bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk of Clonal Hematopoiesis of Indeterminate Potential after Cancer Radiation Therapy
Authors: Crants Shelby A. , Olson Sydney S. , Li Yajing , Bejan Cosmin A. , Vlasschaert Caitlyn , Mack Taralynn M. , Pershad Yash , Kishtagari Ashwin , Reed Sarah C. , Croessmann Sarah , Roden Dan M. , Osterman Travis J. , Shinohara Eric T. , Bick Alexander G. , Park Ben H. , Luo Leo Y.
Published: September 2024

Clonal hematopoiesis of indeterminate potential (CHIP) is a condition associated with aging and increased risk of hematologic malignancies and chronic diseases. While radiation therapy (RT) has been implicated as a risk factor for CHIP, the specific radiation parameters influencing the development of CHIP remain unclear. This study aimed to investigate the association between RT and CHIP and identify relevant radiation parameters affecting CHIP risk. We conducted a retrospective cohort study of cancer patients with RT exposure from an institutional biobank. DNA sequencing was performed to detect mutations in 22 CHIP-associated genes. Multivariable logistic regression models were used to evaluate the association between clinical characteristics, RT parameters, and CHIP. We identified 736 cancer patients with RT exposure and compared their risk of CHIP to a control cohort of 13,605 individuals. RT was found to be an independent risk factor for developing CHIP (OR 1.39, 95% CI 1.08-1.77, p=0.009). The prevalence of CHIP in RT patients was 22.8%. Compared to controls, RT patients showed significantly increased mutations inDNMT3A,PPM1D,TP53,andBRCC3.A positive correlation was observed between CHIP risk and biological equivalent dose of radiation. Stereotactic radiation was also associated with increased CHIP prevalence (OR 2.24, 95% CI 1.14-4.33, p=0.02). This study demonstrates that RT is associated with an increased risk of CHIP development, particularly mutations in DNA damage response genes. These findings have important implications for cancer care and long-term patient monitoring, emphasizing the need for further research into the mechanisms and consequences of RT-related CHIP.

Key Points

Radiation therapy significantly increases the risk of developing clonal hematopoiesis of indeterminate potential (CHIP) in cancer patients

CHIP risk is higher in those who receive higher total dose and stereotactic radiation, with increased mutations in DNA damage repair genes
Gait-to-Contact (G2C) - A novel deep learning framework to predict total knee replacement wear from gait patterns
Authors: Perrone Mattia , Simmons Scott , Malloy Philip , Yuh Catherine , Martin John , Mell Steven P.
Published: September 2024

Background

Total knee replacement (TKR) is the most common inpatient surgery in the US. Studies leveraging finite element analysis (FEA) models have shown that variability of gait patterns can lead to significant variability of wear rates in TKR settings. However, FEA models can be resource-intensive and time-consuming to execute, hindering further research in this area. This study introduces a novel deep learning-based surrogate modeling approach aimed at significantly reducing computational costs and processing time compared to traditional FEA models.

Methods

A published method was used to generate 314 variations of ISO14243-3(2014) anterior/posterior translation, internal/external rotation, flexion/extension, and axial loading time series, and a validated FEA model was used to calculate linear wear distribution on the polyethylene liner. A deep learning model featuring a transformer-CNN based encoder-decoder architecture was trained to predict linear wear distribution using gait pattern time series as input. Model performance was evaluated by comparing the deep learning and FEA model predictions using metrics such as mean absolute percentage error (MAPE) for relevant geometric features of the wear scar, structural similarity index measure (SSIM) and normalized mutual information (NMI).

Results

The deep learning model significantly reduced the computational time for generating wear predictions compared to FEA, with the former training and inferring in minutes, and the latter requiring days. Comparisons of deep learning model wear map predictions to FEA results yielded MAPE values below 6% for most of the variables and SSIM and NMI values above 0.88, indicating a high level of agreement.

