bluuebunny/crossref_metadata_2025 huggingface dataset:
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics
Authors: Lucia-Sanz Adriana , Peng Shengyun , Leung Chung Yin (Joey) , Gupta Animesh , Meyer Justin R. , Weitz Joshua S.
Published: January 2024

The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary – and largely uncharacterized – genetics of adsorption, injection, cell take-over and lysis. Here we present a machine learning approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions amongst 51Escherichia colistrains and 45 phageλstrains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and withouta prioriknowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. We found that the most effective approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, accurately predicting 86% of interactions while reducing the relative error in the estimated strength of the infection phenotype by 40%. Feature selection revealed key phageλandE. colimutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phageλinfections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. The method’s success in recapitulating strain-level infection outcomes arising during coevolutionary dynamics may also help inform generalized approaches for imputing genetic drivers of interaction phenotypes in complex communities of phage and bacteria.
Approaching pathogenicClostridiafrom a One Health perspective
Authors: Cersosimo Laura M. , Worley Jay N. , Bry Lynn
Published: January 2024

Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens includingC.botulinum,C.difficile, andC.perfringensenable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI’s Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
A mouse model to study glutathione limitationin vivo
Authors: Timson Rebecca C. , Khan Artem , Uygur Beste , Saad Marwa , Yeh Hsi-Wen , DelGaudio Nicole , Weber Ross , Alwaseem Hanan , Gao Jing , Yang Chingwen , Birsoy Kıvanç
Published: January 2024

Glutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are linked to many diseases, including cancer and neurodegenerative disorders, determining the function of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme fromStreptococcus Thermophilus(GshF). GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes revealed metabolic liabilities under compartmentalized GSH depletion. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the role of GSH availability in physiology and disease.
Genome-wide patterns of non-coding sequence variation in the major fungal pathogenAspergillus fumigatus
Authors: Brown Alec , Steenwyk Jacob L. , Rokas Antonis
Published: January 2024

A. fumigatusis a deadly fungal pathogen, responsible for >400,000 infections/year and high mortality rates.A. fumigatusstrains exhibit variation in infection-relevant traits, including in their virulence. However, mostA. fumigatusprotein-coding genes, including those that modulate its virulence, are shared betweenA. fumigatusstrains and closely related non-pathogenic relatives. We hypothesized thatA. fumigatusgenes exhibit substantial genetic variation in the non-coding regions immediately upstream to the start codons of genes, which could reflect differences in gene regulation between strains. To begin testing this hypothesis, we identified 5,812 single-copy orthologs across the genomes of 263A. fumigatusstrains.A. fumigatusnon-coding regions showed higher levels of sequence variation compared to their corresponding protein-coding regions. Specifically, we found that 1,274 non-coding regions exhibited <75% nucleotide sequence similarity (compared to 928 protein-coding regions) and 3,721 non-coding regions exhibited between 75% and 99% similarity (compared to 2,482 protein-coding regions) across strains. Only 817 non-coding regions exhibited ≥99% sequence similarity compared to 2,402 protein-coding regions. By examining 2,482 genes whose protein-coding sequence identity scores ranged between 75% and 99%, we identified 478 total genes with signatures of positive selection only in their non-coding regions and 65 total genes with signatures only in their protein-coding regions. 28 of the 478 non-coding regions and 5 of the 65 protein-coding regions under selection are associated with genes known to modulateA. fumigatusvirulence. Non-coding region variation betweenA. fumigatusstrains included single nucleotide polymorphisms and insertions or deletions of at least a few nucleotides. These results show that non-coding regions ofA. fumigatusgenes harbor greater sequence variation than protein-coding regions, raising the hypothesis that this variation may contribute toA. fumigatusphenotypic heterogeneity.
Mapping the tRNA Modification Landscape ofBartonella henselaeHouston I andBartonella quintanaToulouse
Authors: Quaiyum Samia , Sun Jingjing , Marchand Virginie , Sun Guangxin , Reed Colbie J. , Motorin Yuri , Dedon Peter C. , Minnick Michael F. , de Crécy-Lagard Valérie
Published: January 2024

Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens—Bartonella henselaeHouston I andBartonella quintanaToulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications inB. henselaeand 22 genes associated with 23 modifications inB. quintana. Notably, akin to other intracellular and symbiotic bacteria, bothBartonellaspecies have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37.B. quintanaexhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
Nature AND Nurture: Enabling formate-dependent growth inMethanosarcina acetivorans
Authors: Bao Jichen , Somvanshi Tejas , Tian Yufang , Laird Maxime , Garcia Pierre Simon , Schöne Christian , Rother Michael , Borrel Guillaume , Scheller Silvan
Published: January 2024

