrans, is crucial in target search mechanisms studies. Here, we present two single-molecule Förster resonance energy transfer (smFRET)-based assays to study BfiI-DNA interactions. The first assay, smFRET-based DNA looping assay, detects both “Phi” and “U”-shaped DNA looping events. We modified it to only allowin TransBfiI-target DNA interactions to improve specificity and reduce limitations in the observation time. Our TIRF microscopy measurements directly observe the on- and off-target binding events and characterize BfiI binding events. Our results show that BfiI binding events last longer on target sites and that the BfiI rarely changes conformations during binding. This newly developed assay could be useful for other two-targets-binding DNA-interacting proteins and could be employed for dsDNA substrate BfiI-PAINT, which is useful for DNA stretch-assays and other super-resolution fluorescence microscopy studies.
Structure of the human Bre1 complex bound to the nucleosome
Authors: Onishi Shuhei , Uchiyama Kotone , Sato Ko , Okada Chikako , Kobayashi Shunsuke , Nishizawa Tomohiro , Nureki Osamu , Ogata Kazuhiro , Sengoku Toru 
Published: April 2023

SummaryHistone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of Bre1A/RNF20 and Bre1B/RNF40. The Bre1 proteins generally function as tumor suppressors, while in certain cancers, they facilitate cancer cell proliferation. To reveal the structural basis of H2BK120 ubiquitination and its regulation, we determined the cryo-EM structure of the human Bre1 complex bound to the nucleosome. The two RING domains of Bre1A and Bre1B recognize the acidic patch and the nucleosomal DNA phosphates around SHL 6.0, which are ideally located to recruit the E2 enzyme and ubiquitin for H2BK120-specific ubiquitination. Mutational experiments suggest that the two RING domains bind in both orientations and that ubiquitination occurs when Bre1A binds to the acidic patch. Our results provide insights into the relationships between Bre1 proteins and cancer and suggest that H2B monoubiquitination can be regulated by nuclesomal DNA flexibility.
Measuring the impact of genetic heterogeneity and chromosomal inversions on the efficacy of CRISPR-Cas9 gene drives in different strains ofAnopheles gambiae
Authors: Pescod Poppy , Bevivino Giulia , Anthousi Amalia , Shelton Ruth , Margiotta Molly , Shepherd Josephine , Lombardo Fabrizio , Nolan Tony 
Published: April 2023

AbstractThe human malaria vectorAnopheles gambiaeis becoming increasingly resistant to insecticides, spurring the development of genetic control strategies. CRISPR-Cas9 gene drives can modify a population by creating double-stranded breaks at highly specific targets, triggering copying of the gene drive into the cut site (‘homing’), ensuring its inheritance. The DNA repair mechanism responsible requires homology between the donor and recipient chromosomes, presenting challenges for the invasion of lab-developed gene drives into wild populations of target speciesAn. gambiaespecies complex, which show high levels of genome variation.Two gene drives (vas2-5958 andzpg-7280) were introduced into threeAn. gambiaestrains collected across Africa with 5.3-6.6% variation around the target sites, and the effect of this variation on homing was measured. Gene drive homing across different karyotypes of the 2La chromosomal inversion was also assessed. No decrease in gene drive homing was seen despite target site heterology, demonstrating the applicability of gene drives to wild populations.
T9GPred: A Comprehensive Computational Tool for the Prediction of Type 9 Secretion System, Gliding Motility and the Associated Secreted Proteins
Authors: Sahoo Ajaya Kumar , Vivek-Ananth R. P. , Chivukula Nikhil , Rajaram Shri Vishalini , Mohanraj Karthikeyan , Khare Devanshi , Acharya Celin , Samal Areejit 
Published: April 2023