Conclusion

The deep learning approach provides a promising alternative to FEA for predicting wear in TKR, with substantial reductions in computational time and comparable accuracy. Future research will aim to apply this methodology to clinical patient data, which could lead to more personalized and timely interventions in TKR settings.
Optical imaging of micro-droplets of dried saliva for oral squamous cell carcinoma diagnosis
Authors: Foiani Letícia , Nepomuceno Gabrielle , Toledo Julia , Alves Mariana , Rodrigues Nayara , Bandeira Celso , Alves Mônica , Almeida Janete , Martinho Herculano
Published: September 2024

Oral cancer, the sixth most common worldwide, is often diagnosed at an advanced stage, impacting patient survival and mortality. Liquid biopsy offers the potential for cancer diagnosis, enabling dynamic tumor monitoring and disease surveillance. Here we validates a novel diagnostic approach using optical images of dried micro-droplets (volume of oneµl) of saliva samples on glass and platinum substrates, employing Logistic Regression and Support Vector Machine (SVM) models. For each model, accuracy, sensitivity, specificity, and area under the ROC curve were calculated. Our findings indicated that optical density and surface area (SA) obtained from optical images of microdroplets are suitable paramters of discriminating oral cavity squamous cell carcinoma and health individuals. SVM models demonstrate impressive accuracy of 88.10% on glass and 95.00% on Pt substrates, ensuring robust and accurate detection of oral cancer based on these salient features.
Neural and Somatic Mechanisms Driving Clinical Improvements in Post-Acute Schizophrenia Spectrum Disorders
Authors: Roell Lukas , Lindner Christoph , Maurus Isabel , Keeser Daniel , Malchow Berend , Schmitt Andrea , Falkai Peter
Published: September 2024

Background:

A better mechanistic understanding of schizophrenia spectrum disorders is crucial to develop efficient treatment approaches. Therefore, this study investigated longitudinal interrelations between clinical outcomes, brain structure, and somatic health in post-acute individuals from the schizophrenia spectrum.

Methods:

A sample of 63 post-acute patients from two independent physical exercise studies were included in the final analyses. Demographic, clinical, cognitive, and somatic data were acquired at baseline and post-intervention, as were structural magnetic resonance imaging scans. Multivariate cross-lagged panel modelling including mediators was used to study the mutual interrelations over time between the clinical, neural, and somatic level.

Results:

A higher baseline global grey matter volume and larger regional grey matter volumes of the hippocampal formation, precuneus, and posterior cingulate drove improvements in multiple clinical outcomes, such as daily-life functioning, negative symptoms, and cognition. Increases in white matter volume from baseline to post-intervention resulted in significantly reduced positive symptoms and higher daily-life functioning following the intervention.

Conclusion:

Our findings suggest that stimulating neuroplasticity, especially in the hippocampal formation, precuneus, and posterior cingulate gyrus, may represent a promising treatment target in post-acute schizophrenia spectrum disorders. Physical exercise therapies and other lifestyle interventions, and brain stimulation approaches reflect promising treatment candidates. Given the exploratory character of the statistical analysis performed, these findings need to be replicated in independent longitudinal imaging cohorts of patients with schizophrenia spectrum disorders.
Genetic Interplay Between White Matter Hyperintensities and Alzheimer’s Disease: A Brain-Body Perspective
Authors: Singh Manpreet , Shafighi Kimia , Detcheverry Flavie E. , Dabo Fanta , Housni Ikrame , Narayanan Sridar , Gagliano Taliun Sarah A. , Bzdok Danilo , Badhwar AmanPreet
Published: September 2024

MRI-detected white matter hyperintensities (WMH) are often recognized as markers of cerebrovascular abnormalities and an index of vascular brain injury, and are frequently present in individuals with Alzheimer’s disease (AD). Given the emerging bidirectional communication between the brain-body axis in both WMHs and AD, it is important to understand their genetic underpinnings across the whole body. However, literature on this is scarce.

