bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program
Authors: Smith Christina M. , Grow Edward J. , Shadle Sean C. , Cairns Bradley R.
Published: April 2023

The embryonic transcription factor DUX regulates chromatin opening and gene expression in totipotent cleavage-stage mouse embryos, and its expression in embryonic stem cells promotes their conversion to 2-cell embryo-like cells (2CLCs) with extraembryonic potential. However, little is known regarding which domains within mouse DUX interact with particular chromatin and transcription regulators. Here, we reveal that the C-terminus of mouse DUX contains five uncharacterized ∼100 amino acid (aa) repeats followed by an acidic 14 amino acid tail. Unexpectedly, structure-function approaches classify two repeats as ‘active’ and three as ‘inactive’ in cleavage/2CLC transcription program enhancement, with differences narrowed to a key 6 amino acid section. Our proximity dependent biotin ligation (BioID) approach identified factors selectively associated with active DUX repeat derivatives (including the 14aa ‘tail’), including transcription and chromatin factors such as SWI/SNF (BAF) complex, as well as nucleolar factors that have been previously implicated in regulating the Dux locus. Finally, our mechanistic studies reveal cooperativity between DUX active repeats and the acidic tail in cofactor recruitment, DUX target opening, and transcription. Taken together, we provide several new insights into DUX structure-function, and mechanisms of chromatin and gene regulation.
Does social antagonism facilitate supergene expansion? A novel region of suppressed recombination in a 4-haplotype supergene system
Authors: Scarparo Giulia , Palanchon Marie , Brelsford Alan , Purcell Jessica
Published: April 2023

Models of both sex chromosome evolution and the genetic basis of local adaptation suggest that selection acts to lock beneficial combinations of alleles together in regions of reduced or suppressed recombination. Drawing inspiration from such models, we apply similar logic to investigate whether an autosomal supergene underlying colony social organization in ants expanded to include “socially antagonistic” alleles. We tested this premise in aFormicaant species wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. Remarkably, we discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is tightly linked to one of the haplotypes (P2) on chromosome 3, found predominantly in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single queen (monogyne) background, and thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social ‘environments’ (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We also propose that miniaturized queens, 16-20% smaller than queens without 9r, could be incipient intraspecific social parasites.

Significance statement

When sets of gene variants work well together, selection may lead to a reduction in recombination between them. Here, we discover a novel supergene region on chromosome 9 that controls a previously undescribed queen size polymorphism inFormica cinereaants. The haplotype that is found in small queens, 9r, is tightly linked to a supergene haplotype on chromosome 3 that is found in multi-queen colonies. We propose that the region of suppressed recombination expanded to include both chromosome 3 and chromosome 9 because small queens could be successful in the multi-queen but not in the single-queen environment.
A Computational Study of the Role of Counterions and Solvent Dielectric in Determining the Conductance of B-DNA
Authors: Wang Yiren , Demir Busra , Mohammad Hashem , Oren Ersin Emre , Anantram M.P.
Published: April 2023

DNA naturally exists in a solvent environment, comprised of water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the Sodiumion (Na+), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment on charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.
Similar deamination activity but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells
Authors: Rodríguez Milaid Granadillo , Wong Lai , Chelico Linda
Published: April 2023

APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells, to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation andin vitrodeamination. Cell migration, and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activityin vitro. Notably, in nuclear lysates thein vitrodeaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to A3B and A3H in whole cell lysates. Their similar activities in cells nonetheless resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show thatin vitrodeamination data does not always reflect in cell deamination, all three A3s induce somatic mutagenesis, and the impact of each is different.
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
Authors: Müller-Dott Sophia , Tsirvouli Eirini , Vázquez Miguel , Ramirez Flores Ricardo O. , Badia-i-Mompel Pau , Fallegger Robin , Lægreid Astrid , Saez-Rodriguez Julio
Published: April 2023

Gene regulation plays a critical role in the cellular processes that underlie human health and disease. The regulatory relationship between transcription factors (TFs), key regulators of gene expression, and their target genes, the so called TF regulons, can be coupled with computational algorithms to estimate the activity of TFs. However, to interpret these findings accurately, regulons of high reliability and coverage are needed. In this study, we present and evaluate a collection of regulons created using the CollecTRI meta-resource containing signed TF-gene interactions for 1,183 TFs. In this context, we introduce a workflow to integrate information from multiple resources and assign the sign of regulation to TF-gene interactions that could be applied to other comprehensive knowledge bases. We find that the signed CollecTRI-derived regulons outperform other public collections of regulatory interactions in accurately inferring changes in TF activities in perturbation experiments. Furthermore, we showcase the value of the regulons by investigating hallmarks of TF activity profiles inferred from the transcriptomes of three different cancer types. Overall, the CollecTRI-derived TF regulons enable the accurate and comprehensive estimation of TF activities and thereby help to interpret transcriptomics data.

