bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin-modifying enzymes as modulators of nuclear size during lineage differentiation
Authors: Meng Lingjun
Published: May 2022

The mechanism of nuclear size determination and alteration during normal lineage development and cancer pathologies which is not fully understood. As recently reported, chromatin modification can change nuclear morphology. Therefore, we screened a range of pharmacological chemical compounds that impact the activity of chromatin-modifying enzymes, in order to get a clue of the specific types of chromatin-modifying enzymes that remarkably effect nuclear size and shape. We found that interrupted activity of chromatin-modifying enzymes is associated with nuclear shape abnormalities. Furthermore, the activity of chromatin-modifying enzymes perturbs cell fate determination in cellular maintenance and lineage commitment. Our results indicated that chromatin-modifying enzyme regulates cell fate decision during lineage differentiation and is associate with nuclear size alteration.

Significance

Here we described for the first time the modulation of chromatin-modifying enzymes remarkably effects nuclear shape, and perturbs cell fate determination in cellular maintenance and lineage fate commitment in normal stem cells and leukemia cancer cells. We found that the irregularities of nuclear contour were highly related to pharmacological inhibition of chromatin-modifying enzyme activity. After manipulating a histone demethylase named GASC1, we found that upregulation of GASC1 impairs the differentiation of hESCs to terminally differentiated neural cells. Moreover, upregulation of GASC1 impairs the proliferation of leukemia cells due to cell cycle arrest in the G0/G1 phase and indicates misshapen nuclei. This study suggested that chromatin-modifying enzyme regulates the nuclear contour related cell fate decision also including cancer cell fate determination.
Hepatic AMPK activation in response to dynamic REDOX balance is a biomarker of exercise to improve blood glucose control
Authors: Wu Meiling , Zhao Anda , Yan Xingchen , Gao Hongyang , Zhang Chunwang , Liu Xiaomin , Luo Qiwen , Xie Feizhou , Liu Shanlin , Shi Dongyun
Published: May 2022

Antioxidant intervention is considered to inhibit reactive oxygen species (ROS) and alleviates hyperglycemia. Paradoxically, moderate exercise can produce ROS to improve diabetes. The exact redox mechanism of these two different approaches remains largely unclear. Here, by comparing exercise and antioxidants intervention on type 2 diabetic rats, we found moderate exercise upregulated compensatory antioxidant capability and reached a higher level of redox balance in the liver. In contrast, antioxidant intervention achieved a low-level redox balance by inhibiting oxidative stress. Both of these two interventions could promote glycolysis and aerobic oxidation mediated by hepatic AMPK activation, ameliorating diabetes. During exercise, different levels of ROS generated by exercise have differential regulations on the activity and expression of hepatic AMPK. Moderate exercise-derived ROS promoted hepatic AMPK glutathionylation activation. However, excess exercise increased oxidative damage, and inhibited the activity and expression of AMPK. Overall, our results illustrate that both exercise and antioxidant intervention improve blood glucose in diabetes by promoting redox balance, despite the levels of redox balance are different. Moreover, the activation and expression of AMPK could act as a biomarker to reflect the effective treatment range for diabetes. This finding provides theoretical evidence for the precise regulation of diabetes by antioxidants and exercise.
The temporal dynamics of lncRNAFirre-mediated epigenetic and transcriptional regulation
Authors: Much Christian , Lasda Erika L. , Pereira Isabela T. , Vallery Tenaya K. , Ramirez Daniel , Lewandowski Jordan P. , Dowell Robin D. , Smallegan Michael J. , Rinn John L.
Published: May 2022

Numerous studies have now demonstrated that lncRNAs can influence gene expression programs leading to cell and organismal phenotypes. Typically, lncRNA perturbations and concomitant changes in gene expression are measured on the timescale of many hours to days. Thus, we currently lack a temporally grounded understanding of the primary, secondary, and tertiary relationships of lncRNA-mediated transcriptional and epigenetic regulation – despite being a prerequisite to elucidating lncRNA mechanisms. To begin to address when and where a lncRNA regulates gene expression, we genetically engineered cell lines to temporally induce the lncRNAFirre. Using this approach, we were able to monitor lncRNA transcriptional regulatory events from 15 min to four days. We observed that upon induction,FirreRNA regulates epigenetic and transcriptional states,in trans, within 30 min. These early regulatory events result in much larger transcriptional changes after twelve hours, well before current studies monitor lncRNA regulation. Moreover,Firre-mediated gene expression changes are epigenetically remembered for days. Overall, this study suggests that lncRNAs can rapidly regulate gene expression by establishing persistent epigenetic and transcriptional states.
MaLAdapt reveals novel targets of adaptive introgression from Neanderthals and Denisovans in worldwide human populations
Authors: Zhang Xinjun , Kim Bernard , Singh Armaan , Sankararaman Sriram , Durvasula Arun , Lohmueller Kirk E.
Published: May 2022

Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, these outlier-based approaches are vulnerable to a high false-negative rate as the power of different methods vary, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals as AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present an ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selection sweeps, heterosis, and demographic misspecifications. Further, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and on a validation of empirical signals through visual impaction of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data, and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.
Prophylactic treatment of Glycyrrhiza glabra mitigates COVID-19 pathology through inhibition of pro-inflammatory cytokines in the hamster model and NETosis
Authors: Rizvi Zaigham Abbas , Babele Prabhakar , Sadhu Srikanth , Madan Upasna , Tripathy Manas Ranjan , Goswami Sandeep , Mani Shailendra , Kumar Sachin , Awasthi Amit , Dikshit Madhu
Published: May 2022

Severe coronavirus disease (COVID-19) is accompanied with acute respiratory distress syndrome & pulmonary pathology, and is presented mostly with inflammatory cytokine release, dysregulated immune response, skewed neutrophil/ lymphocyte ratio, and hypercoagulable state. Though vaccinations have proved effective in reducing the COVID-19 related mortality, the limitation of use of vaccine against immunocompromised, comorbidity, and emerging variants remains a concern. In the current study we investigate for the first-time the efficacy of Glycyrrhiza glabra (GG) extract, a potent immunomodulator, against SARS-CoV-2 infection in hamsters. Prophylactic treatment with GG showed protection against loss in body weight and 35-40% decrease in lung viral load along with reduced lung pathology in the hamster model. Remarkably, GG reduced the mRNA expression of pro-inflammatory cytokines and Plasminogen activator inhibito-1 (PAI-1). In-vitro, GG acted as potent immunomodulator by reducing Th2 and Th17 differentiation and IL-4 and IL-17A cytokine production. In addition, GG also showed robust potential to suppress ROS, mtROS and NETs generation in a concentration dependent manner in both human polymorphonuclear neutrophils (PMNs) and murine bone marrow derived neutrophils (BMDNs). Taken together, we provide evidence for the protective efficacy of GG against COVID-19 and its putative mechanistic insight, which might be developed as a future immunomodulatory approach against various pathologies with high cytokine production, aberrant neutrophil activation including coronavirus infection.
Enzymatically-active bacterial microcompartments follow substrate gradients and are protected from aggregation in a cell-free system
Authors: Steinkühler Jan , Abrahamson Charlotte H. , Agudo-Canalejo Jaime , Golestanian Ramin , Tullman-Ercek Danielle , Kamat Neha P.
Published: May 2022

The ability to dynamically control organelle movement and position is essential for cellular function. Yet the underlying mechanisms driving this organization have not been fully resolved. Here, we draw from recent experimental observations and theoretical models of enzyme chemotaxis to demonstrate the chemotaxis of a bacterial organelle, the 1,2 propanediol (1,2-PD) utilization bacterial microcompartment (MCP) from Salmonella enterica. Upon encapsulating MCPs in a cell-like, biomimetic compartment, we observed the directed movement of MCPs along an external gradient of substrate. Our analysis shows that MCPs not only chemotax towards their substrate but also that enzymatic activity and substrate turnover protect them against large-scale aggregation. Our results provide a first experimental demonstration of organelle chemotaxis in a synthetic cellular system and support a recent theoretical model of chemotaxis. Together this work reveals a potentially significant driver of organelle organization while contributing to the construction of synthetic cell-like materials.
De Novo Protein Fold Design Through Sequence-Independent Fragment Assembly Simulations
Authors: Pearce Robin , Huang Xiaoqiang , Omenn Gilbert S. , Zhang Yang
Published: May 2022

De novo protein design generally consists of two steps, including structure and sequence design. However, many protein design studies have focused on sequence design with scaffolds adapted from native structures in the PDB, which renders novel areas of protein structure and function space unexplored. Here we developed FoldDesign to create novel protein folds from specific secondary structure (SS) assignments through sequence-independent replica-exchange Monte Carlo (REMC) simulations. The method was tested on 354 non-redundant topologies, where FoldDesign consistently created stable structural folds, while recapitulating on average 87.7% of the SS elements. Meanwhile, the FoldDesign scaffolds had well-formed structures with buried residues and solvent exposed areas that closely matched their native counterparts. Despite the high fidelity to the input SS restraints and local structural characteristics of native proteins, a large portion of the designed scaffolds possessed global folds that were completely different from natural proteins in the PDB, highlighting the ability of FoldDesign to explore novel areas of protein fold space. Detailed data analyses demonstrated that the major contributions to the successful fold design lay in the optimal energy force field, which contains a balanced set of fragment and secondary structure packing terms, and the REMC simulations, which utilize multiple auxiliary movements to efficiently search the conformational space. These results demonstrate FoldDesign’s strong potential to explore both structural and functional space through computational design simulations that natural proteins have not reached through evolution.