Methanogenic archaea are crucial in global carbon cycling as around 1 Gt of the potent greenhouse gas, methane, is produced annually. Major contributors belong to the order Methanosarcinales, which contain some of the most versatile methanogens that are capable of acetotrophic, methylotrophic and CO2-reducing methanogenesis. The genetically tractable model methanogen,Methanosarcina acetivorans, by its nature shows versatility in substrate utilization and energy conservation pathways but cannot utilize formate. In this study, we expanded the primary metabolism ofM. acetivoransto include formate-dependent methanogenesis. By introducing an exogenous formate dehydrogenase, the two metabolically engineeredM. acetivoransstrains acquired the capacity for formate-dependent methanogenesis pathways with one capable of formate-dependent methyl-reduction and the other capable of formate-dependent CO2-reduction. Through nurturing the strain capable of CO2-reduction with adaptive laboratory evolution, we were able to enable growth and methanogenesis ofM. acetivoranssolely on formate, a metabolism only reported in methanogens without cytochromes which are limited by their versatility.M. acetivoransalso showed acetogenic potential where the formate-dependent CO2-reducing strain was able to divert ≈ 10% of carbon to acetate instead of methane. Our results show that even thoughM. acetivoranslacks energy converting hydrogenase and cannot use H2, it has yet-uncharacterized capacity to obtain reduced ferredoxins from oxidizing formate. Our work encourages reevaluation of our understanding of formate utilization in Methanosarcinales. By enabling formate-dependent methanogenesis, we have expanded the substrate spectrum of a versatile model methanogen with cytochromes to include formate as well.
Interactors of sacsin’s DNAJ domain identify function in organellar transport and membrane composition relevant to ARSACS pathogenesis
Authors: Paré Alexandre M. , Cheng-Boivin Zacharie , Dabbaghizadeh Afrooz , Minotti Sandra , Durham Heather D. , Gentil Benoit J.
Published: January 2024

Autosomal Recessive Spastic Ataxia of the Charlevoix Saguenay (ARSACS) is caused by loss of function mutations in theSACSgene encoding sacsin, a 520kDa protein with multiple functional domains. The goal of this study was to identify client proteins interacting with the J domain, a cochaperone domain interacting with Hsp70 chaperones, to gain insights into sacsin’s function and its disruption in experimental models of ARSACS. Pull downs from mouse brain identified Rabs and Rab-associated proteins including Rab1b, ARF5 and endophilin B2, involved in organelle trafficking. In cell and mouse models of ARSACS, higher molecular weight species of Rab1b were identified on SDS-PAGE in addition to the normal 25kDa band and Rab1was retained in the soma along with membranous organelles (i.e., ER, Golgi and ATG9 autophagic vesicles). These changes were reversed by expression of the DNAJ domain or the Ubl domain of sacsin and occurred independent of the formation of abnormal bundles of intermediate filaments, a key feature of ARSACS. Although Rab1b was associated with both Golgi and ER in bothSacs+/+andSacs-/-cells, expression of the DNAJ domain or the Ubl domain of sacsin increased Rab1b association with ER and restored normal electrophoretic mobility. Finally, subcellular distribution of another membrane protein, neuroplastin, a key receptor for synapse formation and plasticity, also was impaired, pointing to a general problem in Rab-dependent membrane trafficking in the absence of sacsin.
The earliest allopolyploidization in tracheophytes revealed by phylotranscriptomics and morphology of Selaginellaceae
Authors: Kang Jong-Soo , Yu Ji-Gao , Xiang Qiao-Ping , Zhang Xian-Chun
Published: January 2024

Selaginellaceae exhibit extraordinary evolutionary history in which they survived and thrived during the Permian–Triassic extinction and did not undergo polyploidization. Here, we reconstructed the phylogenetic relationships of Selaginellaceae by applying large-scale nuclear genes from RNA-seq, and found that each group showed phylogenetic incongruences among single-gene trees with different frequencies. In particular, three different phylogenetic positions of thesanguinolentagroup were recovered by different nuclear gene sets. We evaluated the factors that might lead to the phylogenetic incongruence of thesanguinolentagroup and concluded that hybridization between each ancestor of two superclades is the most likely cause. We presented the supporting evidence from gene flow test, species network inference, and plastome-based phylogeny. Furthermore, morphological characters and chromosomal evidence also lend support to the hybrid origin of this group. The divergence time estimations, using two gene sets respectively, indicated the splits between thesanguinolentagroup and each related superclade happened around the same period, implying that the hybridization event probably occurred during the Early Triassic. This study reveals an ancient allopolyploidization with integrative evidence and robust analyses, which sheds new light on the recalcitrant phylogenetic problem of thesanguinolentagroup and reports the polyploidization in the basal vascular plants, Selaginellaceae.
The ventral hippocampus and nucleus accumbens underlie long-term social memory about female conspecifics in male mice
Authors: Watarai Akiyuki , Ishida Kiyoshi , Okuyama Teruhiro
Published: January 2024