We investigated the brain-body axis by breaking down heritability estimates of these phenotypes across the whole body, – i.e., partitioning heritability. Our aims were to identify genetic underpinnings specific to WMHs, and common between WMHs and AD, by assessing (a) the partitioned heritability of WMHs and AD across the brain-body axis with tissue-specific annotations, (b) the partitioned heritability of WMHs and AD across the brain-body axis with cell-specific annotations, and (c) the genes associated with WMHs and AD, and verifying their expression levels across the whole body.

Our tissue-specific analysis revealed that WMH-associated SNPs were significantly enriched in tissues beyond the brain, namely liver, cardiovascular, and kidney – with liver being a common tissue enriched for both WMHs and AD. Our cell-specific analysis showed enrichment of vascular endothelial cells across the tissue types enriched for WMHs, highlighting their central role in the development of WMHs. Additionally, our gene-level analysis highlighted overlapping patterns of tissue enrichment for both WMHs and AD, and showed interactions between WMH and AD associated genes.

Our findings provide new insights into the systemic influences potentially contributing to WMH pathology, in particular, multi-system endothelial disorder. We hope that our multisystemic genetic findings will stimulate future WMH-research into specific pathways across the brain-body axis.
Design Approaches for Developing Quality Checklists in Healthcare Organizations: A Scoping Review
Authors: Kwong Elizabeth , Cole Amy , Sippo Dorothy , Yu Fei , Adapa Karthik , Shea Christopher M. , Moore Carlton , Das Shiva , Mazur Lukasz
Published: September 2024

Quality checklists have demonstrated benefits in healthcare and other high-reliability organizations, but there remains a gap in the understanding of design approaches and levels of stakeholder engagement in the development of these quality checklists. This scoping review aims to synthesize the current knowledge base regarding the use of various design approaches for developing quality checklists in healthcare. Secondary objectives are to explore theoretical frameworks, design principles, stakeholder involvement and engagement, and characteristics of the design methods used for developing quality checklists. The review followed the Preferred Reporting Items for Systematic Reviews 2020 checklist. Seven databases (PubMed, APA PsycInfo, CINAHL, Embase, Scopus, ACM Digital Library, and IEEE Xplore) were searched for studies using a comprehensive search strategy developed in collaboration with a health sciences librarian. Search terms included “checklist” and “user-centered design” and their related terms. The IAP2 Spectrum of Participation Framework was used to categorize studies by level of stakeholder engagement during data extraction. Twenty-nine studies met the inclusion criteria for this review. Twenty-three distinct design methods were identified that were predominantly non-collaborative in nature (e.g., interviews, surveys, and other methods that involved only one researcher and one participant at a given time). Analysis of the levels of stakeholder engagement revealed a gap in studies that empowered their stakeholders in the quality checklist design process. Highly effective, clear, and standardized methodology are needed for the design of quality checklists. Future work needs to explore how stakeholders can be empowered in the design process, and how different levels of stakeholder engagement might impact implementation outcomes.
Systematic Characterization of the Effectiveness of Alignment in Large Language Models for Categorical Decisions
Authors: Kohane Isaac
Published: September 2024

As large language models (LLMs) are increasingly deployed in high-stakes domains like healthcare, understanding how well their decision-making aligns with human preferences and values becomes crucial, especially when we recognize that there is no single gold standard for these preferences. This paper applies a systematic methodology for evaluating preference alignment in LLMs on categorical decision-making with medical triage as a domain-specific use case. It also measures how effectively an alignment procedure will change the alignment of a specific model. Key to this methodology is a novel simple measure, the Alignment Compliance Index (ACI), that quantifies how effectively a LLM can be aligned to a given preference function or gold standard. Since the ACI measures the effect rather than the process of alignment, it is applicable to alignment methods beyond the in-context learning used in this study.