Significance

Natural proteins were generated following billions of years of evolution and therefore possess limited structural folds and biological functions. There is considerable interest in de novo protein design to generate artificial proteins with novel structures and functions beyond those created by nature. However, the success rate of computational de novo protein design remains low, where extensive user-intervention and large-scale experimental optimization are typically required to achieve successful designs. To address this issue, we developed a new automated open-source program, FoldDesign, for de novo protein fold design which shows improved performance in creating high fidelity stable folds compared to other state-of-the-art methods. The success of FoldDesign should enable the creation of desired protein structures with promising clinical and industrial potential.
Investigating and Modeling the Factors that Affect Genetic Circuit Performance
Authors: Zilberzwige-Tal Shai , Fontanarrosa Pedro , Bychenko Darya , Dorfan Yuval , Gazit Ehud , Myers Chris J.
Published: May 2022

Over the past two decades, synthetic biology has yielded ever more complex genetic circuits able to perform sophisticated functions in response to specific signals. Yet, genetic circuits are not immediately transferable to an outside-the-lab setting where their performance is highly compromised. We propose introducing a scale step to the design-build-test workflow to include factors that might contribute to unexpected genetic circuit performance. As a proof-of-concept, we designed and tested a genetic circuit under different temperatures, mediums, inducer concentrations, and bacterial growth phases. We determined that the circuit’s performance is dramatically altered when these factors differ from the optimal lab conditions. Based on these results, a scaling effort, coupled with a learning process, proceeded to generate model predictions for the genetic circuit’s performance under untested conditions, which is currently lacking in synthetic biology application design. As the synthetic biology discipline transitions from proof-of-concept genetic programs to appropriate and safe application implementations, more emphasis on a scale step is needed to ensure correct and robust performances.
In-VitroEfficacy of Targeted FODMAP Enzymatic Digestion (FODZYME®) in a High-Fidelity Simulated Gastrointestinal Environment
Authors: Ochoa Kenny Castro , Samant Shalaka , Liu Anjie , Duysburgh Cindy , Marzorati Massimo , Singh Prashant , Hachuel David , Chey William , Wallach Thomas
Published: May 2022

Introduction

Irritable bowel syndrome (IBS) is characterized by abdominal pain and changes in bowel habits. FODMAPs are poorly absorbed short-chain carbohydrates that may drive commensal microbial gas production, promoting abdominal pain in IBS. Low-FODMAP diet can result in symptomatic improvement in 50-80% of IBS patients. However, this diet is not meant to be sustained long term, with concern for downstream nutrition and microbial issues. In this study, we evaluate the function of a targeted FODMAP enzymatic digestion food supplement FODZYME® containing an fructan hydrolase enzyme in a simulated gastrointestinal environment.

Methods

Using SHIME®, a multi-compartment simulator of the human gut, FODZYME® dose finding assay in modeled gastrointestinal conditions assessed enzymatic ability to hydrolyze 3 g of inulin. Full intestinal modeling assessing digestion of inulin, absorption of fructose, gas production and other measures of commensal microbial behavior was completed using 1.125 g of FODZYME®.

Results

After 30 minutes, 90% of the inulin was converted to fructose by 1.125 g of FODZYME®.Doubling dosage showed no significant improvement in conversion, whereas a half dose decreased performance to 77.2%. 70% of released fructose was absorbed during simulated small intestinal transit, with a corresponding decrease in microbial gas production, and a small decrease in butyrate and short chain fatty acid (SCFA) production.

Discussion

FODZYME® specifically breaks down inulin in representative gastrointestinal conditions, resulting in decreased gas production while substantially preserving SCFA and butyrate production in the model colon. Our results suggest dietary supplementation with FODZYME® would decrease intestinal FODMAP burden and gas production.
Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria
Authors: Gómez-Pérez Daniel , Schmid Monja , Chaudhry Vasvi , Velic Ana , Maček Boris , Kemen Ariane , Kemen Eric
Published: May 2022

Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein-based, are not well understood. We hypothesize that secreted proteins are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through secretion of proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo colonized leaves combined with machine-learning predictors enabled the selection of candidates for heterologous expression and study of their inhibitory activity. We found that three of the candidate proteins show selective antimicrobial activity on gram-positive bacteria isolated from Arabidopsis thaliana and that these inhibited bacteria are important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulations of the microbiome.
Unsupervised outlier detection applied to SARS-CoV-2 nucleotide sequences can identify sequences of common variants and other variants of interest
Authors: Hahn Georg , Lee Sanghun , Prokopenko Dmitry , Abraham Jonathan , Novak Tanya , Hecker Julian , Cho Michael , Khurana Surender , Baden Lindsey R. , Randolph Adrienne G. , Weiss Scott T. , Lange Christoph
Published: May 2022

