bluuebunny/crossref_metadata_2025 huggingface dataset:
The gut microbiome of the healthy population in Kolkata, India, is a reservoir of antimicrobial resistance genes emphasizing the need of enforcing antimicrobial stewardship
Authors: De Rituparna , Kanungo Suman , Mukhopadhyay Asish Kumar , Dutta Shanta
Published: July 2023

Antimicrobial resistance (AMR) alleviation warrants antimicrobial stewardship (AS) entailing indispensability of epidemiological surveillance. We undertook a small-scale surveillance in Kolkata to detect the presence of antimicrobial resistance genes (ARGs) in the healthy gut microbiome. We found that it was a reservoir of ARGs against common antibiotics. A targeted PCR and sequencing-based ARGs detection against tetracyclines, macrolides, trimethoprim, sulfamethoxazole, aminoglycosides, amphenicol and mobile genetic element (MGE) markers was deployed in twenty-five fecal samples. Relative abundance and frequency of ARGs was calculated. We detected markers against all these classes of antibiotics. 100% samples carried aminoglycoside resistance marker andint1U. A comparison with our previously published diarrheal resistome from the same spatial and temporal frame revealed that a higher diversity of ARGs were detected in the community and a higher rate of isolation oftetC, msrA, tmpandsul-2was found. The presence of common markers in the two cohorts proves that the gut microbiome has been contaminated with ARGs and which are being disseminated among different ecosystems. This is an issue of discerning concern for public health. The study raises an alarming picture of the AMR crisis in low-middle and emergent economies. It emphasizes the strict enforcement of AS in the community.
A nearly complete and phased genome assembly of a ColombianTrypanosoma cruziTcI strain and the evolution of gene families
Authors: Hoyos Sanchez Maria Camila , Ospina Zapata Hader Sebastian , Suarez Brayhan Dario , Ospina Carlos , Barbosa Hamilton Julian , Carranza Martinez Julio Cesar , Vallejo Gustavo Adolfo , Montes Daniel Urrea , Duitama Jorge
Published: July 2023

Chagas is an endemic disease in tropical regions of Latin America, caused by the parasiteTrypanosoma cruzi. High intraspecies variability and genome complexity have been challenges for the development of genomic variation databases, needed to conduct studies in evolution, population genomics, and identification of genomic elements related to virulence and drug resistance inT. cruzi. Here we present a chromosome-level phased assembly of aT. cruzistrain (Dm25), isolated from a reservoir of the speciesDidelphis marsupialislocated at the Tolima department in Colombia, and belonging to the TcI DTU. We obtained a primary haplotype composed of 32 chromosomes, 30 of them assembled in a single contig, and one complete copy of the maxicircle. While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes with a high density of repeat elements show a large divergence, compared to the Brazil A4 assembly. Considering that the distribution of heterozygous sites suggest that Dm25 is diploid, we assembled a second haplotype for 31 chromosomes, achieving an average of three contigs per chromosome. Nucleotide and protein evolution statistics indicate thatT. cruziMarinkellei separated before the diversification ofT. cruziin the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics ofTrypanosomatids.
Mutation of theVinv5′ UTR regulatory region reduces acrylamide levels in processed potato to reach EU food-safety standards
Authors: Shumbe Leonard , Soares Emanoella , Muhovski Yordan , Smit Inga , Vanderschuren Hervé
Published: July 2023

Protein-coding regions of genes have so far been the preferred targets for trait improvement using CRISPR-Cas9 genome editing in plants. Alteration of the reading frame can result in termination of transcription or translation, hence, loss of function of the encoded protein. 5’ UTR sequences also represent a practical target region to alter gene expression and protein abundance. However, editing of 5’ UTRs has so far been scarcely used to engineer trait in crop plants. Here, we demonstrate that insertion of a single adenine nucleotide mediated by Cas9 in the 5’ UTR region of two alleles from the Vacuolar invertase gene (VInv) of the tetraploid potato variety Lady Rosetta (LaRo) is sufficient to substantially lower the content of reducing sugars in the potato under cold-storage conditions. Moreover, the acrylamide content generated during processing of the edited potato lines into crisps was more than three folds lower than the current EU-regulated maximum level of 750 μg/kg in crisps. This gene-editing approach represents a durable strategy to improve food safety of potatoes in varieties widely preferred by the consumers and the industry.
Evolving Membrane-Associated Accessory Protein Variants for Improved Adeno-associated Virus Production
Authors: Schieferecke Adam J. , Lee Hyuncheol , Chen Aleysha , Kilaru Vindhya , Williams Justin Krish , Schaffer David. V.
Published: July 2023

