bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and cryoEM Structure Determination of Escherichia Phage YDC107 Tail Found in a Bacteria-Contaminated Buffer
Authors: Jenkins Matthew C. , Dutta Tahiti , Bobe Daija , Kopylov Mykhailo
Published: December 2024

Cryo-electron microscopy data analysis can yield multiple structures from a single heterogeneous dataset. Here, we show a workflow we used for the identification of a contaminant from a cryoEM grid without prior knowledge of protein sequence. We determined the tail structure of Escherichia phage YDC107 from only several thousand particles. The workflow combines high-resolution single-particle data processing withde novomodel determination using ML-based methods. Structural analysis revealed that the central part of the phage tail has a C6 symmetry, however the overall symmetry of each segment is C3 due to dimerization of a flexible domain.

Abstract Figure
Sequence motif dynamics in RNA pools
Authors: Harth-Kitzerow Johannes , Göppel Tobias , Burger Ludwig , Enßlin Torsten A. , Gerland Ulrich
Published: December 2024

In RNA world scenarios, pools of RNA oligomers form strongly interacting, dynamic systems, which enable molecular evolution. In such pools, RNA oligomers hybridize and dehybridize, ligate and break, ultimately generating longer RNA molecules, which may fold into catalytically active ribozymes. A key process for the elongation of RNA oligomers is templated ligation, which can occur when two RNA strands are adjacently hybridized onto a template strand. Detailed simulations of the dynamics in RNA pools involve a large variety of possible sequences and reactions. Here, we develop a reduced description of these complex dynamics within the space of sequence motifs. We then explore to what extent our reduced description can capture the behavior of detailed simulations that account for the full dynamics in the space of RNA strands. Towards this end, we project the dynamics into a motif space, which accounts only for the abundance of all possible four-nucleotide motifs. A system of ordinary differential equations describes the dynamics of those motifs. Its control parameters are effective rate constants for reactions in motif space, which we obtain from the rate constants for the processes underlying the full dynamics in the space of RNA strands. We find that these reduced motif space dynamics indeed capture important aspects of the informational dynamics of RNA pools in sequence space. This approach could also provide a framework to rationalize and interpret features of the sequence dynamics observed in experimental systems.
Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning
Authors: Wozniak Spencer , Janson Giacomo , Feig Michael
Published: December 2024

Machine learning has emerged as a promising approach for predicting molecular properties of proteins, as it addresses limitations of experimental and traditional computational methods. Here, we introduce GSnet, a graph neural network (GNN) trained to predict physicochemical and geometric properties including solvation free energies, diffusion constants, and hydrodynamic radii, based on three-dimensional protein structures. By leveraging transfer learning, pre-trained GSnet embeddings were adapted to predict solvent-accessible surface area (SASA) and residue-specific pKavalues, achieving high accuracy and generalizability. Notably, GSnet outperformed existing protein embeddings for SASA prediction, and a locally charge-aware variant, aLCnet, approached the accuracy of simulation-based and empirical methods for pKaprediction. Our GNN framework demonstrated robustness across diverse datasets, including intrinsically disordered peptides, and scalability for high-throughput applications. These results highlight the potential of GNN-based embeddings and transfer learning to advance protein structure analysis, providing a foundation for integrating predictive models into proteome-wide studies and structural biology pipelines.
Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum
Authors: Damiani Tito , Smith Joshua , Hebra Teo , Perkovic Milana , Cicak Marijo , Kadlecova Alzbeta , Rybka Vlastimil , Dracinsky Martin , Pluskal Tomas
Published: December 2024

Plant specialized metabolites play key roles in diverse physiological processes and ecological interactions. Identifying structurally novel metabolites, as well as discovering known compounds in new species, is often crucial for answering broader biological questions. The Piper genus (Piperaceae family) is known for its special phytochemistry and has been extensively studied over the past decades. Here, we investigated the alkaloid diversity of Piper fimbriulatum, a myrmecophytic plant native to Central America, using a metabolomics workflow that combines untargeted LC-MS/MS analysis with a range of recently-developed computational tools. Specifically, we leverage open MS/MS spectral libraries and metabolomics data repositories for metabolite annotation, guiding isolation efforts towards structurally-new compounds (i.e., dereplication). As a result, we identified several alkaloids belonging to 5 different classes and isolated one novel seco-benzylisoquinoline alkaloid featuring a linear quaternary amine moiety that we named fimbriulatumine. Notably, many of the identified compounds were never reported in Piperaceae plants. Our findings expand the known alkaloid diversity of this family, and demonstrate the value of revisiting well-studied plant families using state-of-the-art computational metabolomics workflows to uncover previously overlooked chemodiversity. To contextualize our findings into a broader biological context, we employed a workflow for automated mining of literature reports of the identified alkaloid scaffolds and mapped the results onto the angiosperm tree of life. By doing so, we highlight the remarkable alkaloid diversity within the Piper genus and provide a framework for generating hypotheses on the biosynthetic evolution of these specialized metabolites. Many of the computational tools and data resources used in this study remain underutilized within the plant science community. This manuscript demonstrates their potential through a practical application and aims to promote broader accessibility to untargeted metabolomics approaches.
Evolution ofSalmonellaChromosomes and Its Influence on Gene Expression and Chromosomal Conformation
Authors: Hu Yueming , Chen Zewei , Sokaribo Akosiererem S. , Zhao Ziyi , Cao Xin , Zhang Junya , Liu Shuhong , Chen Runhong , Deng Yuping , Bao Hongxia , Hui Xinjie , Sun Ming-an , Zhu Guo-Qiang , Liu Shu-Lin , White Aaron P. , Wang Yejun
Published: December 2024