GRAPHICAL ABSTRACT
Connectivity-based Meta-Bands: A new approach for automatic frequency band identification in connectivity analyses
Authors: Rodríguez-González Víctor , Núñez Pablo , Gómez Carlos , Shigihara Yoshihito , Hoshi Hideyuki , Miguel Ángel Tola-Arribas , Cano Mónica , Ángel Guerrero , García-Azorín David , Hornero Roberto , Poza Jesús
Published: April 2023

The majority of electroencephalographic (EEG) and magnetoencephalographic (MEG) studies filter and analyse neural signals in specific frequency ranges, known as “canonical” frequency bands. However, this segmentation, is not exempt from limitations, mainly due to the lack of adaptation to the neural idiosyncrasies of each individual. In this study, we introduce a new data-driven method to automatically identify frequency ranges based on the topological similarity of the frequency-dependent functional neural network. The resting-state neural activity of 195 cognitively healthy subjects from three different databases (MEG: 123 subjects; EEG1: 27 subjects; EEG2: 45 subjects) was analysed. In a first step, MEG and EEG signals were filtered with a narrow-band filter bank (1 Hz bandwidth) from 1 to 70 Hz with a 0.5 Hz step. Next, the connectivity in each of these filtered signals was estimated using the orthogonalized version of the amplitude envelope correlation to obtain the frequency-dependent functional neural network. Finally, a community detection algorithm was used to identify communities in the frequency domain showing a similar network topology. We have called this approach the “Connectivity-based Meta-Bands” (CMB) algorithm. Additionally, two types of synthetic signals were used to configure the hyper-parameters of the CMB algorithm. We observed that the classical approaches to band segmentation reflect the underlying network topologies at group level for the MEG signals, but they fail to adapt to the individual differentiating patterns revealed by our methodology. On the other hand, the sensitivity of EEG signals to reflect this underlying frequency-dependent network structure is limited. To the best of our knowledge, this is the first study that proposes an unsupervised band segmentation method based on the topological similarity of functional neural network across frequencies. This methodology fully accounts for subject-specific patterns, providing more robust and personalized analyses, and paving the way for new studies focused on exploring the frequency-dependent structure of brain connectivity.
Vangl2 suppresses NF-κB signaling and ameliorates sepsis by targeting p65 for NDP52-mediated autophagic degradation
Authors: Lu Jiansen , Zhang Jiahuan , Jiang Huaji , Hu Zhiqiang , Zhang Yufen , He Lian , Yang Jianwu , Xie Yingchao , Wu Dan , Li Hongyu , Zeng Ke , Tan Peng , Xiao Qingyue , Song Zijing , Pan Chenglong , Bai Xiaochun , Yu Xiao
Published: April 2023

Van Gogh-like 2 (Vangl2), a core planar cell polarity (PCP) component, plays an important role in polarized cellular and tissue morphology induction, growth development and cancer. However, its role in regulating inflammatory responses remains elusive. Here, we report that Vangl2 is upregulated in patients with sepsis and identify Vangl2 as a negative regulator of NF-κB signaling by regulating the protein stability and activation of the core transcription component p65. Mice with myeloid-specific deletion of Vangl2 (Vangl2ΔM) are hypersusceptible to lipopolysaccharide (LPS)-induced septic shock. Vangl2 deficient myeloid cells exhibit enhanced phosphorylation and expression of p65, therefore, promoting the secretion of pro-inflammatory cytokines after LPS stimulation. Mechanistically, NF-κB signaling-induced-Vangl2 recruits E3 ubiquitin ligase PDLIM2 to catalyze K63-linked ubiquitination on p65, which serves as a recognition signal for cargo receptor NDP52-mediated selective autophagic degradation. Taken together, these findings demonstrate Vangl2 as a suppressor of NF-κB mediated inflammation and provide insights into the crosstalk between autophagy and inflammatory diseases.
Characterization of regeneration initiating cells duringXenopus laevistail regeneration
Authors: Radek Sindelka , Pavel Abaffy , Daniel Zucha , Ravindra Naraine , Daniel Kraus , Jiri Netusil , Karel Smetana , Lacina Lukas , Beduya Endaya Berwini , Jiri Neuzil , Martin Psenicka , Mikael Kubista
Published: April 2023

