bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative splicing in 300 human cells and tissues is sparsely distributed and strongly associated with cell identity
Authors: Liang Angelita , Wilkins Marc R 
Published: January 2025

ABSTRACTIn eukaryotes, alternative splicing allows RNA sequences to be changed as required in their cellular context. While the use of gene expression without considering transcript isoforms is commonly used to classify cell types, the significance of alternative splicing to cell identity is not fully understood. Using data-driven classification and clustering methods, we analysed the RNA Atlas, an ultra-deep total RNA and polyA capture sequencing dataset obtained from 300 different types of cell and tissue samples across the human body. We show that splice inclusion values can distinguish cell identity effectively, and sometimes better than gene expression. These specific differences in alternative splicing are biologically relevant, with many splice events expressed in a limited number of cell types. We show that distributions of splice inclusion levels are “sparser” than gene expression levels, being discontinuous and containing outliers – akin to a control dial with a few settings. Gene expression levels display finer variation, taking on a diverse range of values akin to a control dial with many increments. Complementary analysis of comparable RNA-Seq samples from the ENCODE dataset yielded consistent results regardless of the splice event or gene expression quantification tools used, as well as the choice of RiboMinusTMor polyA capture-derived RNA libraries. Our results highlight the utility of alternative splicing data in data-driven and functional analyses, and the unique relationship between alternative splicing and cell identity.
Simulating Longitudinal Single-cell RNA Sequencing Data with RESCUE
Authors: Wynn Elizabeth A. , Mould Kara J. , Vestal Brian E. , Moore Camille M. 
Published: January 2025

AbstractAs single-cell RNA-sequencing (scRNA-seq) becomes more widely used in transcriptomic research, complex experimental designs, such as longitudinal studies, become increasingly feasible. Longitudinal scRNA-seq enables the study of transcriptomic changes over time within specific cell types, yet guidance on analytical approaches and resources for study planning, such as power analysis, remains limited. Data simulation is a valuable tool for evaluating analysis method performance and informing study design decisions, including sample size selection. Currently, most scRNA-seq simulation methods simulate cells for a single sample, thus ignoring the between-sample and between-subject variability inherent to longitudinal scRNA-seq data. Here, we introduce RESCUE (REpeated measures Single Cell RNA-seqUEncing data simulation), a novel method that simulates longitudinal scRNA-seq data using a gamma-Poisson frame-work and incorporates additional variability between samples and subjects. We demonstrate our method’s ability to reproduce important data properties and demonstrate its application in study planning. RES-CUE is implemented as an R package and is available athttps://github.com/ewynn610/RESCUE.
Toxigenecity and Virulence variations ofPseudomonas aeruginosafrom out-patients hospitals in Southwest Nigeria
Authors: Akinboboye Olusola Arinola , Akingbade Olusola Abiodun , Motayo Babatunde O , Olajumoke Akinleye Eunice Folusho , Sesan Aina Emmanuel , Samuel Idowu Adeyemi , Amuche Ede Dorathy , Omotunde Nimotalahi , Amuche Ede Dorathy 
Published: January 2025