Salmonellais one of the most important bacterial pathogens in the world, causing an estimated 120 million infections each year. There is considerable diversity, with ∼2,600 serovars, but it remains unclear how the genomes have evolved as the species and subspecies ofSalmonelladifferentiate. Here, we have reconstructed the ancient orthologous chromosomes of each majorSalmonellalineage and traced their evolutionary process. In total, 911 rearrangement events were identified, with 64% of events occurring in a locus-specific way. Using RNA sequencing and multi-strain association analysis, we demonstrate that genetic rearrangements have a significant effect on gene expression acrossSalmonellalineages. Moreover, we perform chromosome conformation capture (3C) sequencing analysis, which demonstrates large variations for the organization ofterchromosomal interaction domains amongSalmonellalineages. In conclusion, our work delineates the evolutionary trajectory ofSalmonellachromosomes, and demonstrates the influence of rearrangements on gene expression profiles and chromosomal conformation.

Importance

This study reconstructed the ancient orthologous chromosomes of theSalmonellagenus, species and well-recognized subspecies, by which the trajectory of gene flow caused by genetic rearrangements was delineated chronologically. The rearrangements show apparent ‘hotspot’ distribution property and are enriched with genes important for bacterial fitness. Correlation analysis further disclosed the general influence of the rearrangements on gene expression and the organization and conformation of chromosome interaction domains. The results provide new insights on the evolution ofSalmonellachromosomes, especially the genetic rearrangements and their epigenetic consequences.
Development of aDe NovoProtein Binder that Inhibits the Alpha Kinase eEF2K
Authors: Klupt Kody A. , Belrose Ethan , Jia Zongchao
Published: December 2024

Elongation factor 2 kinase (eEF2K) is calmodulin activated and phosphorylates eEF2, a GTPase, that regulates global translation. When eEF2K phosphorylates eEF2, protein translation is halted. This process may be critical to studying how diseases like cancer dysregulate protein synthesis. eEF2K is an alpha kinase and not targeted by conventional kinase inhibitors. Traditional methods of structure-based drug design are incredibly time consuming and expensive, which may involve screening large libraries of small molecules. We have generatedde novosmall binder proteins (∼10kDa) - using RFDiffusion and ProteinMPNN. One promisingde novobinder protein we produced, ‘CAM1’ binds to a hydrophobic patch on the calmodulin binding domain of eEF2K with nanomolar affinity as determined by isothermal titration calorimetry. This binder,in vitro, significantly reduces eEF2 peptide phosphorylation, comparable to the gold-standard small molecule eEF2K inhibitor, A-484954. The predicted structure of CAM1 is a helical bundle which has been confirmed by circular dichroism spectroscopy. Impressively, CAM1 has a melting temperature >800C, and is produced recombinantly in bacteria, greater than 5 mg / culture liter. We have also determined that CAM1 transfection significantly reduces mammalian HeLa cell proliferation comparable to A-484954 treatment and inhibits the phosphorylation of eEF2. Ourde novobinder, the first to our knowledge to inhibit an alpha kinase, and the first non-competitive eEF2K inhibitor, establishes an alternative method of targeting atypical kinase activity.
Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics
Authors: Angelo Murphy , Bhargava Yash , Kierzek Elzbieta , Kierzek Ryszard , Hayes Ryan , Zhang Wen , Vilseck Jonah Z , Aoki Scott Takeo
Published: December 2024

RNA-binding proteins shape biology through their widespread functions in RNA biochemistry. Their function requires the recognition of specific RNA motifs for targeted binding. These RNA binding elements can be composed of both unmodified and chemically modified RNAs, of which over 170 chemical modifications have been identified in biology. Unmodified RNA sequence preferences for RNA-binding proteins have been widely studied, with numerous methods available to identify their preferred sequence motifs. However, only a few techniques can detect preferred RNA modifications, and no current method can comprehensively screen the vast array of hundreds of natural RNA modifications. Prior work demonstrated that λ-dynamics is an accurate in silico method to predict RNA base binding preferences of an RNA-binding antibody. This work extends that effort by using λ-dynamics to predict unmodified and modified RNA binding preferences of human Pumilio, a prototypical RNA binding protein. A library of RNA modifications was screened at eight nucleotide positions along the RNA to identify modifications predicted to affect Pumilio binding. Computed binding affinities were compared with experimental data to reveal high predictive accuracy. In silico force field accuracies were also evaluated between CHARMM and Amber RNA force fields to determine the best parameter set to use in binding calculations. This work demonstrates that λ-dynamics can predict RNA interactions to a bona fide RNA-binding protein without the requirements of chemical reagents or new methods to experimentally test binding at the bench. Advancing in silico methods like λ-dynamics will unlock new frontiers in understanding how RNA modifications shape RNA biochemistry.
Key taxa of the gut microbiome associated with the relationship between environmental sensitivity and inflammation-related biomarkers
Authors: Takasugi Satoshi , Iimura Shuhei , Yasuda Miyabi , Saito Yoshie , Morifuji Masashi
Published: December 2024

Background

Individual differences in environmental sensitivity are linked to stress-related psychiatric symptoms. In previous research, we found that high environmental sensitivity can be a risk factor for increased inflammation and gut permeability, particularly when gut microbiome diversity is low. However, the specific gut bacterial taxa involved in this interaction remain unclear. This study aimed to identify the key gut microbiome taxa associated with this relationship.

