bluuebunny/crossref_metadata_2025 huggingface dataset:
GPU-accelerated homology search with MMseqs2
Authors: Kallenborn Felix , Chacon Alejandro , Hundt Christian , Sirelkhatim Hassan , Didi Kieran , Cha Sooyoung , Dallago Christian , Mirdita Milot , Schmidt Bertil , Steinegger Martin
Published: November 2024

Sensitive search of rapidly growing protein sequence databases for evolutionary information requires continual acceleration. This is achieved by innovating algorithms to filter sequences, or perform alignments. Here, we present GPU-optimized algorithms for gapless filtering, achieving up to 100 TCUPS across eight GPUs, and gapped alignment using protein profiles. Implemented in MMseqs2-GPU, they result in 20× faster and 71× cheaper search on a NVIDIA L40S GPU compared to MMseqs2k-mer on a 128-core CPU. In ColabFold, they accelerate structure prediction 23× at matching accuracy to AlphaFold2. MMseqs2-GPU is open-source software available for CUDA devices atmmseqs.com.
Meta-omic insights into active bacteria mediating N2O mitigation and dissimilatory nitrate reduction to ammonium in an ammonia recovery bioreactor
Authors: Phan Hop V. , Yasuda Shohei , Oba Kohei , Tsukamoto Hiroki , Hori Tomoyuki , Kuroiwa Megumi , Terada Akihiko
Published: November 2024

Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge (MAS) system for retaining ammonia while removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the MAS system is essential to optimize system performance. Here, we employed metagenomics and metatranscriptomics analyses to characterize the microbial community structure and activity during the transition from a microaerophilic to an aerobic condition. A hybrid approach of high-quality Illumina short reads and Nanopore long reads recovered medium-to high-quality 98 non-redundant metagenome-assembled genomes (MAGs) from the MAS communities. The suppressed bacterial ammonia monooxygenase (amoA) expression was upregulated after shifting from a microaerophilic to an aerobic condition. The 73 MAGs (>74% of the total) from 11 bacterial phyla harbored genes encoding proteins involved in nitrate respiration; 39 MAGs (∼53%) carried N2O reductase (nosZ) genes with the predominance of clade IInosZ(31 MAGs), and 24 MAGs (∼33%) possessed nitrite reductase (ammonia forming) genes (nrfA). Clade IInosZandnrfAgenes exhibited the highest and second-highest expressions among nitrogen metabolism genes, indicating robust N2O consumption and ammonification. Non-denitrifying clade IInosZbacteria,Cloacibacteriumspp., in the most abundant and active phylum Bacteroioda, were likely major N2O sinks. Elevated dissolved oxygen (DO) concentration inhibited clade IInosZexpression but notnrfAexpression, potentially switching phenotypes from N2O reduction to ammonification. Collectively, the multi-omics analysis illuminated vital bacteria responsible for N2O reduction and ammonification in microaerophilic and aerobic conditions, facilitating high-performance ammonia recovery.
In vitroFLASH irradiation of A549 lung cancer cells and IMR90 healthy human fibroblasts in the synchrocyclotron room of a clinical proton therapy system
Authors: Zazpe Adrián , del Monte-García Inés , Palao Nerea , Cerrón Fernando , Cueto-Remacha Mateo , Linzoain-Agos Paula , Iniesta-González Minerva , Quartieri Martina , Cuesta Ángel M. , España Samuel , Velasco Guillermo , Vera-Sánchez Juan Antonio , Fraile Luis Mario , Mazal Alejandro , Udías José Manuel , Porras Almudena , Bragado Paloma , Gutierrez-Uzquiza Álvaro , Sánchez-Parcerisa Daniel
Published: November 2024

Purpose

This study aims to investigate the FLASH irradiation effect on lung tumor (A549) and healthy fibroblast (IMR90) cell lines using an irradiation station installed at the synchrocyclotron room of a clinical proton facility without any permanent beamline modifications.

Methods and Materials

An irradiation system composed of a lead scatterer and 3D-printed positioning system was designed and fabricated to operate within the beamline gap of the IBA Proteus One proton therapy facility after the extraction of the beam from the synchrocyclotron. A dosimetric analysis of the produced irradiation field was carried out using radiochromic films. FLASH and conventional-rate irradiations were conducted on relevant cell lines for lung cancer at the isocenter of the treatment room. Biological assessments post-irradiation included clonogenic and viability assays for cell survival, immunofluorescence analysis of p21 protein expression, and flow cytometry analysis for cell cycle arrest evaluation.

Results

The irradiation system successfully delivered homogeneous and repeatable FLASH dose rates (>900 Gy/s) with a positioning accuracy of 1 mm and dose uniformity within 10%. Clonogenic assays revealed no statistically significant differences in survival between FLASH and conventional dose rates for both A549 and IMR90 cell lines, although a trend towards higher viability was observed in IMR90 cells under FLASH conditions. Flow cytometry demonstrated significant differences in cell cycle arrest patterns at doses above 7 Gy, with FLASH-irradiated cells exhibiting a decrease in G2/M phase arrest compared to conventional rates. Immunofluorescence analysis of p21 expression showed no significant differences between irradiation modalities.

