bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence
Authors: Ferguson Scott , Jones Ashley , Murray Kevin , Andrew Rose L. , Bothwell Helen , Schwessinger Benjamin , Borevitz Justin
Published: October 2023

Structural variants (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely relatedEucalyptusspecies to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences, or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals ofE. melliodoraandE. sideroxylon, along with recent high quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads, inE. melliodoraandE. sideroxylonrespectively. Focusing on inversions and translocations, symmetric SVs which are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.
Discovery of two archaeal GDGT lipid modifying enzymes reveals diverse microbes capable of H-GDGT biosynthesis and modification
Authors: Garcia Andy A. , Chadwick Grayson L. , Welander Paula V.
Published: October 2023

Archaea produce unique membrane-spanning lipids, termed glycerol dialkyl glycerol tetraethers (GDGTs), which are thought to aid in adaptive responses to various environmental challenges. GDGTs can be modified in a variety of ways, including cyclization, bridging or cross-linking, methylation, hydroxylation, and desaturation, to give rise to a plethora of structurally distinct GDGT lipids with different properties. Here we report the discovery of a pair of radical SAM enzymes responsible for two of these modifications - an H-GDGT bridge synthase (Hbs), responsible for cross-linking the two hydrocarbon tails of a GDGT to produce H-GDGTs and an H-GDGT methylase (Hgm), responsible for the subsequent methylation of H-GDGTs. Heterologous expression of Hbs proteins from various archaea inThermococcus kodakarensisresults in the production of H-GDGTs in two isomeric forms. Further, co-expression of Hbs and Hgm results in the production of mono- and di-methylated H-GDGTs and minor amounts of tri-methylated H- GDGTs while expression of Hgm alone results in minor production of mono- and di- methylated GDGTs. Phylogenetic analyses reveal the presence of Hbs homologs in diverse archaeal genomes spanning all four archaeal superphyla. We also find Hbs homologs in bacterial genomes that have the genetic potential to synthesize fatty acid- based membrane-spanning lipids such as brGDGTs. We subsequently demonstrate H- GDGT production in three Hbs-encoding archaea, identifying an increase in H-GDGTs in response to elevated temperature in members of the genusArchaeoglobusand observing the production of highly cyclized H-GDGTs with up to 6 rings in the Thermoproteales archaeonVulcanisaeta distributa.Such highly cyclized H-GDGTs are the precursors of ARN acids, a class of tetraprotic naphthenic acids that cause destructive mineral deposition during crude oil processing. Co-occurrence of the H-GDGT synthase with the previously identified GDGT ring synthases in archaeal genomes allowed identification of multiple archaeal phyla with the genetic potential to produce highly cyclized H-GDGTs, with particularly interesting candidates in the class Thermoplasmata from oil rich environments.
Platelet-specific TGFβ1 deficiency aggravates atherosclerosis, vascular inflammation, and hypercholesterolemia in mice
Authors: Tan Shuai , Sun Yang , Sheng Zi , Min Yanan , Gisterå Anton , Zhang Junhao , Ketelhuth Daniel F.J. , Liao Wangjun , Andersson John , Hu Hu , Wang Miao , Hou Ming , Zhang Mingxiang , Peng Jun , Ma Chunhong , Li Nailin
Published: October 2023

Atherosclerosis involves inflammatory and thrombotic mechanisms, to which both platelets and transforming growth factor β (TGFβ) contribute. The effect of platelet-derived TGFβ on atherosclerosis is, however, unknown and therefore investigated. Murine platelet-selective TGFβ-deficiency (plt-TGFβ-/-) was created by aPf4-Cre approach, and an atherosclerotic mouse model was established by functional abrogation ofLdlrand 10-15 weeks of a high-fat diet in plt-TGFβ-/-mice and their non-plt-TGFβ-/-littermates. En face Oil Red O staining of the aorta showed more atherosclerotic lesion formation in plt-TGFβ-/-mice, with significant increases in both lesion size and lesion coverage of the total aortic area. Cryosections of the aortic root confirmed the aggravation of atherogenesis. Platelet-derived TGFβ deficiency increased circulating platelets and plasma levels of total cholesterol, LDL-cholesterol, and triglycerides after a 10 or 15 week high-fat diet period. RNA sequencing and proteomic analyses of the aorta showed signs of CD4+T effector cell and macrophage activation in plt-TGFβ-/-mice. In conclusion, platelet-specific TGFβ deficiency aggravates atherosclerosis, via increasing arterial inflammation and plasma levels of cholesterol. Our findings demonstrate that platelet-derived TGFβ is prominently athero-protective.

Key points

Platelet-specific transforming growth factor β (TGFβ) deficiency markedly enhances atherosclerosis in a high-fat diet-fed murine model.

