bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional characterization of RNA profiles in processing bodies of human embryonic stem cells and mesodermal cells
Authors: Jiang Jin , Shao Qizhe , Xie Sisi , Xiao Xiaoying , Guo Ruisi , Jin Min , Chen Di
Published: November 2023

Processing bodies (P-bodies) are the membraneless organelles that play critical roles in RNA storage and decay. Abnormalities in P-bodies contribute to diseases and developmental disorders. Huge efforts have been applied to the identification of the protein components in P-bodies, however, the dynamics of RNA components of P-bodies in human embryonic stem cells (hESCs) during maintenance and differentiation remain largely elusive. Here, we characterized the RNA profiles of P-bodies from HEK293T cells, hESCs, and hESC-derived mesodermal cells. The number of P-bodies decreases upon hESC differentiation towards mesodermal fate, accompanied with the decreased RNAs within P-bodies. By functional analysis of the P-body enriched and P-body depleted genes across different cell types, we discovered the cell type-specific enrichment of P-body-genes and the potential association with human diseases. We also captured the non-coding RNAs, including long intergenic non-coding RNAs and transposable elements in P-bodies in a cell type-specific manner. Furthermore, we verified the involvement P-bodies in regulating the differentiation of hESCs towards mesoderm by over-expression of LSM14A and knocking down ofSPTAN1. In summary, we characterized the mRNAs and non-coding RNAs in P-bodies of hESCs and hESC-derived mesodermal cells, discovering the potential roles that P-bodies play for the precise differentiation of hESCs.
Boosting performance of generative diffusion model for molecular docking by training on artificial binding pockets
Authors: Voitsitskyi Taras , Bdzhola Volodymyr , Stratiichuk Roman , Koleiev Ihor , Ostrovsky Zakhar , Vozniak Volodymyr , Khropachov Ivan , Henitsoi Pavlo , Popryho Leonid , Zhytar Roman , Yesylevskyy Semen O , Nafiiev Alan , Starosyla Serhii
Published: November 2023

This study introduces the PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule poses in the protein binding pockets. The model utilizes a novel data augmentation technique, involving the creation of numerous artificial binding pockets that mimic the statistical patterns of non-bond interactions found in actual protein-ligand complexes. An algorithmic method was developed to assess and replicate these interaction patterns in the artificial binding pockets built around small molecule conformers. It is shown that the integration of artificial binding pockets into the training process significantly enhanced the model’s performance. Notably, PocketCFDM surpassed DiffDock in terms of non-bond interaction quality, number of steric clashes, and inference speed. Future developments and optimizations of the model are discussed.

Availability

The inference code and final model weights of PocketCFDM are accessible publicly via the GitHub repository:https://github.com/vtarasv/pocket-cfdm.git.
Rifampicin tolerance and growth fitness among isoniazid-resistant clinicalMycobacterium tuberculosisisolates: an in-vitro longitudinal study
Authors: Vijay Srinivasan , Bao Nguyen Le Hoai , Vinh Dao Nguyen , Nhat Le Thanh Hoang , Thu Do Dang Anh , Quang Nguyen Le , Trieu Le Pham Tien , Nhung Hoang Ngoc , Ha Vu Thi Ngoc , Thai Phan Vuong Khac , Ha Dang Thi Minh , Lan Nguyen Huu , Caws Maxine , Thwaites Guy E. , Javid Babak , Thuong Nguyen Thuy Thuong
Published: November 2023

Antibiotic tolerance inMycobacterium tuberculosisleads to less effective bacterial killing, poor treatment responses and resistant emergence. Therefore, we investigated the rifampicin tolerance ofM. tuberculosisisolates, with or without pre-existing isoniazid-resistance. We determined thein-vitrorifampicin survival fraction by minimum duration of killing assay in isoniazid susceptible (IS, n=119) and resistant (IR, n=84)M. tuberculosisisolates. Then we correlated the rifampicin tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs) and isoniazid-resistant mutations. The longitudinal IR isolates collected from patients were analyzed for changes in rifampicin tolerance and associated emergence of genetic variants. The median duration of rifampicin exposure reducing theM. tuberculosissurviving fraction by 90% (minimum duration of killing-MDK90) increased from 1.23 (95%CI 1.11; 1.37) and 1.31 (95%CI 1.14; 1.48) to 2.55 (95%CI 2.04; 2.97) and 1.98 (95%CI 1.69; 2.56) days, for IS and IR respectively, during 15 to 60 days of incubation. This indicated the presence of fast and slow growing tolerant sub-populations. A range of 6 log10-fold survival fraction enabled classification of tolerance as low, medium or high and revealed IR association with increased tolerance with faster growth (OR=2.68 for low vs. medium, OR=4.42 for low vs. high,P-trend=0.0003). The high tolerance in IR isolates was specific to those collected during rifampicin treatment in patients and associated with bacterial genetic microvariants. Furthermore, the high rifampicin tolerant IR isolates have survival potential similar to multi-drug resistant isolates. These findings suggest that IR tuberculosis needs to be evaluated for high rifampicin tolerance to improve treatment regimen and prevent the risk of MDR-TB emergence.
Long-term evolution ofStreptococcus mitisandStreptococcus pneumoniaeleads to higher genetic diversity within rather than between human populations
Authors: Davison Charlotte , Tallman Sam , de Ste-Croix Megan , Antonio Martin , Oggioni Marco R. , Kwambana-Adams Brenda , Freund Fabian , Beleza Sandra
Published: November 2023