Manufacturing sufficient Adeno-Associated Virus (AAV) to meet current and projected clinical needs is a significant hurdle to the growing gene therapy industry. The recently discovered membrane-associated accessory protein (MAAP) is encoded by an alternative open reading frame in the AAVcapgene that is found in all presently reported natural serotypes. Recent evidence has emerged supporting a functional role of MAAP in AAV egress, though the underlying mechanisms of MAAP function remain unknown. Here, we show that inactivation of MAAP from AAV2 by a single point mutation that is silent in the VP1 ORF (AAV2-ΔMAAP) decreased exosome-associated and secreted vector genome production. We hypothesized that novel MAAP variants could be evolved to increase AAV production and thus subjected a library encoding over 1E6 MAAP protein variants to five rounds of packaging selection into the AAV2-ΔMAAP capsid. Between each successive packaging round, we observed a progressive increase in both overall titer and ratio of secreted vector genomes conferred by the bulk selected MAAP library population. Next-generation sequencing uncovered enriched mutational features, and a resulting selected MAAP variant containing missense mutations and a novel C-terminal domain increased overall GFP transgene packaging in AAV2, AAV6, and AAV9 capsids.
Eugenol mimics exercise to promote skeletal muscle fiber remodeling and myokine IL-15 expression by activating TRPV1 channel
Authors: Huang Tengteng , Chen Xiaoling , He Jun , Zheng Ping , Luo Yuheng , Wu Aimin , Yan Hui , Yu Bing , Chen Daiwen , Huang Zhiqing
Published: July 2023

Metabolic disorders are highly prevalent in modern society. Exercise mimetics are defined as pharmacologic compounds that can produce the beneficial effects of fitness. Recently, there has been increased interest in the role of eugenol and transient receptor potential vanilloid 1 (TRPV1) in improving metabolic health. The aim of this study was to investigate whether eugenol acts as an exercise mimetic by activating TRPV1. Here, we showed that eugenol improved endurance capacity, caused the conversion of fast to slow muscle fibers, and promoted white fat browning and lipolysis in mice. Mechanistically, eugenol promoted muscle fiber type transformation by activating TRPV1-mediated CaN signaling pathway. Subsequently, we identified IL-15 as a myokine that is regulated by the CaN/Nuclear factor of activated T cells cytoplasmic 1 (NFATc1) signaling pathway. Moreover, we found that TRPV1-mediated CaN/NFATc1 signaling, activated by eugenol, controlled IL-15 levels in C2C12 myotubes. Our results suggest that eugenol may act as an exercise mimetic to improve metabolic health via activating the TRPV1-mediated CaN signaling pathway.
Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies
Authors: Wainwright J. Benito , Schofield Corin , Conway Max , Phillips Daniel , Martin-Silverstone Elizabeth , Brodrick Emelie A. , Cicconardi Francesco , How Martin J. , Roberts Nicholas W. , Montgomery Stephen H.
Published: July 2023

The striking structural variation seen in arthropod visual systems can be explained by the overall quantity and spatio-temporal structure of light within habitats coupled with developmental and physiological constraints. However, little is currently known about how fine-scale variation in visual structures arise across shorter evolutionary and ecological scales. In this study, we characterise patterns of interspecific (between species), intraspecific (between sexes) and intraindividual (between eye regions) variation in the visual system of four ithomiine butterfly species. These species are part of a diverse 26-Myr-old Neotropical radiation where changes in mimetic colouration are associated with fine-scale shifts in ecology, such as microhabitat preference. By using a combination of selection analyses on visual opsin sequences, in-vivo ophthalmoscopy, micro-computed tomography (micro-CT), immunohistochemistry, confocal microscopy, and neural tracing, we quantify and describe physiological, anatomical, and molecular traits involved in visual processing. Using these data, we provide evidence of substantial variation within the visual systems of Ithomiini, including: i) relaxed selection on visual opsins, perhaps mediated by habitat preference, ii) interspecific shifts in visual system physiology and anatomy, and iii) extensive sexual dimorphism, including the complete absence of a butterfly-specific optic neuropil in the males of some species. We conclude that considerable visual system variation can exist within diverse insect radiations, hinting at the evolutionary lability of these systems to rapidly develop specialisations to distinct visual ecologies, with selection acting at both the perceptual, processing, and molecular level.

Summary statement

Physiological, anatomical, and molecular evidence of extensive visual system variation within a diverse butterfly radiation, hinting at the lability of visual systems to evolve specialisations to distinct visual environments.
Genetic associations of dimensional autistic phenotypes
Authors: Eriksson Tore , Nakamori Chiaki , Iwamoto Kazunari
Published: July 2023

Since there is a large variation in the symptoms shown by persons affected with ASD, analyzing genetics data using a case-control design is not straightforward. To avoid the difficult problem of defining heterogeneous groups, we used four different methods to compute a latent representation of a merged set of three psychometric tests. Computing the genetic contribution of each representation using a subset of participants with genetic data, we showed that factor analysis as well as variable autoencoders separates information contained in psychometric tests into genetically distinct phenotypic domains. Using the individual-level loadings of the domains as quantitative phenotypes in genome-wide association studies we detected statistically significant genetic associations in the domain related to insistence on routine, as well as suggestive genetic signals in other domains. We hope that these results can suggest possible domain-specific interventions in the future.
Dopamine-dependent cerebellar dysfunction enhances beta oscillations and disrupts motor learning in a multiarea model
Authors: Gambosi Benedetta , Sheiban Francesco Jamal , Biasizzo Marco , Antonietti Alberto , D’Angelo Egidio , Mazzoni Alberto , Pedrocchi Alessandra
Published: July 2023