Platelet TGFβ deficiency aggravates hyperlipidemia, with further elevations of total cholesterol, LDL-cholesterol, and triglycerides.
Multi-locus CRISPRi targeting with a single truncated guide RNA
Authors: Moore Molly M , Wekhande Siddarth , Issner Robbyn , Collins Alejandro , Liu Yanjing , Javed Nauman , Buenrostro Jason D , Epstein Charles B , Mattei Eugenio , Doench John G , Bernstein Bradley E , Shoresh Noam , Najm Fadi J
Published: October 2023

A critical goal in functional genomics is evaluating which non-coding elements contribute to gene expression, cellular function, and disease. Functional characterization remains a challenge due to the abundance and complexity of candidate elements. Here, we develop a CRISPRi- based approach for multi-locus screening of putative transcription factor binding sites with a single truncated guide. A truncated guide with hundreds of sequence match sites can reliably disrupt enhancer activity, which expands the targeting scope of CRISPRi while maintaining repressive efficacy. We screen over 13,000 possible CTCF binding sites with 24 guides at 10 nucleotides in spacer length. These truncated guides direct CRISPRi-mediated deposition of repressive H3K9me3 marks and disrupt transcription factor binding at most sequence match target sites. This approach is valuable for elucidating functional transcription factor binding motifs or other repeated genomic sequences and is easily implementable with existing tools.
The grapevine ABC transporter B family member 15 (VvABCB15) is trans-resveratrol transporter out of grapevine cells
Authors: Martínez-Márquez A , Martins V , Sellés-Marchart S , Gerós H , Corchete P , Bru-Martínez R
Published: October 2023

Stilbenes, particularlytrans-resveratrol, play a highly relevant defense role in grapevine as phytoalexin induced in response to stress. Metabolism and transport of stilbenes can be conveniently investigated in grapevine cell culture since large amounts oftrans-resveratrol are accumulated in the extracellular medium upon treatment with the elicitor methylated cyclodextrin, either alone or combined with methyl jasmonate. Aiming at finding trans-resveratrol transporter candidates a proteomic approach on grapevine cells membrane fractions was performed. The candidate VvABCB15 was functionally characterized. Its stable expression in both yeast andSilybum marianumcells heterologous systems led to increasedtrans-resveratrol transport in these hosts. Transient expression inVitiscells showed an enhanced absorbent- or elicitor-assisted accumulation of extracellulartrans-resveratrol in both VvABCB15-expressing or VvGSTU10/VvABCB15-coexpressing cell suspension cultures. Experiments of transient expression inVitiscell suspensions using light-switchable stilbene synthase (pHYH::VvSTS3) and VvABCB15 further confirmed the role of the candidate astrans-resveratrol transporter. VvABCB15-YFP fusion proteins inNicotianaleaf showed localization in plasma membrane, being consistent with a functional role intrans-resveratrol transport. This is the first report providing evidence for the involvement of an ABC transporter B-type, VvABCB15 intrans-resveratrol transport to the extracellular medium of grapevine cells.
A bivalent Adenovirus-Vectored Vaccine induces a robust humoral response, but does not protect cynomolgus macaques against a lethal challenge with Sudan virus
Authors: van Tol Sarah , Fletcher Paige , Feldmann Friederike , Mukesh Reshma K. , Port Julia R. , Gallogly Shane , Schulz Jonathan E. , Rhoderick Joseph F. , Makinson Rebecca , Carmody Aaron , Myers Lara , Lovaglio Jamie , Smith Brian J. , Okumura Atsushi , Shaia Carl , Saturday Greg , Marzi Andrea , Lambe Teresa , Munster Vincent J. , van Doremalen Neeltje
Published: October 2023

The most recent Sudan virus (SUDV) outbreak in Uganda was first detected in September 2022 and resulted in 164 laboratory-confirmed cases and 77 deaths. Currently, there are no approved vaccines or therapeutics against SUDV. In the current study, we investigated the protective efficacy of ChAdOx1-biEBOV in cynomolgus macaques using a prime or a prime-boost regimen. ChAdOx1-biEBOV is a replication-deficient simian adenovirus vector encoding SUDV and Ebola virus (EBOV) glycoproteins (GPs) at the E1 and E4 loci, respectively. Intramuscular vaccination induced SUDV and EBOV GP-specific IgG responses and neutralizing antibodies. Upon challenge with SUDV, vaccinated animals, regardless of vaccination scheme, showed signs of disease like those observed in control animals, and no difference in survival outcomes were measured among all three groups. Viral load in blood samples and in tissue samples obtained after necropsy were not significantly different between groups. Overall, this study highlights the importance of evaluating vaccines in multiple animal models, including nonhuman primates, and demonstrates the importance of understanding protective efficacy in both animal models and human hosts.
Comprehensive Virulence Profiling and Evolutionary Analysis of Specificity Determinants inStaphylococcus aureusTwo-Component Systems
Authors: Ahator Stephen Dela , Wenzl Karoline , Hegstad Kristin , Lentz Christian , Johannessen Mona
Published: October 2023

In theStaphylococcus aureusgenome, a set of highly conserved two-component systems (TCSs) composed of histidine kinases (HKs) with their cognate response regulators (RRs) sense and respond to environmental stimuli, which drive the adaptation of the bacteria. This study investigates the complex interplay between TCSs inS. aureusUSA300, a predominant Methicillin-ResistantS. aureus(MRSA) strain, revealing shared and unique virulence regulatory pathways and genetic variations mediating signal specificity within TCSs. Using TCS-related mutants from the Nebraska Transposon Mutant Library, we analyzed the effects of inactivated TCS HKs and RRs on the production of various virulence factors,in vitroinfection abilities, and adhesion assays. We found that the TCSs influence on virulence determinants was not associated with their phylogenetic relationship, indicating divergent functional evolution. Using the cocrystalized structure of the DesK-DesR fromB. subtilisand modelled structures of the 4 NarL TCSs inS. aureus, we identified interacting residues, revealing specificity determinants and conservation within the same TCS, even from different strain backgrounds. The interacting residues were highly conserved within strains but varied between species due to selection pressures and coevolution of cognate pairs. This study unveils the complex interplay and divergent functional evolution of TCSs, highlighting their potential for future experimental exploration of phosphotransfer between cognate and non-cognate recombinant HK and RRs.