Methods

Environmental sensitivity, gut microbiome composition, gut permeability (lipopolysaccharide-binding protein, LBP) and inflammation (C-reactive protein, CRP) biomarkers were evaluated in 88 participants.

Results

The interaction between environmental sensitivity and the relative abundance of the familyMarinifilaceae(genusButyricimonas) was a predictor of CRP levels. Similarly, the interaction between environmental sensitivity and relative abundance of the familyBarnesiellaceae(genusCoprobacter), the familyAkkermansiace(genusAkkermansia), the genusFamily XIII AD3011 group, the genusGCA-900066225, or the genusRuminiclostridium 1predicted LBP levels. Individuals with high environmental sensitivity exhibited elevated CRP or LBP levels when the relative abundance of these taxa was low. Conversely, highly sensitive individuals had lower CRP or LBP levels when the relative abundance of these taxa was high.

Conclusion

This study suggests that specific taxa serve as one of the protective factors against inflammation and gut permeability in individuals with high environmental sensitivity.
PathOmCLIP: Connecting tumor histology with spatial gene expression via locally enhanced contrastive learning of Pathology and Single-cell foundation model
Authors: Lee Yongju , Liu Xinhao , Hao Minsheng , Liu Tianyu , Regev Aviv
Published: December 2024

Tumor morphological features from histology images are a cornerstone of clinical pathology, diagnostic biomarkers, and basic cancer biology research. Spatial transcriptomics, which provides spatially resolved gene expression profiles overlaid on histology images, offers a unique opportunity to integrate morphological and expression features, thereby deepening our understanding of tumor biology. However, spatial transcriptomics experiments with patient samples in either clinical trials or clinical care are costly and challenging, whereas histology images are generated routinely and available for many legacy prospective cohorts of disease progression and outcomes in well-annotated cohorts. Inferring spatial transcriptomics profiles computationally from these histology images would significantly expand our understanding of tumor biology, but paired data for training multi-modal spatial-histology models remains limited. Here, we tackle this challenge by incorporating performant foundation models pre-trained on massive datasets of pathology images and single-cell RNA-Seq, respectively, which provide useful embeddings to underpin multi-modal models. To this end, we developed PathOmCLIP, a model trained with contrastive loss to create a joint-embedding space between a histopathology foundation model and a single-cell RNA-seq foundation model. We incorporate a set transformer to gather localized neighborhood tumor architecture following contrastive training, which further enhances performance and is necessary to obtain robust results. We validate PathOmCLIP across five tumor types and achieve significant performance improvements in gene expression prediction tasks over other methods. PathOmCLIP can be applied to many archived histology images, unlocking valuable clinical information and facilitating new biomarker discoveries.
The Influence of Rurality on Self-Reported Physical Therapy Utilization Among Patients with Severe Chronic Back Pain in the United States
Authors: McLaughlin Kevin H.
Published: December 2024

Purpose

To examine the association of rurality and physical therapy utilization among a nationally representative sample of individuals with severe chronic back pain.

Methods

This study utilized a publicly available dataset from the 2019 National Health Information Survey (Adult Sample). Individuals with severe chronic back pain were identified based on survey items examining respondents’ pain frequency and location. Physical therapy utilization was identified based on survey questions asking about pain management strategies utilized over the previous 3 months. Rurality was classified aslarge central metro, large fringe metro, medium and small metro, andnonmetropolitan/rural, based on county of residence. Regression was used to examine the association between rurality and physical therapy utilization, while controlling for relevant covariates. National estimates were calculated using provided weighting variables.

Results

We identified 2,925 individuals (weighted = 20,468,134) meeting the criteria for severe chronic back pain. We observed that individuals with severe chronic back pain living in nonmetropolitan/rural areas had 34% lower odds of (weighted OR: 0.66, 95% CI: 0.47, 0.92) utilizing physical therapy compared to individuals living in large central metropolitan areas. We did not observe significant differences in the odds of utilizing physical therapy among individuals living in large fringe metropolitan areas or medium-small metropolitan areas.

