bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tolerance toHaemophilus influenzaeinfection in human epithelial cells: insights from a primary cell-based model
Authors: Kappler Ulrike , Henningham Anna , Nasreen Marufa , Buultjens Andrew H. , Stinear Timothy P. , Sly Peter , Fantino Emmanuelle 
Published: July 2023

AbstractHaemophilus influenzaeis a human respiratory pathogen and inhabits the human respiratory tract as its only niche. Despite this, the molecular mechanisms that allowH. influenzaeto establish persistent infections of human epithelia are not well understood.Here, we have investigated howH. influenzaeadapts to the host environment and triggers the host immune response using a human primary cell-based infection model that closely resembles human nasal epithelia (NHNE).Physiological assays combined with dualRNAseq revealed that NHNE from five healthy donors all responded toH. influenzaeinfection with an initial, ‘unproductive’ inflammatory response that included a strong hypoxia signature but did not produce pro-inflammatory cytokines. Subsequently, an apparent tolerance to large extra- and intracellular burdens ofH. influenzaedeveloped, with NHNE transcriptional profiles resembling the pre-infection state. This occurred in parallel with the development of intracellular bacterial populations, and appears to involve interruption of NFkB signalling. This is the first time that large-scale, persistence-promoting immunomodulatory effects ofH. influenzaeduring infection have been u. Interestingly, NHNE were able to re-activate pro-inflammatory responses towards the end of the 14-day infection resulting in release of pro-inflammatory cytokines (IL8, TNFα). Our data further indicate the presence of infection stage-specific gene expression modules, highlighting fundamental similarities between immune responses in NHNE and canonical immune cells, which merit further investigation.
Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features
Authors: Hoge Carla , de Manuel Marc , Mahgoub Mohamed , Okami Naima , Fuller Zachary , Banerjee Shreya , Baker Zachary , McNulty Morgan , Andolfatto Peter , Macfarlan Todd S. , Schumer Molly , Tzika Athanasia C. , Przeworski Molly 
Published: July 2023

AbstractIn vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, recombination occurs almost exclusively where the protein PRDM9 binds, while in species lacking an intactPRDM9, such as birds and canids, recombination rates are elevated near promoter-like features. To test if PRDM9 also directs recombination in non-mammalian vertebrates, we focused on an exemplar species, the corn snake (Pantherophis guttatus). Unlike birds, this species possesses a single, intactPRDM9ortholog. By inferring historical recombination rates along the genome from patterns of linkage disequilibrium and identifying crossovers in pedigrees, we found that PRDM9 specifies the location of recombination events outside of mammals. However, we also detected an independent effect of promoter-like features on recombination, which is more pronounced on macrothan microchromosomes. Thus, our findings reveal that the uses of PRDM9 and promoter-like features are not mutually-exclusive, and instead reflect a tug of war, which varies in strength along the genome and is more lopsided in some species than others.One sentence summaryWhile the localization of meiotic recombination in vertebrates was previously thought to occur using one of two distinct mechanisms, our analysis of recombination in corn snakes reveals that they and likely other vertebrates use both of these mechanisms.
A fluorescent assay for cryptic transcription inSaccharomyces cerevisiaereveals novel insights into factors that stabilize chromatin structure on newly replicated chromatin
Authors: Gao Ellia , Jung Stephanie , Howe LeAnn J. 
Published: July 2023

AbstractThe disruption of chromatin structure can result in transcription initiating from cryptic promoters. A well-characterized, chromatin-destabilizing stress is the passage of RNA polymerase, and numerous factors function to stabilize chromatin on transcribed genes, suppressing cryptic transcription from sites within gene bodies. DNA replication is also inherently disruptive to chromatin, and multiple replication-coupled histone chaperones suppress cryptic transcription. However, these factors also have documented roles in transcription, and thus whether DNA replication per se can activate cryptic promoters has not been directly examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription inS. cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, Rtt106, Spt6, and Spt16, suppress transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Additionally, for the first time, we demonstrate modest cryptic transcription following the depletion of Rlf2/Cac1, a CAF-1 chromatin assembly complex component. Collectively, these results suggest that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.
Whole-genome Omics delineates the function of CCM1 within the CmPn networks
Authors: Croft Jacob , Grajeda Brian , Aguirre Luis A , Gao Liyuan , Abou-Fadel Johnathan , Sheng Victor , Zhang Jun 
Published: July 2023