Evaluation of the apportionment of genetic diversity of bacterial commensals within and between populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oronasopharingeal healthy-carriageStreptococcus mitisandStreptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119S. mitisgenomes showed higher within- and among-host variation than 810S. pneumoniaegenomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher historical population effective size (Ne) inS. mitis,whose genomic variation been maintained close to mutation-drift equilibrium across (at least many) generations, whereasS. pneumoniaehas been expanding from a smaller ancestral population and has been subjected to adaptive selection. Strikingly, both species show limited differentiation among populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem),we argue that largeNehave led to similar differentiation patterns, even ifmis very low forS. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to largeNe.
Towards new AQP4 inhibitors: ORI-TRN-002
Authors: Thormann Michael , Traube Nadine , Yehia Nasser , Koestler Roland , Galabova Gergana , MacAulay Nanna , Toft-Bertelsen Trine L.
Published: November 2023

Cerebral edema is a life-threatening condition that can cause permanent brain damage or death if left untreated. Existing therapies aim at mitigating the associated elevated intracranial pressure, yet they primarily alleviate pressure rather than preventing edema formation. Prophylactic anti-edema therapy necessitates novel drugs targeting edema formation. Aquaporin 4 (AQP4), an abundantly expressed water pore in mammalian glia and ependymal cells, has been proposed to be involved in cerebral edema formation. A series of novel compounds have been tested for their potential inhibitory effects on AQP4. However, selectivity, toxicity, functional inhibition, sustained therapeutic concentration, and delivery into the central nervous system are major challenges. Employing extensive DFT calculations, we identified a previously unreported thermodynamically stable tautomer of the recently identified AQP4-specific inhibitor TGN-020. This novel form, featuring a distinct hydrogen bonding pattern, served as a template for a COSMOsim-3D based virtual screen of proprietary compounds from Origenis™. The screening identified ORI-TRN-002, an electronic homologue of TGN-020, demonstrating high solubility and low protein binding. Evaluating ORI-TRN-002 on AQP4-expressingXenopus laevisoocytes using a high-resolution volume recording system revealed an IC50of 2.9 ± 0.6 μM, establishing it as a novel AQP4 inhibitor. ORI-TRN-002 exhibits superior solubility and free fraction limitations compared to other reported AQP4 inhibitors, suggesting its potential as a promising antiedema therapy for treating cerebral edema in the future.
Imaging genetics of language network functional connectivity reveals links with language-related abilities, dyslexia and handedness
Authors: Amelink Jitse S. , Postema Merel C. , Kong Xiang-Zhen , Schijven Dick , Castillo Amaia Carrion , Soheili-Nezhad Sourena , Sha Zhiqiang , Molz Barbara , Joliot Marc , Fisher Simon E. , Francks Clyde
Published: November 2023

Language is supported by a distributed network of brain regions with a particular contribution from the left hemisphere. A multi-level understanding of this network requires studying its genetic architecture. We used resting-state imaging data from 29,681 participants (UK Biobank) to measure connectivity between 18 left-hemisphere regions involved in multimodal sentence-level processing, as well as their right-hemisphere homotopes, and interhemispheric connections. Multivariate genome-wide association analysis of this total network, based on genetic variants with population frequencies>1%, identified 14 genomic loci, of which three were also associated with asymmetry of intrahemispheric connectivity. Polygenic dispositions to lower language-related abilities, dyslexia and left-handedness were associated with generally reduced leftward asymmetry of functional connectivity. Exome-wide association analysis based on rare, protein-altering variants (frequencies≤1%) suggested 7 additional genes. These findings shed new light on genetic contributions to language network organization and related behavioural traits.
Pyroptosis leads to loss of centrosomal integrity in macrophages
Authors: Bai Siyi , Martin-Sanchez Fatima , Brough David , Lopez-Castejon Gloria
Published: November 2023

NLRP3 forms a multiprotein inflammasome complex to initiate the inflammatory response when macrophages sense infection or tissue damage, which leads to caspase-1 activation and maturation and release of the inflammatory cytokines interleukin-1β (IL-1β) and IL-18, and Gasdermin-D (GSDMD) mediated pyroptosis. NLRP3 inflammasome activity must be controlled as unregulated and chronic inflammation underlies inflammatory and autoimmune diseases. Several findings uncovered that NLRP3 inflammasome activity is under the regulation of centrosome localized proteins such as NEK7 and HDAC6, however, whether the centrosome composition or structure is altered during the inflammasome activation is not known. Our data show that levels of the centrosomal scaffold protein pericentrin (PCNT) are reduced upon NLRP3 inflammasome activation via different activators in human and murine macrophages. PCNT loss occurs in the presence of membrane stabilizer punicalagin, suggesting this is not a consequence of membrane rupture. We found that PCNT loss is dependent on NLRP3 and active caspases as MCC950 and pan caspase inhibitor ZVAD prevent its degradation. Moreover, caspase-1 and GSDMD are both required for this NLRP3-mediated PCNT loss because absence of caspase-1 or GSDMD triggers an alternative regulation of PCNT via its cleavage by caspase-3 in response to nigericin stimulation. PCNT degradation occurs in response to nigericin, but also other NLRP3 activators including lysomotropic agent L-Leucyl-L-Leucine methyl ester (LLOMe) and hypotonicity. Our work reveals that the NLRP3 inflammasome activation affects centrosome composition and structure which may deepen our understandings of how activated NLRP3 inflammasomes are involved in the pathogenesis of inflammatory diseases.
Comparative single-cell transcriptomic atlases reveal conserved and divergent features of drosophilid central brains
Authors: Lee Daehan , Benton Richard
Published: November 2023

