bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrant glycosylation reveals unexpected clinical outcomes between Luminal B and Basal high stemness index breast cancer cohorts
Authors: Truter Mia , Naidoo Kevin J. 
Published: October 2024

AbstractCancer stem cells facilitate tumorigenesis by hijacking normal developmental pathways, the activity of which are modulated by glycosylation. Aberrant glycosylation is a key hallmark of cancer, but little is known of its functional role within the tumorigenesis system and integrated molecular and cellular cancer landscape. The clinical and phenotypic diversity in breast cancer suggests activation of various biochemical mechanisms, each likely accompanied by unique aberrations in glycosylation. Here we investigate the mechanistic links between glycosylation and breast cancer stemness for subtypes defined by the expression hormone receptors: estrogen (ER), progesterone (PR) and human epidermal growth factor (HER2). Specifically, we consider Basal and Luminal B, the two most highly stem subtypes. These two have significanlty different patient prognoses when accounting for degree of stemness. In the case of patient samples from the Basal subtype, the high stem state is protective, while in samples studied that were identified as Luminal B subtype, the high stem state becomes a risk factor over time. By undertaking a combined machine learning and bioinformatics analysis, we show that patient prognosis varies due to activation of distinct glycosylation pathways that fit into the wider tumorigenic landscape. In the high stem Basal cohort, glycosylation of immune cell surface receptors functions to maintain stemness and facilitates an activated immune response. In comparison, aberrant mannosylation and protein trafficking promote tumorigenesis through metabolic dysregulation in the high stem Luminal B cohort. These findings suggest that glycosylation plays an integral role in tumorigenesis far more so than the important role that has been identified for specific glycans, glycoenzymes or glycogens. In a systems analysis of Basal and Luminal B subtypes, we find that their aberrant glycosylation to be specific and different from each other particular with respect to high stem cases. This opens up an avenue for personalised glycosylation-based cancer diagnostics and therapeutics discovery.SignificanceAberrant glycosylation gene expression screening of Basal and Luminal B breast cancer subtypes reveals differences in their phenotypic and clinical outcomes as a function of stemness helpful for personalised diagnostic and treatment.
Mechanistic insights into the inhibition of dengue virus NS5 methyltransferase by herbacetin
Authors: Bhutkar Mandar , Verma Shalja , Singh Vishakha , Kumar Pravindra , Tomar Shailly 
Published: October 2024

AbstractHerbacetin (HC) is a naturally occurring flavonoid compound with a dual antiviral mechanism. It inhibits the polyamine biosynthetic pathway and targets the methyltransferase (MTase) enzyme of the dengue and chikungunya virus. However, understanding the detailed inhibition mechanism of DENV MTase by HC remains unclear. The crystal structure of DENV3 nonstructural protein 5 (NS5) MTase in complex with HC and S-adenosyl-L-homocysteine presented in this study gives structural insights into the inhibition mechanism. Structural analysis revealed that HC binds to the cap 0 RNA site near the GTP binding site in the DENV3 NS5 MTase, and fluorescence polarization assay demonstrated HC inhibits GTP binding with an inhibition constant Kivalue of ∼ 0.43 µM. This is the first study that identified an inhibitor that targets the conserved RNA-binding region of NS5 MTase, suggesting its potential as a highly effective scaffold for broad-spectrum antiviral agents against orthoflaviviruses.ImportanceDengue virus (DENV) is a vector-borne disease affecting global health, and no antiviral treatment is available for Dengue fever. DENV NS5 methyltransferase (DENV NS5 MTase) is a viral RNA capping enzyme essential for the virus replication. This study demonstrated that herbacetin (HC), a natural flavonoid, blocked the binding of GTP to NS5 MTase and inhibited the enzyme. In addition to DENV3, HC effectively inhibited the replication of DENV1,2, and 4 serotypes. The crystal structure of the DENV3 NS5 MTase in complex with HC revealed that HC binds at the cap 0 RNA binding site, which is close to the GTP binding site and thereby perturbs the spatial arrangement of GTP binding site residues. HC, as the first identified inhibitor that targets the conserved RNA-binding site of DENV3 NS5 MTase, presents a potential scaffold for the development of new antiviral drugs.
Characterisation ofPseudomonas aeruginosa’smetal-responsive TonB-dependent transporters
Authors: Ferry Manon , Ferriz Hortense , Sharp Connor , Paschalidis Christos , Boutant Emmanuel , Schalk Isabelle J. , Cunrath Olivier 
Published: October 2024