AbstractIntroductionCerebral cavernous malformations (CCMs) are abnormal dilations of brain capillaries that increase the risk of hemorrhagic strokes. Mutations in the KRIT1, MGC4607, and PDCD10 genes cause CCMs, with mutations in CCM1 accounting for about 50% of familial cases. The disorder exhibits incomplete penetrance, meaning that individuals with CCM may appear normal initially, but once symptoms manifest, their brains have already suffered irreversible damage. Compromised blood-brain barrier (BBB) is crucial in regulating the flow of substances between the blood and the central nervous system, which can result in hemorrhagic CCMs. Progesterone and its derivatives have been studied for their impact on maintaining BBB integrity. CCM2 interacts with CCM1 and CCM3, forming the CCM signaling complex (CSC), which connects classic and non-classic progesterone signaling to establish the CmPn signaling network, vital in preserving BBB integrity.MethodsThe study aimed to explore the relationship between CCM1 and key pathways of the CmPn signaling network, utilizing a toolset comprising three mouse embryonic fibroblast lines (MEFs) with distinct CCM1 expression levels. Omics and systems biology analysis were performed to investigate Ccm1-mediated signaling within the CmPn signaling network.ResultsThe findings suggest that CCM1 plays a critical role in controlling cellular processes in response to different progesterone-mediated actions within CmPn/CmP signaling networks, partly by regulating gene transcription. This function is crucial for preserving the integrity of microvessels, indicating that targeting CCM1 could hold promise as a therapeutic approach for this condition.
LC3B conjugation machinery promotes autophagy-independent HIV-1 entry in CD4+ T lymphocytes
Authors: Pradel Baptiste , Deffieu Maïka S. , Robert-Hebmann Véronique , Cantaloube Guilhem , Faure Mathias , Chazal Nathalie , Gaudin Raphaël , Espert Lucile 
Published: July 2023

AbstractHIV-1 entry into CD4+ T lymphocytes relies on the viral and cellular membranes’ fusion, leading to viral capsid delivery in the cytoplasm of target cells. The conjugation of ATG8/LC3B protein, process referred to as ATG8ylation and mainly studied in the context of autophagy, occurs transiently in the early stages of the HIV-1 replication cycle in CD4+ T lymphocytes. Despite numerous studies investigating the interplays of HIV-1 with autophagy machinery, the impact of ATG8ylation in the early stages of HIV-1 infection remains unknown. Here we found that HIV-1 exposure leads to the rapid enrichment of LC3B towards the target cell plasma membrane, in close proximity with the incoming viral particles. Furthermore, we demonstrated that ATG8ylation is a key event that facilitates HIV-1 fusion with target CD4+ T cells. Interestingly, this effect is independent of the canonical autophagy pathway as ATG13 silencing does not prevent HIV-1 entry. Together, our results provide an unconventional role of LC3B conjugation subverted by HIV-1 to achieve a critical early step of its replication cycle.TeaserHIV-1 induces LC3B enrichment towards its target cell entry site and uses the conjugation of this protein to favor its entry step.
Exercise on cytokine responses in males and females: Effect of leucine, HMB and BCAA
Authors: Brown Alexander D. , Grammenou Maria , Tee Chris C.L. , Chong Mee Chee , Stewart Claire E. 
Published: July 2023