Parkinson’s disease (PD) is a chronic degenerative disorder of the central nervous system that affects the motor system. The discovery that PD motor symptoms result from the death of dopaminergic cells in the substantia nigra led to focus most of PD research on the basal ganglia. However, recent findings point to an active involvement of the cerebellum in PD. Here, we have developed a multiscale computational model of the rodent brain’s basal ganglia-cerebellar network. Simulations showed that a direct effect of dopamine depletion on the cerebellum must be taken into account to reproduce the alterations of PD neural activity, particularly the increased beta oscillations widely reported in PD patients. Moreover, dopamine depletion indirectly impacted spike-time-dependent plasticity at the parallel fiber-Purkinje cell synapses, degrading associative motor learning as observed in PD. Overall, these results suggest a relevant involvement of cerebellum in PD motor symptoms.

Significance Statement

This study highlights the role of cerebellum in Parkinson’s disease (PD). While most studies on PD concentrate on dopaminergic mechanisms in the basal ganglia, here we show that dopamine depletion impacts also on the cerebellum, generating a complex dysfunctional interaction between the two subcortical circuits. To investigate this interaction, we developedde novoa multiarea multiscale network model that mechanistically addresses the effects of dopamine depletionon the cerebellum. Our study demonstrates that this aspect is crucial to reproduce experimental data, particularly the increased beta wave activity. Moreover, alterations in spike-time-dependent plasticity at the parallel fibre – Purkinje cell synapse of cerebellum can explain the link between dopamine depletion to motor learning impairment. These simulations indicate that the cerebellum warrants more attention in future PD research.
Mitochondrial variation inAnopheles gambiaeandAn. coluzzii: phylogeographic legacy of species isolation and mito-nuclear associations with metabolic resistance to pathogens and insecticides
Authors: Romero Jorge E. Amaya , Chenal Clothilde , Chehida Yacine Ben , Miles Alistair , Clarkson Chris S. , Pedergnana Vincent , Wertheim Bregje , Fontaine Michael C.
Published: July 2023

Mitochondrial DNA (mtDNA) has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mtDNA variation inAn. gambiaeandAn. coluzzii, in perspective with other species in theAnopheles gambiaecomplex (AGC), by assembling the mitogenomes of 1219 mosquitoes across Africa. The mtDNA phylogeny of the AGC was consistent with a previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, An. arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three salt-water tolerant species (An. merus, An. melas, An. bwambae) in the AGC also suggested that introgression and possibly selection shaped mtDNA evolution. MtDNA variation inAn. gambiaeandAn. coluzziiacross Africa revealed significant partitioning among populations and species. A peculiar mtDNA lineage found predominantly inAn. coluzziiand in the hybrid taxon of the African “far-west”exhibited divergence comparable to the inter-species divergence in the AGC, with a geographic distribution matching closelyAn. coluzzii’s geographic range. This phylogeographic relict of theAn. coluzziiandAn. gambiaesplit was associated with population and species structuration, but not withWolbachiaoccurrence. The lineage was significantly associated with SNPs in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline the mito-nuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticide inAnopheles.
Adaptation of theMycobacterium tuberculosistranscriptome to biofilm growth
Authors: Youngblom Madison A. , Smith Tracy M. , Pepperell Caitlin S.
Published: July 2023

Mycobacterium tuberculosis(M. tb), the causative agent of tuberculosis (TB), is a leading global cause of death from infectious disease. Biofilms are increasingly recognized as a relevant growth form duringM. tbinfection and may impede treatment by enabling bacterial drug and immune tolerance.M. tbhas a complicated regulatory network that has been well-characterized for many relevant disease states, including dormancy and hypoxia. However, despite its importance, our knowledge of the genes and pathways involved in biofilm formation is limited. Here we characterize the biofilm transcriptomes of fully virulent clinical isolates and find that the regulatory systems underlying biofilm growth vary widely between strains and are also distinct from regulatory programs associated with other environmental cues. We used experimental evolution to investigate changes to the transcriptome during adaptation to biofilm growth and found that the application of a uniform selection pressure resulted in loss of strain-to-strain variation in gene expression, resulting in a more uniform biofilm transcriptome. The adaptive trajectories of transcriptomes were shaped by the genetic background of theM. tbpopulation leading to convergence on a sub-lineage specific transcriptome. We identified widespread upregulation of non-coding RNA (ncRNA) as a common feature of the biofilm transcriptome and hypothesize that ncRNA function in genome-wide modulation of gene expression, thereby facilitating rapid regulatory responses to new environments. These results reveal a new facet of theM. tbregulatory system and provide valuable insight into howM. tbadapts to new environments.