AbstractPseudomonas aeruginosa, a versatile bacterium, relies on several TonB-dependent transporters (TBDTs) for nutrient acquisition (such as iron-siderophore complexes) and adaptation to various environments. While some TBDTs are well characterized, a significant number remain unexplored despite their potential role in pathogenicity. In this study, we developed fluorescent reporter plasmids to investigate TBDT promoter activity. Initially, we characterized their promoter activity in commonly used laboratory conditions, revealing diverse expression patterns among all TBDTs. Subsequently, we classified the TBDTs into distinct metal-responsive groups based on their stress-responsive behaviour, shedding light on their functional roles. Additionally, we show that these reporter constructs can be used as a powerful tool for siderophore detection. Finally, single cell analysis of TBDT promoter activity during coculture with an enterobactin-producingKlebsiella pneumoniaestrain shows homogenous expression of key TBDT inP. aeruginosa. Our findings provide valuable insights into the expression profiles and functional diversity ofP. aeruginosaTBDTs in complex conditions, reaching from commonly used lab media to complex co-culturing conditions.
Bacteroides thetaiotaomicron enhances H2S production in Bilophila wadsworthia
Authors: Davies Jade , Mayer Melinda J. , Juge Nathalie , Narbad Arjan , Sayavedra Lizbeth 
Published: October 2024

AbstractSulfate- and sulfite-reducing bacteria (SRB) are a group of strict anaerobes found within the human gut.Bilophila wadsworthia, a sulfite-reducing bacterium which produces hydrogen sulfide (H2S) from taurine and isethionate respiration is a common member of the healthy commensal human gut microbiota, but has been implicated in several disease states including inflammatory bowel disease and colorectal cancer.Bacteroides thetaiotaomicron, one of the most prominent gut bacteria, has sulfatases which release sulfate, serving as a potential substrate for sulfate-reducing bacteria. Here, we showed that whenB. thetaiotaomicronandB. wadsworthiawere in co-culture, there was a significant increase inB. thetaiotaomicron’s growth and in H2S production byB. wadsworthia. Differential gene expression analysis revealed increased expression ofB. wadsworthia’sdsrMKJOPcomplex in co-culture, which delivers electrons for sulfite reduction to H2S. This was accompanied by a decreased expression of genes associated with taurine, sulfolactate and thiosulfate respiration, indicating thatB. thetaiotaomicronmay provide an alternative source of sulfite toB. wadsworthia. We hypothesised adenosine 5’-phosphosulfate (APS) to be this intermediate. Indeed,B. wadsworthiawas able to grow using APS or sulfite as electron acceptors. Endometabolomic and transcriptomic analyses revealed decreased production of indole byB. thetaiotaomicronin co-culture withB. wadsworthiadue to enhanced tryptophan utilisation byB. wadsworthia. The results of this microbe-microbe interaction could have significant pro-inflammatory effects in the human gut environment.
Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson’s disease and cognitive decline pathophysiology
Authors: Clasen Frederick , Yildirim Suleyman , Arıkan Muzaffer , Garcia-Guevara Fernando , Hanoğlu Lütfü , Yılmaz Nesrin H. , Şen Aysu , Demir Tuğçe Kahraman , Yıldız Zeynep , Mardinoglu Adil , Uhlen Mathias , Shoaie Saeed 
Published: October 2024

ABSTRACTThe human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson’s Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with either mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of the gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.
Spatial organization of supercoil dynamics during DNA replication
Authors: Kusano Yoshiharu , Shinkai Soya , Nozawa Ryu-Suke , Sun Jiying , Onami Shuichi , Tashiro Satoshi , Hirota Toru 
Published: October 2024

AbstractProgression of DNA replication inevitably generates helical tension and resulting super-helical structures, or supercoils, that originate from the double helix of DNA. As DNA polymerases progress, negative supercoils accumulate in the wake of the replication fork, thereby impeding fork progression unless the supercoils are resolved topologically. Using super-resolution microscopy combined with spatial distribution analysis, here we describe that SMC5/6-mediated confinement of negative supercoils lies at the basis of releasing them by topoisomerase Top2A. Along with DNA replication, SMC5/6 progressively associates with chromatin and locally increases the density of supercoil clusters behind the fork, allowing Top2A to efficiently target and release the accumulated supercoils. These processes are essential to complete DNA replication prior to mitosis and therefore to ensure genome stability. Remarkably, we found that HeLa cells over-accumulate poorly confined negative supercoils beyond the processing capacity of cellular SMC5/6, which may exemplify the condition associated with genome instability of cancer cells.
TRPM8 channels control Golgi morphology through an AR-dependent induction of the Scd1 gene and modulation of unsaturated lipid content
Authors: Wehbi Mariam , Gouriou Yves , Borowiec Anne-sophie , Geoffray Juliette , Badawi Sally , Chouabe Christophe , Slomianny Christian , Gordienko Dmitri , Gonnot Fabrice , Dewailly Etienne , Delcourt Philippe , Ferrera René , Pais-de-Barros Jean-Paul , Kurdi Mazen , Héliot Laurent , Van Coppenolle Fabien , Lemonnier Loic , Prevarskaya Natalia , Bidaux Gabriel 
Published: October 2024