Embryos are regeneration and wound healing masters. They not only rapidly close their wounds, remodel injured tissue without a scar, but also regenerate body parts. Many animal models with variable regenerative capabilities have already been studied. Additionally, with the introduction of high throughput techniques, novel regeneration mechanisms including genes and signaling pathways, and specialized cell types required for regeneration control in spatial and temporal aspects have been identified. Until now our knowledge has been limited to primarily the late phases of regeneration (> 1 day post injury). In this paper, we reveal the critical steps for regeneration initiation. We have discovered Regeneration Initiating Cells (RICs) using single cell and spatial transcriptomic analyses during tail regeneration inXenopus laevis. RICs are formed transiently from the basal epidermal cells and are critical for the modification of the surrounding extracellular matrix to allow for migration of other cell types such as regeneration organizing cells that further promote regeneration. Absence or deregulation of RICs leads to excessive extracellular matrix deposition and regeneration defects.
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

Switch/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

Background

Determining 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.

Results

We 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.

Conclusions

QUEEN 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

Fluorescence 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 statement

This 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

The 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

The 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

Monitoring 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

Histone 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

The 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

Type 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

Sterol-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

Single-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 summary

Aneuploidy 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

A 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

The 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

The 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 STATEMENT

The vasopressin type 2 receptor promotes dual Gαsand Gαq/11signaling at early endosomes in β-arrestin-dependent and -independent manners.
Livestock species rather than grazing intensity shape plant guild proportions in interaction with multiple environmental drivers in grassland from the Pyrenees
Authors: Rodríguez Antonio , Ibanez Mercedes , Chocarro Cristina , Sebastià M.‐Teresa
Published: April 2023

Questions

Does grazing management shape the proportion of plant guilds (grasses, legumes, forbs and sedges) in mountain grasslands?

Which properties of grazing management have the greatest effect on the proportion of plant guilds: grazer diversity/identity or grazing intensity?

Are the effects of grazing management on guild proportion modified by other environmental variables that explain plant guild distribution at broad spatial scales?

Location

Mountains in the Pyrenees.

Methods

We modelled the proportion of grasses, legumes, forbs and sedges using data from the PASTUS database (n = 96), which contains a wide range of environmental and management conditions due to the high variety of environmental conditions in mountain grasslands in the Pyrenees. We used a machine‐learning algorithm to find those variables that best explained the proportions of each plant guild. We focussed on the differences between the levels of grazing intensity and the grazing species included in the model, and on detecting interactions between grazing variables and climate, topography and soil conditions.

Results

The proportion of forbs and grasses strongly depended on the grazing livestock species at broad spatial scales. Only soil pH showed a higher overall explanatory power on guild distribution. In general, forbs were favoured in cattle‐ and grasses in sheep‐grazed grasslands, the latter also being favoured on acidic soils, while forbs were favoured in more alkaline soil conditions. However, the effects of those factors (grazing species and soil pH) were modulated through interactions with several other environmental variables, including soil Mg, K and P, and terrain slope. In contrast, grazing intensity was a minor driver of guild distribution.

Conclusions

Our results provide information about the relationship between plant functional diversity, indicated by the different plant guild proportions, and grazing management in the Pyrenean grasslands. This information could be useful for developing hypotheses for future experimental studies and for designing policies to improve the management of mountain grasslands.
Application of AIS‐ and flyover‐based methods to monitor illegal and legal fishing in Canada's Pacific marine conservation areas
Authors: Iacarella Josephine C. , Burke Lily , Clyde Georgia , Wicks Adam , Clavelle Tyler , Dunham Anya , Rubidge Emily , Woods Paul
Published: April 2023

New approaches are required to undertake the substantial task of monitoring ongoing fishing activity in marine conservation areas to ensure conservation goals are achieved. To address this need, we applied previously developed, yet currently underused, vessel tracking methods based on Automatic Identification System (AIS) and aerial surveillance (“flyovers”) to Canada's Pacific marine conservation areas from 2012 to 2019. We used satellite and terrestrial‐based AIS receivers and flyover‐based visual observations to estimate illegal and legal fishing activity after 185 conservation area (CA) enactments (i.e., static, geographically defined areas with fishing regulations). We compared the effectiveness in detecting fishing activity between the AIS‐ and flyover‐based methods, and used the latter to determine that 93% of vessels were actively fishing in CAs without AIS. The AIS‐based method still detected 3303 h of fishing in CAs after enactment, and both methods estimated 22%–24% of fishing activity in CAs was illegal. The application of these methods also shed light on the complexity of fishing regulations across CAs (i.e., varying and CA‐specific restrictions). This highlighted the need to better align vessel tracking fishing gear classifications with CA regulation specifications, and conversely to simplify regulations (e.g., no‐take), for more accurate monitoring and evaluation moving forward.
Deep brain stimulation of fornix in Alzheimer's disease: From basic research to clinical practice
Authors: Liu Zhikun , Shu Kai , Geng Yumei , Cai Chang , Kang Huicong
Published: April 2023