Importance

Understanding mechanisms of resistance and tolerance inMycobacterium tuberculosis(M. tb) can help us develop new treatments that capitalize onM. tb’s vulnerabilities. Here we used transcriptomics to study both the regulation of biofilm formation in clinical isolates as well as how those regulatory systems adapt to new environments. We find that closely related clinical populations have diverse strategies for growth under biofilm conditions, and that genetic background plays a large role in determining the trajectory of evolution. These results have implications for future treatment strategies that may be informed by our knowledge of the evolutionary constraints on strain(s) from an individual infection. This work provides new information about the mechanisms of biofilm formation inM. tband outlines a framework for population level approaches for studying bacterial adaptation.
Regulation of BCR-mediated Ca2+mobilization by MIZ1-TIMBIM4 safeguards IgG1+GC B cell positive selection
Authors: Zhang Lingling , Toboso-Navasa Amparo , Gunawan Arief , Camara Abdouramane , Nakagawa Rinako , Finsterbusch Katja , Chakravarty Probir , Newman Rebecca , Zhang Yang , Eilers Martin , Andreas Wack , Tolar Pavel , Toellner Kai-Michael , Calado Dinis Pedro
Published: July 2023

The transition from IgM to affinity-matured IgG antibodies is vital for effective humoral immunity. This is facilitated by germinal centers (GCs) through affinity maturation and preferential accumulation of IgG+B cells over IgM+B cells. However, it is not known whether the positive selection of the different immunoglobulin isotypes within GCs varies in its dependency on specific transcriptional mechanisms. Here, we identified IgG1+GC B cell transcription factor dependency using CRISPR-Cas9 and conditional mouse genetics. We found that MIZ1 was specifically required for IgG1+GC B cell survival during positive selection, whereas IgM+GC B cells were largely independent. Mechanistically, MIZ1 induced TMBIM4, an ancestral anti-apoptotic protein that regulated inositol trisphosphate receptor mediated Ca2+mobilization downstream of IgG1. The MIZ1-TMBIM4 axis prevented mitochondrial dysfunction-induced IgG1+GC cell death caused by excessive Ca2+accumulation. This study uncovers a unique immunoglobulin isotype-specific dependency, on a hitherto unidentified mechanism in GC positive selection.
Smooth muscle-derived adventitial progenitor cells promote key cell type transitions controlling plaque stability in atherosclerosis in a Klf4-dependent manner
Authors: Dubner Allison M , Lu Sizhao , Jolly Austin J , Strand Keith A , Mutryn Marie F , Hinthorn Tyler , Noble Tysen , Nemenoff Raphael A , Moulton Karen S , Majesky Mark W , Weiser-Evans Mary CM
Published: July 2023

We previously established that vascular smooth muscle-derived adventitial progenitor cells (AdvSca1-SM) preferentially differentiate into myofibroblasts and contribute to fibrosis in response to acute vascular injury. However, the role of these progenitor cells in chronic atherosclerosis has not been defined. Using an AdvSca1-SM lineage tracing model, scRNA-Seq, flow cytometry, and histological approaches, we confirmed that AdvSca1-SM cells localize throughout the vessel wall and atherosclerotic plaques, where they primarily differentiate into fibroblasts, SMCs, or remain in a stem-like state. Klf4 knockout specifically in AdvSca1-SM cells induced transition to a more collagen-enriched myofibroblast phenotype compared to WT mice. Additionally, Klf4 depletion drastically modified the phenotypes of non-AdvSca1-SM-derived cells, resulting in more contractile SMCs and atheroprotective macrophages. Functionally, overall plaque burden was not altered with Klf4 depletion, but multiple indices of plaque vulnerability were reduced. Collectively, these data support that modulating the AdvSca1-SM population confers increased protection from the development of unstable atherosclerotic plaques.
Oxygen isotopes in orangutan teeth reveal recent and ancient climate variation
Authors: Smith Tanya M. , Arora Manish , Austin Christine , Ávila Janaína N. , Duval Mathieu , Lim Tze Tshen , Piper Philip J. , Vaiglova Petra , Vos John de , Williams Ian S. , Zhao Jian-xin , Green Daniel R.
Published: July 2023

Studies of climate variation commonly rely on chemical and isotopic changes recorded in sequentially-produced growth layers, such as in corals, shells and tree rings, as well as in accretionary deposits—ice and sediment cores, and speleothems. Oxygen isotopic compositions (δ18O) of tooth enamel are a direct method of reconstructing environmental variation experienced by an individual animal. Here we utilize long-forming orangutan dentitions (Pongospp.) to probe recent and ancient rainfall trends on a weekly basis over ∼ 3–11 years per individual. We first demonstrate the lack of any consistent isotopic enrichment effect during exclusive nursing, supporting the use of primate first molar teeth as environmental proxies. Comparisons of δ18O values (n = 2016) in twelve molars from six modern Bornean and Sumatran orangutans reveal a high degree of overlap, with more consistent annual and bimodal rainfall patterns in the Sumatran individuals. Comparisons with fossil orangutan δ18O values (n = 955 measurements from six molars) reveal similarities between modern and late Pleistocene fossil Sumatran individuals, but differences between modern and late Pleistocene/early Holocene Bornean orangutans. These suggest drier and more open environments with reduced monsoon intensity during this earlier period in northern Borneo, consistent with other Niah Caves studies and long-term speleothem δ18O records in the broader region. This approach can be extended to test hypotheses about the paleoenvironments that early humans encountered in southeast Asia.
A Plant Flavonol Rescues a Pathogenic Mutation Associated with Kinesin in Neurons
Authors: Chai Yongping , Li Dong , Gong Weibin , Ke Jingyi , Tian Dianzhe , Chen Zhe , Guo Angel , Guo Zhengyang , Li Wei , Feng Wei , Ou Guangshuo
Published: July 2023