To explore how brains change upon species evolution, we generated single-cell transcriptomic atlases of the central brains of three closely-related but ecologically-distinct drosophilids: the generalistsDrosophila melanogasterandDrosophila simulans, and the noni fruit specialistDrosophila sechellia. The global cellular composition of these species’ central brains is well-conserved, but we predicted a few cell types (perineurial glia, sNPF and Dh44 peptidergic neurons) with divergent frequencies. Gene expression analysis revealed that distinct cell types within the central brain evolve at different rates and patterns; notably, glial cell types exhibit the greatest divergence between species. Compared toD. melanogaster, the cellular composition and gene expression patterns of the central brain inD. sechelliadisplay greater deviation than those ofD. simulans- despite their similar phylogenetic distance fromD. melanogaster- that the distinctive ecological specialization ofD. sechelliais reflected in the structure and function of its brain. Expression changes inD. sechelliaencompass metabolic and ecdysone signaling genes, suggestive of adaptations to its novel ecological demands. Additional single-cell transcriptomic analysis onD. sechelliarevealed genes and cell types responsive to dietary supplement with noni, pointing to glia as sites for both physiological and genetic adaptation to novel conditions. Our atlases represent the first comparative analyses of “whole” central brains, and provide a comprehensive foundation for studying the evolvability of nervous systems in a well-defined phylogenetic and ecological framework.
Utilization of the genetically encoded calcium indicator Salsa6F in cardiac applications
Authors: Márquez-Nogueras Karla M. , Bovo Elisa , Cao Quan , Zima Aleksey V. , Kuo Ivana Y.
Published: November 2023

Calcium signaling is a critical process required for cellular mechanisms such as cardiac contractility. The inability of the cell to properly activate or regulate calcium signaling can lead to contractile dysfunction. In isolated cardiomyocytes, calcium signaling has been primarily studied using calcium fluorescent dyes, however these dyes have limited applicability to whole organs. Here, we crossed the Salsa6f mouse which expresses a genetically encoded ratiometric cytosolic calcium indicator with a cardiomyocyte specific inducible cre to temporally-induce expression and studied cytosolic calcium transients in isolated cardiomyocytes and modified Langendorff heart preparations. Isolated cardiomyocytes expressing Salsa6f or Fluo-4AM loaded were compared. We also crossed the Salsa6f mouse with a floxed Polycystin 2 (PC2) mouse to test the feasibility of using the Salsa6f mouse to measure calcium transients in PC2 heterozygous or homozygous knock out mice. Although there are caveats in the applicability of the Salsa6f mouse, there are clear advantages to using the Salsa6f mouse to measure whole heart calcium signals.
YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing
Authors: Bowness Joseph S , Almeida Mafalda , Nesterova Tatyana B , Brockdorff Neil
Published: November 2023

X chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions incisto silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. Chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing. In this study, we integrate time-course data of gene silencing and decreasing inactive X (Xi) chromatin accessibility in mouse embryonic stem cell lines with an inducibleXistallele (iXist-ChrX mESCs). Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results indicate that YY1 acts as barrier to Xist-mediated silencing that is removed only at late stages of the XCI process.
Cadherins modulate the self-organizing potential of gastruloids
Authors: Mayran Alexandre , Kolly Dominique , Lopez-Delisle Lucille , Romaniuk Yuliia , Leonardi Maxine , Cossy Anne-Catherine , Lacroix Theo , Amândio Ana Rita , Osteil Pierre , Duboule Denis
Published: November 2023

Gastruloids have recently emerged as an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning. They undergo gastrulation-like processes leading to the self-organization into highly reproducible biological objects. Here, we sought to uncover the molecular and cellular mechanism underlying this remarkable property. We report that self-organization competence is associated with a cell-specific coordination of a Cadherin switch. We find that N-Cadherin hinders gastruloids morphogenetic competence, for its inactivation leads to the formation of trunk-like structures in absence of extra-cellular matrix analogues. In contrast,E-Cadherinrepression bySnai1is critical for self-organization:Snai1establishes a cell-specific repressive pace by triggering the repression of a pluripotency-associated transcription program and its chromatin landscape, thus allowing a proper transition from E-to N-Cadherin to occur. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the observed self-organizing potential of gastruloids.
Using Environmental DNA to Reconstruct Amphibian Communities at Sites Infected withBatrachochytrium salamandrivoransin the Netherlands
Authors: Davison Anna M. , Spitzen–van der Sluijs Annemarieke , O’Donnell Matthew J. , Prasetyo Andhika P. , Broadhurst Holly A. , Sales Naiara G. , Herder Jelger E. , Coscia Ilaria , McDevitt Allan D.
Published: November 2023