Conclusions

The developed irradiation station effectively facilitates FLASH radiotherapy experiments in a clinical proton facility, achieving the necessary dose rates without hardware modification or extra tuning of the facility. Our analysis reported notable alterations in cell cycle dynamics suggesting distinct biological responses between FLASH and conventional rates in both healthy and tumor cells. These findings contribute to the emerging understanding of the FLASH effect and support the potential for its differential impact on cancerous versus healthy tissues.
Fast-Part: Fast and Accurate Data Partitioning for Biological Sequence Analysis
Authors: Ahmed Shafayat , Emon Muhit Islam , Moumi Nazifa Ahmed , Zhang Liqing
Published: November 2024

Developing effective machine learning models for classifications of biological sequences depends heavily on the quality of the training and test datasets split. Existing tools are either computationally expensive, unable to maintain the desired level of similarity between the training and test datasets, or unable to retain training: test ratio stratification. Here, we present Fast-Part, a fast and accurate sequence data partitioning tool that ensures strict homology separation between the training and test datasets and the best possible training: test stratification ratio, and at the same time is computationally fast. Evaluation of Fast-Part on multiple protein sequence datasets shows that it performs data partitioning with exceptional speed and maintains strict partitioning compared to the existing tools. Fast-Part can handle massive datasets like CD-HIT[1] and MMseq[2] and maintain strict homology partitioning like GraphPart[3].
Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer
Authors: Ireland Abbie S. , Hawgood Sarah B. , Xie Daniel A. , Barbier Margaret W. , Lucas-Randolph Scarlett , Tyson Darren R. , Zuo Lisa Y. , Witt Benjamin L. , Govindan Ramaswamy , Dowlati Afshin , Moser Justin C. , Puri Sonam , Rudin Charles M. , Chan Joseph M. , Elliott Andrew , Oliver Trudy G.
Published: November 2024

Summary paragraph

Neuroendocrine and tuft cells are rare, chemosensory epithelial lineages defined by expression of ASCL1 and POU2F3 transcription factors, respectively1,2. Neuroendocrine cancers, including small cell lung cancer (SCLC), frequently display tuft-like subsets, a feature linked to poor patient outcomes3–13. The mechanisms driving neuroendocrine–tuft tumour heterogeneity, and the origins of tuft-like cancers are unknown. Using multiple genetically-engineered animal models of SCLC, we demonstrate that a basal cell of origin (but not the accepted neuroendocrine origin) generates neuroendocrine–tuft-like tumours that highly recapitulate human SCLC. Single-cell clonal analyses of basal-derived SCLC further uncovers unexpected transcriptional states and lineage trajectories underlying neuroendocrine–tuft plasticity. Uniquely in basal cells, introduction of genetic alterations enriched in human tuft-like SCLC, including high MYC, PTEN loss, and ASCL1 suppression, cooperate to promote tuft-like tumours. Transcriptomics of 944 human SCLCs reveal a basal-like subset and a tuft-ionocyte-like state that altogether demonstrate remarkable conservation between cancer states and normal basal cell injury response mechanisms14–18. Together, these data suggest that the basal cell is a plausible origin for SCLC and other neuroendocrine-tuft cancers that can explain neuroendocrine–tuft heterogeneity—offering new insights for targeting lineage plasticity.
HIGH PRECISION CHARACTERIZATION OF RCCX REARRANGEMENTS IN A 21-HYDROXYLASE DEFICIENCY LATIN AMERICAN COHORT USING OXFORD NANOPORE LONG READ SEQUENCING
Authors: Claps Aldana , Kolomenski Jorge E. , Fernandez Franco , Macchiaroli Natalia , Ingravidi Marina L. , Delea Marisol , Fernandez Cecilia , Castro Tania , Laiseca Julieta , Kamenetzky Laura , Taboas Melisa I. , Dain Liliana B.
Published: November 2024

The gene CYP21A2, mapped to the RCCX module in 6p21.3, is responsible for the 21-hydroxylase deficiency (21OHD). In this work, we used Oxford Nanopore Technology (ONT) Long Reads (LR) sequencing to analyze samples from a large Argentinian cohort of 21OHD. Our goal was to gain additional information about the GVs involved in the rearrangements, to obtain higher resolution for the breakpoints of converted alleles and to retrieve new data of TNX and CYP21A1P genes. A total of 34 samples were sequenced in 2 amplicons of 8.5 Kb covering the centromeric and telomeric RCCX modules. The number of GVs found varied between 17-106 and all expected pathogenic GVs and new ones were obtained with the LR sequencing workflow developed. From the 21 alleles with macroconverted or chimeric genes containing the promoter of the CYP21A1P, we uncovered 5 of them lacking GVs commonly expected to be involved in 21OHD rearrangements. Importantly, we reclassified one patient with a deletion that had been overlooked with the current diagnostic technologies applied. These new findings change the genetic counseling for the patient and his family related to the presence of a carrier allele for Congenital Adrenal Hyperplasia and Ehlers-Danlos Syndrome (CAH-X). Furthermore, by addressing the study of the centromeric and the telomeric RCCX modules, we found 19 GVs for CYP21A1P and 29 GVs for TNXA not previously described in Latin American populations or not reported in any of the consulted databases. This study may represent the first one applying ONT LR in clinical studies in Latin America, highlighting the importance of LR sequencing as a high-resolution method of diagnosis and better cost-effective balance. It allows us to better understand the diversity of the RCCX modules and to gain knowledge of the molecular pathogenesis of the disease.
Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets ofcis-regulation
Authors: Thakur Rohit , Xu Mai , Sowards Hayley , Yon Joshuah , Jessop Lea , Myers Timothy , Zhang Tongwu , Chari Raj , Long Erping , Rehling Thomas , Hennessey Rebecca , Funderburk Karen , Yin Jinhu , Machiela Mitchell J. , Johnson Matthew E. , Wells Andrew D. , Chesi Alessandra , Grant Struan F.A. , Iles Mark M. , Landi Maria Teresa , Law Matthew H. ,   Melanoma Meta-Analysis Consortium, Choi Jiyeon , Brown Kevin M.
Published: November 2024