IMPORTANCE

Given the widespread conservation of Two-Component Systems (TCSs) in bacteria and their pivotal role in regulating metabolic and virulence pathways, they present a compelling target for anti-microbial agents—especially in the face of rising multi-drug resistant infections. Harnessing TCSs therapeutically necessitates a profound understanding of their evolutionary trajectory in signal transduction, as this underlies their unique or shared virulence regulatory pathways. Such insights are critical for effectively targeting TCS components, ensuring an optimized impact on bacterial virulence and mitigating the risk of resistance emergence via the evolution of alternative pathways. Our research offers an in-depth exploration of virulence determinants controlled by TCSs in S. aureus, shedding light on the evolving specificity determinants that orchestrate interactions between their cognate pairs.
H2S preconditioning induces long-lived perturbations in O2metabolism
Authors: Hanna David A. , Diessl Jutta , Guha Arkajit , Kumar Roshan , Andren Anthony , Lyssiotis Costas , Banerjee Ruma
Published: October 2023

Hydrogen sulfide exposure in moderate doses can induce profound but reversible hypometabolism in mammals. At a cellular level, H2S inhibits the electron transport chain (ETC), augments aerobic glycolysis, and glutamine-dependent carbon utilization via reductive carboxylation; however, the durability of these changes is unknown. We report that despite its volatility, H2S preconditioning increasesP50(O2), the O2pressure for half maximal cellular respiration, and has pleiotropic effects on oxidative metabolism that persist up to 24-48 h later. Notably, cyanide, another complex IV inhibitor, does not induce this type of metabolic memory. Sulfide-mediated prolonged fractional inhibition of complex IV by H2S is modulated by sulfide quinone oxidoreductase, which commits sulfide to oxidative catabolism. Since induced hypometabolism can be beneficial in disease settings that involve insufficient or interrupted blood flow, our study has important implications for attenuating reperfusion-induced ischemic injury, and/or prolonging shelf life of biologics like platelets.
A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A
Authors: Porter Robert S. , Nagai Masayoshi , An Sojin , Gavilan Maria C. , Murata-Nakamura Yumie , Bonefas Katherine M. , Zhou Bo , Dionne Olivier , Manuel Jeru Manoj , St-Germain Joannie , Browning Liam , Laurent Benoit , Cho Uhn-Soo , Iwase Shigeki
Published: October 2023

How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associatedPHF21Amissense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing ofPHF21A-n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.
Genome-wide CRISPR/Cas9 screen identifies MAT2A as a critical host factor for BK Polyomavirus
Authors: Caller Laura , Ho Sophia , Brown Katherine , Dupont Liane , Zalatel Tjasa , Beale Rupert , Lehner Paul J. , Crump Colin M.
Published: October 2023

BK polyomavirus (BKPyV) is a ubiquitous human pathogen that causes major complications for renal transplant patients (polyomavirus-associated nephropathy) and hematopoietic stem cell transplant patients (haemorrhagic cystitis). There are currently no effective antivirals available against BKPyV. As polyomaviruses are small DNA viruses that express very few proteins and utilise host DNA polymerases for their replication, there is limited possibility of targeting viral proteins for therapeutic intervention. As such, there is increasing interest in targeting host pathways to inhibit these viruses. To identify host genes required for BKPyV infection we have conducted the first genome-wide CRISPR/Cas9 screen in BKPyV infected cells. This led to the identification of methionine adenosyltransferase 2A (MAT2A), which we have validated as a host dependency factor for BKPyV infection. MAT2A is a druggable host enzyme that synthesises S-adenosylmethionine, the principal co-factor and methyl donor within cells. We have found that a small molecule inhibitor of MAT2A is a potent antiviral drug inhibiting BKPyV replication, offering a new therapeutic option for treatment of BKPyV diseases.
Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation
Authors: Hong Seong Ho , Osa Akane , Huang Oscar W. , Wertz Ingrid E. , Nomura Daniel K.
Published: October 2023