KIF1A, a microtubule-based motor protein responsible for axonal transport, is linked to a group of neurological disorders known as KIF1A-associated neurological disorder (KAND). Current therapeutic options for KAND are limited. Here, we introduced the clinically relevant KIF1A(R11Q) variant into theC. eleganshomolog UNC-104, resulting in uncoordinated animal behaviors. Through genetic suppressor screens, we identified intragenic mutations in UNC-104’s motor domain that rescued synaptic vesicle localization and coordinated movement. We showed that two suppressor mutations partially recovered motor activity in vitro by counteracting the structural defect caused by R11Q at KIF1A’s nucleotide-binding pocket. We found that supplementation with fisetin, a plant flavonol, improved KIF1A(R11Q) worms’ movement and morphology. Notably, our biochemical and single-molecule assays revealed that fisetin directly restored the ATPase activity and processive movement of human KIF1A(R11Q) without affecting wild-type KIF1A. These findings suggest fisetin as a potential intervention for enhancing KIF1A(R11Q) activity and alleviating associated defects in KAND.
A global, integrated view of the ubiquitylation site occupancy and dynamics
Authors: Prus Gabriela , Satpathy Shankha , Weinert Brian T. , Narita Takeo , Choudhary Chunaram
Published: July 2023

Ubiquitylation regulates virtually all proteins and biological processes in a cell. However, the global site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have never been quantified. Here, we present the first integrated picture of ubiquitylation site occupancy and half-life. Ubiquitylation occupancy spans four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and the regulation of sites by proteasome inhibitors show strong interrelationships. These properties can discriminate signaling-relevant sites from the sites involved in proteasomal degradation. The sites strongly upregulated by proteasome inhibitors have a longer half-life, and the half-life increases with increasing protein length. Importantly, a previously unknown surveillance mechanism rapidly deubiquitylates all ubiquitin-specific E1 and E2 enzymes and protects them against bystander ubiquitylation accumulation. This work reveals general principles of ubiquitylation-dependent governance and offers conceptual insights into the dynamic regulation of the cell.

Highlights

Ubiquitylation site occupancy is 3 orders of magnitude lower than phosphorylation

The highest 80% and the lowest 20% occupancy sites have distinct properties

High occupancy sites are concentrated in the cytoplasmic domains of SLC proteins

A dedicated mechanism prevevents ubiquitylation accumulation in E1s and E2s
Towards Modular Engineering of Cell Signalling: Topographically-Textured Microparticles Induce Osteogenesis via Activation of Canonical Hedgehog Signalling
Authors: Ghuloum Fatmah I. , Stevens Lee A. , Johnson Colin A. , Riobo-Del Galdo Natalia A. , Amer Mahetab H.
Published: July 2023

Polymer microparticles possess great potential as functional building blocks for advanced bottom-up engineering of complex tissues. Tailoring the three-dimensional architectural features of culture substrates has been shown to induce osteogenesis in mesenchymal stem cellsin vitro, but the molecular mechanisms underpinning this remain unclear. This study proposes a mechanism linking the activation of Hedgehog signalling to the osteoinductive effect of surface-engineered, topographically-textured polymeric microparticles. In this study, mesenchymal progenitor C3H10T1/2 cells were cultured on smooth and dimpled poly(D,L-lactide) microparticles to assess differences in viability, cellular morphology, proliferation, and expression of a range of Hedgehog signalling components and osteogenesis-related genes. Dimpled microparticles induced osteogenesis and activated the Hedgehog signalling pathway relative to smooth microparticles and 2D-cultured controls without the addition of exogenous biochemical factors. We observed upregulation of the osteogenesis markersRunt-related transcription factor2(Runx2) andbone gamma-carboxyglutamate protein 2(Bglap2), as well as the Hedgehog signalling components,glioma associated oncogene homolog 1(Gli1),Patched1(Ptch1), andSmoothened(Smo). Treatment with the Smo antagonist KAAD-cyclopamine confirmed the involvement of Smo inGli1target gene activation, with a significant reduction in the expression ofGli1,Runx2andBglap2(p≤0.001) following KAAD-cyclopamine treatment. Overall, our study demonstrates the role of the topographical microenvironment in the modulation of Hedgehog signalling, highlighting the potential for tailoring substrate topographical design to offer cell-instructive 3D microenvironments. Topographically-textured microparticles allow the modulation of Hedgehog signallingin vitrowithout adding exogenous biochemical agonists, thereby eliminating potential confounding artefacts in high-throughput drug screening applications.