Abstract

The recently discoveredBatrachochytrium salamandrivorans(Bsal) fungus can cause high mortality rates in some European salamanders and newts (urodelans) and has the potential to expand its currently small invasive range in Europe. Therefore, monitoring its distribution and better understanding both the species threatened and the mechanics of infection are essential in mitigating the damageBsalmay cause. Environmental DNA (eDNA) has emerged as a promising non-invasive method for detecting both this fungal pathogen and the amphibian communities in infected areas. We applied these methods in the province Gelderland, the Netherlands where the pathogen has previously been detected and is expanding its range, with the goal of detecting the natural amphibian community present. We sampled 27 water bodies in the region surrounding the known outbreak sites. We used data from aBsal-specific qPCR assay to determine its presence-absence and applied an eDNA metabarcoding approach to characterize the amphibian communities using two different primer sets. The 12S vertebrate primer set outperformed the 16S amphibian primer set and detected all the expected amphibians in the study area:Bufo bufo, Lissotriton vulgaris, Pelobates fuscus, Pelophylax spp.,Rana temporariaandTriturus cristatus.Bsalwas detected at eight of the ponds. A distance-based redundancy analysis found a weak but significant relationship betweenBsalpresence and the composition of amphibian communities using eDNA. This study provides the foundation for future studies onBsaland its relationship with amphibian communities in Europe, highlighting the need for further research into the mechanisms of persistence and transmission between water bodies.
Regulation of adipocyte dedifferentiation at the skin wound edge
Authors: Yao Longbiao , Jeong Sunhye , Kwon Hae Ryong , Olson Lorin E.
Published: November 2023

Adipocytes have diverse roles in energy storage and metabolism, inflammation, and tissue repair. Mature adipocytes have been assumed to be terminally differentiated cells. However, recent evidence suggests that adipocytes retain substantial phenotypic plasticity, with potential to dedifferentiate into fibroblast-like cells under physiological and pathological conditions. Here, we develop a two-step lineage tracing approach based on the observation that fibroblasts express platelet-derived growth factor receptor alpha (Pdgfra) while adipocytes express Adiponectin (Adipoq) but notPdgfra. Our approach specifically tracesPdgfra+cells that originate fromAdipoq+adipocytes. We find many traced adipocytes and fibroblast-like cells surrounding skin wounds, but only a few traced cells localize to the wound center. In agreement with adipocyte plasticity, traced adipocytes incorporate EdU, downregulate Plin1 and PPARγ, and upregulate αSMA. We also investigate the role of potential dedifferentiation signals using constitutively active PDGFRα mutation,Pdgfraknockout, orTgfbr2knockout models. We find that PDGF and TGFβ signaling both promote dedifferentiation, and PDGFRα does so independently of TGFβR2. These results demonstrate an intersectional genetic approach to trace the hybrid cell phenotype ofPdgfra+adipocytes, which may be important for wound repair, regeneration and fibrosis.
baRulho: an R package to quantify degradation in animal acoustic signals
Authors: Araya-Salas Marcelo , Grabarczyk Erin E. , Quiroz-Oliva Marcos , García-Rodríguez Adrián , Rico-Guevara Alejandro
Published: November 2023

Animal acoustic signals are shaped by selection to convey information based on their tempo, intensity, and frequency. However, sound degrades as it propagates over space and across physical obstacles (e.g., vegetation or infrastructure), which affects communication potential. Therefore, transmission experiments are designed to quantify change in signal structure in a given habitat by broadcasting and re-recording animal sounds at increasing distances.

We introduce ‘baRulho’, an R package designed to simplify the implementation of sound transmission experiments. We highlight the package features with a case study testing the effects of habitat and acoustic structure on signal transmission. Synthesized sounds that varied in frequency, duration, and frequency and amplitude modulation were broadcast and re-recorded at five increasing distances in open and closed understory at the Bosque de Tlalpan, Mexico City. With this data, we showcase baRulho’s functions to prepare master sound files, annotate re-recorded test sounds, as well as to calculate and visualize measures that quantify degradation of acoustic signals in the time and frequency domain.

Degradation measures in baRulho adequately quantified acoustic degradation, following predicted patterns of sound transmission in natural environments. Re-recorded signals degraded less in open habitats compared to closed habitats, with higher-frequency sounds exhibiting more degradation. Furthermore, frequency modulated sounds degraded to a greater extent than pure tones. The increased attenuation and reverberation observed in higher frequency sounds and closed habitats suggest that factors such as absorption and scattering by vegetation play significant roles in transmission patterns.