Targeted protein degradation with Proteolysis Targeting Chimeras (PROTACs) is a powerful therapeutic modality for eliminating disease-causing proteins through targeted ubiquitination and proteasome-mediated degradation. Most PROTACs have exploited substrate receptors of Cullin-RING E3 ubiquitin ligases such as cereblon and VHL. Whether core, shared, and essential components of the Cullin-RING E3 ubiquitin ligase complex can be used for PROTAC applications remains less explored. Here, we discovered a cysteine-reactive covalent recruiter EN884 against the SKP1 adapter protein of the SKP1-CUL1-F-box containing SCF complex. We further showed that this recruiter can be used in PROTAC applications to degrade neo-substrate proteins such as BRD4 and the androgen receptor in a SKP1- and proteasome-dependent manner. Our studies demonstrate that core and essential adapter proteins within the Cullin-RING E3 ubiquitin ligase complex can be exploited for targeted protein degradation applications and that covalent chemoproteomic strategies can enable recruiter discovery against these targets.
Variant-Specific Landscape of Mutual Exclusivity Among BRAF, EGFR, and KRAS Oncogenes in Human Cancer
Authors: Vaeyens Freya , Hetzel Jan-Patrick , Mernberger Marco , Eggermont Carolien , Olsen Catharina , Maes Ken , Vlaeminck Jelle , Hes Frederik , Pichler Martin , Giron Philippe , Timofeev Oleg , Noeparast Maxim
Published: October 2023

In this cross-sectional study, we report the findings of our investigation into the mutual exclusivity (ME) and co-occurrence (CO) patterns of BRAF, KRAS, and EGFR mutations in human cancer. Our analysis acknowledges previously overlooked mutational subtypes with distinct clinical implications. Creating an automated R framework, we analyzed mutation data from 64807 unique cBioPortal samples, 1570 cell lines, and 2714 unique Belgian cancer samples. Consistently, across all three datasets, we observe that co-occurrence is less likely among class I BRAF, Hydrolysis KRAS, and Classical-like EGFR mutations. Bilateral variant-assigned CO matrices uncover novel inter-class and inter-type CO and ME scenarios, encompassing conventional and atypical mutations. Besides Class I BRAF, various mutation classes exhibit diverse CO patterns, justifying the need to refine mutational classifications. We provide a variant-specific database for precision oncology showcasing ME among three actionable oncogenes. These findings may guide the discovery of novel synthetically lethal interactions for targeted cancer therapy.
Towards Understanding Autism Heterogeneity: Identifying Clinical Subgroups and Neuroanatomical Deviations
Authors: Meijer Jente , Vieira Bruno Hebling , Elleaume Camille , Baranczuk-Turska Zofia , Langer Nicolas , Floris Dorothea L.
Published: October 2023

Autism Spectrum Disorder (‘autism’) is a neurodevelopmental condition characterized by substantial behavioural and neuroanatomical heterogeneity. This poses significant challenges to understanding its neurobiological mechanisms and developing effective interventions. Identifying phenotypically more homogeneous subgroups and shifting the focus from average group differences to individuals is a promising approach to addressing heterogeneity. In the present study, we aimed to parse clinical and neuroanatomical heterogeneity in autism by combining clustering of clinical features with normative modeling based on neuroanatomical measures (cortical thickness [CT] and subcortical volume) within the ABIDE datasets (N autism=861, N neurotypical=886, age-range 5-64). First, model-based clustering was applied to autistic symptoms as measured by the Autism Diagnostic Observation Schedule to identify clinical subgroups of autism. Next, we examined whether clinical subgrouping resulted in increased neurobiological homogeneity within the subgroups compared to the entire autism group by comparing their spatial overlap of neuroanatomical deviations. We further investigated whether the identified subgroups improved the accuracy of autism classification based on the neuroanatomical deviations using supervised machine learning with cross-validation. Results yielded two clinical subgroups primarily differing in restrictive and repetitive behaviours (RRB). Both subgroups showed increased homogeneity in localized deviations with the high-RRB subgroup showing increased volume deviations in cerebellum and the low-RRB subgroup showing decreased CT deviations predominantly in the postcentral gyrus and fusiform cortex. Nevertheless, substantial within-group heterogeneity remained highlighted by the failure of the classifier to distinguish between the subgroups. Identifying subgroups of autism has substantial clinical implications opening the potential for more tailored behavioural interventions and improving clinical outcomes.

General Scientific Summary

Autism is characterized by pronounced behavioural and neurobiological heterogeneity. This study suggests that reducing this heterogeneity at the clinical level by employing subgrouping also results in more similar neuroanatomical profiles in the identified clinical subgroups. Although we could demonstrate that clinical subgrouping reduces neuroanatomical heterogeneity, simultaneously, there remained substantial heterogeneity potentially pointing towards multiple pathways resulting in high RRBs and neurobiological subgroups with similar clinical phenotypes.
Bagged Fuzzy-Rough Nearest Neighbors (BFRNNs): A Novel Ensemble Learning Algorithm for Disease Diagnosis and Prognosis Prediction
Authors: Cheruvu Aashish , Martin Lockheed
Published: October 2023