For many social animals, including humans, the ability to remember and recognize conspecifics (i.e., having social memory), especially a mating partner, is essential for adaptive reproductive strategies. Our previous studies have shown that social memory about same-sex conspecifics, namely male-to-male social memory, is stored in hippocampal ventral CA1 (vCA1) neurons and that neural projections from the vCA1 to the nucleus accumbens (NAc) are crucial for social discriminatory behavior. However, how the memory of an opposite-sex conspecific, specifically male-to-female social memory, and how the social memory modulates sexual behavior in males remain unknown. Herein, we investigated the ultrasonic vocalizations (USVs) and socially approaching behavior of males toward a female before and after social memory formation. We found that the total duration of USVs was reduced when the male mice interacted with a familiar female. This reduction in USV emission was blocked by optogenetic inhibition of vCA1 neurons, as well as D1- and D2-dopamine receptor (D1R and D2R) expressing neurons in the NAc. Furthermore, fiber photometry recordings in the NAc revealed that the activities of both D1R and D2R neuronal populations were altered during social interaction with familiar or novel females after the process of familiarization. The response of D1R-neurons was reduced only when interacting with familiar females. In contrast, although responses of D2R-neurons were reduced toward both familiar and novel females after social memory formation, the reduction towards novel females was significantly more pronounced compared to that towards familiar females. Our findings suggested that the activities of both vCA1 neurons and D1R- and D2R-expressing NAc neurons in males were differentially modulated by the presence of social memory about females during adaptive reproductive strategies.

Significance Statement

Long-term social memory about females modulates male sexual behavior, specifically ultrasonic vocalization emissions, mediated by hippocampal ventral CA1 and dopamine receptor expressing neurons in the nucleus accumbens.
Primary oocytes with cellular senescence features are involved in ovarian aging in mice
Authors: Yan Hao , Diaz Miranda Edgar Andres , Jin Shiying , Wilson Faith , An Kang , Godbee Brooke , Zheng Xiaobin , Brau-Rodríguez Astrid Roshealy , Lei Lei
Published: January 2024

In mammalian females, quiescent primordial follicles serve as the ovarian reserve and sustain normal ovarian function and egg production via folliculogenesis. The loss of primordial follicles causes ovarian aging. Cellular senescence, characterized by cell cycle arrest and production of the senescence-associated secretory phenotype (SASP), is associated with tissue aging. In the present study, we report that some quiescent primary oocytes in primordial follicles become senescent in adult mouse ovaries. The senescent primary oocytes share senescence markers characterized in senescent somatic cells. The senescent primary oocytes were observed in young adult mouse ovaries, remained at approximately 15% of the total primary oocytes during ovarian aging from 6 months to 12 months, and accumulated in aged ovaries. Administration of a senolytic drug ABT263 to 3-month-old mice reduced the percentage of senescent primary oocytes and the transcription of the SASP cytokines in the ovary. In addition, led to increased numbers of primordial and total follicles and a higher rate of oocyte maturation and female fertility. Our study provides experimental evidence that primary oocytes, a germline cell type that is arrested in meiosis, become senescent in adult mouse ovaries and that senescent cell clearance reduced primordial follicle loss and mitigated ovarian aging phenotypes.
Nationwide Inclusive Facilitator Training: Mindsets, Practices and Growth
Authors: Codding Diane , Yen Alexandria H. , Lewis Haley , Johnson-Ojeda Vanessa , Frey Regina F. , Hokanson Sarah Chobot , Goldberg Bennett B.
Published: January 2024

Advancing diversity in STEM requires competent and confident faculty and staff who can lead local professional development in inclusive teaching to improve classroom instruction and support all learners. This paper examines how a facilitator training model designed to promote inclusive facilitation impacted inclusive learning community facilitator self-reported confidence and practices. This mixed methods study reports on survey data from project trained facilitators (n=71) collected over four course runs. Facilitators reported significant increases in confidence, with the largest effect sizes in areas related to diversity, equity, and inclusion (DEI) and identity. Qualitative findings indicate the training model effectively aligned facilitators with our approach to inclusive facilitation. Findings demonstrate that professional development in inclusive teaching, and by extension in other equity and diversity topics, can be successfully done at a national scale by centering identity, power, and positionality while upholding ‘do no harm.’ This paper provides a strategy for how DEI-focused faculty development efforts can select, train, and support facilitators on a national scale while maintaining high fidelity to project values and goals.
Concordance of high blood pressure among middle-aged and older same-sex couples in the USA
Authors: Varghese Jithin Sam , Curtis Michael G. , Opara Samuel C.O. , Patel Shivani A. , Sheth Anandi N. , Hussen Sophia A.
Published: January 2024