The R package ‘baRulho’ provides an open-source, user-friendly suite of tools designed to facilitate analysis of animal sound degradation. Notably, it offers similar results to other sound analysis software but with significantly reduced processing time. Moreover, the package minimizes the potential for user error through automated test file annotation and verification procedures. We hope that baRulho can help enhance accessibility to transmission experiments within the research community, ultimately contributing to a deeper understanding of the ecological drivers of animal communication systems.
A Novel Role for Phospholamban in the Thalamic Reticular Nucleus
Authors: Klocke Benjamin , Britzolaki Aikaterini , Saurine Joseph , Ott Hayden , Krone Kylie , Bahamonde Kiara , Thelen Connor , Tzimas Christos , Sanoudou Despina , Kranias Evangelia G. , Pitychoutis Pothitos M.
Published: November 2023

The thalamic reticular nucleus (TRN) is a critical brain region that greatly influences vital neurobehavioral processes, including executive functioning and the generation of sleep rhythms. Recently, TRN dysfunction was suggested to underlie hyperactivity, attention deficits, and sleep disturbances observed across various devastating neurodevelopmental disorders, including autism, schizophrenia and attention-deficit/hyperactivity disorder (ADHD). Notably, a highly specialized sarco- endoplasmic reticulum calcium (Ca2+) ATPase 2 (SERCA2)-dependent Ca2+signaling network operates in the dendrites of TRN neurons to regulate their high-frequency bursting activity. Phospholamban (PLN) is a prominent regulator of the SERCA2 with an established role in maintaining Ca2+homeostasis in the heart; although the interaction of PLN with SERCA2 has been largely regarded as cardiac-specific, our findings challenge this view and suggest that the role of PLN extends beyond the cardiovascular system to impact brain function. Specifically, we found PLN to be expressed in the TRN neurons of the adult mouse brain and utilized global constitutive and innovative conditional genetic mouse models, in combination with 5-choice serial reaction time task (5-CSRTT) and electroencephalography (EEG)-based somnography to assess the role of PLN in regulating executive functioning and sleep, two complex behaviors that map onto thalamic reticular circuits. Overall, the results of the present study show that perturbed PLN function in the TRN results in aberrant thalamic reticular behavioral phenotypes in mice (i.e., hyperactivity, impulsivity and sleep deficits) and support a novel role for PLN as a critical regulator of the SERCA2 in the thalamic reticular neurocircuitry.
Reconstitution of a Biofilm Adhesin System from a Sulfate-Reducing Bacterium inPseudomonas fluorescens
Authors: Karbelkar Amruta A. , Font Maria E. , Smith T. Jarrod , Sondermann Holger , O’Toole George A.
Published: November 2023

Biofilms of the sulfate reducing bacterium (SRB)Desulfovibrio vulgarisHildenborough (DvH) can facilitate metal corrosion in various industrial and environmental settings leading to substantial economic losses; however, the mechanisms of biofilm formation by DvH are not yet well-understood. Evidence suggests that a large adhesin, DvhA, may be contributing to biofilm formation in DvH. ThedvhAgene and its neighbors encode proteins that resemble the Lap system, which regulates biofilm formation byPseudomonas fluorescens, including a LapG-like protease DvhG and effector protein DvhD, which has key differences from the previously described LapD. By expressing the Lap-like adhesion components of DvH inP. fluorescens, our data support the model that the N-terminal fragment of the large adhesin DvhA serves as an adhesin “retention module” and is the target of the DvhG/DvhD regulatory module, thereby controlling cell-surface location of the adhesin. By heterologously expressing the DvhG/DvhD-like proteins in aP. fluorescensbackground lacking native regulation (ΔlapGΔlapD) we also show that cell surface regulation of the adhesin is dependent upon the intracellular levels of c-di-GMP. This study provides insight into the key players responsible for biofilm formation by DvH, thereby expanding our understanding of Lap-like systems.

Significance

Corrosion leads to ∼2.5 trillion US dollars in economic losses, 20% of which are estimated to be microbially induced. Biofilms of sulfate reducing bacteria (SRB), especially the genusDesulfovibrio, are important members of the corrosion consortium and accelerate deterioration of metals. Understanding how biofilms are formed by SRB can provide important clues to mitigate this challenge. In this study, we used genetic and biochemical tools to investigate the mechanism of biofilm formation byDesulfovibrio vulgarisHildenborough. Our study reveals critical genes responsible for regulating the secretion of a large adhesin known to be required for biofilm formation.
Inhibition of FAM19A5 restores synaptic loss and improves cognitive function in mouse models of Alzheimer’s disease
Authors: Kim Han-Byul , Yoo Sangjin , Kwak Hoyun , Ma Shi-Xun , Kim Ryunhee , Lee Minhyeok , Ha Nui , Pyo Soonil , Kwon Soon-Gu , Cho Eun-Ho , Lee Sang-Myeong , Jang Juwon , Kim Wonkyum , Park Hae-Chul , Baek Minkyung , Park Yosub , Park Ji-Young , Park Jin-Woo , Hwang Sun Wook , Hwang Jong-Ik , Seong Jae Young
Published: November 2023

Introduction

Alzheimer’s disease (AD) is characterized by the dysregulation of synaptic balance, with progressive loss of synapses outpacing formation, ultimately leading to cognitive decline. However, the lack of effective strategies for restoring lost synapses poses a major barrier to improving clinical outcomes.

Methods

We developed NS101, a monoclonal antibody targeting FAM19A5, a brain-secreted protein. Its preclinical efficacy in restoring synapses and cognition was evaluated using APP/PS1 and P301S mice. The clinical safety and target engagement of NS101 were examined in human participants.