Genome-wide association studies (GWAS) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be established. Capture-HiC is an assay that links fine-mapped risk variants to candidate target genes by comprehensively mapping cell-type specific chromatin interactions. We performed a melanoma GWAS region-focused capture-HiC assay in human primary melanocytes to identify physical interactions between fine-mapped risk variants and potential causal melanoma susceptibility genes. Overall, chromatin interaction data alone nominated potential causal genes for 61 of the 68 melanoma risk signals, identifying many candidates beyond those reported by previous studies. We further integrated these data with cell-type specific epigenomic (chromatin state, accessibility), gene expression (eQTL/TWAS), DNA methylation (meQTL/MWAS), and massively parallel reporter assay (MPRA) data to prioritize potentiallycis-regulatory variants and their respective candidate gene targets. From the set of fine-mapped variants across these loci, we identified 140 prioritized candidate causal variants linked to 195 candidate genes at 42 risk signals. In addition, we developed an integrative scoring system to facilitate candidate gene prioritization, integrating melanocyte and melanoma datasets. Notably, at several GWAS risk signals we observed long-range chromatin connections (500 kb to >1 Mb) with distant candidate target genes. We validated several suchcis-regulatory interactions using CRISPR inhibition, providing evidence for known cancer driver genesMDM4andCBL, as well as the SRY-box transcription factorSOX4, as likely melanoma risk genes.
Comorbidities associated with chronic kidney disease among young people living with HIV in Uganda. A nested case control study
Authors: Nasuuna Esther M , Tomlinson Laurie A , Kalyesubula Robert , Castelnuovo Barbara , Nanyeenya Nicholus , Dziva Chikwari Chido , Weiss Helen A
Published: November 2024

Introduction

Chronic kidney disease (CKD) is often complicated by disorders in multiple body systems, associated with higher mortality and morbidity. Young people living with HIV (YPLHIV) have an increased risk of multisystem chronic comorbidities. However, there are few data describing comorbidities associated with CKD among YPLHIV.

Methods

We conducted a case-control study in seven ART clinics in Kampala, Uganda. Cases were YPLHIV (aged 10-24 years) diagnosed with CKD and controls were those without CKD. We collected data on demographic and clinical factors: blood pressure, fasting glucose levels, anaemia, electrolytes, parathyroid hormone, and cognitive impairment. We summarized the demographic and clinical factors and used logistic regression to estimate odds ratios (OR) and 95% confidence intervals for associations between CKD comorbidities, adjusted for age, sex and viral suppression.

Results

A total of 292 participants (96 cases and 196 controls) were recruited. Cases were mostly male (59.4% vs 36.5%), and younger (88.5% vs 46.4% aged <17 years) compared to controls. CKD was associated with having a detectable HIV viral load (OR=3.73; 95% CI 1.53-9.12) and proteinuria (aOR=4.19; 95% CI 2.28-7.72). CKD was also associated with low haematocrit, hypochloraemia, hyperphosphatemia, and high mean corpuscular volume. There was no evidence of an association of CKD with hypertension, anaemia, or stunting.

Conclusion

The pattern of comorbidities among YPLHIV with CKD is uncertain and difficulties may relate to difficulty determining true kidney function and normal ranges in this population. Further studies are needed to discern the pattern of CKD complications to improve management efforts and clinical outcomes.
Matching Clinical Profiles with Interventions to Optimize Daily Stepping in People with Stroke
Authors: McCartney Kiersten M. , Pohlig Ryan T. , Miller Allison , Thompson Elizabeth D. , Reisman Darcy
Published: November 2024

Background

Individualizing interventions is imperative to optimize physical activity in people with chronic stroke. This secondary analysis grouped individuals with chronic stroke into clinical profiles based on baseline characteristics and examined if these clinical profiles preferentially benefitted from a specific rehabilitation intervention to improve daily step-activity.

Methods

Participants had non-cerebellar strokes ≥6 months prior to enrollment, were 21-85 years old, had walking speeds of 0.3-1.0 m/s, and took <8,000 steps-per-day. Participants were randomized to 1 of 3 interventions: high-intensity treadmill training (FAST), a step-activity behavioral intervention (SAM), or a combined intervention (FAST+SAM). The primary outcome was the interaction of latent class (clinical profile) and intervention group (FAST, SAM, FAST+SAM) on a change in steps-per-day. Key clinical characteristics to identify the latent classes included walking speed, walking endurance, balance self-efficacy, cognition, and area deprivation.

Results

Of the 190 participants with complete pre- and post-intervention data (mean [SD] age, 64 [12] years; 93 females [48.9%]), 3 distinct profiles of people with chronic stroke were identified. Within our sample, class 1 had the lowest walking capacity (speed and endurance), lowest balance self-efficacy, and highest area deprivation, and had the greatest change in step-activity when enrolled in the SAM (mean[95%CI], 1624 [426 – 2821]) or FAST+SAM (1150 [723 – 1577]) intervention. Class 2 had walking capacity, baseline steps-per-day, and self-efficacy values between Class 1 and 3, and had the greatest change in step-activity when enrolled in the SAM (2002 [1193–2811]) intervention. Class 3 had the highest walking capacity, highest self-efficacy, and lowest area deprivation and the greatest change in step-activity when enrolled in the FAST+SAM (1532 [915–2150]) intervention.