AbstractPurposeTo identify the effects of leucine, β-hydroxy β-methylbutyrate (HMB) and branched chain amino acid (BCAA) on post-exercise cytokine responses in females and males.MethodsMales (n=53) and females (n=37) completed 100 drop jumps and consumed either no supplement, leucine (3g/d), HMB (3g/d) or BCAA (4.5g/d) from 1d pre to 14d post-exercise. Muscle soreness, squat jumps, chair rises and creatine kinase (CK) were measured at pre, post, 24h, 48h, 7 and 14d. Blood lactate (pre, post), 10 cytokines (pre, 24h, 48h, 7d) and oestradiol (pre, 7d) were also measured.ResultsWithout supplementation post-exercise, soreness was induced in both males (6-fold) and females (5-fold). With supplementation, there were no increases in CK or oestradiol in females and no impact on muscle soreness, performance, or function in both sexes. In males, CK was elevated in untreated (48%) and leucine (69%) conditions vs baseline, but these were suppressed with HMB and BCAA. IL-7 was elevated in females vs males at baseline (6.3-fold), leucine increased IL-7 concentrations in females at 24h (17.0-fold), 48h (5.1-fold) vs males. With HMB, TNFr1-α increased in females at 24h (2.2-fold), 48h (2.3-fold) and 7d (2.3-fold) vs males. In males with BCAA, TNFr1-α decreased (P=0.06) from pre to 24h (6.8-fold), then increased (P<0.05) from 24 to 48h (8.0-fold).ConclusionAlthough supplements were without effect on soreness following exercise, the cytokine response was evoked by exercise and impacted significantly by leucine, HMB and BCAA in females vs males. This improved cytokine response in females could lead to improved resistance to damage.
Seasonal influenza viruses decay more rapidly at intermediate humidity in droplets containing saliva compared to respiratory mucus
Authors: Rockey Nicole C. , Le Sage Valerie , Marr Linsey C. , Lakdawala Seema S. 
Published: July 2023

AbstractExpulsions of virus-laden aerosols or droplets are an important source of onward respiratory virus transmission and can originate from both the oral and nasal cavity of an infected host. However, the presence of infectious influenza virus in the oral cavity during infection has not been widely considered, and thus little work has explored the environmental persistence of influenza virus in oral cavity expulsions that may facilitate transmission. Using the ferret model, we detected infectious virus in the nasal and oral cavities, suggesting that virus can be expelled into the environment from either anatomical site. We also assessed the stability of two influenza A viruses (H1N1 and H3N2) in droplets of human saliva or respiratory mucus over a range of relative humidities. We observed that influenza virus infectivity decays rapidly in saliva droplets at intermediate relative humidity, while viruses in airway surface liquid droplets retain infectivity. Virus inactivation was not associated with bulk protein content, salt content, or droplet drying time. Instead, we found that saliva droplets exhibited distinct inactivation kinetics during the wet and dry phases at intermediate relative humidity and that droplet residue morphology may lead to the elevated first-order inactivation rate observed during the dry phase. Additionally, distinct differences in crystalline structure and nanobead localization were observed between saliva and airway surface liquid droplets. Together, our work demonstrates that different respiratory fluids exhibit unique virus persistence profiles and suggests that influenza viruses expelled from the oral cavity may contribute to virus transmission in low and high humidity environments.ImportanceDetermining how viruses persist in the environment is important for mitigating transmission risk. Expelled infectious droplets and aerosols are composed of respiratory fluids, including saliva and complex mucus mixtures, but how influenza viruses survive in such fluids is largely unknown. Here, we find that infectious influenza virus is present in the oral cavity of infected ferrets, suggesting that saliva-containing expulsions can play a role in onward transmission. Additionally, influenza virus in droplets composed of saliva degrades more rapidly than virus within respiratory mucus. Droplet composition impacts the crystalline structure and virus localization in dried droplets. These results suggest that viruses from distinct sites in the respiratory tract could have variable persistence in the environment, which will impact viral transmission fitness.
The length of haplotype blocks and signals of structural variation in reconstructed genealogies
Authors: Ignatieva Anastasia , Favero Martina , Koskela Jere , Sant Jaromir , Myers Simon R. 
Published: July 2023