Conclusions

Individuals living in rural parts of the US have lower odds of using physical therapy for management of their severe chronic back pain. Additional research is needed to examine the factors that contribute to these differences and improve access to care.
A case-cluster of aseptic meningitis associated with a newly identified recombinant echovirus6/CoxsackievirusB1 enterovirus
Authors: Cherabuddi Kartikeya , Tagliamonte Massimiliano S. , Lednicky John A. , Ostrov David A. , Moquin Tracey L. , Thoomkuntla Vishal Kaushik , Bourgeois Brian , Iovine Nicole M. , Myers Paul D. , Salemi Marco , Morris J. Glenn
Published: December 2024

A daycare teacher presented to a local Emergency Department (ED) with complaints of headache, neck stiffness, and fever. Preliminary analysis of cerebral spinal fluid (CSF) raised concerns about meningococcal meningitis and prompted notification of the county health department, which then notified the daycare. Ten children presented to a University referral hospital for evaluation, four of whom were febrile. CSF from the teacher and nasal swabs from the febrile children were all RT-PCR positive for enterovirus. A novel recombinant enterovirus was cultured from the teacher’s CSF and from two of the nasal swabs. The amino-terminal portion of the recombinant virus was derived from an Echovirus E6 with the carboxy-terminal portion originating from a Coxsackievirus B1; recombinant segments were most closely related to similar segments from strains isolated in France. Recombination occurred within the C-2 gene which encodes a multifunctional protein that functions as an RNA-stimulated ATPase associated with virus replication and virion morphogenesis. Structural modeling predicted that the recombinant protein was capable of forming hexameric and heptameric assemblies. Our data highlight the ongoing potential for recombination among enteroviruses groups, leading to modifications within viral proteins which may impact virulence.

Brief Article Summary

After a daycare teacher was diagnosed with meningitis, ten children were referred by the county health department to a University Hospital for evaluation. Cerebral Spinal Fluid (CSF) from the teacher and nasal swabs from symptomatic children were positive for a novel recombinant enterovirus, with the amino-terminal portion of the virus derived from Echovirus E6 and the carboxy-terminal portion originating from a Coxsackievirus B1.
Machine Learning Analysis of PD-L1 and CD8 Expression Patterns in Penile Squamous Cell Carcinoma: Implications for Immunotherapy
Authors: Canete-Portillo Sofia , Taheri Diana , del Carmen Rodriguez-Peña María , Eich Marie-Lisa , Cocks Margaret , Cubilla Antonio L. , Netto George J. , Chaux Alcides
Published: December 2024

Introduction

In 2023, the US reported an estimated 2,050 new penile squamous cell carcinoma (SCC) cases, with mortality rates rising to 23%. Despite therapeutic advancements, the need to identify molecular and immunotherapeutic targets, especially PD-L1 and CD8, has become increasingly evident as immunotherapy emerges as a promising treatment strategy.

Methods

Tissue samples from 108 SCC patients were examined using four tissue microarrays (TMA). Alongside the assessment of histologic features and PD-L1 and CD8 expressions, a machine learning model was employed. This model, constructed in Python, leveraged various statistical tests and methodologies to discern the predictive relationships between PD-L1/CD8 expression and pathologic features, with potential implications for immunotherapy selection.

Results

Histologic subtype was predominant in PD-L1 expression in tumor cells, explaining 13.5% variability, whereas combined with host response, it reached 20%. For intratumoral lymphocytes, host response stood out, explaining 11.2% of PD-L1 and 15% of CD8 variability. In peritumoral lymphocytes, host response again dominated, accounting for 21.1% of CD8 variability. These findings align with recent studies showing the importance of immune markers in predicting treatment response and prognosis.

Conclusions

The study highlighted the crucial relationship between penile SCC’s pathologic features and PD-L1/CD8 expression, emphasizing their potential as both prognostic and predictive biomarkers. By integrating traditional histopathology with machine learning, we provide valuable insights for patient stratification and personalized immunotherapeutic strategies in penile SCC.
Depression is Associated with Treatment Response Trajectories in Adults with Prolonged Grief Disorder: A Machine Learning Analysis
Authors: Calderon Adam , Irwin Matthew , Simon Naomi M. , Katherine Shear M. , Mauro Christine , Zisook Sidney , Reynolds Charles F. , Malgaroli Matteo
Published: December 2024

Although evidence-based treatments for Prolonged Grief Disorder (PGD) exist, pretreatment characteristics associated with differential improvement trajectories have not been identified. To identify clinical factors relevant to optimizing PGD treatment outcomes, we used unsupervised and supervised machine learning to study treatment effects from a double-blinded, placebo-controlled, randomized clinical trial. Participants were randomized into four treatment groups for 20 weeks: citalopram with grief-informed clinical management, citalopram with prolonged grief disorder therapy (PGDT), pill placebo with PGDT, or pill placebo with clinical management. The trial included 333 PGD patients aged 18–95 years (Mage= 53.9;SD± 14.4), predominantly female (77.4%) and white (84.4%). Symptom trajectories were assessed using latent growth mixture modeling based on Inventory for Complicated Grief scores collected at six time points every 4 weeks. The relationship between patient-level characteristics and assigned trajectories was examined using logistic regression with elastic net regularization based on the administration of citalopram, PGDT, and risk factors for developing PGD. Three distinct response trajectories were identified: lesser severity responders (60%, n = 200), greater severity responders (18.02%, n = 60), and non-responders (21.92%, n = 73). Differences between greater severity responders and non-responders emerged as statistically significant by Week 8. The elastic net model demonstrated acceptable discrimination between responders and non-responders (AUC = .702; accuracy = .684). Higher baseline depression severity, grief-related functional impairment, and absence of PGDT were associated with reduced treatment response likelihood. These findings underscore the importance of early identification of clinical factors to optimize individualized PGD treatment strategies.