Conclusions

People with chronic stroke require different interventions to optimize a change in step-activity. Clinicians can use clinically relevant measures to personalize intervention selection to augment step-activity in people with chronic stroke.

Trial Registration

NCT02835313;https://clinicaltrials.gov/ct2/show/NCT02835313
Prevent with Pleasure: A systematic review of HIV public communication campaigns incorporating a pleasure-based approach
Authors: Muschialli Luke , Ford Jessie V. , Gonsalves Lianne , Pralat Robert
Published: November 2024

Previous research suggests integrating pleasure into HIV prevention programming improves health outcomes. There are no existing reviews on how exactly pleasure is used within HIV public communications campaigns (PCCs). This manuscript investigates: (1) how HIV PCCs operationalise pleasure; and (2) the efficacy of pleasure-based HIV PCCs. EMBASE, Web of Science Core Collection and PsycINFO were searched for articles that present pleasure-based HIV PCCs on 13/12/2023 (PROSPERO ID: CRD42023487275) with no language restrictions. A narrative synthesis on pleasure operationalisation centred around three inductively coded categories:Enjoyment,Emotional ConnectionandEmpowerment. Another narrative synthesis summarised efficacy data around six categories of HIV-related outcomes. 19,238 articles were retrieved, with 47 articles included in analysis, describing 29 campaigns. 65.5% of interventions operationalisedEmpowerment, 48.3%Enjoyment, and 31.0%Emotional Connection, with narrative synthesis highlighting the diverse ways this was achieved across target communities. An analysis of efficacy identified heterogeneous outcome reporting with inconsistent results across studies, but important outcomes, such as stigma reduction and condom use, were positively associated with intervention exposure across all interventions. We highlight a range of mechanisms through which pleasure can be operationalised, which should inform future intervention development, even if the extant literature weakly supports the efficacy of such interventions.
Inappropriate Dosing of Direct Oral Anticoagulants Among Very Elderly Inpatients With Atrial Fibrillation
Authors: Zhang Ya-Tong , Liu Jun-Peng , ZHAO Zinan , Gu Hong-Qiu , NA Yifan , ZHANG Tianqi , Dong Min , Wan Yuhao , ZENG Min , Sun Ning , Wu Cheng , Yang Jiefu
Published: November 2024

Background: Among very elderly patients with atrial fibrillation, the frequency of inappropriate direct oral anticoagulant (DOAC) dosing, associated factors, and temporal trends in practice are unknown. Objective: To investigate the frequency of inappropriate DOAC dosing, associated factors, and temporal trends in very elderly patients with atrial fibrillation. Methods: We retrospectively enrolled consecutive very elderly inpatients (≥80 years of age) diagnosed with atrial fibrillation at Beijing Hospital from January 2018 to August 2023, and discharged on DOACs were stratified according to receipt of underdosing, overdosing, or recommended dosing. Risk factors associated with underdosing or overdosing were identified using logistic regression. Cochran-Mantel-Haenszel analyses were used to assess temporal trends. Results: We included 676 inpatients aged ≥80 years with atrial fibrillation (mean age 84.4±3.5 years, 53.1% female) prescribed a DOAC at hospital discharge (22.9% dabigatran, 62.3% rivaroxaban, 14.8% edoxaban). Recommended dosing occurred in 338 (50.6%) patients, underdosing in 308 (45.6%), and overdosing in 30 (4.4%). The overall rate of inappropriate dosing was 49.4%. Risk factors associated with underdosing included older age (OR = 1.98, 95% CI: 1.52-2.60, p < 0.001), lower CrCl (OR = 0.98, 95% CI: 0.97-0.99, p = 0.01), and non-internal medicine ward (OR = 2.15, 95% CI: 1.33-3.45, p = 0.002). The risk factor associated with overdosing was younger age (OR = 0.38, 95% CI: 0.19-0.75, p = 0.005). Over the study period, recommended dosing increased over time with a corresponding decline in inappropriate dosing, but these changes were not statistically significant. Conclusions: Inappropriate DOAC dosing, especially underdosing, remains common in very elderly AF inpatients. This issue persists despite years passing, emphasizing the need for patient-focused, collaborative AF management and thorough prognostic studies.
Whole-Slide ECM Imaging Reveals Dense Fibrous Matrix as a High-Risk Factor for Recurrence in Stage II Colon Cancer
Authors: Ravensbergen C.J. , Colaco V.S. , Putter H. , Crobach A.S.L.P. , Boonstra J. , Lindeman J.H.F. , Tollenaar R.A.E.M. , Mesker W.E.
Published: November 2024

Introduction

The extracellular matrix (ECM) supports tumor progression by influencing tumor cell migration and invasion. This study examines the link between peritumoral ECM morphology and five-year recurrence risk in TNM Stage II colon cancer, using quantitative whole-slide ECM imaging. We hypothesize that loose ECM regions are associated with increased recurrence risk due to enhanced tumor budding (TB) or poorly differentiated clusters (PDC).

Methods

In a case-control study of 100 TNM Stage II colon cancer patients (25 with recurrence and 75 controls matched by lymph node sampling and tumor extent), Picrosirius red-stained sections were imaged to quantify ten ECM parameters across 798 regions of interest (ROIs). Conditional logistic regression assessed associations between ECM morphologies, TB, PDCs, and recurrence.