As of June 2022, the GISAID database contains more than one million SARS-CoV-2 genomes, including several thousand nucleotide sequences for the most common variants such as delta or omicron. These SARS-CoV-2 strains have been collected from patients around the world since the beginning of the pandemic. We start by assessing the similarity of all pairs of nucleotide sequences using the Jaccard index and principal component analysis. As shown previously in the literature, an unsupervised cluster analysis applied to the SARS-CoV-2 genomes results in clusters of sequences according to certain characteristics such as their strain or their clade. Importantly, we observe that nucleotide sequences of common variants are often outliers in clusters of sequences stemming from variants identified earlier on during the pandemic. Motivated by this finding, we are interested in applying outlier detection to nucleotide sequences. We demonstrate that nucleotide sequences of common variants (such as alpha, delta, or omicron) can be identified solely based on a statistical outlier criterion. We argue that outlier detection might be a useful surveillance tool to identify emerging variants in real time as the pandemic progresses.
Primary cilia regulate Meibomian glands development and dimensions without impairing lipid composition of the meibum
Authors: Portal Céline , Lin Yvonne , Rastogi Varuni , Peterson Cornelia , Foster James , Wilkerson Amber , Butovich Igor , Iomini Carlo
Published: May 2022

Purpose

Primary cilia regulate the development of various ectoderm-derived tissues, including the corneal epithelium, skin, hair follicle and sebaceous glands. We aimed to investigate their role in meibomian gland (MG) development.

Methods

Primary cilium ablation in MGs was achieved by crossing a floxed Ift88 mouse (Ift88fl/fl) with a mouse expressing the Cre recombinase under the keratin 14 (K14) promoter, to generateK14-Cre;Ift88fl/flmice. MG morphology was evaluated by histology and immunostaining, as well as lipid staining and 2-photon microscopy on whole mount tarsal plates. MG lipid profiles were assessed by chromatography.

Results

We showed that most of MG cells are ciliated during early stages of MG development and that MG ciliated rate decreases throughout morphogenesis. In morphologically mature glands, only the MG central duct and ductules are ciliated, and meibocytes lose their cilia as they differentiate and become filled with lipids. Primary cilium ablation induces enlargement of MGs, dilation of the MG central duct, and an increased production of lipids, without dramatically changing the lipid profiles. In addition, primary cilia regulate MG elongation and the spatial distribution of proliferating and dying cells within MGs, without changing the total cell proliferation and death rates.

Conclusions

These findings indicate that primary cilia are not necessary for normal MG development. However, they promote MG enlargement and lipid production, suggesting that primary cilia could be an interesting target for treatments of ocular surface diseases involving MGs, like dry eye disease.
Activity of Tricyclic Pyrrolopyrimidine Gyrase B Inhibitor against Mycobacterium abscessus
Authors: Madani Abdeldjalil , Negatu Dereje A. , El Marrouni Abdellatif , Miller Randy R. , Boyce Christopher , Murgolo Nicholas , Bungard Christopher J. , Zimmerman Matthew D. , Dartois Véronique , Gengenbacher Martin , Olsen David B. , Dick Thomas
Published: May 2022

Tricyclic pyrrolopyrimidines (TPPs) are a new class of antibacterials inhibiting the ATPase of DNA gyrase. TPP8, a representative of this class, is active against Mycobacterium abscessus in vitro. Spontaneous TPP8 resistance mutations mapped to the ATPase domain of M. abscessus DNA gyrase and the compound inhibited DNA supercoiling activity of recombinant M. abscessus enzyme. Further profiling of TPP8 in macrophage and mouse infection studies demonstrated proof-of-concept activity against M. abscessus ex vivo and in vivo.
Enhancement of Cell Adhesion by Anaplasma phagocytophilum Nucleolin-interacting Protein AFAP
Authors: Tang Hongcheng , Zhu Jiafeng , Wu Shuyan , Niu Hua
Published: May 2022

Anaplasma phagocytophilum, the aetiologic agent of human granulocytic anaplasmosis (HGA) is an obligate intracellular Gram-negative bacterium. During infection, A. phagocytophilum enhances the adhesion of neutrophils to infected endothelial cells. However the bacterial factors contributing to this phenomenon remain unknown. In this study, we characterized a type IV secretion system substrate of A. phagocytophilum, AFAP (an actin filament-associated Anaplasma phagocytophilumprotein), and found it enhanced cell adhesion. Tandem affinity purification combined with mass spectrometry identified host nucleolin as an AFAP-binding protein. Further study showed disruption of nucleolin by RNA interference and treatment of a nucleolin-binding DNA aptamer AS1411 attenuated AFAP-mediated cell adhesion. The characterization of AFAP with enhancement effect on cell adhesion and identification of its interaction partner may help understand the mechanism underlying A. phagocytophilum-promoting cell adhesion, facilitating elucidation of HGA pathogenesis.