Heterosexual couples in romantic relationships are known to influence each other’s hypertension risk. However, the role of partners on an individual’s hypertension status in same-sex relationships is less understood. Our objective is to characterize the burden of high blood pressure among middle-aged and older couples consisting of men who have sex with men (MSM) and women who have sex with women (WSW) living in the US. Among 81 same-sex couples from the Health and Retirement Study 2006-18, 72.4% (95%CI: 23.4-95.7) MSM couples and 61.0% (95%CI: 30.4-84.8) WSW couples consisted of both partners with hypertension. Same-sex couples demonstrate high concordance of hypertension and related risk factors, suggesting a need to develop novel interventions targeting MSM and WSW couples
Protection afforded by post-infection SARS-CoV-2 vaccine doses: a cohort study in Shanghai
Authors: Zheng Bo , Gonçalves Bronner , Deng Pengfei , Wang Weibing , Tian Jie , Liang xueyao , Yao Ye , Xue Caoyi
Published: January 2024

ABSTRACT

Background:In many settings, a large fraction of the population has both been vaccinated against and infected by SARS-CoV-2. Hence, quantifying the protection provided by post-infection vaccination has become critical for policy. We aimed to estimate the protective effect against SARS-CoV-2 reinfection of an additional vaccine dose after an initial Omicron variant infection.

Methods:We report a retrospective, population-based cohort study performed in Shanghai, China, using electronic databases with information on SARS-CoV-2 infections and vaccination history. We compared reinfection incidence by post-infection vaccination status in individuals initially infected during the April-May 2022 Omicron variant surge in Shanghai and who had been vaccinated before that period. Cox models were fit to estimate adjusted hazard ratios (aHR).

Results:275,896 individuals were diagnosed with RT-PCR-confirmed SARS-CoV-2 infection in April-May 2022; 199,312/275,896 were included in analyses on the effect of a post-infection vaccine dose. Post-infection vaccination provided protection against reinfection (aHR 0.82; 95% CI 0.79-0.85). For patients who had received one, two or three vaccine doses before their first infection, hazard ratios for the post-infection vaccination effect were 0.84 (0.76-0.93), 0.87 (0.83-0.90) and 0.96 (0.74-1.23), respectively. Vaccination within 30 and 90 days before the second Omicron wave provided different degrees of protection (in aHR): 0.51 (0.44-0.58), and 0.67 (0.61-0.74), respectively. Moreover, for all vaccine types, but to different extents, a post-infection dose given to individuals who were fully vaccinated before first infection was protective.

Conclusions:In previously vaccinated and infected individuals, an additional vaccine dose provided protection against Omicron variant reinfection. These observations will inform future policy decisions on COVID-19 vaccination in China and other countries.
Hippocampus Glutathione S Reductase Potentially Confers Genetic Resilience to Cognitive Decline in the AD-BXD Mouse Population
Authors: Saul Michael C. , Litkowski Elizabeth M. , Hadad Niran , Dunn Amy R. , Boas Stephanie M. , Wilcox Jon A. L. , Robbins Julia E. , Wu Yiyang , Philip Vivek M. , Merrihew Gennifer E. , Park Jea , De Jager Philip L. , Bridges Dave E. , Menon Vilas , Bennett David A. , Hohman Timothy J. , MacCoss Michael J. , Kaczorowski Catherine C.
Published: January 2024

Alzheimer’s disease (AD) is a prevalent and costly age-related dementia. Heritable factors account for 58-79% of variation in late-onset AD, but substantial variation remains in age-of- onset, disease severity, and whether those with high-risk genotypes acquire AD. To emulate the diversity of human populations, we utilized the AD-BXD mouse panel. This genetically diverse resource combines AD genotypes with multiple BXD strains to discover new genetic drivers of AD resilience. Comparing AD-BXD carriers to noncarrier littermates, we computed a novel quantitative metric for resilience to cognitive decline in the AD-BXDs. Our quantitative AD resilience trait was heritable and genetic mapping identified a locus on chr8 associated with resilience to AD mutations that resulted in amyloid brain pathology. Using a hippocampus proteomics dataset, we nominated the mitochondrial glutathione S reductase protein (GR or GSHR) as a resilience factor, finding that the DBA/2J genotype was associated with substantially higher GR abundance. By mapping protein QTLs (pQTLs), we identified synaptic organization and mitochondrial proteins coregulated in trans with a cis-pQTL for GR. We found four coexpression modules correlated with the quantitative resilience score in aged 5XFAD mice using paracliques, which were related to cell structure, protein folding, and postsynaptic densities. Finally, we found significant positive associations between humanGSRtranscript abundance in the brain and better outcomes on AD-related cognitive and pathology traits in the Religious Orders Study/Memory and Aging project (ROSMAP). Taken together, these data support a framework for resilience in which neuronal antioxidant pathway activity provides for stability of synapses within the hippocampus.
SURF2 is a MDM2 antagonist in triggering the nucleolar stress response
Authors: Tagnères Sophie , Santo Paulo Espirito , Radermecker Julie , Rinaldi Dana , Froment Carine , Provost Quentin , Capeille Solemne , Watkins Nick , Marcoux Julien , Gleizes Pierre-Emmanuel , Marcel Virginie , Plisson-Chastang Célia , Lebaron Simon
Published: January 2024