AbstractRecent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correlation structure between genealogical local trees, we evaluate how this structure is reconstructed by leading approaches. Despite identifying pervasive biases, we show that applying a simple correction recovers the desired distributions for one algorithm, Relate. We develop a statistical test to identify clades spanning unexpectedly long genomic regions, likely reflecting regional suppression of recombination in some individuals. Our approach allows a systematic scan for inter-individual recombination rate variation at an intermediate scale, between genome-wide differences and individual hotspots. Using genealogies reconstructed with Relate for 2 504 human genomes, we identify 50 regions possessing clades with unexpectedly long genomic spans (p <1·10−12). The strongest signal corresponds to a known inversion on chromosome 17. The second strongest uncovers a novel 760kb inversion on chromosome 10, common (21%) in S. Asians and correlated with GWAS hits for a range of phenotypes. Other regions indicate additional genomic rearrangements: inversions (8), copy number changes (2), or other variants (12). The remaining regions appear to reflect recombination suppression by previously unevidenced mechanisms. They are enriched for precisely spanning single genes (p= 5·10−10), specifically those expressed in male gametogenesis, and for eQTLs (p= 2·10−3). This suggests an extension of previously hypothesised crossover suppression within meiotic genes, towards a model of suppression varying across individuals with different expression levels. Our methods can be readily applied to other species, showing that genealogies offer previously un-tapped potential to study structural variation and other phenomena impacting evolution.
Efficient PCR-based gene targeting in isolates of the non-conventional yeastDebaryomyces hansenii
Authors: Alhajouj Sondos , Turkolmez Selva , Abalkhail Tarad , Alwan Zeena Hadi Obaid , Gilmour D. James , Mitchell Phil J. , Hettema Ewald H. 
Published: July 2023

AbstractDebaryomyces hanseniiis a yeast with considerable biotechnological potential as an osmotolerant, stress tolerant oleaginous microbe. However, targeted genome modification tools are limited and require a strain with auxotrophic markers. Gene targeting by homologous recombination has been reported to be inefficient but here we describe a set of reagents and a method that allows gene targeting at high efficiency in wild type isolates. It uses a simple PCR-based amplification that extends a completely heterologous selectable marker with 50 bp flanks identical to the target site in the genome. Transformants integrate the PCR product through homologous recombination at high frequency (>75%). We illustrate the potential of this method by disrupting genes at high efficiency and by expressing a heterologous protein from a safe chromosomal harbour site. These methods should stimulate and facilitate further analysis ofD. hanseniistrains and open the way to engineer strains for biotechnology.
Improved Protocol for Reproducible Human Cortical Organoids Reveals Early Alterations in Metabolism withMAPTMutations
Authors: Bertucci Taylor , Bowles Kathryn R. , Lotz Steven , Qi Le , Stevens Katherine , Goderie Susan K. , Borden Susan , Oja Laura Maria , Lane Keith , Lotz Ryan , Lotz Hailey , Chowdhury Rebecca , Joy Shona , Arduini Brigitte L. , Butler David C. , Miller Michael , Baron Heide , Sandhof Carl Alexander , Silva M. Catarina , Haggarty Stephen J. , Karch Celeste M. , Geschwind Daniel H. , Goate Alison M. , Temple Sally 
Published: July 2023