Purpose of the study is to develop a novel machine learning (ML) algorithm that can accurately predict malignant versus benign tumors. A novel ML hybrid ensemble model called “Bagged Fuzzy-Rough k-Nearest Neighbors” (BFRNN) was developed. BFRNN is an improvement over the widely used k-Nearest Neighbors algorithm due to its use of fuzzy-rough logic and an unique ensemble voting algorithm. Initially, graphical libraries were used to visualize the Wisconsin Breast Cancer biomarker dataset (WBCBD) to capture useful insights about the data. Following preprocessing of the data (e.g. encoding categorical data snd removing outliers), a small subset of the most important breast cancer biomarkers were chosen based on feature selection technique and applying breast cancer domain knowledge. The performance of BFRNN was compared with a sample of five commonly used ML classification algorithms. The criteria for the evaluation the performance of ML was based on accuracy, area under the Receiver Operating Characteristic curve, and the ability to overcome overfitting. Discussion: Among the algorithms evaluated, BFRNN was the best classifier of WBCBD achieving an average training score of 98.47% and an average testing score of 99.09%. Among the other common ML algorithms evaluated, the highest test accuracy observed was 95.1% for Random Forest, with significant overfitting. In addition, outlier removal from the dataset and Pearson’s Correlation evaluation steps can be avoided for the implementation of the BFRNN algorithm. BFRNN has shown high accuracy in classifying the malignant versus benign characteristics and this algorithm could be a useful tool in disease diagnosis.
Multilevel Plasticity and Altered Glycosylation Drive Aggressiveness in Hypoxic and Glucose-Deprived Bladder Cancer Cells
Authors: Peixoto Andreia , Ferreira Dylan , Miranda Andreia , Relvas-Santos Marta , Freitas Rui , Veth Tim S. , Brandão Andreia , Ferreira Eduardo , Paulo Paula , Cardoso Marta , Gaiteiro Cristiana , Cotton Sofia , Soares Janine , Lima Luís , Teixeira Filipe , Ferreira Rita , Palmeira Carlos , Heck Albert J. R. , Oliveira Maria José , Silva André M. N. , Santos Lúcio Lara , Ferreira José Alexandre
Published: October 2023

Bladder tumours with aggressive characteristics often present with microenvironmental niches marked by low oxygen levels (hypoxia) and limited glucose supply due to inadequate vascularization. The molecular mechanisms facilitating cellular adaptation to these stimuli remain largely elusive. Employing a multi-omics approach, we discovered that hypoxic and glucose- deprived cancer cells enter a quiescent state supported by mitophagy, fatty acidβ-oxidation, and amino acid catabolism, concurrently enhancing their invasive capabilities. Reoxygenation and glucose restoration efficiently reversed cell quiescence without affecting cellular viability, highlighting significant molecular plasticity in adapting to microenvironmental challenges. Furthermore, cancer cells exhibited substantial perturbation of proteinO-glycosylation, leading to simplified glycophenotypes with shorter glycosidic chains. Exploiting glycoengineered cell models, we established that immature glycosylation contributes to reduced cell proliferation and increased invasion. Our findings collectively indicate that hypoxia and glucose deprivation trigger cancer aggressiveness, reflecting an adaptive escape mechanism underpinned by altered metabolism and protein glycosylation, providing grounds for clinical intervention.
Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes
Authors: Kieft Rudo , Zhang Yang , Yan Haidong , Schmitz Robert J. , Sabatini Robert
Published: October 2023

The genomes ofLeishmaniaand trypanosomes are organized into polycistronic transcription units flanked by a modified DNA base J involved in promoting RNA polymerase II (Pol II) termination. We recently characterized aLeishmaniacomplex containing a J-binding protein, PP1 protein phosphatase 1, and PP1 regulatory protein (PNUTS) that controls transcription termination potentially via dephosphorylation of Pol II by PP1. WhileT. bruceicontains eight PP1 isoforms, none purified with the PNUTS complex, suggesting a unique PP1-independent mechanism of termination. We now demonstrate that the PP1-binding motif of TbPNUTS is required for function in terminationin vivoand that TbPP1-1 modulates Pol II termination inT. bruceiinvolving dephosphorylation of the C-terminal domain of the large subunit of Pol II. PP1-1 knock-down results in increased cellular levels of phosphorylated large subunit of Pol II accompanied by readthrough transcription and pervasive transcription of the entire genome by Pol II, including Pol I transcribed loci that are typically silent, such as telomeric VSG expression sites involved in antigenic variation and production of TERRA RNA. These results provide important insights into the mechanism underlying Pol II transcription termination in primitive eukaryotes that rely on polycistronic transcription and maintain allelic exclusion of VSG genes.
Identification and full-genome assembly of novel Colorado potato beetle iflavirus and solinvi-like virus with SISPA Sequencing
Authors: Antonets Maria , Bodnev Sergei , Rotskaya Ulyana , Kosman Elena , Tregubchak Tatyana , Bauer Tatyana , Azaev Mamedyar , Kryukov Vadim , Antonets Denis
Published: October 2023