Results

Unsupervised clustering identified three ECM morphologies: dense fibrous, loose sparse, and complex tortuous. Dense fibrous ECM correlated strongly with recurrence (aOR 9.43, 95% CI 3.29-29.30,p< 0.001), while loose sparse and complex tortuous ECMs were associated with reduced recurrence risk (aOR 0.33, 95% CI 0.11-0.91,p= 0.040, and aOR 0.14, 95% CI 0.02-0.53,p= 0.012, respectively). TB was highest in loose sparse ECM (mean 9.3), and PDCs were highest in dense fibrous ECM (mean 5.5).

Discussion

Our findings suggest that ECM morphology, particularly dense fibrous ECM, predicts recurrence in Stage II colon cancer, highlighting ECM profiling as a promising tool for patient stratification beyond traditional staging.
Deciphering the function of Com_YlbF domain-containing proteins in Staphylococcus aureus
Authors: Corredor-Rozo Zayda , Marquez-Ortiz Ricaurte , Velandia-Romero Myriam L. , Abril-Riaño Deisy , Madroñero Johana , Prada Luisa F. , Vanegas-Gomez Natasha , García Begoña , Echeverz Maite , Calderón-Peláez María Angélica , Chaparro-Olaya Jacqueline , Morales Liliana , Nieto-Clavijo Carlos , Escobar-Perez Javier
Published: November 2024

The com_ylbF domain-containing proteins that inhibit sporulation, competition, and biofilm formation by affecting the activity of Ribonuclease RNase-Y inBacillus subtilis. Similar Com_YlbF proteins are found inStaphylococcus aureus, but their function is yet to be determined. This study investigates the role of com_ylbF domain-containing proteins (Qrp/YheA, YmcA, and YlbF) inS. aureusby evaluating the impact ofqrp/yheA,ymcA,andylbFgene deletion on biofilm formation, PIA/PNAG production, and hemolytic capacity. It was found that deletion of the threeqrp/yheA,ymcA,andylbFgenes inS. aureusproduced a decrease in biofilm formation, a slight decrease in PIA/PNAG production, and a decrease in its hemolytic capacity. Global transcriptional analysis in the mutant strain showed dysregulation of several genes associated with pathogenesis, notably a decreased expression of theagrAgene (quorum sensing system), thedelta,alpha,andgammahemolysins, as well as thesdrCgenes,eap/map(adhesion proteins). It also showed-an attenuation of virulence, manifesting as enhanced survival amongGalleria mellonellalarvae, and BALB/c mice, possibly associated due to disrupted RNase-Y activity when theqrp/yheA,ymcA,andylbFare deleted. In conclusion, this work supports the hypothesis that this new family of proteins containing a com_ylbF domain is involved in the regulation of genes related to biofilm formation, hemolysis, and virulence inS. aureusthrough a change in RNase-Y activity.
TSSK homologue regulates the expression ofprotamineandmosquito testes specificgenes inAnopheles stephensi
Authors: Meghwanshi Keshav Kumar , Choudhary Chhavi , Rohilla Pooja , Dixit Rajnikant , Saxena Vishal Kumar , Shukla Jayendra Nath
Published: November 2024

The testis-specific serine/threonine-protein kinase (tssk) gene is known to play an important role in spermiogenesis in mammals. This study identifiestsskhomologues,As_tssk3andAea_tssk1inAnopheles stephensiandAedes aegypti, respectively. BothAs_tssk3andAea_tssk1were found to express in a male-specific manner throughout the development. Efficient knockdown in the expression ofAs_tssk3gene was observed upon feedingAn. stephensilarvae with target dsRNA.As_tssk3knockdown led to a reduced sperm reservoir in male adults. Additionally, the knockdown ofAs_tssk3resulted in the reduced expression of two male specifically expressed genes,protamine & mosquito testes specific(mts-a sperm-specific marker) homologues ofAn. stephensi.In-silicointeraction analysis suggests that As_TSSK3 protein interacts with the Nucleosome Assembly Protein1 like-4 (NAP1like-4), a putative transcription factor. We hypothesize that As_TSSK3 regulates the transcription ofprotamineandmtsgenes via NAP, as both NAP andprotaminehave previously been shown to function in the establishment and maintenance of chromatin dynamics, in independent studies. The study presented here is the first report of characterisation oftsskhomologues in any mosquito species. The knockout studies and phosphorylation assays would provide more insights to explore the mechanism by whichAs_tssk3regulatesprotamineandmtsgenes inAnopheles stephensi.

Highlights

This study identifies thetsskhomologues inAe. aegyptiandAn. stephensiand showed their male-specific expression in both the mosquito species.

dsRNA mediated knockdown ofAs_TSSK3resulted into the males with a reduced size of sperm reservoir.

dsRNA mediated knockdown ofAs_TSSK3led to the reduction in the expression ofAs_protandAs_mts, homologues of protamine and mosquito testis specific, genes inAn. stephensi.

In-silico studies suggest that As_TSSK3 regulates the expression ofAs_protandAs_mtsgenes via NAP.
Sla2 is a core interaction hub for Clathrin Light Chain and the Pan1/End3/Sla1 Complex
Authors: Draper-Barr George , Defelipe Lucas A. , Ruiz-Carrillo David , Gustavsson Emil , Landau Meytal , García-Alai Maria
Published: November 2024

The interaction network of Sla2, a vital adaptor protein in the endocytic mid-coat, undergoes constant rearrangement incorporating or replacing interacting proteins over time. Sla2 serves as a scaffold linking the membrane to the actin cytoskeleton, with this role modulated by Clathrin Light Chain (CLC), which inhibits Sla2’s function under certain conditions. We show that Sla2 has two independent binding sites for CLC: one previously described in homologs of Fungi (Sla2) and Metazoa (Hip1R), and a second found only in Fungi. We present the structural model of the Sla2 actin-binding domains in the context of regulatory structural domains by electron cryo-microscopy. We provide an interaction map of Sla2 and the regulatory proteins Sla1 and Pan1, predicted by AI modelling and confirmed by molecular biophysics techniques. Pan1 competes with CLC for the conserved binding site on Sla2. These results enhance the mapping of crucial interactions at endocytic checkpoints and highlight the divergence between Metazoa and Fungi in this vital process.