Results

FAM19A5 binds to LRRC4B, a postsynaptic adhesion molecule, leading to synapse reduction. Blocking this interaction with NS101 normalized the rate of synapse elimination in AD mice. This synaptic rebalancing restored the number and function of synapses, resulting in improved cognition. Systemically administered NS101 facilitated the transport of brain FAM19A5 into the bloodstream.

Discussion

Targeting FAM19A5 may hold clinical promise for treating AD by restoring synaptic balance.
Genome-wide detection of somatic mosaicism at short tandem repeats
Authors: Sehgal Aarushi , Ziaei-Jam Helyaneh , Shen Andrew , Gymrek Melissa
Published: November 2023

Motivation

Somatic mosaicism, in which a mutation occurs post-zygotically, has been implicated in several developmental disorders, cancers, and other diseases. Short tandem repeats (STRs) consist of repeated sequences of 1-6bp and comprise more than 1 million loci in the human genome. Somatic mosaicism at STRs is known to play a key role in the pathogenicity of loci implicated in repeat expansion disorders and is highly prevalent in cancers exhibiting microsatellite instability. While a variety of tools have been developed to genotype germline variation at STRs, a method for systematically identifying mosaic STRs (mSTRs) is lacking.

Results

We introduce prancSTR, a novel method for detecting mSTRs from individual high-throughput sequencing datasets. Unlike many existing mosaicism detection methods for other variant types, prancSTR does not require a matched control sample as input. We show that prancSTR accurately identifies mSTRs in simulated data and demonstrate its feasibility by identifying candidate mSTRs in whole genome sequencing (WGS) data derived from lymphoblastoid cell lines for individuals sequenced by the 1000 Genomes Project. Our analysis identified an average of 76 and 577 non-homopolymer and homopolymer mSTRs respectively per cell line as well as multiple cell lines with outlier mSTR counts more than 6 times the population average, suggesting a subset of cell lines have particularly high STR instability rates.

Availability

prancSTR is freely available athttps://github.com/gymrek-lab/trtools.

Documentation

Detailed documentation is available athttps://trtools.readthedocs.io/

Contact

mgymrek@ucsd.edu
Rapid and prolonged response of oligodendrocyte lineage cells in standard acute cuprizone demyelination model revealed byin situhybridization
Authors: He Yuehua , Xie Hua , Zhang Liuning , Feng Yuanyu , Long Yu , Xu ZhengTao , Zou Yanping , Zheng Wei , Wang Shuming , He Yongxiang , Li Jiong , Xiao Lin
Published: November 2023

Dietary administration of a copper chelator, cuprizone (CPZ), has long been reported to induce intense and reproducible demyelination of several brain structures such as the corpus callosum (CC) in mice, followed by spontaneous remyelination after drug withdrawal. Despite the widespread use of CPZ as an animal model for demyelinating diseases such as multiple sclerosis (MS), the mechanism by which it induces demyelination and then allows robust remyelination is still unclear. An intensive mapping of the oligodendrocyte (OL) lineage cell dynamics during the de-and remyelination course would be of particular importance for a deeper understanding of this model. Here, using a panel of OL lineage cell markers asin situhybridization (ISH) probes, includingPdgfra, Plp, Mbp, Mog, Enpp6, combined with immunofluorescence staining of CC1, SOX10, we provide a detailed dynamic profile of OL lineage cells during the entire course of the model from 3.5 days, 1, 2, 3, 4,5 weeks of CPZ treatment, i.e. the demyelination period, as well as after 1, 2, 3, 4 weeks of recovery (drug withdrawal) from 5 weeks of CPZ treatment, i.e. the remyelination period. The result showed an unexpected early death of mature OLs and response of OL progenitor cells (OPCs) in vivo upon CPZ challenge, and a prolonged upregulation of myelin-forming OLs compared to the intact control even 4 weeks after CPZ withdrawal. These data may point to the need to optimize the timing windows for the introduction of pro-remyelination therapies in demyelinating diseases such as MS, and may serve as a basic reference system for future studies of the effects of any intervention on demyelination and remyelination using the CPZ model.
Enhanced surface accessibility of SARS-CoV-2 Omicron spike protein due to an altered glycosylation profile
Authors: Wang Dongxia , Zhang Zijian , Baudys Jakub , Haynes Christopher , Osman Sarah H. , Zhou Bin , Barr John R. , Gumbart James C.
Published: November 2023

SARS-CoV-2 spike (S) proteins undergo extensive glycosylation, aiding proper folding, enhancing stability, and evading host immune surveillance. In this study, we used mass spectrometric analysis to elucidate the N-glycosylation characteristics and disulfide bonding of recombinant spike proteins derived from the SARS-CoV-2 Omicron variant (B.1.1.529) in comparison with the D614G spike variant. Furthermore, we conducted microsecond-long molecular dynamics simulations on spike proteins to resolve how the different N-glycans impact spike conformational sampling in the two variants. Our findings reveal that the Omicron spike protein maintains an overall resemblance to the D614G spike variant in terms of site-specific glycan processing and disulfide bond formation. Nonetheless, alterations in glycans were observed at certain N-glycosylation sites. These changes, in synergy with mutations within the Omicron spike protein, result in increased surface accessibility of the macromolecule, including ectodomain, receptor-binding domain, and N-terminal domain. These insights contribute to our understanding of the interplay between structure and function, thereby advancing effective vaccination and therapeutic strategies.