Using a dataset of simulated patient pairs, three frontier LLMs (GPT4o, Claude 3.5 Sonnet, and Gemini Advanced) were assessed on their ability to make triage decisions consistent with an expert clinician’s preferences. The models’ performance before and after alignment attempts was evaluated using various prompting strategies. The results reveal significant variability in alignment effectiveness across models and alignment approaches. Notably, models that performed well, as measured by ACI, pre-alignment sometimes degraded post-alignment, and small changes in the target preference function led to large shifts in model rankings.

The implicit ethical principles, as understood by humans, underlying the LLMs’ decisions were also explored through targeted questioning. These findings highlight the complex, multifaceted nature of decision-making and the challenges of robustly aligning AI systems with human values. They also motivate the use of a practical set of methods and the ACI, in the near term, to understand the correspondence between the variety of human and LLM decision-making values in specific scenarios.
Postoperative Lymphatic Exudate is a Proximal Source of ctDNA and Detects Recurrence in HPV-negative Head and Neck Cancer
Authors: Lazare Seka , Gu Zhuosheng , Earland Noah , Harmon Adam , Pacula Maciej , Long Megan , Tellis Ashley , Whitfield Damion , Benson Adam , Gerndt Sophie , Harris Peter , Khalil Lucien , Ramirez Ricardo , Xu Zhongping , Wahle Benjamin , Puram Sid , Adkins Doug , Thorstad Wade , Zandberg Daniel , Chernock Rebecca , Skinner Heath , Seethala Raja , Ferris Robert L. , Francis Marra S. , Winckler Wendy , Chaudhuri Aadel A. , Zevallos Jose P.
Published: September 2024

Relapse is a major cause of failure after surgery in HPV-human papillomavirus (HPV) negative head and neck squamous cell carcinoma (HNSCC),), with up to 50% of patients recurring within 2 years. While clinicopathologic criteria exist for adjuvant treatment, these criteria are imprecise and have not changed for decades. However, no reliable method exists to tailor adjuvant therapy for individual patients based on risk of recurrence after surgery. Using an ultra-sensitive targeted sequencing approach, we demonstrate that circulating tumor DNA (ctDNA) in lymphatic exudate collected via surgical drains (“lymph”) 24 hours after surgery accurately identifies MRD and outperforms plasma in an initial cohort of 36 HNSCC patients. We then applied the lymph ctDNA test to an independent, multi-site cohort of 37 HNSCC patients, replicating the original finding. Lymph performance was particularly enhanced in locoregional relapse in both cohorts and generalized to early stage (I-II) patients. Analysis of matched plasma collected at this early timepoint was not predictive of recurrence. We demonstrate a liquid biopsy approach using a historically overlooked biofluid to potentially enable precision adjuvant therapy and achieve superior oncologic outcomes.

SIGNIFICANCE

Postoperative lymphatic exudate represents a novel proximal analyte for MRD detection in HPV-HNSCC designed specifically for use in the immediate post-surgical window when adjuvant therapy decisions must be made. Accurate MRD identification at this early timepoint has potential to augment traditional pathology and personalize adjuvant treatment paradigms in HPV-negative HNSCC.
Synthetic Data Generation in Motion Analysis: A Generative Deep Learning Framework
Authors: Perrone Mattia , Mell Steven , Martin John , Nho Shane J. , Simmons Scott , Malloy Philip
Published: September 2024