Alzheimer's disease (AD) is one of the most common progressive neurodegenerative diseases associated with the degradation of memory and cognitive ability. Current pharmacotherapies show little therapeutic effect in AD treatment and still cannot prevent the pathological progression of AD. Deep brain stimulation (DBS) has shown to enhance memory in morbid obese, epilepsy and traumatic brain injury patients, and cognition in Parkinson's disease (PD) patients deteriorates during DBS off. Some relevant animal studies and clinical trials have been carried out to discuss the DBS treatment for AD. Reviewing the fornix trials, no unified conclusion has been reached about the clinical benefits of DBS in AD, and the dementia ratings scale has not been effectively improved in the long term. However, some patients have presented promising results, such as improved glucose metabolism, increased connectivity in cognition‐related brain regions and even elevated cognitive function rating scale scores. The fornix plays an important regulatory role in memory, attention, and emotion through its complex fibre projection to cognition‐related structures, making it a promising target for DBS for AD treatment. Moreover, the current stereotaxic technique and various evaluation methods have provided references for the operator to select accurate stimulation points. Related adverse events and relatively higher costs in DBS have been emphasized. In this article, we summarize and update the research progression on fornix DBS in AD and seek to provide a reliable reference for subsequent experimental studies on DBS treatment of AD.
Principal component analysis for particle size‐based classification of gorgon nut flour and their morphological, structural, thermal and pasting characteristics
Authors: Sharma Rajiv , Kotwaliwale Nachiket , Jindal Navdeep , Saxena Dharmesh C.
Published: April 2023

The effect of differential particle size on morphological, structural, thermal and pasting properties of raw gorgon nut flour was studied. Flour was sieved into five size fractions (250–75 μm). XRD spectra were of “A” type with strong diffraction peaks at 15 & 23, and an unresolved doublet at 17 & 18 degree. A strong negative correlation was observed between relative crystallinity and amylose content. The peak glass transition temperature (70.13–78.81 °C) and enthalpy (12.06–60.96 J g−1) differed significantly. Among all fractions, the peak viscosity, trough viscosity, onset temperature, enthalpy, peak & conclusion temperature, and amylose content were inversely correlated to setback, breakdown, relative crystallinity, pasting temperature, and pasting time of gorgon nut flour. Principal component analysis categorised flour fractions into three distinct sub‐groups viz. coarse (<250 μm), medium (<180 μm), and fine (<106 μm), exhibiting diverse behaviour. It could be inferred that peak viscosity and setback of finer fractions could be considered as the key property of gorgon nut flour. The finer fractions may be appropriate for sauces and soups whereas, coarser fractions may be used to prepare stronger dough for baked products.
Volarisation of Brewer's spent grain for noodles preparation and its potential assessment against obesity
Authors: Anisha Anisha , Kaushik Deepika , Kumar Mukul , Kumar Ashwani , Esatbeyoglu Tuba , Proestos Charalampos , Khan Mohammad Rizwan , Elobeid Tahra , Kaur Jasjit , Oz Fatih
Published: April 2023

Brewer's spent grain is the most prevalent low‐cost by‐product of brewing industry, contributing to about 85% of all by‐products produced. It is of interest for food industry applications because of its high nutritional value (fibres, protein and bioactive substances). The objective of this study was to determine the effects of different brewer's spent grain composition usage on various quality criteria of noodles as well as to investigate the possible usage opportunities and assessments of them in the production of noodles against obesity. For this purpose, noodle production was carried out using five different compositions of brewer's spent grain barley, barley and wheat, barley and rice, barley and maize, barley and finger millets, all at different concentrations (5%, 10%, 15% and 20%). Various quality criteria of the noodles were determined. Noodles made with the addition of barley and maize spent grains were found to be high in physio‐chemical and nutritional properties, and amylase and lipase inhibition assay. Concentration above 15% of spent grains affected the texture of the noodles. From the sensory evaluation, 10% concentration of barley and maize noodles was selected as it had good texture, colour and appearance. It was comparatively good in taste and aroma from other samples.