Trial Registration:clinicaltrials.govIdentifier:NCT01179568.
Severe outcomes and length of stay among people with schizophrenia hospitalized for COVID-19: A population-based retrospective cohort study
Authors: Gronsbell Jessica , Wang John , Thurston Hilary , Gao Jianhui , Shi Yaqi , Train Anthony D. , Butt Debra , Gershon Andrea , O’Neill Braden , Tu Karen
Published: December 2024

Background and Hypothesis

Schizophrenia is associated with substantial physical and psychiatric comorbidities that increase the risk of severe outcomes in COVID-19 infection. However, few studies have examined the differences in care and outcomes among people with schizophrenia throughout the pandemic. We hypothesized that rates of in-hospital mortality, admission to the intensive care unit (ICU), and length of stay differed among people with and without schizophrenia.

Study Design

We conducted a population-based retrospective cohort study using administrative health data from Ontario, Canada that included individuals hospitalized for COVID-19 between February 2020 and October 2023. We compared mortality, ICU admission, and length of stay using regression models adjusted for age, sex, comorbidities, vaccination status, and sociodemographic characteristics.

Study Results

We evaluated 66,959 hospital admissions, 4.3% (2,884) of which involved people with schizophrenia. People with schizophrenia had a significantly decreased rate of ICU admission (adjusted OR: 0.74, [0.67, 0.82]), a longer length of stay (adjusted RR: 1.25, [1.21, 1.30]), but a similar risk of mortality (adjusted OR: 1.09, [0.98, 1.22]) as people without schizophrenia. Age modified the relationship between schizophrenia and ICU admission. People with schizophrenia aged 60-75 were substantially less likely to be admitted to the ICU relative to those without (18.4% vs. 26.5%, p < .001).

Conclusions

Our findings underscore disparities in care among people with and without schizophrenia. These disparities vary by age and suggest that people with schizophrenia may not be receiving the same level of care as people without schizophrenia hospitalized for COVID-19.
Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in MLL leukaemia
Authors: Gordon Shellaina J. V. , Perner Florian , MacPherson Laura , Wenge Daniela V. , Bourgeois Wallace , Fennell Katie , Klaus Tabea , Petrovic Jelena , Horvath Jakub , Cao Joan , Lapek John , Uryu Sean , White Jeffrey , Lam Enid Y. N. , Mu Xinmeng Jasmine , Chan Yih-Chih , Gillespie Andrea , Blyth Benjamin , Camerino Michelle A. , Bozikis Ylyva E. , Holze Henrietta , Knezevic Kathy , Balic Jesse , Stupple Paul A. , Street Ian P. , Monahan Brendon J. , Sharma Shikhar , Wainwright Elanor N. , Vassiliadis Dane , Paul Thomas A. , Armstrong Scott A. , Dawson Mark A.
Published: December 2024

Understanding the molecular pathogenesis of MLL fusion oncoprotein (MLL-FP) leukaemia has spawned epigenetic therapies that have improved clinical outcomes in this often-incurable disease. Using genetic and pharmacological approaches, we define the individual and combined contribution of KAT6A, KAT6B and KAT7, in MLL-FP leukaemia. Whilst inhibition of KAT6A/B is efficacious in some pre-clinical models, simultaneous targeting of KAT7, with the novel inhibitor PF-9363, increases the therapeutic efficacy. KAT7 interacts with Menin and the MLL complex and is co-localised at chromatin to co-regulate the MLL-FP transcriptional program. Inhibition of KAT6/KAT7 provides an orthogonal route to targeting Menin to disable the transcriptional activity of MLL-FP. Consequently, combined inhibition rapidly evicts the MLL-FP from chromatin, potently represses oncogenic transcription and overcomes primary resistance to Menin inhibitors. Moreover, PF-9363 or genetic depletion of KAT7 can also overcome acquired genetic/non-genetic resistance to Menin inhibition. These data provide the molecular rationale for rapid clinical translation of combination therapy in MLL-FP leukaemia.
The Swiss Army Knife of Alginate Manipulation – A Gut Bacterium Alginate Lyase with Diverse Catalytic Activities
Authors: Tandrup Tobias , Rivas-Fernández José Pablo , Madsen Mikkel , Rønne Mette E. , Petersen Agnes B. , Klau Leesa J. , Tøndervik Anne , Wilkens Casper , Aachmann Finn L. , Rovira Carme , Svensson Birte
Published: December 2024

