bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractArchaea 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

AbstractAtherosclerosis 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 pointsPlatelet-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

AbstractA 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

ABSTRACTStilbenes, 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

AbstractThe 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

ABSTRACTIn 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.IMPORTANCEGiven 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

ABSTRACTHydrogen 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

AbstractHow 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

AbstractBK 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

AbstractTargeted 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

AbstractIn 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

AbstractAutism 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 SummaryAutism 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

AbstractPurpose 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.