Graphical Abstract
Chemically Induced Degradation of Native Proteins by Direct Recruitment to the 26S Proteasome
Authors: Balzarini Madeline , Gui Weijun , Jayalath Isuru M. , Schell Bin-Bin , Tong Joel , Kodadek Thomas
Published: July 2023

Targeted protein degradation (TPD) is a promising strategy for drug development. Most degraders function by forcing the association of the target protein (TP) with an E3 Ubiquitin ligase, which in favorable cases results in the poly-Ubiquitylation of the TP and its subsequent degradation by the 26S proteasome. Here we explore the feasibility of a different TPD strategy in which the TP is recruited directly to the proteasome without the requirement for poly-Ubiquitylation. Using an engineered cell line in which the HaloTag protein is fused to one of the Ubiquitin receptors, we show that native protein targets can be degraded in this fashion when the cells are exposed to a chemical dimerizer containing a chloroalkane and a TP ligand. The potential advantages and disadvantages of Ubiquitin-independent degraders vs. traditional proteolysis-targeting chimeras are discussed.
Identification ofLactuca sativatranscription factors impacting resistance toBotrytis cinereathrough predictive network inference
Authors: Pink Harry , Talbot Adam , Carter Ryan , Hickman Richard , Cooper Oliver , Law Rebecca , Higgins Gillian , Yao Chenyi , Gawthrop Frances , Hand Paul , Pink David , Clarkson John , Denby Katherine
Published: July 2023

Lettuce is susceptible to a wide range of plant pathogens including the fungal pathogensBotrytis cinereaandSclerotinia sclerotiorum, causal agents of grey mould and lettuce drop, respectively. Chemical control is routinely used but there is an urgent need to develop varieties with enhanced resistance given the economic and environmental costs of preventative pesticide sprays, the prevalence of fungicide-resistant isolates of both pathogens in the field, and the increasing withdrawal of approved fungicides through legislation. Resistance againstBotrytis cinereaandSclerotinia sclerotiorumis quantitative, governed by multiple small-medium impact loci, with plant responses involving large-scale transcriptional reprogramming. The elucidation of the gene regulatory networks (GRNs) mediating these responses will not only identify key transcriptional regulators but also interactions between regulators and show how the defence response is fine-tuned to a particular pathogen. We generated high-resolution (14 time points) time series expression data from lettuce leaves following mock-inoculation or inoculation withB. cinerea, capturing the dynamics of the transcriptional response to infection. Integrating this data with a time series dataset fromS. sclerotioruminfection of lettuce identified a core set of 4362 genes similarly differentially expressed in response to both pathogens. Using the expression data for these core genes (with additional single time point data from 21 different lettuce accessions) we inferred a GRN underlying the lettuce defence response to these pathogens. Using the GRN, we have predicted and validated key regulators of lettuce immunity, identifying both positive (LsBOS1) and negative (LsNAC53) regulators of defence againstB. cinerea, as well as downstream target genes. These data provide a high level of detail on defence-induced transcriptional change in a crop species and a GRN with the ability to predict transcription factors mediating disease resistance both in lettuce and other species.
A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Authors: Du Ze-Zhen , He Jia-Bao , Jiao Wen-Biao
Published: July 2023

Background

Although sequencing technologies have boosted the measurement of the sequencing diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods have been developed to address this issue and tested for human genomes, however, their performance in plant genomes remains largely elusive. Furthermore, pipelines integrating the advantages of current genotyping methods might be required, considering the different complexity of plant genomes.

Results

Here we comprehensively evaluate eight such genotypers in different scenarios in terms of variant type and size, sequencing parameters, genomic context, and complexity, as well as graph size, using both simulated and read data sets from representative plant genomes. Our evaluation reveals that there are still great challenges to applying existing methods to plants, such as excessive repeats and variants or high resource consumption. Therefore, we propose a pipeline called Ensemble Variant Genotyper (EVG) that can achieve better genotype concordances without increasing resource consumption. EVG can achieve comparably higher genotyping recall and precision even using 5× reads. Furthermore, we demonstrate that EVG is more robust with an increasing number of variants, especially for insertion and deletion.

Conclusions

Our study will provide new insights into the development and application of graph-based genotyping algorithms. We conclude that EVG provides an accurate, unbiased, and cost-effective way for genotyping both small and large variations and will be potentially used in population-scale genotyping for large, repetitive, and heterozygous plant genomes.
A cautionary note on the use of N-acetylcysteine as a reactive oxygen species antagonist to assess copper mediated cell death
Authors: Graham Rebecca E. , Elliott Richard J. R. , Munro Alison F. , Carragher Neil O.
Published: July 2023

A new form of cell death has recently been proposed involving copper-induced cell death, termed cuproptosis. This new form of cell death has been widely studied in relation to a novel class of copper ionophores, including elesclomol and disulfiram. However, the exact mechanism leading to cell death remains contentious. The oldest and mostly widely accepted biological mechanism is that the accumulated intracellular copper leads to excessive build-up of reactive oxygen species and that this is what ultimately leads to cell death. Most of this evidence is largely based on studies using N-acetylcysteine (NAC), an antioxidant, to relieve the oxidative stress and prevent cell death. However, here we have demonstrated using inductively coupled mass-spectrometry, that NAC pretreatment significantly reduces intracellular copper uptake triggered by the ionophores, elesclomol and disulfiram, suggesting that reduction in copper uptake, rather than the antioxidant activity of NAC, is responsible for the diminished cell death. We present further data showing that key mediators of reactive oxygen species are not upregulated in response to elesclomol treatment, and further that sensitivity of cancer cell lines to reactive oxygen species does not correlate with sensitivity to these copper ionophores. Our findings are in line with several recent studies proposing the mechanism of cuproptosis is instead via copper mediated aggregation of proteins, resulting in proteotoxic stress leading to cell death.