Generative deep learning has emerged as a promising data augmentation technique in recent years. This approach becomes particularly valuable in areas such as motion analysis, where it is challenging to collect substantial amounts of data. The current study introduces a data augmentation strategy that relies on a variational autoencoder to generate synthetic data of kinetic and kinematic variables. The kinematic and kinetic variables consist of hip and knee joint angles and moments, respectively, in both sagittal and frontal plane, and ground reaction forces. Statistical parametric mapping (SPM) did not detect significant differences between real and synthetic data for each of the biomechanical variables considered. To further evaluate the effectiveness of this approach, a long-short term model (LSTM) was trained both only on real data (R) and on the combination of real and synthetic data (R&S); the performance of each of these two trained models was then assessed on real test data unseen during training. The predictive model achieved comparable results in terms of nRMSE when predicting knee joint moments in the frontal (R&S: 9.86% vs R:10.72%) and sagittal plane (R&S: 9.21% vs R: 9.75%), and hip joint moments in the frontal (R&S: 16.93% vs R:16.79%) and sagittal plane (R&S: 13.29% vs R:14.60%). These findings suggest that the proposed methodology is an effective data augmentation approach in motion analysis settings.
Evaluating large language model workflows in clinical decision support: referral, triage, and diagnosis
Authors: Gaber Farieda , Shaik Maqsood , Franke Vedran , Akalin Altuna
Published: September 2024

Accurate medical decision-making is critical for both patients and clinicians. Patients often struggle to interpret their symptoms, determine their severity, and select the right specialist. Simultaneously, clinicians face challenges in integrating complex patient data to make timely, accurate diagnoses. Recent advances in large language models (LLMs) offer the potential to bridge this gap by supporting decision-making for both patients and healthcare providers. In this study, we benchmark multiple LLM versions and an LLM-based workflow incorporating retrieval-augmented generation (RAG) on a curated dataset of 2,000 medical cases derived from the Medical Information Mart for Intensive Care database. Our findings show that these LLMs are capable of providing personalized insights into likely diagnoses, suggesting appropriate specialists, and assessing urgent care needs. These models may also support clinicians in refining diagnoses and decision-making, offering a promising approach to improving patient outcomes and streamlining healthcare delivery.
A New Approach to Identifying Elite Winter Sport Athletes’ Risk of Relative Energy Deficiency in Sport (REDs)
Authors: Smith Emily M. , Drager Kelly , Groves Erik M. , Gabel Leigh , Boyd Steven K. , Burt Lauren A.
Published: September 2024

Objectives

Relative Energy Deficiency in Sport (REDs) is a syndrome resulting from problematic low energy availability (LEA). Low areal bone mineral density (aBMD) is a primary indicator of LEA, measured by dual X-ray absorptiometry (DXA). High-resolution peripheral quantitative computed tomography (HR-pQCT) is an advanced imaging device that provides measures of volumetric BMD (vBMD), bone microarchitecture, geometry, and strength. The objective of this study was to assess prevalence of REDs in elite winter sport athletes and to observe the associations in bone parameters using HR-pQCT in athletes identified as at-risk or not at-risk of REDs.

Methods

Participants included 101 elite athletes (24.1±4.4 SD years; 52% female). The REDs Clinical Assessment Tool (CAT2) was used to determine REDs risk. HR- pQCT scans of the non-dominant radius and left tibia were analyzed upon REDs risk grouping.

Results

Seventeen athletes (17%; 71% female) were at-risk based on the REDs CAT2. After covarying for lean mass, odds ratios (OR) suggested higher likelihood of REDs risk classification for athletes with low cortical thickness, cortical area, total vBMD, and bone strength.

Conclusions

Impaired total vBMD, bone strength and cortical bone parameters were approximately twice as likely (OR: 1.9-3.0) in athletes at-risk of REDs. Results agree with the consensus statement that HR-pQCT may identify impaired bone health in athletes at-risk of REDs. Future directions should use HR-pQCT to explore REDs risk longitudinally, utilizing bone change over time as this may provide greater insight. Using advanced imaging to explore REDs risk in a population of winter high-performance athletes is novel.
Evaluating the clinical utility of hand performance information from at-home egocentric video in outpatient neurorehabilitation
Authors: Kadambi Adesh , Manzone Damian M. , Zariffa José
Published: September 2024

Background

Restoring hand function is a primary focus of neurorehabilitation after stroke and spinal cord injury. However, monitoring hand use outside the clinic remains challenging. This study aims to evaluate how therapists perceive and would utilise information from a clinical decision support system (CDSS) that uses egocentric video to monitor patients’ hand use at home.