ABSTRACTType 9 secretion system (T9SS) is one of the least characterized secretion systems exclusively found in theBacteroidetesphylum which comprise various environmental and economically relevant bacteria. While T9SS plays a central role in bacterial movement termed gliding motility, survival and pathogenicity, there is an unmet need for a comprehensive tool that predicts T9SS, gliding motility and proteins secreted via T9SS. In this study, we develop such a computational tool, Type 9 secretion system and Gliding motility Prediction (T9GPred). To build this tool, we manually curated published experimental evidence and identified mandatory components for T9SS and gliding motility prediction. We also compiled experimentally characterized proteins secreted via T9SS and determined the presence of three unique types of C-terminal domain signals, and these insights were leveraged to predict proteins secreted via T9SS. Notably, using recently published experimental evidence, we show that T9GPred has high predictive power. Thus, we used T9GPred to predict the presence of T9SS, gliding motility and associated secreted proteins across 693 completely sequencedBacteroidetesstrains. T9GPred predicted 402 strains to have T9SS, of which 327 strains are also predicted to exhibit gliding motility. Further, T9GPred also predicted putative secreted proteins for the 402 strains. In a nutshell, T9GPred is a novel computational tool for systems-level prediction of T9SS and streamlining future experimentation. The source code of the computational tool is available in our GitHub repository:https://github.com/asamallab/T9GPred. The tool and its predicted results are compiled in a web server available at:https://cb.imsc.res.in/t9gpred/.
Selective inhibition of OSBP blocks retrograde trafficking by inducing partial Golgi degradation
Authors: He Nianzhe , Depta Laura , Rossetti Cecilia , Cigler Marko , Michon Marine , Dan Oliver Rafn , Hoock Joseph , Barbier Julien , Gillet Daniel , Forrester Alison , Winter Georg E. , Laraia Luca 
Published: April 2023

AbstractSterol-binding proteins are important regulators of lipid homeostasis and membrane integrity; however, the discovery of selective small molecule modulators can be challenging due to structural similarities in the sterol binding domains. We report the discovery of highly potent and selective inhibitors of oxysterol binding protein (OSBP), which we termoxybipins. Sterol-containing chemical chimeras aimed at identifying new sterol binding proteins by targeted degradation, led to a significant reduction in Golgi-associated proteins. The degradation was found to occur at lysosomes, concomitant with changes in general protein glycosylation, indicating that the degradation of Golgi proteins was a downstream effect. By establishing a sterol transport protein biophysical assay panel, we discovered that theoxybipinspotently inhibited OSBP, resulting in blockage of retrograde trafficking and attenuating Shiga toxin toxicity. As theoxybipinsdo not target any other sterol transporters tested, we advocate their use as chemical tools to study OSBP function and therapeutic relevance.
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing
Authors: Patruno Lucrezia , Milite Salvatore , Bergamin Riccardo , Calonaci Nicola , D’Onofrio Alberto , Anselmi Fabio , Antoniotti Marco , Graudenzi Alex , Caravagna Giulio 
Published: April 2023

AbstractSingle-cell RNA and ATAC sequencing technologies allow one to probe expression and chromatin accessibility states as a proxy for cellular phenotypes at the resolution of individual cells. A key challenge of cancer research is to consistently map such states on genetic clones, within an evolutionary framework. To this end we introduce CONGAS+, a Bayesian model to map single-cell RNA and ATAC profiles generated from independent or multimodal assays on the latent space of copy numbers clones. CONGAS+ can detect tumour subclones associated with aneuploidy by clustering cells with the same ploidy profile. The framework is implemented in a probabilistic language that can scale to analyse thousands of cells thanks to GPU deployment. Our tool exhibits robust performance on simulations and real data, highlighting the advantage of detecting aneuploidy from two distinct molecules as opposed to other single-molecule models, and also leveraging real multi-omic data. In the application to prostate cancer, lymphoma and basal cell carcinoma, CONGAS+ did retrieve complex subclonal architectures while providing a coherent mapping among ATAC and RNA, facilitating the study of genotype-phenotype mapping, and their relation to tumour aneuploidy.Author summaryAneuploidy is a condition caused by copy number alterations (CNAs), which brings cells to acquire or lose chromosomes. In the context of cancer progression and treatment response, aneuploidy is a key factor driving cancer clonal dynamics, and measuring CNAs from modern sequencing assays is therefore important. In this framing, we approach this problem from new single-cell assays that measure both chromatin accessibility and RNA transcripts. We model the relation between single-cell data and CNAs and, thanks to a sophisticated Bayesian model, we are capable of determining tumour clones from clusters of cells with the same copy numbers. Our model works when input cells are sequenced independently for both assays, or even when modern multi-omics protocols are used. By linking aneuploidy to gene expression and chromatin conformation, our new approach provides a novel way to map complex genotypes with phenotype-level information, one of the missing factors to understand the molecular basis of cancer heterogeneity.
A Screen Reveals Bexarotene, Sorafenib and Certain of its Analogues as Common and Effective Inhibitors of Growth of Bacteria that Grow on LB but not on McConkey Agar
Authors: Scheerer J. 
Published: April 2023