ABSTRACTTransient receptor potential melastatin 8 (TRPM8), the cold and menthol receptor is essential to thermosensation, although its roles in organs within the body are still unclear. Besides TRPM8, we previously cloned several isoforms, like 4TM-TRPM8, which can be expressed with or without TRPM8.In this study, we characterize the human TRPM8(85) in ER membranes in the vicinity of Golgi apparatus (GA) and mitochondria in prostate epithelial cells. Silencing of TRPM8(85) induces lipid droplet accumulation, GA expansion and fragmentation associated with a drop in the vesicular trafficking to plasmalemma. Furthermore, lipidomic analysis reveals a strong shift in unsaturated fatty acids (UFAs), induced by TRPM8(85) silencing and to a lesser extent silencing of TRPM8. UFAs increase is caused by the induction of Δ9 stearoyl desaturase (Scd1) gene. Silencing SCD1 or palmitate incubation prevent GA expansion in TRPM8(85)-silenced cells. Finally, we demonstrated that TRPM8 regulates SCD1 via the androgen receptor.
Membrane-bound Guanylyl Cyclase COP5/HKR1 changes ciliary beat pattern and biases cell steering during chemotaxis inChlamydomonas reinhardtii
Authors: Strain Alexis , Kratzberg Nathan , Vu Dan , Miller Emmaline , Wakabayashi Ken-ichi , Melvin Adam , Kato Naohiro 
Published: October 2024

AbstractThis study investigates the control of ciliary beat patterns during ammonium chemotaxis in the model ciliate microalgaeChlamydomonas reinhardtii. Screening the chemotaxis response of mutant strains with ciliary defects revealed that a strain lacking CAV2, the alpha subunit of the voltage-gated Ca2+channel, is deficient in ammonium chemotaxis. CAV2 regulates the switching of the ciliary beat pattern from the asymmetric to the symmetric waveform. Strains lacking COP5/HKR1 (chlamyopsin 5/histidine kinase rhodopsin 1), a membrane-bound guanylyl cyclase, are also deficient in ammonium chemotaxis. Conversely, strains defective in phototaxis perform ammonium chemotaxis normally.Cell motility analysis revealed wild-type cells reduce the incidences of switching the ciliary beat pattern from the asymmetric to symmetric waveform when swimming up the ammonium gradient. In contrast, the COP5/HKR1 disrupted strain does not bias ciliary beat pattern switching in the gradient. This finding reveals that a membrane-bound guanylyl cyclase plays a critical role inChlamydomonaschemotaxis signaling transduction, similarly to animal chemotaxis. On the other hand, ciliary beat pattern switching induces randomized directional changes, analogous to run-and-tumble chemotaxis of bacteria and archaea. This study reveals thatChlamydomonassignaling transduction is similar to the eukaryotic mechanism, yet the cellular locomotion follows the bacteria and archaea mechanism.
Farm exposure is associated with human breast milk immune profile and microbiome
Authors: Swaney Mary Hannah , Steidl Olivia Rae , Tackett Anastasia , Fye Samantha , Lee Kristine E. , Ong Irene M. , Bendixsen Casper , Spicer Gretchen , DeLine James , Gern James E , Lucey John , Seroogy Christine M. , Kalan Lindsay , Singh Anne Marie 
Published: October 2024

SUMMARYPrenatal and early life farm exposure, and breastfeeding, are associated with protection from allergic diseases. We hypothesize that farm exposure influences the human breast milk microbiome and immune proteins. The immune protein profiles and microbial communities of 152 human breast milk samples were compared among three maternal farm exposure groups (traditional agrarian, farm, and non-farm) in rural Wisconsin to identify signatures associated with farm status and atopic disease. We found significant differences between farm groups for 23 immune proteins (p-adj<0.05), microbiome diversity (p=2.2E-05), and microbiome richness (p=8.0e-06). Traditional agrarian human breast milk had the highest immune protein levels and microbiome diversity and richness, followed by farm and non-farm human breast milk. Furthermore, Gram-positive bacterial species correlated with IL-23 mediated signaling events (p-adj<1.0E-05). These data suggest that increased farm exposures promotes human breast milk that is more microbially-diverse and rich in immune-associated proteins, ultimately influencing immune development in the infant.
Genome-wide analysis ofEnterococcus faecalisgenes that facilitate interspecies competition withLactobacillus crispatus
Authors: Lam Ling Ning , Savage Kathryn E. , Shakir Camille N. , Lemos José A. 
Published: October 2024