ABSTRACTBackgroundMultidrug resistant (MDR)Pseudomonas aeruginosaisolates harboring genes for virulence and antibiotic resistance, have grown more prevalent lately. These strains pose a major threat to the general population, especially in tertiary care settings. There is a paucity of information on toxigenic and virulence diversity of multidrug resistantP. aeruginosain Nigeria, hence, the need to characterize and determine the variations of the virulence genes.MethodsSix hundred clinical samples from different anatomical sites were collected aseptically from Lagos University Teaching Hospital (LUTH), University of Medical Sciences, Ondo (UNIMED) and Federal Medical Centre, Abeokuta (FMC).Pseudomonas aeruginosawas isolated using cetrimide agar identified using biochemical tests. Antibiotic sensitivity was done by disc diffusion method. Protease, phospholipase C (lecithinase), caseinase and gelatinase presence were assayed for. Genomic DNA was extracted fromP. aeruginosaisolates and screened for the presence of N-Acetylneuraminate synthase (NaN), Elastase B (LasB), Exotoxin A (ExoA), Exoenzyme S (ExoS) and Exoenzyme U (ExoU) virulence genes by PCR.ResultsThree hundred and sixty bacterial isolates identified from clinical samples are as follows:Pseudomonas aeruginosa(11.3%),Escherichia coli(18.0%),Klebsiella pneumoniae(14.3%),Staphylococcus aureus(10.2%),Proteus mirabilis(3.2%),Streptococcus pnuemoniae(2.3%), Enterobacter aerogenes(0.5%) andAcinetobacter baumanni(0.1%). Enzymes detected in theP. aeruginosaisolates were Phospholipase C (77.9%), caseinase (83.9%), gelatinase (98.5%) and protease (88.2%). TheP. aeruginosaisolates were all resistant to ampicillin and cloxacillin; 26 (38.2 %) strains exhibited multidrug resistance. VirulenceLasB elastase gene was detected in all 14 multi resistantP. aeruginosa, ExoA was detected in 5, ExoS in 4, ExoU in 5 and NaN in 4 isolates: Four (28.6%)ConclusionThe study confirmed presence and variations of toxic genes inPseudomonas aeruginosaisolated from all the three tertiary hospitals.
MULTIPLE PRIMARY CANCERS IN LUNG CANCER PATIENTS IN ATLANTIC CANADA AND IMPLICATIONS FOR SCREENING AND MANAGEMENT
Authors: Coyle Kassandra M. , Gao Yingtong , Murphy Rowan E. , Martinez Victor , Goodarzi Aaron , Dellaire Graham , Wallace Alison 
Published: January 2025

AbstractBackgroundLung cancer incidence rates in Atlantic Canada significantly exceed those of other Canadian provinces, with underlying causes remaining poorly understood. This regional disparity suggests potential genetic or environmental factors unique to Atlantic Canada. Here we present for the first-time data indicating that accompanying the high lung cancer rates in Atlantic Canada is an intricate landscape of multiple malignancies. This represents a phenomenon of multiple primary cancers that is unprecedented in the literature and presents unique challenges in the diagnosis and treatment of individuals diagnosed with lung cancer in Atlantic Canada.MethodsWe performed a retrospective chart review of 1,151 patients referred to the thoracic surgeons at the Queen Elizabeth II Health Sciences Centre between 2019 and 2023 with the new diagnosis of lung cancer. The primary focus was to assess the incidence of multiple primary cancers (as documented in pathology reports) and analyze demographic, clinical, and geographical factors through Fisher’s exact tests and Student’s t-tests.ResultsForty-three precent (43.3%) of Atlantic Canadian patients presented with multiple primary cancers. Of 1,949 cancers identified, 1,440 were of primary lung origin. Sixty percent (60.0%) of our cohort was female. Thirty-one percent (31.3%) were self-reported current tobacco smokers, 50.3% were former tobacco smokers, and 18.4% reported no tobacco use. The average age and body mass index (BMI) at first diagnosis was similar between those patients with and without multiple primary cancers, averaging 67 years and 27.7 kg/m2, respectively. Thirty-nine percent (39.2%) of our study participants lived in more densely populated centers (>100,000 people), 10.2% in intermediate centers (∼98,000 people) and 50.7% in more sparsely populated centers (<55,000 people).ConclusionsWe have uncovered an unprecedented phenomenon in Atlantic Canada of a cohort of patients with lung cancer having multiple primary cancers of different tissue origin at a rate that is four times greater than previously described. The implications of this study are that Atlantic Canadians are disproportionately burdened with cancers of multiple origins that are not explained by smoking rates or BMI. Future studies will investigate the contribution of genetic predisposition, environmental exposures, and socioeconomic factors unique to Atlantic Canada underlying the high rates of multiple primary cancers documented here in a lung cancer cohort. Such studies will be essential to develop effective cancer prevention and screening strategies in Atlantic Canada.
The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure
Authors: Haddox Hugh K. , Angehrn Georg , Sesta Luca , Jennings-Shaffer Chris , Temple Seth D. , Galloway Jared G. , DeWitt William S. , Bloom Jesse D. , Matsen Frederick A. , Neher Richard A. 
Published: January 2025

AbstractRNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g.,A→C,A→G, etc.) and can vary between sites in the viral genome. Understanding this variation can shed light on the mutational processes at play, and is crucial for quantitative modeling of viral evolution. Using the millions of available SARS-CoV-2 full-genome sequences, we estimate rates of synonymous mutations for all 12 possible nucleotide mutation types and examine how much these rates vary between sites. We find a surprisingly high level of variability and several striking patterns: the rates of four mutation types suddenly increase at one of two gene boundaries; the rates of most mutation types strongly depend on a site’s local sequence context, with up to 56-fold differences between contexts; consistent with a previous study, the rates of some mutation types are lower at sites engaged in RNA secondary structure. A simple log-linear model of these features explains ∼15-60% of the fold-variation of mutation rates between sites, depending on mutation type; more complex models only modestly improve predictive power out of sample. We estimate the fitness effect of each mutation based on the number of times it actually occurs versus the number of times it is expected to occur based on the model. We identify several small regions of the genome where synonymous or noncoding mutations occur much less often than expected, indicative of strong purifying selection on the RNA sequence that is independent of protein sequence. Overall, this work expands our basic understanding of SARS-CoV-2’s evolution by characterizing the virus’s mutation process at the level of individual sites and uncovering several striking mutational patterns that arise from unknown mechanisms.
A stress-activated mid-insula to BNST pathway regulates susceptibility to abstinence-induced negative affect in female mice
Authors: Williams Benjamin M. , Little Jincy R. , O’Connell Nathaniel S. , Centanni Samuel W. 
Published: January 2025

ABSTRACTStress is central to many neuropsychiatric conditions, including alcohol use disorder (AUD). Stress influences the initiation and continued use of alcohol, the progression to AUD, and relapse. Identifying the neurocircuits activated during stress, and individual variability in these responses is critical for developing new treatment targets for AUD, particularly to mitigate stress-induced relapse. Using a longitudinal approach, this study examined the relationship between sub-chronic stress exposure and negative affect during protracted abstinence following chronic ethanol exposure. Sub-chronic restraint stress heightened negative affect-like behavior in protracted abstinence. Interestingly, this was driven by a subset of “stress-susceptible” female mice. We examined the mid-insula, a hub in the brain’s salience network, as a driver of this effect, given its role in emotional regulation and links to alcohol craving, consumption, and abstinence-induced negative affect. Mid-insula GCaMP fiber photometry revealed that GCaMP activity during stress exposure was positively correlated with activity during the novelty-suppressed feeding test (NSFT) two weeks into abstinence. A distinct subset of mice exhibited increasing activity during the consummatory phase, implicating the mid-insula as a neural basis for heightened negative affect in abstinence. Chemogenetic inhibition of mid-insula neurons projecting to the dorsal BNST during stress disrupted the emergence of stress susceptibility, highlighting this circuit as a key determinant of susceptibility to abstinence-induced negative affect. These outcomes were female-specific, addressing a critical gap in understanding AUD risk in women. Furthermore, female mice exhibited higher struggling behavior during stress than males. However, this effect was blocked by chemogenetic inhibition of the insula-BNST pathway during stress. By linking pre-alcohol stress response with abstinence outcomes, this work positions the insula-BNST pathway as a potential AUD circuit activity biomarker and therapeutic target.
Adipocyte Aldosterone in Obstructive Sleep Apnea
Authors: Dong Yunzhou , Bock Josh , Karim Shahid , Singh Prachi , Somers Virend K. 
Published: January 2025