Highlights

Anaplasma phagocytophilum AFAP localized to cell periphery.

AFAP enhanced cell adhesion.

AFAP interacted with host nucleolin.

Disruption of nucleolin attenuated AFAP-mediated cell adhesion.
Genome dynamics in mosses: Extensive synteny coexists with a highly dynamic gene space
Authors: Kirbis Alexander , Rahmatpour Nasim , Dong Shanshan , Yu Jin , van Gessel Nico , Waller Manuel , Reski Ralf , Lang Daniel , Rensing Stefan A. , Temsch Eva M. , Wegrzyn Jill L. , Goffinet Bernard , Liu Yang , Szövényi Péter
Published: May 2022

Background

While genome evolutionary processes of seed plants are intensively investigated, very little is known about seed-free plants in this respect. Here, we use one of the largest groups of seed-free plants, the mosses, and newly generated chromosome-scale genome assemblies to investigate three poorly known aspects of genome dynamics and their underlying processes in seed-free plants: (i) genome size variation, (ii) genomic collinearity/synteny, and (iii) gene set differentiation.

Results

Comparative genomic analyses on the model moss Physcomitrium (Physcomitrella) patens and two genomes of Funaria hygrometrica reveal that, like in seed plants, genome size change (approx. 140 Mbp) is primarily due to transposable element expansion/contraction. Despite 60 million years of divergence, the genomes of P. patens and F. hygrometrica show remarkable chromosomal stability with the majority of homologous genes located in conserved collinear blocks. In addition, both genomes contain a relatively large set of lineage-specific genes with no detectible homologs in the other species’ genome, suggesting a highly dynamic gene space fueled by the process of de novo gene birth and loss rather than by gene family diversification/duplication.

Conclusions

These, combined with previous observations suggest that genome dynamics in mosses involves the coexistence of a collinear homologous and a highly dynamic species-specific gene sets. Besides its significance for understanding genome evolution, the presented chromosome-scale genome assemblies will provide a foundation for comparative genomic and functional studies in the Funariaceae, a family holding historical and contemporary model taxa in the evolutionary biology of mosses.
Radiation-Induced Metabolic Reprogramming of Fibroblasts Regulates the Breast Cancer Microenvironment
Authors: Corn Kevin C. , Britto Lucy S. , Mohamed Youssef K. , Ivanova Yoanna I. , Zhu Tian , Rafat Marjan
Published: May 2022

Patients with triple negative breast cancer (TNBC) continue to have high recurrence rates despite current interventions, including radiation therapy (RT). Radiation-resistant TNBC cells and circulating tumor cells thought to be involved in recurrence survive due to changes in their metabolic profiles, which may be influenced by their interactions with radiation-damaged stromal cells, such as fibroblasts, following treatment. How fibroblasts metabolically respond to RT and influence the metabolism of TNBC cells is poorly understood. In this study, we identify that radiation-damaged fibroblasts accumulate lipids due to increased autophagic flux. The radiation damage response allows fibroblasts to maintain increased fatty acid oxidation, overall mitochondrial respiration, and aerobic glycolysis rates, leading to increased lactate secretion. TNBC cells respond to these metabolic changes by increasing migration rates and tumor spheroid growth. Our work reveals how metabolic crosstalk between irradiated fibroblasts and TNBC cells leads to a microenvironment conducive to recurrence.

Although radioresistant and circulating tumor cell survival has been attributed to altered metabolism, the metabolic impact of radiation therapy on stromal cells is unknown. The authors provide a burgeoning mechanism for radiation-induced metabolic crosstalk between fibroblasts and breast cancer cells that may influence recurrence.

Graphical Abstract
Substrate adhesion determines migration during mesenchymal cell condensation in chondrogenesis
Authors: Casanellas Ignasi , Jiang Hongkai , David Carolyn M. , Vida Yolanda , Pérez-Inestrosa Ezequiel , Samitier Josep , Lagunas Anna
Published: May 2022

Effective cartilage development relies on the successful formation of mesenchymal cell condensates. Mesenchymal condensation is a prevalent morphogenetic transition, which involves the upregulation of the adhesive extracellular glycoprotein fibronectin (FN). During condensation, there is an active directional migration of cells from the surrounding loose mesenchyme towards regions of increasing matrix adherence (the condensation centers). In this study, we live imaged the first 40 h of mesenchymal condensation during chondrogenesis on nanopatterns of the cell-adhesive peptide arginine-glycine-aspartic acid (RGD), present in FN. Results show cell-substrate adhesions modulate both single-cell and collective cell migration during mesenchymal condensation. Single cell tracking analysis showed that substrate adhesion determines the migration mode, protrusion formation and the directionality of the cell movement. Cells on the more adhesive nanopatterns presented traits among amoeboid and mesenchymal modes of migration facilitating a more directional movement and reducing contact inhibition of locomotion (CIL), which allows merging and condensation. Inhibition experiments demonstrated that neural cadherin (N-Cad) is required in cell-cell interactions, enabling cells to coordinate their movement and directionality in a multicellular environment and to maintain the group cohesiveness during migration. Altogether, this contributes to create a sufficiently dynamic scenario, in which there is a balance between cell-substrate and cell-cell adhesions for condensates to grow. Our results provide a framework for the regulation of single and collective cell migration during mesenchymal condensation, through nanoscale cell-substrate adherence.