Teaser

Through mass spectrometry and molecular dynamics simulations, SARS-CoV-2 Omicron spike is found to be less covered by glycans when compared to the D614G spike variant.
A communication hub for phosphoregulation of kinetochore-microtubule attachment
Authors: Zahm Jacob A. , Harrison Stephen C.
Published: November 2023

The Mps1 and Aurora B kinases regulate and monitor kinetochore attachment to spindle microtubules during cell division, ultimately ensuring accurate chromosome segregation. In yeast, the critical attachment components are the Ndc80 and Dam1 complexes (Ndc80c and DASH/Dam1c, respectively). Ndc80c is an 600-Å long heterotetramer that binds microtubules through a globular “head” at one end and centromere-proximal kinetochore components through a globular knob at the other end. Dam1c is a heterodecamer that forms a ring of 16-17 protomers around the shaft of the single kinetochore microtubule in point-centromere yeast. The ring coordinates the approximately eight Ndc80c rods per kinetochore. In published work, we showed that a site on the globular “head” of Ndc80c, including residues from both Ndc80 and Nuf2, binds a bipartite segment in the long, C-terminal extension of Dam1. Results reported here show, both by in vitro binding experiments and by crystal structure determination, that the same site binds a conserved segment in the long N-terminal extension of Mps1 and a similarly conserved segment in the N-terminal extension of Ipl1 (yeast Aurora B). Together with results from experiments in yeast cells and from biochemical assays reported in two accompanying papers, the structures and graded affinities identify a communication hub for ensuring uniform bipolar attachment and for signaling anaphase onset.
Phylogeny Inference Under Time-Decaying Migration and Varying Information Content
Authors: Shaik Zaynab , Bergh Nicola G. , Verboom G. Anthony , Oxelman Bengt
Published: November 2023

Abstract

Postspeciation gene flow is widespread across the Tree of Life but is ignored as a cause of gene tree discordance under the standard multispecies coalescent. Where interspecific migration has occurred but is not modelled explicitly, effective population sizes, divergence times and topology can be seriously misestimated. Isolation-with-migration and multispecies coalescent-with-introgression models explicitly model migration but include additional parameters that limit their computational viability with even moderately sized molecular data sets. Here we simulate the evolution of sequences which vary in molecular information content under the coalescent while allowing continuous, tree-wide gene flow/migration between contemporaneous branches, the rate of which decreases with time since divergence. Using simulated sequences, we evaluate the performance of DENIM under rapidly to gradually time-decaying migration and benchmark its performance against the standard MSC method StarBeast3. DENIM consistently outperforms StarBeast3, both in phylogenetic accuracy and computational performance per core. Rapidly decaying migration is associated with improved topology and divergence time estimates under both DENIM and StarBeast3. While species tree estimation accuracy is not improved by increasing the number of loci from 30 to 60 under either method, model convergence is slowed considerably. By contrast, increasing sequence length to 10,000 bp has no clear effect on convergence rates, but shows a tendency towards increased accuracy in DENIM. We apply DENIM and StarBeast3 with a 36-locus empirical bat data set and recover species trees identical in topology to those obtained with 12,931 loci. Our work demonstrates that DENIM can deliver accurate phylogenetic estimates in the presence of both deep coalescence and empirically realistic migration patterns using as few as 30 loci with single-core runtimes of 2-3 days.
Cancer-associated fibroblasts serve as decoys to suppress NK cell anti-cancer cytotoxicity
Authors: Ben-Shmuel Aviad , Gruper Yael , Levi-Galibov Oshrat , Rosenberg-Fogler Hallel , Carradori Giulia , Stein Yaniv , Dadiani Maya , Naumova Mariia , Nevo Reinat , Morzaev-Sulzbach Dana , Yagel Gal , Mayer Shimrit , Gal-Yam Einav Nili , Scherz-Shouval Ruth
Published: November 2023

Cancer associated fibroblasts (CAFs) are among the most abundant components of the breast tumor microenvironment (TME) and major contributors to immune modulation. CAFs are well-known to regulate the activity of diverse types of immune cells including T cells, macrophages and dendritic cells, however little is known about their interaction with Natural killer (NK) cells, which constitute an important arm of anti-tumor immunity. Here we find, using mouse models of cancer and ex-vivo co-cultures, that CAFs inhibit NK cell cytotoxicity towards cancer cells. We unravel the mechanism by which this suppression occurs, through ligand-receptor engagement between NK cells and CAFs leading to CAF cytolysis, which in turn diminishes the expression of activating receptors on NK cells, promoting cancer escape from NK cell surveillance. Analysis of breast cancer patient samples reveals enrichment of NK cells in CAF-rich regions, and upregulation of NK binding ligands on CAFs which is correlated with poor disease outcome. These results reveal a CAF-mediated immunosuppressive decoy mechanism with implications for treatment of solid tumors.
RNAmigos2: Fast and accurate structure-based RNA virtual screening with semi-supervised graph learning and large-scale docking data
Authors: Carvajal-Patiño Juan G. , Mallet Vincent , Becerra David , Niño V. L. Fernando , Oliver Carlos , Waldispühl Jérôme
Published: November 2023

RNAs constitute a vast reservoir of mostly untapped drug targets. Structure-based virtual screening (VS) methods screen large compound libraries for identifying promising candidate molecules by conditioning on binding site information. The classical approach relies on molecular docking simulations. However, this strategy does not scale well with the size of the small molecule databases and the number of potential RNA targets. Machine learning emerged as a promising technology to resolve this bottleneck. Efficient data-driven VS methods have already been introduced for proteins, but these techniques have not yet been developed for RNAs due to limited dataset sizes and lack of practical use-case evaluation.