AbstractAldosterone, a hormone synthesized by the adrenal glands, plays a pivotal role in regulating both blood pressure and electrolyte balance and may contribute to long term cardiovascular risk. Recent findings suggest that adipose tissue might serve as a source for aldosterone production and secretion. Patients suffering from obstructive sleep apnea (OSA) often exhibit elevated blood pressure levels and increased cardiovascular risk. Therefore, we sought to investigate whether increased aldosterone synthesis in fat tissue could contribute to the increase in hypertension and cardiovascular disease in OSA patients. To address this, we conducted a comparative analysis of adipocyte aldosterone level in OSA patients versus Age and BMI matched healthy individuals. Our data revealed no significant differences in aldosterone content between the two groups. Further examination involved measuring the expression of the key enzyme CYP11B2 responsible for aldosterone synthesis. We observed comparable expression levels of CYP11B2 in both the OSA and control groups. To corroborate these findings, we isolated stromal vascular fraction (SVF) from human fat tissues. The SVF cells were cultured in preadipocyte medium and subjected to normoxia and intermittent hypoxia (IH), mimicking OSA conditions as per established protocol. Subsequent analysis of aldosterone levels in cell lysates and conditioned medium revealed no significant differences. Similarly,in vitroexamination of CYBP11B2 expression was not different in normoxic versus IH conditions. In conclusion, our study did not discern significant differences in adipocyte aldosterone production and secretion between patients with OSA and matched control subjects, nor in human preadipocytes under normoxicversusIH conditions.
Molecular docking, validation, dynamic simulation and pharmacokinetic prediction of natural compounds againstMycobacterium tuberculosisBeta-lactamase BlaC
Authors: Sreekumar Sandra , Bhagya Jyothi J.L , Liji S.S , Pani Subhash Chandra , Rajee Niya Elizaba , Stephanie Aguero Pizzolo , Raphael Terreux , Dhanasingh Immanuel 
Published: January 2025

ABSTRACTTuberculosis, caused byMycobacterium tuberculosisranks second globally in terms of infectious disease-related deaths, after HIV. The resistance ofM. tuberculosisto existing beta-lactam antibiotics is primarily due to chromosomally encoded gene blaC, which can hydrolyse predominantly available beta-lactam antibiotics. Despite the available beta-lactamase inhibitors with beta-lactam ring such as clavulanate, being efficacious, they lead the bacteria to develop an inhibitor escape mechanism. In contrast, the natural product inhibitors without beta-lactam ring that might resist bacterial escape mechanisms have the additional advantage of fewer side effects, higher bioavailability, and better bioremediation towards environmental sustainability. This study identifies novel natural inhibitors against BlaC, from the Natural Products Atlas database of PubChem and ZINC comprising 10,000 compounds using molecular docking and Molecular Dynamics (MD) simulations. The virtual screening and docking experiments demonstrated that the top 10 compounds exhibited favourable docking scores in the range of -7.59 to -9.63 kcal/mol compared to the reference molecule, Doripenem (-7.35 kcal/mol). Following targeted docking and ADMET analysis, three lead compounds Lecanorafuran A, Tryptoquivaline K, and Deacetylisowortmin A were selected for MD simulations for a period of 100 ns to evaluate the stability of the protein-ligand complexes. Based on Root Mean Square Deviation, Root Mean Square Fluctuation, Radius of gyration and Solvent Accessible Surface Area, PCA, and FEL analysis, it was found that Tryptoquivaline K exhibited consistent stability throughout the simulation. Additionally, Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis was conducted to assess the binding affinity of the complex. All these analyses validate that the natural compound Tryptoquivaline K exhibits potential as a promising BlaC inhibitor but warrants further validation through experimental studies in this aspect.
Higher adaxial stomatal density is associated with lower grain yield in spring wheat
Authors: Samantara Kajal , Ivandi Elena , Tulva Ingmar , Jalakas Pirko , Khalegh Doust Banafsheh , Ingver Anne , Kärp Merko , Brazauskas Gintaras , Bleidere Mara , Tamm Ilmar , Hõrak Hanna , Merilo Ebe 
Published: January 2025