ABSTRACTEnterococci are opportunistic pathogens notorious for causing a variety of infections. While bothEnterococcus faecalisandLactobacillus crispatusare commensal residents of the vaginal tract, the molecular mechanisms that enableE. faecalisto outcompeteL. crispatus,and consequently cause vaginal infections remains unknown. To begin to address this, we need to gain a better understanding of the competitive interactions betweenE. faecalisandL. crispatus. Here, we show thatL. crispatuseradicatesE. faecalisin a contact-independent manner. Using transposon sequencing to identifyE. faecalisOG1RF transposon (Tn) mutants that are either under-represented or over-represented when co-cultured withL. crispatus, we found that Tn mutants with disruption in thedltABCDoperon, that encodes the biosynthetic pathway for D-alanylation of teichoic acids, andOG1RF_11697encoding for an uncharacterized hypothetical protein are more susceptible to killing byL. crispatus. Inversely, Tn mutants with disruption inldh1,that encodes for L-lactate dehydrogenase, are more resistant toL. crispatus killing. Using theGalleria mellonellainfection model, we show that co-injection ofL. crispatuswithE. faecalisOG1RF enhances larvae survival while thisL. crispatus-mediated protection was lost in larvae co-infected with eitherL. crispatusandE. faecalisΔldh1or Δldh1Δldh2strains. Last, using RNA sequencing to identifyE. faecalisgenes that are differently expressed in the presence ofL. crispatus, we found major changes in expression of genes associated with glycerophospholipid metabolism, central metabolism and general stress responses. The findings in this study provide insights on howE. faecalismitigate assaults byL. crispatus.IMPORTANCEEnterococcus faecalisis an opportunistic pathogen notorious for causing a multitude of infections. WhileE. faecalismust compete withLactobacillus crispatusto cause vaginal infections, howE. faecalisovercomesL. crispatuskilling remains unknown. We show thatL. crispatuseradicatesE. faecalistemporally in a contact-independent manner. Using high throughput molecular approaches, we identified genetic determinants that enableE. faecalisto compete withL. crispatus. This study represents an important first step for the identification of adaptive genetic traits required for enterococci to compete with lactobacilli.
DIO-SPOTlight Transgenic Mouse to Functionally Monitor Protein Synthesis Regulated by the Integrated Stress Response
Authors: Oliver Matthew L. , Caffall Zachary F. , Eatman Callie B. , Faw Timothy D. , Calakos Nicole 
Published: October 2024

ABSTRACTThe integrated stress response (ISR) is a core pathway for maintaining cellular proteostasis and a key regulator of translation in processes beyond the cellular response to stress. For example, the ISR regulates developmental axonogenesis, learning and memory, and synaptic plasticity in the brain. One barrier to uncovering ISR roles in health and disease is the challenge of monitoring its activity. The transient nature of regulatory phosphorylation events and lack of transgenic ISR reporter mouse lines make visually capturing the molecular hallmarks of ISR activation in specific cell types especially difficult. We recently developed the SPOTlight (SelectivePhospho-eIF2αOpen reading frameTracking light) reporter, which uniquely provides a readout of the functional state of protein synthesis initiation dynamics that are regulated by the ISR. Here, we report the generation of a transgenic mouse line with Cre-dependent expression of SPOTlight. This resource enables selective visualization of ISR-regulated functional activity across genetically defined cell populations body-wide. Using a pan-neuronal Cre line (Nestin-Cre), we demonstrate the reporter’s performance and applications for cell-specific discovery, live tissue assessments and quantitative comparisons across broad physical space. We also specifically investigated the extent to which the property of steady-state basal ISR activation, recently described in dorsal striatal cholinergic interneurons, extends to other classes of cholinergic neurons and provide a CNS-wide atlas of SPOTlight activity in these cells. The DIO-SPOTlight mouse enables a wide range of studies in all organ systems and functional monitoring opportunities not previously accessible.
Improving the annotation of amino acid biosynthesis pathways: GapMind 2024
Authors: Price Morgan N. , Shiver Anthony L. , Day Leslie A. , Torres Marta , Lesea Hira P. , Owens Trenton K. , Deutschbauer Adam M. , Arkin Adam P. 
Published: October 2024

AbstractGapMind is an automated web-based tool for annotating amino acid biosynthesis pathways in bacterial and archaeal genomes. We updated GapMind to include recently identified enzymes, including new enzymes that we identified by using high-throughput genetics and comparative genomics. Across 206 prokaryotes that have high-quality genomes and are reported to grow in minimal media, the average number of unexplained missing steps or gaps dropped from 1.4 per genome to 0.8 per genome. The majority of the remaining gaps involve the gain or loss of phosphate groups.
Role of ribosomal protein bS1 in orthogonal mRNA start codon selection
Authors: Boyko Kristina V. , Bernstein Rebecca A. , Kim Minji , Cate Jamie H. D. 
Published: October 2024

ABSTRACTIn many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3′-end of 16S ribosomal RNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create “orthogonal” ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here we engineered theEscherichia coliribosome to prevent binding of bS1 to the 30S subunit, to separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomesin vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of bS1 binding to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.