SummaryCerebral cortical-enriched organoids derived from human pluripotent stem cells (hPSCs) are valuable models for studying neurodevelopment, disease mechanisms, and therapeutic development. However, recognized limitations include the high variability of organoids across hPSC donor lines and experimental replicates. We report a 96-slitwell method for efficient, scalable, reproducible cortical organoid production. When hPSCs were cultured with controlled-release FGF2 and an SB431542 concentration appropriate for theirTGFBR1/ALK5expression level, organoid cortical patterning and reproducibility were significantly improved. Well-patterned organoids included 16 neuronal and glial subtypes by single cell RNA sequencing (scRNA-seq), frequent neural progenitor rosettes and robust BCL11B+ and TBR1+ deep layer cortical neurons at 2 months by immunohistochemistry. In contrast, poorly-patterned organoids contain mesendoderm-related cells, identifiable by negative QC markers includingCOL1A2. Using this improved protocol, we demonstrate increased sensitivity to study the impact of differentMAPTmutations from patients with frontotemporal dementia (FTD), revealing early changes in key metabolic pathways.
Viral infection arrests coccolithophore calcification and nutrient consumption, and triggers shifts in organic stoichiometry
Authors: Dikstein Tamar , Antler Gilad , Pellerin Andre , Sharoni Shlomit , Frada Miguel J. 
Published: July 2023

AbstractBlooms of the coccolithophoreEmiliania huxleyiare routinely infected by a specific lytic virus (EhV), which rapidly kills host cells triggering bloom termination and organic and inorganic carbon export. However, the impact of EhV on the dynamic of resource acquisition and cellular stoichiometry remains unknown, limiting the current understanding of the ecological and biogeochemical significance ofE. huxleyiblooms. To tackle this knowledge gap, we used algal and EhV cultures to determine over the course of infections the dynamics of alkalinity, modulated by calcification, nitrate and phosphate consumption and organic matter stoichiometry. We found that within 24hr alkalinity concentration stabilized and nutrient uptake declined to background levels. In parallel, the stoichiometric ratio of carbon to nitrogen was about 15% higher and the nitrogen to phosphorus ratio was about 12% lower during infections relative to controls. These variations likely resulted from lipid accumulation required for viral replication and the differential retention of phosphorus-rich macromolecular pools in decaying cells, respectively. Finally, after host population decay a progressive enrichment in phosphorus relative to nitrogen and carbon was detected in the remaining cell lysates. We estimate that this stoichiometric shift post-infection was driven by the progressive accumulation of heterotrophic bacteria involved in the degradation of organic material. Viral-mediated cell remodeling and consequent shifts in biomass stoichiometry likely impacts the patterns of nutrient cycling and biological carbon pump efficiency during large-scale blooms in the oceans.
The arginine/ornithine binding protein ArgT plays an essential role inBrucellato prevent intracellular killing and contribute to chronic persistence in the host
Authors: Mallik Sushree Rekha , Joshi Kiranmai , Radhakrishnan Girish K. 
Published: July 2023

ABSTRACTBrucellaspecies are facultative intracellular bacterial pathogens that cause the contagious zoonotic disease, brucellosis.Brucellaspp. infect a wide range of animals, including livestock, wild animals, and marine mammals. Brucellosis remains endemic to various parts of the world, affecting the economic growth of many countries because of its impact on public health and livestock productivity. There are no human vaccines for brucellosis, and controlling the disease in susceptible animals is crucial for limiting human infections. Although the available live-attenuated vaccines have protective efficacy in animals, they have many disadvantages, including infectivity in humans. Compared with other invasive bacterial pathogens, minimal information is available on the virulence factors ofBrucellathat enable them to survive in the host. Here, we performed transposon-based random mutagenesis ofB. neotomaeand identified the arginine/ornithine binding protein, ArgT, as the crucial virulence determinant ofBrucella. DeletingArgTfromB. melitensisresulted in its attenuation in macrophages, which was restored upon complementation with anArgTexpression plasmid. We observed that macrophages infected with ΔArgT-Brucellaproduced elevated levels of NO due to the inability of ΔArgT Brucellato deplete the host intracellular arginine through its importer. Furthermore, defective survival of ΔArgT B. melitensiswas observed in the infected mice, which correlated with enhanced NO production in the mice. Our studies revealed thatArgTinBrucellaplays a vital role in preventing intracellular killing and contributes to the chronic persistence ofBrucellain the host. This study highlights the essential role of arginine in clearing intracellular infections and the subversion of this host defense mechanism by intracellular pathogens for their chronic persistence.