The Colorado potato beetle is one of the most devastating potato pests widespread in the world. However, its viral pathogens remain highly unexplored. Here using SISPA high-throughput sequencing of Colorado potato beetle (CPB) samples derived from prepupal larvae that died from an unknown infection, we have identified two previously unknown viruses and assembled their full-length genomic sequences. The subsequent genetic and phylogenetic analysis of the obtained sequences demonstrated that the isolated viruses, namedLeptinotarsa iflavirus 1andLeptinotarsa solinvi-like virus 1, are the novel representatives ofIflaviridaeandSolinviviridaeviral families, respectively. To the best of our knowledge, these are the first sequencing-confirmed insect viruses derived directly from CPB samples. And we also propose thatLeptinotarsa iflavirus 1may be associated with lethal disease in CPB.
In Vitro Safety Signals for Potential Clinical Development of the Anti-Inflammatory Pregnane X Receptor Agonist FKK6
Authors: Dvořák Zdeněk , Vyhlídalová Barbora , Pečinková Petra , Li Hao , Anzenbacher Pavel , Špičáková Alena , Anzenbacherová Eva , Chow Vimanda , Liu Jiabao , Krause Henry , Wilson Derek , Berés Tibor , Tarkowski Petr , Chen Dajun , Mani Sridhar
Published: October 2023

Background and purpose

Based on the mimicry of microbial metabolites, functionalized indoles were demonstrated as the ligands and agonists of the pregnane X receptor (PXR). The lead indole, FKK6, displayed PXR-dependent protective effects in DSS-induced colitis in mice andin vitrocytokine-treated intestinal organoid cultures. Here, we performed the initialin vitropharmacological profiling of FKK6.

Experimental approach

A complex series of cell-free and cell-based assays were employed. The organic synthesis, and advanced analytical chemistry methods were used.

Key results

FKK6-PXR interactions were characterized by hydrogen-deuterium exchange mass spectrometry. Screening FKK6 against potential cellular off-targets revealed high PXR selectivity. FKK6 has poor aqueous solubility but was highly soluble in simulated gastric and intestinal fluids. FKK6 was bound to plasma proteins and chemically stable in plasma. The partition coefficient of FKK6 was 2.70, and FKK6 moderately partitioned into red blood cells. In Caco2 cells, FKK6 displayed high permeability (A-B: 22.8 × 10-6cm.s-1) and no active efflux. These data are indicative of essentially completein vivoabsorption of FKK6. FKK6 was rapidly metabolized by cytochromes P450, notably by CYP3A4 in human liver microsomes. Two oxidized FKK6 derivatives, including N6-oxide and C19-phenol, were detected, and these metabolites had 5-7 × lower potency as PXR agonists than FKK6. This implies that despite high intestinal absorption, FKK6 is rapidly eliminated by the liver, and its PXR effects are predicted to be predominantly in the intestines.

Conclusion and implications

The PXR ligand and agonist FKK6 has a suitable pharmacological profile supporting its potential preclinical development.

BULLET POINT SUMMARY

What is already known:

Microbial metabolite mimic FKK6 is a hPXR agonist with anti-inflammatory properties in mice and human.

Thein vitroPXR binding, absorption, and metabolism have not been completely characterized.

What this study adds:

PXR selectivity with unique binding mode, high intestinal cell permeability, rapid and complex microsomal metabolism.

Initial testing for predicted metabolites shows reduced potency as PXR agonists.

Clinical significance:

PXR effects of FKK6 are predicted to be predominantly in the intestines.

FKK6 has a suitable pharmacological profile supporting its potential preclinical development.
A spatial-temporal map of glutamatergic neurogenesis in embryonic cerebellar nuclei uncovers a high degree of cellular heterogeneity
Authors: Casoni Filippo , Croci Laura , Marroni Francesca , Demenego Giulia , Cremona Ottavio , Codazzi Franca , Consalez G. Giacomo
Published: October 2023

The nuclei are the main output structures of the cerebellum. Each and every cerebellar cortical computation reaches several areas of the brain by means of CN processing and integration. Nevertheless our knowledge of these structures is still limited compared to the cerebellar cortex. Here, we present a genetic inducible fate mapping study characterizing rhombic lip-derived glutamatergic neurons of the nuclei, the most conspicuous family of long-range cerebellar efferent neurons. Glutamatergic neurons mainly occupy dorsal and lateral territories of the lateral and interposed nuclei, as well as the entire medial nucleus. They are born starting from about embryonic day 9.5, with a peak between 10.5 and 12.5, and invade the nuclei with a lateral to medial progression. While some markers label a heterogeneous population of neurons sharing a common location (Brn2), others appear to be lineage specific (Tbr1, Lmx1a, Meis2). A comparative analysis of Tbr1 and Lmx1a distributions reveals an incomplete overlap in their expression domains, in keeping with the existence of separate efferent subpopulations. Finally, some tagged glutamatergic progenitors are not labeled by any of the markers used in this study, disclosing further complexity. Taken together, our results obtained in late embryonic nuclei shed light on the heterogeneity of the excitatory neuron pool, underlying the diversity in connectivity and functions of this largely unexplored cerebellar territory. Our findings lay the groundwork for focused functional analyses of individual subpopulations of nuclear neurons.
EdTech applications and their adoption in Indian education sector–a bibliometric analysis and systematic literature review
Authors: Aaradhi Vaibhav , Chakraborty Debarun
Published: October 2023

Purpose

This research intends to analyse the trend in educational technology (EdTech) over the last 20 years using systematic scientific mapping and bibliometric analysis and how it relates to the Indian context. Considering the anticipated growth in this field over the previous three years post-pandemic, an existing literature analysis is required. This study aims to map the existing intellectual structure in EdTech applications to extend the knowledge base further in this field. This study also intends to research how the Indian education sector compares in terms of the research output for the EdTech sector, considering the increased government focus on online learning as per the education policy in 2020. The study's findings will pave the way for sustainable research that will be extended in the future.