The alginate-degrading enzymeBoPL38 of the human gut bacteriumBacteroides ovatusCP926 degrades the three polysaccharide structures found in alginate, a major constituent of brown macroalgae with numerous industrial applications. However, the detailed mechanisms of alginate-degrading enzymes remain unclear. Crystal structures ofBoPL38 complexes with alginate oligosaccharides, now shed light on the enzyme’s catalytic machinery. QM/MM simulations reveal distinct conformational and reaction pathways, highlighting different transition states for mannuronate and guluronate conversion. C5 proton abstraction at subsite +1 by Y298 and H243 facilitatessyn-andanti-β-elimination reactions, respectively. Substrate recognition relies on R292 distorting the sugar at subsite +1 into a preactivated conformation, while stabilizing the active site tunnel through a salt bridge. Furthermore, NMR spectroscopy found thatBoPL38 also catalyze mannuronate to guluronate epimerization in addition to its lyase function, thereby paving the way for future enzymatic alginate modification.
Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA
Authors: Cornwell-Arquitt Robert L. , Nigh Riley , Hathaway Michael T. , Yesselman Joseph D. , Hendrix David A.
Published: December 2024

RNA molecules adopt complex structures that perform essential biological functions across all forms of life, making them promising candidates for therapeutic applications. However, our ability to design new RNA structures remains limited by an incomplete understanding of their folding principles. While global metrics such as the minimum free energy are widely used, they are at odds with naturally occurring structures and incompatible with established design rules. Here, we introduce local stability compensation (LSC), a principle that RNA folding is governed by the local balance between destabilizing loops and their stabilizing adjacent stems, challenging the focus on global energetic optimization. Analysis of over 100, 000 RNA structures revealed that LSC signatures are particularly pronounced in bulges and their adjacent stems, with distinct patterns across different RNA families that align with their biological functions. To validate LSC experimentally, we systematically analyzed thousands of RNA variants using DMS chemical mapping. Our results demonstrate that stem reactivity correlates strongly with LSC (R² = 0.458 for hairpin loops) and that structural perturbations affect folding primarily within ∼6 nucleotides from the loop. These findings establish LSC as a fundamental principle that could enhance the rational design of functional RNAs.

Graphical Abstract
Knockdown-resistance (kdr) mutations in IndianAedes aegyptipopulations: lack of recombination among haplotypes bearing V1016G, F1534C, and F1534Lkdralleles
Authors: Kaur Taranjeet , Kushwah Rajababu S. , Pradhan Sabyasachi , Das Manoj K. , Kona Madhavinadha P , Anushrita  , Weetman David , Dixit Rajnikant , Singh Om P.
Published: December 2024

Background

Knockdown resistance (kdr) mutations in the voltage-gated sodium channel (VGSC) gene are a key mechanism of insecticide resistance in mosquitoes. In AsianAedes aegyptipopulations two main VGSC haplogroups withkdrmutations have been identified: one carrying the F1534C mutation and another with V1016G and/or S989P mutations. Functional studies have demonstrated that these three mutations on a single haplotype confer up to a 1100-fold increase in pyrethroid resistance, underscoring the need to monitor these triple mutations within distinct populations. This study investigates the prevalence ofkdrmutations in Indian populations and explores the linkage association between these mutations and two distinct conserved types of introns located between exons 20 and 21.

Methods

Ae. aegyptispecimens collected from eight different locations were genotyped forkdralleles and intron (between exons 20 and 21) haplotypes using PCR-based assays. Representative samples underwent DNA sequencing of VGSC regions.

Results

Fivekdrmutations namely S989P, V1016G, T1520I, F1534C, and F1534L, were identified, each exhibiting varying distribution and frequencies across different geographical regions. Two distinct and stably-diverged intron haplotypes, designated as intron-A and intron-B, were identified between exons 20 and 21. Seven haplotypes, including two wild-type variants, were observed among Indian populations. Thekdr-bearing haplotypes can be classified into three distinct haplogroups: haplogroup G (V1016G with/or without S989P and with intron-A), haplogroup L (F1534L and intron-A), and haplogroup C (F1534C with/or without T1520I and with intron-B). Importantly, no evidence of recombination within Indian populations was detected among these three haplogroups.

Conclusions

Fivekdrmutations were identified in the VGSC of IndianAe. aegyptipopulations, each showing a definitive linkage with one of the two types of intron haplotypes. The lack of recombination among haplogroups bearing 1016G with 989P, 1534C and 1534L mutations suggests that the most potent insecticide resistance haplotype, bearing the triplekdrmutation, is currently absent. This finding has significant operational implications, as it may indicate that current vector control measures remain effective against these populations, potentially delaying the emergence of highly resistant phenotypes
Cell types associated with human brain functional connectomes and their implications in psychiatric diseases
Authors: Nie Pengxing , Zhan Yafeng , Chen Renrui , Qi Ruicheng , Liu Cirong , Wang Guang-Zhong
Published: December 2024

Cell types are fundamental to the functional organization of the human brain, yet the specific cell clusters contributing to functional connectomes remain unclear. Using human whole-brain single-cell RNA sequencing data, we investigated the relationship between cortical cell cluster distribution and functional connectomes. Our analysis identified dozens of cell clusters significantly associated with resting-state network connectivity, with excitatory neurons predominantly driving positive correlations and inhibitory neurons driving negative correlations. Many of these cell clusters are also conserved in macaques. Notably, functional network connectivity is predicted by cellular communication among these clusters. We further identified cell clusters linked to various neuropsychiatric disorders, with several clusters implicated in multiple conditions. Comparative analysis of schizophrenia and autism spectrum disorder revealed distinct expression patterns, highlighting disease-specific cellular mechanisms. These findings underscore the critical role of specific cell clusters in shaping functional connectomes and their implications for neuropsychiatric diseases.
Did Energy Costs of Walking Limit the Evolution of a Larger Human Birth Canal?
Authors: Stansfield Ekaterina , Egner Clara , Mitteroecker Philipp , Kainz Hans
Published: December 2024