Summary statement

The fine tuning of substrate adherence through nanopatterning allows control of mesenchymal cell migration and determines condensation during chondrogenesis in vitro.
Pervasive tandem duplications and convergent evolution shape coral genomes
Authors: Noel Benjamin , Denoeud France , Rouan Alice , Buitrago-López Carol , Capasso Laura , Poulain Julie , Boissin Emilie , Pousse Mélanie , Da Silva Corinne , Couloux Arnaud , Armstrong Eric , Carradec Quentin , Cruaud Corinne , Labadie Karine , Lê-Hoang Julie , Tambutté Sylvie , Barbe Valérie , Moulin Clémentine , Bourdin Guillaume , Iwankow Guillaume , Romac Sarah ,   Tara Pacific Consortium Coordinators, Allemand Denis , Planes Serge , Gilson Eric , Zoccola Didier , Wincker Patrick , Voolstra Christian R , Aury Jean-Marc
Published: May 2022

Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to these ecosystems, providing habitat and food to a great diversity of species. In the frame of the Tara Pacific expedition, we generated two coral genomes,Porites lobataandPocillopora meandrinawith vastly improved contiguity that allowed us to study the functional organisation of these genomes. We annotated their gene catalog and report a relatively higher gene number (43,000 and 32,000 genes respectively) than that found in other public coral genome sequences. This finding is explained by a high number of tandemly duplicated genes (almost a third of the predicted genes). We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to immune system and disease-resistance, which we suggest to be functionally linked to coral host resilience. At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
Single cell kinetic modeling of redox-based drug metabolism in head and neck squamous cell carcinoma
Authors: Raddatz Andrew D. , Furdui Cristina , Bey Erik , Kemp Melissa L.
Published: May 2022

Head and neck squamous cell carcinoma (HNSCC) cells are highly heterogeneous in their metabolism and typically experience elevated reactive oxygen species (ROS) levels in the tumor microenvironment. The tumor cells survive under these chronic oxidative conditions by upregulating antioxidant systems compared to healthy cells. Radiation and the majority of chemotherapies used clinically for treatment of HNSCC rely directly or indirectly upon the generation of short-lived ROS to induce cancer cell death. To investigate the heterogeneity of cellular responses to chemotherapeutic ROS generation in tumor and healthy tissue, we leveraged single cell RNA-sequencing (scRNA-seq) data to perform redox systems-level simulations of quinone-cycling β-lapachone treatment as a source of NQO1-dependent rapid superoxide and hydrogen peroxide (H2O2) production. Transcriptomic data from 10 HNSCC patient tumors was used to populate over 4000 single cell antioxidant enzymatic models. The simulations reflected significant systems-level differences between the redox states of healthy and cancer cells, demonstrating in some patient samples a targetable cancer cell population or in others statistically indistinguishable effects between non-malignant and malignant cells. Subsequent multivariate analyses between healthy and malignant cellular models point to distinct contributors of redox responses between these phenotypes. This model framework provides a mechanistic basis for explaining mixed outcomes of NQO1-bioactivatable therapeutics despite the tumor specificity of these drugs as defined by NQO1/catalase expression.
A conserved enzyme of smut fungi facilitates cell-to-cell movement in the plant bundle sheath
Authors: Ökmen Bilal , Jaeger Elaine , Schilling Lena , Finke Natalie , Lee Yoon Joo , Wemhöner Raphael , Pauly Markus , Neumann Ulla , Doehlemann Gunther
Published: May 2022

The smut fungi are one of the largest groups of fungal plant pathogens, causing disease in all cereal crops. They directly penetrate their hosts and establish a biotrophic interaction. During colonization of the plant, smut fungi secrete a wide range of effector proteins, which suppress plant immunity and modulate cellular functions as well as development of the host, thereby determining the pathogen’s life-style and virulence potential.

The conserved effector Erc1 (enzyme required for cell-to-cell movement) contributes to virulence of the corn smut Ustilago maydis in maize leaves, but not on the tassel. Erc1 binds to host cell wall components and has a 1,3-β-glucanase activity, which is required to attenuate β-glucan-induced defense responses in host leaves. Confocal microscopy revealed that Erc1 has a cell type-specific virulence function, being necessary for fungal cell-to-cell movement in the plant bundle sheath. This cell type-specific virulence function of Erc1 is fully conserved in the barley pathogen Ustilago hordei, which has a functionally conserved Erc1 orthologue.