Design/methodology/approach

Bibliometric analysis is conducted on the manuscripts extracted from Web of Science databases for the last 20 years (from 2003 to 2023). This study uses a descriptive research approach for bibliometric analysis as, by nature, this is an exploratory investigation, and no physical or existing experiment can be performed on the quantification, characteristic or productivity of EdTech applications. VoS Viewer and R software are extensively considered for a detailed bibliometric analysis.

Findings

E-learning, blended learning and distance education emerged as the most frequently used keywords. The results reveal that technology adoption, higher education, technology and modelling are the most researched topics in this field.

Research limitations/implications

This research is limited to the last 20 years' database obtained from the Web of Science database and limited to educational, management and operation databases only.

Practical implications

The paper intends to analyse the global scenario of EdTech research and ensures that the paper will effectively connect with researchers, educators, policymakers and practitioners from different parts of the world. The results derived from the bibliometric analysis, cluster analysis and identification of key authors, journals and countries can contribute towards the improved contribution in this area.

Originality/value

The paper discusses the research in EdTech over the last two decades and effectively tries to bridge the gap in global research. Integrating systematic scientific mapping and bibliometric analysis is an innovative way to assess the growth and impact of EdTech. Considering the post-pandemic scenario and the government's emphasis on online learning, these are consistent with current developments.
Institutional investors' information needs in the context of the sustainable finance disclosure regulation (EU/2019/2088): the implications for companies' sustainability reporting
Authors: Gebhardt Maria , Schneider Anne , Seefloth Marcel , Zülch Henning
Published: October 2023

Purpose

The paper aims to provide companies with a better understanding of the needs of institutional investors to improve the disclosure of sustainability information by companies. The study investigates the changed information needs of institutional investors resulting from the Sustainable Finance Disclosure Regulation (SFDR).

Design/methodology/approach

This study uses an internet-based survey instrument amongst institutional investors to gain insights into their needs regarding sustainability information. The authors received 155 responses in total and use descriptive statistics and t-tests to analyse the survey data.

Findings

The results demonstrate that the implementation of the SFDR challenges institutional investors, as it affects their decision process. Additionally, the findings still indicate a lack of available corporate sustainability information, making it even more challenging for institutional investors to make appropriate investment decisions. Respondents suggest that information on climate-related risks is more important than the European Union (EU) Taxonomy metrics for meeting the SFDR requirements.

Research limitations/implications

The findings are mainly restricted to the opinion of European investors. However, the evidence contributes to the existing literature by investigating institutional investors' information needs in the new regulatory landscape.

Practical implications

As the study provides insights into institutional investors' needs, reporting companies recognise the relevance of transparently providing sustainability information to be further considered in the investment process of institutional investors despite the regulation. The findings can help regulators develop uniform and global sustainability reporting standards.

Originality/value

This paper is the first to provide evidence on sustainability information requested on the institutional investors' side. The survey gathers primary data from professional investment members unavailable in databases or reports.
The encroachment strategy under eco-innovation collaboration with delayed realized efficiency information
Authors: Li Yating , Chen Ting , Zhang Xinxin , Yuan Jiahang
Published: October 2023

Purpose

Eco-innovation products, which means achieving more efficient and responsible use of resources and reducing the detrimental impact on the environment, can win a competitive advantage for the enterprises. But it is not easy to implement due to the high cost of eco-innovative technologies development, the uncertainty of market needs and return risk of investment. Many enterprises seek collaborations from their upstream suppliers to jointly carry out eco-innovation, such as Apple, IBM and Nike. A unique feature of collaboration is that efforts by one party enhance the marginal value of the other party's efforts. However, the collaboration will make the partner know the eco-innovation technology and prompt the partner to encroach the market to sell competitive products by herself. Motivated by this observation, this paper considers the optimal collaboration strategy on eco-innovation between upstream and downstream supply chain member and the optimal encroachment strategy of upstream supplier in a supply chain.

Design/methodology/approach

This paper models a supply chain wherein a supplier provides products or materials for her manufacturer and cooperates with her manufacturer in eco-innovation. Also, the supplier could encroach on the market to sell similar products by herself. Then this paper uses game theory and mathematical modeling to do relative analysis.

Findings

The analysis reveals several interesting insights. First, eco-innovation collaboration makes supplier encroachment no longer only rely on the encroachment cost. The delayed realized eco-innovation efficiency information also plays a vital role. Second, different from previous research, the authors find the manufacturer's preference for supplier encroachment depends on the uncertainty of eco-innovation efficiency and potential market demand. Third, both partial and full encroachment strategies of the supplier can effectively improve the eco-innovation level.