Cancer cells are addicted to strong ribosome production to sustain their proliferation rate. Many chemotherapies impede ribosome production which is perceived by cells as “nucleolar stress” (NS), triggering p53-dependent and independent response pathways leading to cell cycle arrest and/or apoptosis. The 5S RNP particle, a sub-ribosomal particle, is instrumental to NS response. Upon ribosome assembly defects, the 5S RNP accumulate as free form. This free form is able to sequester and inhibit MDM2, thus promoting p53 stabilization. To investigate how cancer cells can resist to NS, we purified free-5S RNP and uncovered a new interaction partner, SURF2. Functional characterization of SURF2 shows that its depletion increases cellular sensitivity to NS, while its overexpression promotes their resistance to it. Consistently, SURF2 expression level negatively correlates with the overall survival in adrenocortical and head and neck squamous cell carcinomas. Our data demonstrate that SURF2 buffers free-5S RNP particles, and can modulate their activity. SURF2 regulates NS responses, and is a key player in both ribosomopathies and oncogenic mechanisms.
Lupus-associated innate receptors drive extrafollicular evolution of autoreactive B cells
Authors: Zhu Danni Yi-Dan , Maurer Daniel P. , Castrillon Carlos , Deng Yixiang , Mohamed Faez Amokrane Nait , Ma Minghe , Schmidt Aaron G. , Lingwood Daniel , Carroll Michael C.
Published: January 2024

In systemic lupus erythematosus, recent findings highlight the extrafollicular (EF) pathway as prominent origin of autoantibody-secreting cells (ASCs). CD21loCD11c+B cells, associated with aging, infection, and autoimmunity, are contributors to autoreactive EF ASCs but have an obscure developmental trajectory. To study EF kinetics of autoreactive B cell in tissue, we adoptively transferred WT and gene knockout B cell populations into the 564Igi mice - an autoreactive host enriched with autoantigens and T cell help. Time-stamped analyses revealed TLR7 dependence in early escape of peripheral B cell tolerance and establishment of a pre-ASC division program. We propose CD21locells as precursors to EF ASCs due to their elevated TLR7 sensitivity and proliferative nature. Blocking receptor function reversed CD21 loss and reduced effector cell generation, portraying CD21 as a differentiation initiator and a possible target for autoreactive B cell suppression. Repertoire analysis further delineated proto-autoreactive B cell selection and receptor evolution toward self-reactivity. This work elucidates receptor and clonal dynamics in EF development of autoreactive B cells, and establishes modular, native systems to probe mechanisms of autoreactivity.
Plasmodium falciparummitochondrial complex III, the target of atovaquone, is essential for progression to the transmissible sexual stages
Authors: Sheokand Pradeep Kumar , Mühleip Alexander , Sheiner Lilach
Published: January 2024

The Plasmodium mitochondrial electron transport chain (mETC) is responsible for essential metabolic pathways such as de novo pyrimidine synthesis and ATP synthesis. The mETC complex III (cytochrome bc1 complex) is responsible for transferring electrons from ubiquinol to cytochrome c and generating a proton gradient across the inner mitochondrial membrane, which is necessary for the function of ATP synthase. Recent studies revealed that the composition of Plasmodium complex III is divergent from human, highlighting its suitability as a target for specific inhibition. Indeed, complex III is the target of the clinically used anti-malarial atovaquone and of several inhibitors undergoing pre-clinical trials, yet its role in parasite biology have not been thoroughly studied. We provide evidence that the universally conserved subunit, PfRieske, and the new parasite subunit, PfC3AP2, are part of Plasmodium falciparum complex III (PfCIII), with the latter providing support for the prediction of its divergent composition. Using inducible depletion, we show that PfRieske, and therefore PfCIII as a whole, is essential for asexual blood stage parasite survival, in line with previous observations. We further found that depletion of PfCIII results in gametocyte maturation defect. These phenotypes are linked to defects in mitochondrial functions upon PfRieske depletion, including increased sensitivity to mETC inhibitors in asexual stages and decreased cristae abundance alongside abnormal mitochondrial morphology in gametocytes. This is the first study which explores the direct role of the PfCIII in gametogenesis via genetic disruption, paving the way for a better understanding of the role of mETC in the complex life cycle of these important parasites and providing further support for the focus of antimalarial drug development on this pathway.
Kernel-smoothed permutation for extreme P-value estimation in genetic association studies
Authors: Bian Jiayi , Li Caifeng , Wu Jingjing , Long Quan
Published: January 2024