Overall, it is vital to disseminate this key piece of information regarding NAC’s activity on copper uptake since new research attributing the effect of NAC on copper ionophore activity to quenching of reactive oxygen species is being published regularly and our studies suggest their conclusions may be misleading.
Methanolic extracts of the edible halophyteCrithmum maritimumenhance oxidative stress resistance inCaenorhabditis elegansthrough hormetic mechanisms
Authors: Martins-Noguerol Raquel , Mata-Cabana Alejandro , Olmedo María , DeAndrés-Gil Cristina , Moreira Xoaquín , Francisco Marta , Moreno-Pérez Antonio J. , Cambrollé Jesús
Published: July 2023

Halophytes are promising sources of bioactive phenolic compounds for the food and pharmaceutical industries. However, their phenolic composition is influenced by environmental conditions, and thein vivoantioxidant activity of their phytochemicals is largely unknown. We evaluated the antioxidant capacity of phenolic-rich methanolic extracts from the edible halophyteCrithmum maritimum, grown in wild and greenhouse conditions. Additionally, theirin vivoantioxidant capacity was analyzed for the first time using the modelCaenorhabditis elegans. Wild plant extracts showed higher phenolic content and diversity, andin vitroantioxidant activity. Both extracts enhanced oxidative stress resistance and increased nematode survival rates, albeit to varying extents, and increased reactive oxygen species production in nematodes, without affecting their lifespan, suggesting a hormetic mechanism. Although no neuroprotective effects were observed in models of neurodegenerative diseases, these findings highlight the potential ofC. maritimumas a valuable source of phenolics with antioxidant properties for the food industry.
Shedding light on the Ophel biome: The Trans-Tethyan phylogeography of the sulfide shrimpTethysbaena(Peracarida: Thermosbaenacea) in the Levant
Authors: Guy-Haim Tamar , Kolodny Oren , Frumkin Amos , Achituv Yair , Velasquez Ximena , Morov Arseniy R.
Published: July 2023

Tethysbaenaare small peracarid crustaceans found in extreme environments such as subterranean lakes and thermal springs, represented by endemic species found around the ancient Tethys, including the Mediterranean, Arabian Sea, Mid-East Atlantic, and the Caribbean Sea. TwoTethysbaenaspecies are known from the Levant:T. relicta, inhabiting the Dead Sea-Jordan Rift Valley, andT. ophelicola, found in the Ayyalon cave complex in the Israeli coastal plain, both belonging to the same species-group based on morphological cladistics. Along the biospeleological research of the Levantine subterranean fauna, three biogeographic hypotheses determining their origins were proposed: (1) Pliocenic transgression, (2) Mid-late Miocenic transgression, and (3) The Ophel Paradigm, according to which these are inhabitants of a chemosynthetic biome as old as the Cambrian. We have used mtDNA COI gene and a molecular clock approach to establish the phylogeny and assess the divergence times of the LevantineTethysbaena. Contrary to prior hypotheses, our results indicate a two-stage colonization pattern: a late Oligocene transgression, through a marine gulf extending from the Arabian Sea, leading to the colonization ofT. relictain the Dead Sea-Jordan Rift Valley, and a Miocene transgression in the emerging Mediterranean region, carryingT. ophelicolato the coastal plain of Israel.
Sleep maintains excitatory synapse diversity in the cortex and hippocampus
Authors: Koukaroudi Dimitra , Qiu Zhen , Fransén Erik , Gokhale Ragini , Bulovaite Edita , Komiyama Noboru H. , Seibt Julie , Grant Seth G.N.
Published: July 2023

How sleep deprivation affects cognition remains elusive. Synaptome mapping of excitatory synapses in 125 regions of the mouse brain revealed that sleep deprivation selectively reduces synapse diversity in the cortex and hippocampus. Sleep deprivation targeted specific types and subtypes of excitatory synapses while maintaining total synapse density. Altered synaptic responses to neural oscillations in a computational model suggest that sleep prevents cognitive impairments by maintaining normal brain synaptome architecture.
Cold temperature induces a TRPM8-independent calcium release from the endoplasmic reticulum in human platelets
Authors: Stratiievska Anastasiia , Filippova Olga , Özpolat Tahsin , Byrne Daire , Lawrence Bailey S. , Mollica Molly Y. , Harris Jeff , Esancy Kali , Chen Junmei , Dhaka Ajay K. , Sniadecki Nathan J. , López José A , Stolla Moritz
Published: July 2023