Originality/value

The paper is the first to take the interplay between collaboration and encroachment into account in a supply chain. The results caution enterprises and policymakers to take vertical collaboration and delayed realized information into account in the competitive supply chain before making any operational decisions. Furthermore, the authors propose that governmental intervention aimed at stimulating supplier encroachment in appropriate circumstances can contribute to the improved environmental performance of products.
Clinical pharmacology of prochlorperazine in healthy young males.
Authors: Isah AO , Rawlins MD , Bateman DN
Published: October 2023

1. The pharmacokinetics and pharmacodynamics of prochlorperazine (PCZ) have been studied in healthy young males following single 12.5 mg i.v. and 50 mg oral doses, and during repeated doses (25 mg twice daily) for 14 days. 2. Oral bioavailability was low and an N‐desmethyl metabolite was detected. Plasma clearance was high (0.98 1 kg‐1 h) and the volume of distribution was large (12.9 1 kg‐1) after i.v. dosing. 3. The terminal elimination half‐life of PCZ was 9 +/‐ 1 h and 8 +/‐ 2 h after i.v. and single oral dosing, respectively. The urinary recoveries of drug and metabolite were low. 4. Accumulation of PCZ and its metabolite occurred following repeated dosing. The half‐life at the end of 14 days therapy was 18 +/‐ 4 h. 5. Postural tachycardia, decreased salivary flow, impaired psychomotor function and a diminished level of arousal were observed after intravenous PCZ. Similar effects, but of lower magnitude were observed after single oral doses. During chronic dosing postural tachycardia and antihistaminic effects were observed, the latter not being observed after single doses. 6. After single intravenous dosing the maximal drug effects occurred 2‐4 h after peak plasma drug concentrations for all measures except for plasma prolactin and self‐scored restlessness 7. An antagonist action at dopamine (D2), muscarinic‐cholinergic and alpha‐adrenoceptors is postulated after single doses, with antihistaminic effects during chronic dosing, possibly indicating the presence of an active metabolite.
Lack of systematic effects of the 5‐hydroxytryptamine 3 receptor antagonist ICS 205‐930 on gastric emptying and antral motor activity in patients with primary anorexia nervosa.
Authors: Stacher G , Bergmann H , Granser‐Vacariu GV , Wiesnagrotzki S , Wenzelabatzi TA , Gaupmann G , Kugi A , Steinringer H , Schneider C , Hobart J
Published: October 2023

1. The 5‐hydroxytryptamine 3 receptor antagonist, ICS 205‐930, has been reported to have potent effects on gastric smooth muscle and to enhance gastric emptying in animals, but findings in man have been inconsistent. 2. This study investigated the effects of ICS 205‐930 on gastric emptying of an isotopically labelled semisolid 1168 kJ meal and on antral contractility in patients with primary anorexia nervosa, a condition frequently associated with impaired gastric motor function. 3. Thirteen female patients (age 18‐39 years, median 22 years; percentage of ideal body weight 52‐90%, median 66%) participated each in two studies, in which 0.15‐0.18 mg kg‐1 ICS 205‐930 or placebo were infused i.v. in crossover, double‐blind fashion. Gastric emptying and antral contractility were recorded scintigraphically for 50 min. 4. ICS 205‐930 did not affect gastric emptying: the mean percentage of meal remaining in the stomach after 50 min (69.6% +/‐ 3.2 s.e. mean) was nearly identical to that after placebo (70.7 +/‐ 3.3%). 5. Amplitude, frequency and propagation velocity of antral contractions differed only little after ICS 205‐930 and placebo, respectively. 6. The results show that ICS 205‐930 has no effect on the impaired gastric motor activity in primary anorexia nervosa and thus provide further evidence that the compound does not have prominent prokinetic effects in man.
Gastric emptying in healthy volunteers after multiple doses of levodopa.
Authors: Waller DG , Roseveare C , Renwick AG , Macklin B , George CF
Published: October 2023

1. Oral levodopa frequently produces an episodic delay in gastric emptying which leads to multiple peak concentrations of the drug in plasma. We have studied the effects of multiple dosing of levodopa on gastric emptying and levodopa absorption in eight healthy young volunteers in a randomised two‐way cross‐over study. 2. The plasma concentration‐time curves for levodopa were measured after three oral doses of 125 mg given at 2 h intervals and compared with the concentration‐time curve for levodopa following administration of two doses of placebo and a single oral dose of 125 mg. 3. A low incidence of multiple peak plasma concentrations of levodopa was detected after all doses of levodopa. The area under the plasma concentration‐time curves (AUC) for the final dose of levodopa (150.8 +/‐ 22.0 micrograms ml‐1 min) was lower than for the two preceding doses (205.7 +/‐ 41.8 and 199.5 +/‐ 51.8 micrograms ml‐1 min) but not different from that of the single dose given at the same time of day (141.7 +/‐ 29.1 micrograms ml‐1 min). This indicates that the lower AUC of the final dose of levodopa was related to the time of administration and not a result of the two preceding doses. 4. The absence of any significant effects of preceding doses of levodopa on gastric emptying was confirmed a) by co‐administration of soluble paracetamol, as a marker of gastric emptying, with the second dose of levodopa or placebo and b) by co‐administration of radiolabelled DTPA and gamma‐camera imaging with the final dose of levodopa on the multiple dosing day and the single dose of levodopa on the placebo day.(ABSTRACT TRUNCATED AT 250 WORDS)