Energetic disadvantages of a wider pelvis have long been central to explanations of the small human birth canal and the relatively risky birth process, iconic for antagonistic selection in evolution. While static mechanics predict such effects, recent empirical studies question this view. By altering a generic musculoskeletal model beyond modern human variation one parameter at a time and applying predictive forward modelling of human gait, we examined how body dimensions impact locomotion efficiency and inferred selective pressures on past morphologies. Our findings confirm that a wider pelvis increases abductor muscle demands, as lever mechanics suggest. However, dynamic walking compensates via other muscles, minimizing the total transport cost. Moreover, slightly longer legs easily offset the modest energetic costs of a larger birth canal. We propose that other factors, such as pelvic floor stability, likely constrained the evolution of the human birth canal, rather than energetic disadvantages alone.
FAK modulates glioblastoma stem cell energetics via regulation of glycolysis and glutamine oxidation
Authors: Masalmeh Roza H. A. , Dawson John C. , Garcia Virginia Alvarez , Muir Morwenna T. , Carter Roderick N. , Hardingham Giles , Davies Cameron , Graham Rosina , von Kriegsheim Alex , Marques Junior Jair , Pednekar Chinmayi , Pollard Steven M. , Carragher Neil O. , Brunton Valerie G. , Frame Margaret C.
Published: December 2024

Glycolysis and the TCA cycle are reprogrammed in cancer cells to meet bioenergetic and biosynthetic demands, including by engagement with the extracellular matrix (ECM). We show that focal adhesion kinase (FAK), a mediator of integrin-ECM signalling, is driving cellular energetics in a stem cell model of glioblastoma (GBM). FAK gene deletion inhibits both glycolysis and glutamine oxidation, with increased mitochondrial fragmentation and elevated phosphorylation of the mitochondrial protein MTFR1L at S235. Simultaneously, FAK loss causes a mesenchymal to epithelial transition, enhanced acto-myosin contractility as shown by phospho-myosin light chain (p-MLC S19) and impaired cell migration/invasiveness. Rho-kinase (ROCK) inhibitors suppress p-MLC (S19) and restore glutamine oxidation and elongation of mitochondria. Thus, FAK is a key regulator of both glycolysis and glutamine oxidation mediated by acto-myosin contractility that controls both cell and mitochondrial morphology. Moreover, FAK-dependent cellular energetics are coincident properties with GBM stem cell migration, invasiveness and tumour growth in vivo.
Rapid Surge of Reassortant A(H1N1) Influenza Viruses in Danish Swine and their Zoonotic Potential
Authors: Ryt-Hansen Pia , George Sophie , Hjulsager Charlotte Kristiane , Trebbien Ramona , Krog Jesper Schak , Ciucani Marta Maria , Langerhuus Sine Nygaard , DeBeauchamp Jennifer , Crumpton Jeri Carol , Hibler Taylor , Webby Richard J. , Larsen Lars Erik
Published: December 2024

In 2018, a single detection of a novel reassortant swine influenza A virus (swIAV) was made in Denmark. The hemagglutinin (HA) of the virus was from the H1N1 pandemic 2009 (H1N1pdm09) lineage and the neuraminidase (NA) from the H1N1 Eurasian avian-like swine lineage (H1N1av). By 2022, the novel reassortant virus (H1pdm09N1av) constituted 27 % of swIAVs identified through the Danish passive swIAV surveillance program. Sequencing detected two H1pdm09N1av genotypes; Genotype 1 contained an internal gene cassette of H1N1pdm09 origin, Genotype 2 differed by carrying an NS gene segment of H1N1av origin. The internal gene cassette of Genotype 2 became increasingly dominant, not only in the H1pdm09N1av population, but also in other Danish enzootic swIAV subtypes. Phylogenetic analysis of the HA genes from H1pdm09N1av viruses revealed a monophyletic source, a higher substitution rate compared to other H1N1pdm09 viruses and genetic differences with human seasonal and other swine adapted H1N1pdm09 viruses. Correspondingly, H1pdm09N1av viruses were antigenically distinct from human H1N1pdm09 vaccine viruses. Both H1pdm09N1av genotypes transmitted between ferrets by direct contact, but only Genotype 1 was capable of efficient aerosol transmission. The rapid spread of H1pdm09N1av viruses in Danish swine herds is concerning for swine and human health. Their zoonotic threat is highlighted by the limited pre-existing immunity observed in the human population, aerosol transmission in ferrets and the finding that the internal gene cassette of Genotype 2 was present in the first two zoonotic infections ever detected in Denmark.
Calmodulin binding is required for calcium mediated TRPA1 desensitization
Authors: Sanders Justin H. , Taiwo Kehinde M. , Adekanye Glory A. , Bali Avnika , Zhang Yuekang , Paulsen Candice E.
Published: December 2024