Teaser

Sla2 forms complexes with three regulatory proteins in the endocytic pit, two of which compete for the same site
Quantification of Cyclin-CDK dissociation constants in living cells using fluorescence cross-correlation spectroscopy with green and near-infrared fluorescent proteins
Authors: Toyama Aika , Goto Yuhei , Yamauchi Yuhei , Sugiyama Hironori , Kondo Yohei , Mochizuki Atsushi , Aoki Kazuhiro
Published: November 2024

The cell cycle is a highly coordinated process governed by cyclin-bound cyclin-dependent kinases (CDKs). While the interaction between cyclin and CDK are well-documented, the dissociation constants (Kd) between specific cyclin-CDK pairs within living cells remain poorly understood. Fluorescence cross-correlation spectroscopy (FCCS) enables the quantification of the Kd, but challenges remain in selecting an optimal pair of fluorescent molecules for FCCS in a living cell. In this study, we demonstrate that mNeonGreen and phycocyanobilin-bound miRFP670 represent a suitable pair for FCCS in living cells from the viewpoint of high photostability and low bleed-through. This fluorescent protein pair enables us to measure the Kdvalues of the cyclin-dependent kinase Cdc2 and B-type cyclin Cdc13 in fission yeast cells. Moreover, we conducted a comprehensive analysis of the Kdvalues for 36 cyclin-CDK complexes, formed by 9 distinct cyclins and 4 CDKs, in mammalian cells, including unconventional cyclin-CDK pairs. These findings provide insights into the redundancy of cyclin-CDK binding in cell cycle progression, with potential implications for understanding cell cycle regulation in both fission yeast and higher eukaryotes.
Multi-view BLUP: a promising solution for post-omics data integrative prediction
Authors: Wu Bingjie , Xiong Huijuan , Zhuo Lin , Xiao Yingjie , Yan Jianbing , Yang Wenyu
Published: November 2024

Phenotype prediction is a promising strategy for accelerating molecular plant breeding. Data from multiple sources (called multi-view data) can provide complementary information to characterize a biological object from various aspects. By integrating multi-view information into phenotype prediction, a multi-view best linear unbiased prediction (MVBLUP) method was proposed in this paper. By assigning different weights to measure the importance of different views of data and using a differential evolution algorithm with an early stopping mechanism to adjust the weight vector adaptively, a multi-view kinship matrix was obtained first and then incorporated into the BLUP model for phenotype prediction. To validate the efficiency of MVBLUP, we conducted numerical experiments on four multi-view datasets.

Compared to the average performance of the single-view method, the prediction accuracy of the MVBLUP method has improved by a range of 0.038 to 0.201.The results demonstrate that the MVBLUP model is an effective method of integrating multi-view data.
Hallmarks of glucocorticoid receptor condensates involvement in transcription regulation
Authors: Benítez Belén , Stortz Martin , De Rossi María Cecilia , Presman Diego M. , Levi Valeria
Published: November 2024

Several proteins necessary for mRNA production concentrate in intranuclear condensates, which are proposed to affect transcriptional output. The glucocorticoid receptor (GR) is a ligand-activated transcription factor that regulates the expression of hundreds of genes relevant to many physiological and pathological processes. As with all members of the steroid receptor family, GR forms condensates of unknown function. Here, we examine whether GR condensates are involved in transcription regulation using Airyscan super-resolution microscopy and nano-antibodies targeting initiation and elongating states of RNA polymerase II (Pol2). We observed subpopulations of GR condensates colocalizing with initiating and, surprisingly, elongating Pol2 foci. The analysis of GR mutants with different transcriptional outputs suggests a correlation between condensate formation capability and transcription initiation. Moreover, the number of GR molecules within initiation and elongation condensates appears to be linked to transcriptional activity. Taken together, our data suggests an involvement of GR condensates in transcription initiation and elongation.
Visual physiology of Australian stingless bees
Authors: Penmetcha Bhavana , Ryan Laura A , Ogawa Yuri , Hart Nathan S , Narendra Ajay
Published: November 2024

Stingless bees engage in a range of visually guided behaviours that require relatively high spatial resolution and contrast sensitivity. Although the eyes of honeybees, bumblebees, carpenter bees, and sweat bees have been studied extensively, there is limited knowledge of stingless bees. Here, we studied two sympatric Australian species,Tetragonula carbonariaandAustroplebeia australis, which are important crop pollinators. The biggerA. australishad more and larger ommatidial facets compared toT. carbonaria. Using pattern electrophysiology, we showed thatA. australishad higher contrast sensitivity (13.07) compared toT. carbonaria(5.99), but their spatial resolving power did not differ (0.53 cycles deg-1). We discuss these differences in visual physiology in the context of the distinct foraging behaviours of the two species.
Structural insights into the opening mechanism of C1C2 channelrhodopsin
Authors: Mulder Matthias , Hwang Songhwan , Broser Matthias , Brünle Steffen , Skopintsev Petr , Schattenberg Caspar , Schnick Christina , Hartmann Sina , Church Jonathan , Schapiro Igor , Dworkowski Florian , Weinert Tobias , Hegemann Peter , Sun Han , Standfuss Jörg
Published: November 2024