Platelets are sensitive to temperature changes and akin to sensory neurons, are activated by a decrease in temperature. However, the molecular mechanism of this temperature-sensing ability is unknown. Yet, platelet activation by temperature could contribute to numerous clinical sequelae, most importantly to reduced quality ofex vivo-stored platelets for transfusion. In this interdisciplinary study, we present evidence for the expression of the temperature-sensitive ion channel transient receptor potential cation channel subfamily member 8 (TRPM8) in human platelets and precursor cells. We found the TRPM8 mRNA and protein in MEG-01 cells and platelets. Inhibition of TRPM8 prevented temperature-induced platelet activation and shape change. However, chemical agonists of TRPM8 did not seem to have an acute effect on platelets. When exposing platelets to below-normal body temperature, we detected a cytosolic calcium increase which was independent of TRPM8 but was completely dependent on the calcium release from the endoplasmic reticulum. Because of the high interindividual variability of TRPM8 expression, a population-based approach should be the focus of future studies. Our study suggests that the cold response of platelets is complex and TRPM8 appears to play a role in early temperature-induced activation of platelets, while other mechanisms likely contribute to later stages of temperature-mediated platelet response.
Insight into the risk-resistant function of ESG performance: An organizational management perspective
Authors: Zhang Yue , Zhang Changjiang , Zhang Sihan , Yang Yuqi , Lan Kai
Published: July 2023

Purpose

This study aims to examine the risk-resistant role of environmental, social and governance (ESG) performance in the capital market, focusing on an organizational standpoint. Furthermore, it aims to offer management decision advice to companies seeking protection against stock market risks. Conclusions obtained through this research have the potential to enrich the economic consequences of ESG performance, provide practical implications for enhancing corporate ESG performance, improving corporate information quality and stabilizing capital market development.

Design/methodology/approach

Based on the data of Chinese A-share listed companies from 2009 to 2020, this study examines the risk-resistant function of ESG performance in the capital market. The impact of ESG performance on management behavior is analyzed from the perspective of organizational management and the three mechanisms of pre-event, during the event and post-event.

Findings

This paper demonstrates that companies that effectively implement ESG practices are capable of effectively mitigating risks associated with stock price crashes. Heterogeneity analysis reveals that the inhibitory effect of ESG performance on stock price crash risk is more pronounced in nonstate-owned enterprises and enterprises with higher levels of marketization. After controlling for issues such as endogeneity, the conclusions of this paper are still valid. The mechanism analysis indicates that ESG performance reduces the risk of stock price crash through three paths of organizational management: pre-event, during the event and post-event. That is, ESG performance plays the role of restraining managers’ opportunistic behavior, reducing information asymmetry and boosting investor sentiment.

Originality/value

This paper provides new insights into the relationship between ESG performance and stock price crash risk from an organizational management perspective. This study establishes three impact mechanisms (governance effect, information effect and insurance effect), offering a theoretical basis for strategic corporate decisions of risk management. Additionally, it comprehensively examines the contextual differences in the role of ESG performance, shedding light on the specific domains where ESG practices are influential. These findings offer valuable insights for promoting stable development in the capital market and fostering the healthy growth of the real economy.
Family influences on entrepreneurial orientation in immigrant entrepreneurship
Authors: Ljungkvist Torbjörn , Evansluong Quang , Boers Börje
Published: July 2023

Purpose

This study explores how the family influences the entrepreneurial orientation (EO) process in immigrant businesses.

Design/methodology/approach

The paper draws on inductive multiple-case studies using 34 in-depth interviews. This paper relies on three cases of immigrant entrepreneurs originating from Mexico and Colombia that established firms in Sweden.

Findings

The results suggest that EO development trajectories vary in the presence of family roles (i.e. inspirers, backers and partners), resulting in the immigrant family business configurations of family-role-influenced proactiveness, risk-taking and innovation.

Originality/value

The immigrant family configurations drive three EO-enabling scenarios: (1) home-country framing, (2) family backing and (3) transnational translating. Immigrant family dynamics facilitate the development of EO over time through reciprocal interaction processes across contexts. This study indicates that, through family dynamics, EO develops as mutually interactive processes between the immigrant entrepreneur's family in the home and host countries.
Market segmentation based on customer experience dimensions extracted from online reviews using data mining
Authors: Pandey Shweta , Pandey Neeraj , Chawla Deepak
Published: July 2023

Purpose

This study aims to develop a practical and effective approach for market segmentation using customer experience dimensions derived from online reviews.

Design/methodology/approach

The research investigates over 6,500 customer evaluations of food establishments on Taiwan’s Yelp platform through the Latent Dirichlet allocation (LDA) data mining approach. By using the LDA-derived experience dimensions, cluster analysis discloses market segments. Subsequently, sentiment analysis is used to scrutinize the emotional scores of each segment.

Findings

Mining online review data helps discern divergent and new customer experience dimensions and sheds light on the divergent preferences among identified customer segments concerning these dimensions. Moreover, the polarity of sentiments expressed by consumers varies across such segments.

Research limitations/implications

Analyzing customer attributes extracted from online reviews for segmentation can enhance comprehension of customers’ needs. Further, using sentiment analysis and attributes of online reviews result in rich profiling of the identified segments, revealing gaps and opportunities for marketers.

Originality/value

This research presents a new approach to segmentation, which surmounts the restrictions of segmentation methods dependent on survey-based information. It contributes to the field and provides a valuable means for conducting customer-focused market segmentation. Furthermore, the suggested methodology is transferable across different sectors and not reliant on particular data sources, creating possibilities in diverse scenarios.