Calcium (Ca2+) ions affect nearly all aspects of biology. Excessive Ca2+entry is cytotoxic and Ca2+- mobilizing receptors have evolved diverse mechanisms for tight regulation that often include Calmodulin (CaM). TRPA1, an essential Ca2+-permeable ion channel involved in pain signaling and inflammation, exhibits complex Ca2+regulation with initial channel potentiation followed by rapid desensitization. The molecular mechanisms of TRPA1 Ca2+regulation and whether CaM plays a role remain elusive. We find that TRPA1 binds CaM best at basal Ca2+concentration, that they co-localize in resting cells, and that CaM suppresses TRPA1 activity. Combining biochemical, biophysical, modeling, NMR spectroscopy, and functional approaches, we identify an evolutionarily conserved, high-affinity CaM binding element in the distal TRPA1 C-terminus (DCTCaMBE). Genetic or biochemical perturbation of Ca2+/CaM binding to the TRPA1 DCTCaMBE yields hyperactive channels that exhibit drastic slowing of desensitization with no effect on potentiation. Ca2+/CaM TRPA1 regulation does not require the N-lobe, raising the possibility that CaM is not the Ca2+sensor,per se. Higher extracellular Ca2+can partially rescue slowed desensitization suggesting Ca2+/CaM binding to the TRPA1 DCTCaMBE primes an intrinsic TRPA1 Ca2+binding site that, upon binding Ca2+, triggers rapid desensitization. Collectively, our results identify a critical regulatory element in an unstructured TRPA1 region highlighting the importance of these domains, they reveal Ca2+/CaM is an essential TRPA1 auxiliary subunit required for rapid desensitization that establishes proper channel function with implications for all future TRPA1 work, and they uncover a mechanism for receptor regulation by Ca2+/CaM that expands the scope of CaM biology.
Effects of prey abundance and foliage structure in plant selection by insectivorous birds in the central Monte desert
Authors: Guerra-Navarro Carolina , Cueto Victor R.
Published: December 2024

Foraging behavior allows a direct examination of how birds use their habitats and provides the possibility to understand what environment factors can determine those patterns. We analyzed the woody plant selection, height and substrate use, and attack maneuver by Greater Wagtail-tyrant (Stigmatura budytoides), Grey-crowned Tyrannulet (Serpophaga griseicapilla) and Ringed Warbling-Finch (Microspingus torquata) in the main habitats of central Monte desert. The three bird species selectedProsopis flexuosatrees and avoided the most abundant shrub species:Larrea divaricataandLarrea cuneifoliain mesquite woodland and creosotebush habitats. The importance ofP. flexuosawas due because this plant constitute an abundant food patch of great diversity of arthropods. Our results about how bird species use their habitat and which factors were influencing these selection pattern are important to management and conservation of insectivorous birds in the central Monte desert.
Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines
Authors: Bangaru Sandhya , Jackson Abigail M. , Copps Jeffrey , Fernández-Quintero Monica L. , Torres Jonathan L. , Richey Sara T. , Nogal Bartek , Sewall Leigh M. , Torrents de la Peña Alba , Rehman Asma , Guebre-Xabier Mimi , Girard Bethany , Das Rituparna , Corbett-Helaire Kizzmekia S. , Seder Robert A. , Graham Barney S. , Edwards Darin K. , Patel Nita , Smith Gale , Ward Andrew B.
Published: December 2024

Current COVID-19 vaccines are largely limited in their ability to induce broad, durable immunity against emerging viral variants. Design and development of improved vaccines utilizing existing platforms requires an in-depth understanding of the antigenic and immunogenic properties of available vaccines. Here we examined the antigenicity of two of the original COVID-19 vaccines, mRNA-1273 and NVX-CoV2373, by electron microscopy-based polyclonal epitope mapping (EMPEM) of serum from immunized non-human primates (NHPs) and clinical trial donors. Both vaccines induce diverse polyclonal antibody (pAb) responses to the N-terminal domain (NTD) in addition to the receptor-binding domain (RBD) of the Spike protein, with the NTD supersite being an immunodominant epitope. High-resolution cryo-EMPEM studies revealed extensive pAb responses to and around the supersite with unique angles of approach and engagement. NTD supersite pAbs were also the most susceptible to variant mutations compared to other specificities, indicating that ongoing Spike ectodomain-based vaccine design strategies should consider immuno-masking this site to prevent induction of these strain-specific responses.
Regulatory interactions between APOBEC3B N- and C-terminal domains
Authors: Braza Mac Kevin E. , Demir Özlem , Ahn Surl-Hee , Morris Clare K. , Calvó-Tusell Carla , McGuire Kelly L. , de la Peña Avalos Bárbara , Carpenter Michael A. , Chen Yanjun , Casalino Lorenzo , Aihara Hideki , Herzik Mark A. , Harris Reuben S. , Amaro Rommie E.
Published: December 2024

APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) active site is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared dynamics of the truncated (A3Bctd) to the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD-CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics of fl-A3B, which may offer new avenues for therapeutic intervention in cancer.