We propose a data-driven VS pipeline that deals with the unique challenges of RNA molecules through coarse grained modeling of 3D structures and heterogeneous training regimes using synthetic data augmentation and RNA-centric self supervision. We report strong prediction and generalizability of our framework, ranking active compounds among inactives in the top 2.8% on average on a structurally distinct drug-like test set. Those predictions are sensitive, but robust to pockets alterations, opening the door to its use on binding site detection methods outputs. Our model results in a ten thousand-times speedup over docking techniques while obtaining higher performance. Finally, we deploy our model on a recently publishedin-vitrosmall molecule microarray experiment with 20,000 compounds and report a mean enrichment factor at 1% of 2.93 on four unseen RNA riboswitches. To our knowledge, this is the first experimental evidence of success for structure-based deep learning methods in RNA virtual screening. Our source code and data, as well as a Google Colab notebook for inference, are available on GitHub.1
Microtubule length correlates with spindle length inC. elegansmeiosis
Authors: Zimyanin Vitaly , Redemann Stefanie
Published: November 2023

The accurate segregation of chromosomes during female meiosis relies on the precise assembly and function of the meiotic spindle, a dynamic structure primarily composed of microtubules. Despite the crucial role of microtubule dynamics in this process, the relationship between microtubule length and spindle size remains elusive. LeveragingC. elegansas a model system, we combined electron tomography and live imaging to investigate this correlation. Our analysis revealed significant changes in spindle length throughout meiosis, coupled with alterations in MT length. Surprisingly, while spindle size decreases during the initial stages of anaphase, the size of antiparallel microtubule overlap decreased as well. Detailed electron tomography shows a positive correlation between microtubule length and spindle size, indicating a role of microtubule length in determining spindle dimensions. Notably, microtubule numbers displayed no significant association with spindle length, highlighting the dominance of microtubule length regulation in spindle size determination. Depletion of the microtubule depolymerase KLP-7 led to elongated metaphase spindles with increased microtubule length, supporting the link between microtubule length and spindle size. These findings underscore the pivotal role of regulating microtubule dynamics, and thus microtubule length, in governing spindle rearrangements during meiotic division, shedding light on fundamental mechanisms dictating spindle architecture.
Single-cell imaging of protein dynamics of paralogs reveals mechanisms of gene retention
Authors: Dandage Rohan , Papkov Mikhail , Greco Brittany M. , Fishman Dmytro , Friesen Helena , Wang Kyle , Styles Erin , Kraus Oren , Grys Benjamin , Boone Charles , Andrews Brenda , Parts Leopold , Kuzmin Elena
Published: November 2023

Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is a largely unexplored mechanism of functional divergence. We performed a systematic single-cell imaging analysis of protein dynamics and screened subcellular redistribution of proteins, capturing their localization and abundance changes, providing insight into forces determining paralog retention. Paralogs showed dependency, whereby proteins required their paralog to maintain their native abundance or localization, more often than compensation. Network feature analysis suggested the importance of functional redundancy and rewiring of protein and genetic interactions underlying redistribution response of paralogs. Translation of non-canonical protein isoform emerged as a novel compensatory mechanism. This study provides new insights into paralog retention and evolutionary forces that shape genomes.
Air India-Vistara merger – maneuvering “Vihaan.AI” through the turbulence
Authors: Chaudhary Prashant
Published: November 2023

Learning outcomes

The expected learning outcomes are to understand the complexities involved in the integration of two carriers with different business strategies and approaches, the merger of two brands with distinct personas and identities and the confluence of two different cultures; figure out the strategic options in front of the Tata Group and how it can deal with various macro- and micro-level business challenges, defy the financial hiccups and manoeuvre the operational complexities to accomplish mission Vihaan.AI; and develop a pragmatic approach to macro and micro business environmental scanning for making strategic business decisions.

Case overview/synopsis

In November 2022, Tata Group, the salt to software conglomerate, announced the merger of Air India (AI) and Vistara. This would lead to the formation of the full-service airline under the brand name “Air India”. The obvious reason behind this was the higher recognition, salience and recall of the brand AI as compared with Vistara in the global market. The Tata Group envisaged the brand AI to be a significant international aviation player with the heritage, persona and ethos of the brand Vistara in the renewed manifestation of AI. To realise these goals, Tata Group laid down an ambitious plan called “Vihaan.AI”, which was aimed at capturing a domestic market share of 30% by 2027.

Complexity academic level

This case study can be taught as part of undergraduate- and postgraduate-level management programmes.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 11: Strategy.