Methods

Five patient-therapist dyads were recruited. Patients recorded daily activities using head-mounted cameras. Therapists reviewed dashboards of processed video data from their patients and completed semi-structured interviews and structured questionnaires. A mixed-methods approach with thematic analysis was used to evaluate the CDSS’s clinical usefulness.

Results

Therapists preferred video footage over graphical data, valuing its rich insights into their patients’ real-world activities. The information was perceived as useful for understanding patient performance at home and potentially influencing therapy planning.

Conclusions

This study demonstrates the potential of using egocentric video to inform clinical decision-making in neurorehabilitation, particularly for hand function. Therapists found the CDSS valuable for assessing real-world hand use but noted implementation challenges. Despite this, therapists across technical familiarity levels expressed trust in the system and willingness to use it regularly, indicating it could enhance their ability to tailor therapy plans to patients’ real-world activities.
Generative machine learning of ADAR substrates for precise and efficient RNA editing
Authors: Jiang Yue , Bagepalli Lina R. , Banjanin Bora S. , Savva Yiannis A. , Cao Yingxin , Guo Lan , Briggs Adrian W. , Booth Brian , Hause Ronald J.
Published: September 2024

Adenosine Deaminase Acting on RNA (ADAR) converts adenosine to inosine within certain double-stranded RNA structures. However, ADAR’s promiscuous editing and poorly understood specificity hinder therapeutic applications. We present an integrated approach combining high-throughput screening (HTS) with generative deep learning to rapidly engineer efficient and specific guide RNAs (gRNAs) to direct ADAR’s activity to any target. Our HTS quantified ADAR-mediated editing across millions of unique gRNA sequences and structures, identifying key determinants of editing outcomes. We leveraged these data to develop DeepREAD (Deep learning forRNAEditing byADARDesign), a diffusion-based model that elucidates complex design rules to generate novel gRNAs outperforming existing design heuristics. DeepREAD’s gRNAs achieve highly efficient and specific editing, including challenging multi-site edits. We demonstrate DeepREAD’s therapeutic potential by designing gRNAs targeting the MECP2R168Xmutation associated with Rett syndrome, achieving both allelic specificity and species cross-reactivity. This approach significantly accelerates the development of ADAR-based RNA therapeutics for diverse genetic diseases.
Transcriptional memories mediate the plasticity of sulfide stress responses to enable acclimation inUrechis unicinctus
Authors: Zhang Wenqing , Liu Danwen , Yang Heran , Yang Tianya , Zhang Zhifeng , Ma Yubin
Published: September 2024

To cope with environmental stresses, organisms often adopt a memory response upon primary stress exposure to facilitate a quicker and/or stronger reaction to recurring stresses. Somatic stress memory is essential in dealing with contemporary stress. The earliest sign of somatic stress memory is a change in gene transcription levels, which alters physiology and phenotype to better cope with stress. Sulfide is a common environmental pollutant; however, some organisms have successfully colonized sulfur-rich environments. Whether stress memory plays important role in sulfide stress adaptation remains unclear. In this study, to determine whetherUrechis unicinctus, a sulfur-tolerant organism, retains the memory of previous sulfide stress, we simulated a repetitive sulfide stress/recovery system. The results showed that the tolerance ofU. unicinctusto sulfide stress was significantly increased after priming with 50 µM sulfide. Further, transcriptional memory genes (TMGs) involved in regulating sulfide stress memory were identified, classified according to their expression patterns, and functionally analyzed. TMGs involved in sulfide metabolism, sugar metabolism, and protein homeostasis pathway showed an enhanced response, whereas those related to DNA repair pathway demonstrated a modified response pattern. Our study indicated thatU. unicinctusretains memory of sulfide stress priming, which mediates plasticity to accelerate sulfide stress adaptation.
Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis
Authors: Hakim Samuel Edward , Choudhary Nancy , Malhotra Karan , Peng Jian , Arafa Ahmed , Bültemeier Arne , Friedhoff Ronja , Bauer Maximilian , Witte Claus-Peter , Herde Marco , Heretsch Philipp , Pucker Boas , Franke Jakob
Published: September 2024