Channelrhodopsins, light-gated cation channels, enable precise control of neural cell depolarization or hyperpolarization with light in the field of optogenetics. This study integrates time-resolved serial crystallography and atomistic molecular dynamics (MD) simulations to resolve the structural changes during C1C2 channelrhodopsin activation. Our observations reveal that within the crystal environment, C1C2 predominantly remains in a light-activated state with characteristics of the M390intermediate. Here, rearrangement of retinal within its binding pocket partially opens the central gate towards the extracellular vestibule. These structural changes initiate channel opening but were insufficient to allow K+flow. Adjusting protonation states to represent the subsequent N520intermediate in our MD simulations induced further conformational changes, including rearrangements of transmembrane helices 2 and 7, that opened the putative ion- translocation pathway. This allows spontaneous but low cation but not anion conduction, that matches experiments. Our findings provide critical structural insights into key intermediates of the channel opening mechanism, enhancing our understanding of ion conduction and selectivity in channelrhodopsins at an atomistic level.
Characterising Protein Search Drift using exhaustive protein search and Alphafold2
Authors: Buchan Daniel WA
Published: November 2024

In this paper we present the first exhaustive analysis of iterative protein search drift and show how such results may impact downstream modelling. Assembling and extracting evolutionary information from families of related proteins is a core challenge in the studey of molecular evolution. For instance, iterative protein search is a common first step in a wide variety of bioinformatics tools and pipelines. And the output of such searches often form the inputs for modelling tools such as Alphafold2. Here we characterise profile drift; the tendency for some searches to become contaminated with sequences outside of the intended evolutionary family. We observe that drift occurs in nearly 15% of searches and can be observed to have measurable impacts on downstream predictive tasks such as structure prediction.
InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
Authors: Simon Elana , Zou James
Published: November 2024

Abstract

Protein language models (PLMs) have demonstrated remarkable success in protein modeling and design, yet their internal mechanisms for predicting structure and function remain poorly understood. Here we present a systematic approach to extract and analyze interpretable features from PLMs using sparse autoencoders (SAEs). By training SAEs on embeddings from the PLM ESM-2, we identify thousands of human-interpretable latent features per layer that highlight hundreds of known biological concepts such as binding sites, structural motifs, and functional domains. In contrast, examining individual neurons in ESM-2 reveals significantly less conceptual alignment, suggesting that PLMs represent most concepts in superposition. We further demonstrate that a larger PLM (ESM-2 with 650M parameters) captures substantially more interpretable concepts than a smaller PLM (ESM-2 with 8M parameters). Beyond capturing known annotations, we show that ESM-2 learns coherent concepts that do not map onto existing annotations and propose a pipeline using language models to automatically interpret novel latent features learned by the SAEs. As practical applications, we demonstrate how these latent features can fill in missing annotations in protein databases and enable targeted steering of protein sequence generation. Our results demonstrate that PLMs encode rich, interpretable representations of protein biology and we propose a systematic framework to uncover and understand these latent features. In the process, we recover both known biology and potentially new protein motifs. As community resources, we introduce InterPLM (interPLM.ai), an interactive visualization platform for investigating learned PLM features, and release code for training and analysis at github.com/ElanaPearl/interPLM.
The microbiota of wooden cheese ripening boards is a rich source of antimicrobial-producing bacteria againstListeria monocytogenes
Authors: Chen Yuxing , Chaves Ibrahim Zuniga , Suen Garret , Huynh TuAnh N.
Published: November 2024

Wooden boards are essential tools in cheese ripening and there are accumulating observations suggesting their antimicrobial effect against foodborne bacterial pathogens, such asListeria monocytogenes. However, poor bacterial recovery of bacteria from wood can confound quantification of pathogen burdens. To assessL. monocytogenessurvival on wooden cheese boards, we applied a disruptive grinding method and tracked native board-associated bacterial counts as controls. Our data revealed thatL. monocytogenesdeclines on clean zones of wooden boards, but can replicate on areas where there is suitable cheese. Our microbiota analysis revealed diverse bacterial communities on wooden board surfaces, with a prominent presence ofBrevibacterium,Brachybacterium, andStaphylococcusgenera. We further identified seven bacterial species that inhibitL. monocytogenes, belonging toBacillus,Staphylococcus, andSerratiaphyla, as well asLactococcus lactis. We focused on aBacillus safensisisolate as a novel biocontrol agent candidate, and found it to potently inhibitL. monocytogenesvia secreted antimicrobial factors. Our genomic, bioinformatic, and biochemical analyses indicate that those factors are likely antimicrobial peptides encoded by multiple biosynthetic gene clusters, several of which are unique toB. safensisand have not been characterized. A sub-inhibitory concentration ofB. safensissupernatant induces a significant down-regulation of prophage elements and up-regulation antimicrobial stress response inL. monocytogenes. Taken together, our findings indicate that the wooden board microbiota is a rich source of antimicrobial-producing bacteria with potential applications in foodborne pathogen control strategies.