In genetic studies, permutation tests serve as a cornerstone to estimate P-values. This is because researchers may design new test statistics without a known closed-form distribution, or the assumption of a well-established test may not hold. However, permutation tests require vast number of permutations which is proportional to the magnitude of the actual P-values. When it comes to genome-wide association studies where multiple-test corrections are routinely conducted, the actual P-values are extremely small, requiring a daunting number of permutations that may be beyond the available computational resources. Existing models that reduce the required number of permutations all assume a specific format of the test statistic to exploit its specific statistical properties. We propose Kernel-smoothed permutation which is a model-free method universally applicable to any statistic. Our tool forms the null distribution of test statistics using a kurtosis-driven transformation, followed by a kernel-based density estimation (KDE). We compared our Kernel-smoothed permutation to Naïve permutation using statistics from known closed-form null distributions. Based on three frequently used test statistics in association studies, i.e., t-test, sequence kernel association test (SKAT), and chi-squared test, we demonstrated that our model reduced the required number of permutations by a magnitude with the same or higher accuracy.
The astrovirus N-terminal nonstructural protein anchors replication complexes to the perinuclear ER membranes
Authors: Ali Hashim , Noyvert David , Hankinson Jacqueline , Lindsey Gemma , Lulla Valeria
Published: January 2024

An essential aspect of viral replication is the anchoring of the replication complex (RC) to cellular membranes. Positive-sense RNA viruses employ diverse strategies, including co-translational membrane targeting through signal peptides and co-opting cellular membrane trafficking components. Often, N-terminal nonstructural proteins play a crucial role in linking the RC to membranes, facilitating the early association of the replication machinery. Astroviruses utilize a polyprotein strategy to synthesize nonstructural proteins, relying on subsequent processing to form replication-competent complexes. In this study, we provide evidence for the perinuclear ER membrane association of RCs in five distinct human astrovirus strains. Using tagged recombinant classical human astrovirus 1 and neurotropic MLB2 strains, we establish that the N-terminal domain guides the ER membrane association. Through mutational analysis of the N-terminal domain in replicon and reverse genetics systems, we identified di-arginine motifs responsible for the perinuclear ER retention and formation of functional RCs. Our findings highlight the intricate virus-ER interaction mechanism employed by astroviruses, potentially leading to the development of novel antiviral intervention strategies.

Author Summary

Human astroviruses are a significant cause of acute gastroenteritis, accounting for up to 9% of cases in young children. Immunocompromised individuals and infants experience more critical symptoms, such as severe and persistent diarrhea, as well as sporadic systemic and even fatal diseases. To date, no drugs have been developed to protect against astrovirus infection. Our study provides the first evidence that the integrity of the N-terminal domain of nsP1a is essential for establishing early replication. Central to this process, the di-arginine motifs in the N-terminal domain are responsible for ER retention, the formation of functional replication complexes, and viral replication. Therefore, selectively targeting N-terminal domain-mediated ER retention could be a promising therapeutic strategy to effectively control astrovirus infection.
PIRCHE application versions 3 and 4 lead to equivalent T cell epitope mismatch scores in solid organ and stem cell transplantation modules
Authors: Matern Benedict M , Niemann Matthias
Published: January 2024

Elevated PIRCHE scores between recipient and donor in organ and stem cell transplantation have been shown to correlate with increased risk of donor-specific HLA antibodies and graft-versus-host disease, respectively. With each revision of the PIRCHE application server, it is critical to completely evaluate the predicted scores, and compare with previous revisions. This manuscript compares the newly introduced PIRCHE version 4.2 with its predecessor version 3.3, which has been widely used in retrospective studies, using a virtual cohort of 10,000 transplant pairs. In the stem cell transplantation module, both versions yield identical results for 100% of the test population. In the solid organ transplantation module, 97% of the test population has identical PIRCHE scores in both versions. The deviating cases could be attributed to a refinement in the PIRCHE algorithm’s specification. For the 3% of cases with deviations, the determined magnitude of the difference is likely to be below the detection limit for clinical effects. We hereby confirm the equivalence in PIRCHE scores generated by the application server versions 3.3 and 4.2.
De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome
Authors: White Benjamen , Lux Thomas , Rusholme-Pilcher Rachel , Juhász Angéla , Kaithakottil Gemy , Duncan Susan , Simmonds James , Rees Hannah , Wright Jonathan , Colmer Josh , Ward Sabrina , Joynson Ryan , Coombes Benedict , Irish Naomi , Henderson Suzanne , Barker Tom , Chapman Helen , Catchpole Leah , Gharbi Karim , Bose Utpal , Okada Moeko , Handa Hirokazu , Nasuda Shuhei , Shimizu Kentaro K. , Gundlach Heidrun , Lang Daniel , Naamati Guy , Legg Erik J. , Bharti Arvind K. , Colgrave Michelle L. , Haerty Wilfried , Uauy Cristobal , Swarbreck David , Borrill Philippa , Poland Jesse A. , Krattinger Simon G. , Stein Nils , Mayer Klaus F.X. , Pozniak Curtis ,   10+ Wheat Genome Project, Spannagl Manuel , Hall Anthony
Published: January 2024

Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome level the genomes of nine wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome withde novoannotation and differential expression analysis for these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of thesede novoannotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homeolog expression and identified cultivar-specific expression profiles. In a case study utilising both the newly constructed wheat pan-genome and pan-transcriptome we demonstrate prevalent variation in the prolamin superfamily and immune-reactive proteins across the pan-cultivars.In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.
Appropriate glycemic management protects the germline but not uterine environment in type 1 diabetes
Authors: Zhao Allan , Jiang Hong , Palomares Arturo Reyes , Larsson Alice , He Wenteng , Grünler Jacob , Zheng Xiaowei , Rodriguez Wallberg Kenny A. , Catrina Sergiu-Bogdan , Deng Qiaolin
Published: January 2024

Emerging evidence indicates that parental diseases can impact the health of subsequent generations through epigenetic inheritance. Recently, it was shown that maternal diabetes alters the metaphase II oocyte transcriptome, causing metabolic dysfunction in offspring. However, the type 1 diabetes (T1D) mouse models frequently utilized in previous studies may be subject to several confounding factors as a result of severe hyperglycemia. This limits clinical translatability due to improvements in glycemic control for T1D subjects. Therefore, we optimized a T1D mouse model to investigate the effects of appropriately managed maternal glycemic levels on oocytes and intrauterine development. We show that diabetic mice with appropriate glycemic control exhibited better long-term health outcomes, which maintains the oocyte transcriptome and chromatin accessibility. Moreover, we find that human oocytes undergoing in vitro maturation challenged with mildly increased levels of glucose, reflecting appropriate glycemic management, also retained their transcriptome. However, the fetal growth and placental function were still affected despite appropriate glycemic control, underscoring the uterine environment rather than the germline as a pathological factor for developmental programming in appropriately managed diabetes.
Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria
Authors: Kropp Ashleigh , Gillett David L. , Venugopal Hari , Gonzálvez Miguel A. , Lingford James P. , Barlow Christopher K. , Zhang Jie , Greening Chris , Grinter Rhys
Published: January 2024

Diverse bacteria and archaea use atmospheric carbon monoxide (CO) as an energy source during long-term survival. This process enhances the biodiversity of soil and marine ecosystems globally and removes 250 million tonnes of a toxic, climate-relevant pollutant from the atmosphere each year. Bacteria use [MoCu]-carbon monoxide dehydrogenases (Mo-CODH) to convert CO to carbon dioxide, then transfer the liberated high-energy electrons to the aerobic respiratory chain. However, given no high-affinity Mo-CODH has been purified, it is unknown how these enzymes oxidise CO at low concentrations and interact with the respiratory chain. Here we resolve these knowledge gaps by analysing Mo-CODH (CoxSML) and its hypothetical partner CoxG fromMycobacterium smegmatis. Kinetic and electrochemical analyses show purified Mo-CODH is a highly active high-affinity enzyme (Km= 139 nM,kcat= 54.2 s-1). Based on its 1.85 Å resolution cryoEM structure, Mo-CODH forms a CoxSML homodimer similar to characterised low-affinity homologs, but has distinct active site coordination and narrower gas channels that may modulate affinity. We provide structural, biochemical, and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chainviathe membrane-bound menaquinone-binding protein CoxG. Consistently, CoxG is required for CO-driven respiration, extracts menaquinone from mycobacterial membranes, and binds quinones in a hydrophobic pocket. Finally, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of a biogeochemically and ecologically important process, while demonstrating that the newly discovered process of long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.
RNA regulates cohesiveness and porosity of a biological condensate
Authors: Chou Han-Yi , Aksimentiev Aleksei
Published: January 2024