Thus, Erc1 is an enzymatically active core virulence factor with a cell type-specific virulence function in different hosts, which is important for cell-to-cell movement during host colonization of pathogenic smut fungi.
Extraintestinal roles of intestinal vitamin D receptor in protecting against dysbiosis and tumorigenesis in breast cancer
Authors: Zhang Yong-Guo , Zhang Jilei , Deb Shreya , Garrett Shari , Xia Yinglin , Sun Jun
Published: May 2022

The microbiota play critical roles in regulating the function and health of intestine and extraintestinal organs. A fundamental question is whether there is an intestinal-microbiome-breast axis during the development of breast cancer. If yes, what are the roles of host factors? Vitamin D receptor (VDR) involves host factors and the human microbiome. Vdr gene variation shapes the human microbiome and VDR deficiency leads to dysbiosis. We hypothesized that intestinal VDR protects hosts against tumorigenesis in breast. Reduced VDR mRNA expression was observed in patients with breast cancer. We used a 7,12-dimethylbenzanthracene (DMBA)-induced breast cancer model in intestinal epithelial VDR knockout (VDRΔIEC) mice. We reported that VDRΔIEC mice with dysbiosis are more susceptible to breast cancer induced by DMBA. Intestinal and breast microbiota analysis showed that lacking VDR leads to bacterial profile shift from normal to susceptible carcinogenesis. We found enhanced bacterial staining within breast tumors. At the molecular and cellular levels, we identified the mechanisms by which intestinal epithelial VDR deficiency led to increased gut permeability, disrupted tight junctions, microbial translocation, and enhanced inflammation, thus increasing the tumor size and number in breast. Furthermore, treatment with beneficial bacterial metabolite butyrate or probiotic Lactobacillus plantarum reduced the breast tumors, enhanced the tight junctions, and inhibited inflammation in the VDRΔIEC mice. Gut microbiome contribute to the pathogenesis of diseases, not only in the intestine, but also in the breast. Our study provides new insights into the mechanism by which intestinal VDR dysfunction and gut dysbiosis led to high risk of extraintestinal tumorigenesis. Gut-tumor-microbiome interactions indicate a new target in the prevention and treatment of breast cancer.

Abstract Figure
HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design
Authors: Panei F. P. , Torchet R. , Menager H. , Gkeka P. , Bonomi M.
Published: May 2022

RNA molecules are implicated in numerous fundamental biological processes and many human pathologies, such as cancer, neurodegenerative disorders, muscular diseases, and bacterial infections. Modulating the mode of action of disease-implicated RNA molecules can lead to the discovery of new therapeutical agents and even address pathologies linked to 8undruggable9 protein targets. This modulation can be achieved by direct targeting of RNA with small molecules. As of today, only a few RNA-targeting small molecules are used clinically. One of the main obstacles that has hampered the development of a rational drug design protocol to target RNA with small molecules is the lack of a comprehensive understanding of the molecular mechanisms at the basis of RNA-small molecule recognition. Here, we present HARIBOSS, a curated collection of RNA-small molecule structures determined by X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-electron microscopy. HARIBOSS facilitates the exploration of drug-like compounds known to bind RNA, the analysis of ligands and pockets properties, and ultimately the development of in silico strategies to identify RNA-targeting small molecules. HARIBOSS can be explored via a web interface available at http://hariboss.pasteur.cloud.
Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep
Authors: Cheng Hong , Zhang Zhuangbiao , Wen Jiayue , Lenstra Johannes A. , Heller Rasmus , Cai Yudong , Guo Yingwei , Li Ming , Li Ran , Li Wenrong , He Sangang , Wang Jintao , Shao Junjie , Song Yuxuan , Zhang Lei , Billah Masum , Wang Xihong , Liu Mingjun , Jiang Yu
Published: May 2022

The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population due to reduced recombination.
The Proteomic Landscape of Genome-Wide Genetic Perturbations
Authors: Messner Christoph B. , Demichev Vadim , Muenzner Julia , Aulakh Simran , Röhl Annika , Herrera-Domínguez Lucía , Egger Anna-Sophia , Kamrad Stephan , Lemke Oliver , Calvani Enrica , Mülleder Michael , Lilley Kathryn S. , Kustatscher Georg , Ralser Markus
Published: May 2022

Functional genomic strategies help to address the genotype phenotype problem by annotating gene function and regulatory networks. Here, we demonstrate that combining functional genomics with proteomics uncovers general principles of protein expression, and provides new avenues to annotate protein function. We recorded precise proteomes for all non-essential gene knock-outs in Saccharomyces cerevisiae. We find that protein abundance is driven by a complex interplay of i) general biological properties, including translation rate, turnover, and copy number variations, and ii) their genetic, metabolic and physical interactions, including membership in protein complexes. We further show that combining genetic perturbation with proteomics provides complementary dimensions of functional annotation: proteomic profiling, reverse proteomic profiling, profile similarity and protein covariation analysis. Thus, our study generates a resource in which nine million protein quantities are linked to 79% of the yeast coding genome, and shows that functional proteomics reveals principles that govern protein expression.