AbstractA screen of 61 compounds identified bexarotene and sorafenib as inhibitors of bacterial isolates that grew on LB agar but not on McConkey agar. The effect of bexarotene was durable, whereas sorafenib simply retarded growth. Two sorafenib analogues, previously not described, dubbed JSR-A40 and JSR-N42, displayed durable effects. Upon extending this to a larger group of bacteria from different sources it was found that both bexarotene and JSR-N42 were active in concentrations from between 1.25-10 µM in 42 of bacteria growing in LB but not McConkey medium, whereas bacteria growing on McConkey agar were all found to be insensitive at that concentration. Both bexarotene and N42 displayed rather broad characteristics similar to clindamycin, however non-overlapping. Sensitivity to clindamycin, if observed, was generally higher. It was found that the urea type compound N42 at 5 µM was broader active than clindamycin at 5 µM in this set of isolates.
Three small partner proteins facilitate the type VII-dependent secretion export of an antibacterial nuclease
Authors: Yang Yaping , Boardman Eleanor , Deme Justin , Alcock Felicity , Lea Susan , Palmer Tracy 
Published: April 2023

SummaryThe type VIIb protein secretion system (T7SSb) plays a role in interbacterial competition in Gram-positive Firmicute bacteria and secretes various toxic effector proteins. The mechanism of secretion and the roles of numerous conserved genes within T7SSb gene clusters remain unknown. EsaD is a nuclease toxin secreted by theStaphylococcus aureusT7SSb, which forms a complex with its cognate immunity protein, EsaG, and chaperone EsaE. Encoded upstream of EsaD are three small secreted proteins, EsxB, EsxC and EsxD. Here we show that EsxBCD bind to the transport domain of EsaD and function as EsaD export factors. We report the first structural information for a complete T7SSb substrate pre-secretion complex. Cryo-EM of the EsaDEG trimer and the EsaDEG-EsxBCD hexamer shows that incorporation of EsxBCD confers a conformation comprising a flexible globular cargo domain attached to a long narrow shaft that is likely to be crucial for efficient toxin export.
β-arrestin-dependent and -independent endosomal G protein activation by the vasopressin type 2 receptor
Authors: Daly Carole , Guseinov Akim Abdul , Hahn Hyunggu , Wright Adam , Tikhonova Irina G. , Thomsen Alex Rojas Bie , Plouffe Bianca 
Published: April 2023

ABSTRACTThe vasopressin type 2 receptor (V2R) is an essential GPCR in renal regulation of water homeostasis. Upon stimulation, the V2R activates Gαsand Gαq/11, which is followed by robust recruitment of β-arrestins and receptor internalization into endosomes. Unlike canonical GPCR signaling, the β-arrestin association with the V2R does not terminate Gαsactivation, and thus, Gαs-mediated signaling is sustained while the receptor is internalized. Here, we demonstrate that this V2R ability to co-interact with G protein/β-arrestin and promote endosomal G protein signaling is not restricted to Gαs, but also involves Gαq/11. Furthermore, our data implies that β-arrestins potentiate Gαs/Gαq/11activation at endosomes rather than terminating their signaling. Surprisingly, we found that the V2R internalizes and promote endosomal G protein activation independent of β-arrestins to a minor degree. These new observations challenge the current model of endosomal GPCR signaling and suggest that this event can occur in both β-arrestin-dependent and -independent manners.IMPACT STATEMENTThe vasopressin type 2 receptor promotes dual Gαsand Gαq/11signaling at early endosomes in β-arrestin-dependent and -independent manners.