Biological condensates have emerged as key elements of a biological cell function, concentrating disparate biomolecules to accomplish specific biological tasks. RNA was identified as a key ingredient of such condensates, however, its effect on the physical properties of the condensate was found to depend on the condensate’s composition while its effect on the microstructure has remained elusive. Here, we characterize the physical properties and the microstructure of a protein–RNA condensate by means of large-scale coarse-grained (CG) molecular dynamics simulations. By developing a custom CG model of RNA compatible with a popular CG model of proteins, we systematically investigate the structural, thermodynamic, and kinetic properties of condensate droplets containing thousands of individual protein and RNA molecules over a range of temperatures. While we find RNA to increase the condensate’s cohesiveness, its effect on the condensate’s fluidity is more nuanced with longer molecules compacting the condensate and making it less fluid. We show that a biological condensate has a sponge-like morphology of interconnected channels of size that increases with temperature and decreases in the presence of RNA. Our results suggest that longer RNA form a dynamic scaffold within a condensate, regulating not only its fluidity but also permeability to intruder molecules.
Hydrophobic bulk conservation and genetic code determine the pattern of prokaryotic genome organization
Authors: Teng Wenkai , Zhou Yangkai , Zheng Lingling , Xu Yongqian , Rao Yangzhi , Chen Siruo , Xia Tian , Shu Wensheng , Chen Mengyun
Published: January 2024

Prokaryotic genomes in general exhibit marked organizational asymmetry, and differ substantially in GC-skew, AT-skew, and GS-bias (gene strand bias). Despite enigmatic origins, these organizational features and genomic GC-content have been described to be widely associated with each other recently, providing an opportunity to probe the evolutionary mechanisms. By analyzing sequence data of 4,012 leading strands from all available representative genomes, we found that the unusual nucleotide usage of coding genes under low GC-content contributed to a shift between two organizational patterns in the context of mutational biases. Analysis of artificially established neutral and natural models further suggests that in genes both GC-skew and AT-skew increase with decreasing GC-content, mostly contributed by synonymous substitutions because of genetic code, and by nonsynonymous substitutions because of hydrophobic bulk conservation in amino acid usage, respectively. This novel mechanistic framework in our study highlights the importance of evolutionary processes “operating at lower levels of organization” in the microbial world.
Stimulus-induced gamma sources reduce in power but not in spatial extent with healthy aging in human EEG
Authors: Biswas Ankan , Kumar Wupadrasta Santosh , Sharma Kanishka , Ray Supratim
Published: January 2024

Aging alters brain structure and function, and studying such changes may help understand the neural basis underlying aging and devise interventions to detect deviations from healthy progression. Electroencephalogram (EEG) offers an effective way to study healthy aging owing to its high temporal resolution and affordability. Recent studies have shown that narrow- band stimulus-induced gamma oscillations (20-70 Hz) in EEG, induced with cartesian gratings in a fixation task paradigm, weaken with healthy aging and onset of Alzheimer’s Disease (AD) while remaining highly reproducible for a given subject, and thus hold promise as potential biomarkers. However, functional connectivity (FC) sometimes changes in a different way compared to sensor power with aging. This difference could be potentially addressed by studying how underlying gamma sources change with aging, since either a reduction in source power or a shrinkage of the sources (or both) could reduce the power in the sensors but may have different effects on other measures such as FC. We therefore reconstructed EEG gamma sources through a linear inverse method called exact Low-resolution Tomography Analysis (eLORETA) on a large (N=217) cohort of healthy elderly subjects (>50 years). We further characterized gamma distribution in cortical space as an exponential fall-off from a seed voxel with maximal gamma source power to delineate a reduction in magnitude versus shrinkage. We found significant reduction in magnitude but not shrinkage with healthy aging. Overall, our results shed light on changes in EEG gamma source distribution with healthy aging, which could provide clues about underlying neural mechanisms.
Measuring concentration of nanoparticles in polydisperse mixtures using interferometric nanoparticle tracking analysis (iNTA)
Authors: Kashkanova Anna D. , Albrecht David , Küppers Michelle , Blessing Martin , Sandoghdar Vahid
Published: January 2024

Quantitative measurements of nanoparticle concentration in liquid suspensions are in high demand, for example, in the medical and food industries. Conventional methods remain unsatisfactory, especially for polydisperse samples with overlapping size ranges. Recently, we introduced interferometric nanoparticle tracking analysis (iNTA) as a new method for high-precision measurement of nanoparticle size and refractive index. Here, we show that by counting the number of trajectories that cross the focal plane, iNTA can measure concentrations of subpopulations in a polydisperse mixture in a quantitative manner and without the need for a calibration sample. We evaluate our method on both monodisperse samples and mixtures of known concentrations. Furthermore, we assess the concentration of SARS-CoV-2 in supernatant samples obtained from infected cells.