IMPORTANCE

Despite stringent food safety measures,L. monocytogenesfoodborne outbreaks remain frequent with high hospitalization and mortality rates. Removal ofL. monocytogenesfrom food processing environments is extremely challenging, because this pathogen is ubiquitous and encodes a wide array of stress response mechanisms that enable it to thrive under harsh conditions. Our study found that clean wooden boards used in cheese ripening inhibitL. monocytogenes, causing a noticeable decline in pathogen population following surface inoculation. Bacterial communities on wooden cheese boards are rich and diverse, and harbor many species that produce antimicrobial compounds againstL. monocytogenes, with the example of a newB. safensisisolate. Therefore, wooden board microbiota is a promising source for future antimicrobial discovery efforts.
Disordered glass nanowire substrates produce in vivo-like astrocyte morphology revealed by optical diffraction tomography
Authors: Anantha Pooja , Kim Joo Ho , Saracino Emanuela , Raj Piyush , Lucarini Ivano , Tanwar Swati , Chen Jessica , Gu Luo , Agrawal Jay , Convertino Annalisa , Barman Ishan
Published: November 2024

Astrocytes, integral components of the central nervous system (CNS), fulfill crucial roles such as maintaining ion homeostasis, providing neuroprotection, and contributing to the blood-brain barrier. Their distinctive, star-like morphology is essential to these functions, and abnormalities in astrocyte structure are linked to numerous neurological disorders. However, our understanding of astrocyte morphology, particularlyin vivo, remains limited. Traditional imaging methods, such as fluorescence microscopy, introduce challenges like restricting continuous observation and comprehensive morphological analysis. In this study, we present a novel approach utilizing optical diffraction tomography (ODT), an advanced imaging technique that generates 3D refractive index profiles, to image and quantify detailed astrocyte morphology. We demonstrate, for the first time, the application of ODT to image samples through and on disordered glass nanowire (NW) substrates, overcoming the typical challenges posed by nanostructures, which can disrupt phase reconstruction. Crucially, we show that disordered glass nanowire (NW) substrates can inducein vivo-like astrocyte morphology in cultured rat cortical astrocytes. Compared to traditional glass substrates, astrocytes grown on disordered glass NWs substrates exhibited enhanced process branching and greater total arbor length—features typically observed in their natural,in vivostate, a state of advanced maturation. This finding underscores the significant influence of substrate topography on astrocyte structure and highlights the unique potential of nanostructured environments to mimic physiological conditions. By leveraging ODT, we were able to monitor astrocyte behavior on these substrates, providing unprecedented insights into their morphological dynamics. Our study pioneers the use of nanostructured substrates for reconstructing astrocyte morphology and sets the stage for further exploration of how microenvironmental cues shape astrocyte morphology and behavior.
The D15 color arrangement test retains its diagnostic value regardless of display accuracy: A modeling study
Authors: Árpádffy-Lovas Tamás , Tóth-Molnár Edit
Published: November 2024

Color vision testing is often considered a resource-intensive examination, requiring an anomaloscope, or at least color plates and specialized lighting equipment. Multiple novel, digital color vision testing algorithms have also been described, but were only verified using calibrated displays. In this work, we assessed if color vision testing could be performed with any computer display using two arrangement type color vision tests, the D15 and desaturated D15 panels. Established mathematical models of human color vision deficiencies (CVDs) and publicly available colorimetric data of real world computer screens were used to model how the panel colors would be displayed on computer screens and then perceived and arranged by subjects with varying levels of CVD. A total of 627,431 arrangements were evaluated. We found that all of the modeled displays, including ones with a low color accuracy of deltaE=6, were characterized by specificity above 86%, and the sensitivity of the desaturated D15 panel remained above 85% as well, with negative predictive values above 90% to detect any form of CVD compared to using the unmodifed colors. These findings suggest that any digital screen could be utilized for color vision screening, even without calibration, enabling reliable high-throughput screening utilizing equipment that is already present at virtually all healthcare providers. Since 8% of the population is affected by some form of CVD, simplifeid screening would unlock notable benefits for all stakeholders. Furthermore, the described algorithm could also be used to optimize other digital color vision tests for general use.
Consumption of legumes and risk of hepatobiliary diseases among humans aged 2+ years: a scoping review
Authors: Langmann Fie , Jensen Christopher Fisker , Mortensen Vibeke Lie , Rosendal Line , Bock Niels , Dahm Christina C.
Published: November 2024

Objectives

To identify and map the literature regarding human consumption of legumes and potential relationships with hepatobiliary diseases.

Background

Consuming legumes might reduce lipid accumulation in the liver while potentially impeding the functionality of the bile duct and gallbladder. As dietary trends shift toward promoting legume consumption, exploring the positive and negative impacts on hepatobiliary health becomes crucial.

Methods

This scoping review explored the intake of dietary pulses and legumes (excluding broader dietary patterns) and their relation to hepatobiliary diseases like non-alcoholic fatty liver disease, gallstones, and gallbladder removal among individuals above the age of two years. The review included textbooks, expert opinions, and searches in four databases (PubMed, CINAHL Complete, Embase, and Web of Science). Two reviewers extracted data independently from each article. The synthesis of results was presented narratively by hepatobiliary outcomes. Unpublished studies and grey literature sources were sought out.

Results

From 19,881 records retrieved, 29 were included - 17 on non-alcoholic fatty liver disease and 12 on gallbladder diseases. Most studies were observational, but a few were narrative reviews. Some studies found a protective association between legume consumption and non-alcoholic liver disease, while others found no association. Overall, there was no clear association between legume consumption and gallbladder diseases. The studies varied in methodological quality, and confidence in the findings was low.

Conclusion

The association between legume consumption and non-alcoholic fatty liver disease was inverse or non-significant. The association between legume consumption and gallbladder disease was inconclusive. Further research is needed to draw firmer conclusions.Keywords: Dietary pulses; Gallstone; Hepatobiliary health; Legumes; Non-alcoholic fatty liver disease