AbstractIn land plants, stomatal pores on leaf surfaces developed to control gas exchange between leaf and surrounding air, but also to enable nutrient uptake and leaf cooling. Traits such as stomatal density (SD), guard cell size, stomatal distribution between the upper (adaxial) and lower (abaxial) leaf surfaces (stomatal ratio), and stomatal aperture width exhibit notable variation across different genotypes and environments. These traits influence leaf photosynthesis, water loss, growth, productivity, and pathogen susceptibility. Here, we studied different stomatal traits of spring wheat flag leaves and their relationship with grain yield in field experiments during 2022-2023. Significant genotypic variation among adaxial and abaxial SDs and stomatal ratios was detected, whereas stomatal conductance was mostly affected by annual differences in weather. A strong negative relationship between adaxial stomatal density and grain yield was detected under all conditions, when abiotic factors (water stress or nutrient limitation) resulted in yield losses, whereas under favourable conditions, there was no significant relationship between adaxial stomatal density and grain yield. The effects of leaf surface-specific traits on yield are often overlooked in physiological and breeding experiments. Our results indicate that higher-than-optimal adaxial SD values may result in wheat yield losses under stresses imposed by future climate conditions.
Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control
Authors: Rodschinka Geraldine , Forcelloni Sergio , Behrens Andrew , Riemenschneider Henrick , Edbauer Dieter , Wani Sascha , Nedialkova Danny 
Published: January 2025

AbstractThe translation of mRNA into proteins in multicellular organisms needs to be carefully tuned to changing proteome demands in development and differentiation, and defects in translation often have a disproportionate impact in distinct cell types. Here we used inducible CRISPR interference screens to compare the essentiality of genes with functions in mRNA translation in human induced pluripotent stem cells (hiPSC) and hiPSC-derived neural and cardiac cells. We find that core components of the mRNA translation machinery are broadly essential, but the consequences of perturbing translation-coupled quality control factors are highly cell type-dependent. Human stem cells critically depend on pathways that detect and rescue slow or stalled ribosomes, and on the E3 ligase ZNF598 to resolve a novel type of ribosome collisions at translation start sites on endogenous mRNAs with highly efficient initiation. Our findings underscore the importance of cell identity for deciphering the molecular mechanisms of translational control in metazoans.
RNA G-Quadruplex Emerges from a Coil-Like Ensemble via Multiple Pathways
Authors: Pokorná Pavlína , Mlýnský Vojtěch , Šponer Jiří , Stadlbauer Petr 
Published: January 2025

AbstractRNA G-quadruplexes (rG4s) are vital structural elements in gene regulation and genome stability. In untranslated regions of mRNAs, rG4s influence translation efficiency and mRNA localization. Additionally, rG4s of long non-coding RNAs and telomeric RNA play roles in RNA processing and cellular aging. Despite their significance, atomic-level folding mechanisms of rG4s remain poorly understood due to their complexity. We used enhanced-sampling all-atom molecular dynamics simulations to model the folding of an r(GGGA)3GGG sequence into a parallel-stranded rG4. The folding pathways suggest that RNA initially adopts a compact coil- like ensemble, marked by dynamic guanine stacking and pairing. The three-quartet rG4 builds up gradually from the coil via diverse routes involving strand rearrangements and guanine incorporations. While the folding mechanism is multi-pathway, various two-quartet rG4s seem to be a common transitory ensemble for most routes. Our simulations also exposed force-field imbalances, with the predicted folding free energy of +12.5 kcal/mol deviating from experiments. Additionally, the enhanced sampling protocol, combining well-tempered metadynamics with solute tempering, faced productivity challenges on the multidimensional free-energy surface. Overall, this study provides atomistic insights into rG4 folding, emphasizing compact coil-like ensembles as key precursors, while revealing limitations in simulating non-canonical RNA structures.