Highlights

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Nine million protein quantities recorded in ~4,600 non-essential gene deletions in S. cerevisiae reveal principles of how the proteome responds to genetic perturbation

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Genome-scale protein expression is determined by both functional relationships between proteins, as well as common biological responses

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Broad protein expression profiles in slow-growing strains can be explained by chromosomal aneuploidies

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Protein half-life and ribosome occupancy are predictable from protein abundance changes across knock-outs

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Functional proteomics annotates missing gene function in four complementary dimensions
Identifying novel regulators of placental development using time series transcriptomic data and network analyses
Authors: Vu Ha T. H. , Kaur Haninder , Kies Kelby R. , Starks Rebekah R. , Tuteja Geetu
Published: May 2022

The placenta serves as a connection between the mother and the fetus during pregnancy, and provides the fetus with oxygen, nutrients, and growth hormones. However, the regulatory mechanisms and dynamic gene interaction networks underlying early placental development are understudied. Here, we generated RNA sequencing (RNA-seq) data from mouse fetal placenta tissues at embryonic day (e) 7.5, e8.5 and e9.5 to identify genes with timepoint-specific expression, then inferred gene interaction networks to analyze highly connected network modules. We determined that timepoint-specific gene network modules associated with distinct developmental processes, and with similar expression profiles to specific human placental cell populations. From each module, we obtained hub genes and their direct neighboring genes, which were predicted to govern placental functions. We confirmed that four novel candidate regulators identified through our analyses regulate cell migration in the HTR-8/SVneo cell line. Upon conclusion of this study, we were able to predict several novel regulators of placental development using network analysis of bulk RNA-seq data. Our findings and analysis approaches will be valuable for future studies investigating the transcriptional landscape of early placental development.
The Effects of Negative Periocular Pressure on Biomechanics of the Optic Nerve Head and Cornea: A Computational Modeling Study
Authors: Safa Babak N. , Bleeker Adam , Berdahl John P. , Ethier C. Ross
Published: May 2022

Purpose

To evaluate the effects of negative periocular pressure (NPP), and concomitant intraocular pressure (IOP) lowering, on the biomechanics of the optic nerve head (ONH) and cornea.

Methods

We developed a validated finite element (FE) model of the eye to compute tissue biomechanical strains induced in response to NPP delivered using the Multi-Pressure Dial (MPD) system. The model was informed by clinical measurements of IOP lowering and was based on published tissue properties. We also conducted sensitivity analyses by changing pressure loads and tissue properties.

Results

Application of -7.9 mmHg NPP decreased strain magnitudes in the ONH by c. 50% while increasing corneal strain magnitudes by c. 25%. Comparatively, a similar increase in corneal strain was predicted to occur due to an increase in IOP of 4 mmHg. Sensitivity studies indicated that NPP lowers strain in the ONH by reducing IOP and that these effects persisted over a range of tissue stiffnesses and spatial distributions of NPP.

Conclusions

NPP is predicted to considerably decrease ONH strain magnitudes. It also increases corneal strain but to an extent expected to be clinically insignificant. Thus, using NPP to lower IOP and hence decrease ONH mechanical strain is likely biomechanically beneficial for glaucoma patients.

Translational Relevance

This study provides the first description of how NPP affects ONH biomechanics and explains the underlying mechanism of ONH strain reduction. It complements current empirical knowledge about the MPD system and guides future studies of NPP as a treatment for glaucoma.
Comparison of simple RNA extraction methods for molecular diagnosis of hepatitis C virus in plasma
Authors: Hongjaisee Sayamon , Jabjainai Yosita , Sakset Suthasinee , Preechasuth Kanya , Ngo-Giang-Huong Nicole , Khamduang Woottichai
Published: May 2022

We evaluated the efficacy of four simple RNA extraction methods for the detection of hepatitis C virus (HCV) in plasma samples: silica-membrane-based, magnetic beads-based, boiling with Diethyl Pyrocarbonate (DEPC)-treated distilled water or a commercial lysis buffer. HCV RNA was detected using both real time reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop mediated isothermal amplification (RT-LAMP). The magnetic beads-based extraction can be used as an alternative RNA extraction method for on-site HCV detection. Boiling with DEPC-treated distilled water was not appropriate for low HCV load samples and boiling with a lysis buffer was not recommended.