Withanolides are steroidal lactones from nightshade (Solanaceae) plants. Of the over 1,200 known representatives, many possess potent biological activities, but their drug potential has not been fully realised up until now. A central obstacle is the limited availability of minor withanolides, caused by a lack of knowledge about the underlying biosynthetic pathways. Here, we combine phylogenomics with metabolic engineering to overcome this limitation. By sequencing the genome of the medicinal plant and archetypical withanolide producer ashwagandha (Withania somnifera) and comparing the genome sequences of nine Solanaceae species, we discovered a conserved gene cluster for withanolide biosynthesis, consisting of two sub-gene clusters which differ in their expression patterns. To investigate the functions of the encoded enzymes, we established metabolic engineering platforms in yeast (Saccharomyces cerevisiae) and the model plantNicotiana benthamiana. This allowed us to reconstitute the first three oxidative steps of withanolide biosynthesis, catalysed by the cytochrome P450 monooxygenases CYP87G1, CYP88C7, and CYP749B2, leading to the aglycone of the known compound withanoside V. Our work sets the basis for the biotechnological production of withanolides in heterologous hosts and will therefore help to fully harness the drug potential of these plant steroids in the future.
The snoRNP chaperone snR190 and the Npa1 complex form a macromomecular assembly required for 60S ribosomal subunit maturation
Authors: Hamze Hussein , Jaafar Mariam , Khreiss Ali , Dominique Carine , Bourdeaux Jessie , Méndez-Godoy Alfonso , Kressler Dieter , Humbert Odile , Albert Benjamin , Henras Anthony K. , Henry Yves
Published: September 2024

The early steps of large-ribosomal-subunit assembly feature among the least understood steps of ribosome synthesis in eukaryotes. InSaccharomyces cerevisiae, the snR190 box C/D snoRNP chaperone and the Npa1 complex, composed of the α-solenoid scaffold proteins Npa1 and Npa2, the DEAD-box helicase Dbp6, the RNA-binding protein Nop8 and Rsa3, are likely involved in early 25S rRNA folding events. Here, we report for the first time the existence outside pre-ribosomal particles of an independent macromolecular assembly constituted by the Npa1 complex and the snR190 snoRNP chaperone. Nop8 mediates the formation of this assembly and can associate on its own with free snR190. Moreover, Nop8 RRM domain helps tether the snR190 snoRNP to pre-ribosomal particles. snR190 features a specific central stem-loop structure, which is required for high-affinity binding between free snR190 and the Npa1 complex. Deleting this extension does not prevent snR190 association with pre-ribosomal particles but impairs snR190 activity in early pre-rRNA processing events. This work establishes the importance of association with auxiliary protein complexes for optimum snoRNP chaperone activity during rRNA folding events.
Characterizing the soil microbial community associated with the fungal pathogenCoccidioides immitis
Authors: Radosevich Molly , Head Jennifer , Couper Lisa , Gomez-Weaver Amanda , Camponuri Simon , Montoya Liliam , Taylor John , Remais Justin
Published: September 2024

Coccidioidomycosis is a fungal disease affecting humans and other mammals, caused by environmental pathogens of the genusCoccidioides. Understanding the ecological factors that shape the distribution ofCoccidioidesin soils is important for minimizing the risk of human exposure, though this remains challenging due to the pathogen’s highly variable spatial distribution. Here, we examined associations between the soil microbial community andCoccidioides immitispresence within the Carrizo Plain National Monument—a minimally disturbed grassland ecosystem, and the site of a longitudinal study examining the effects of rodents and their burrows onC. immitispresence in soils. Using internal transcribed spacer 2 (ITS2) and 16S sequencing to characterize the soil fungal and bacterial communities, we found over 30 fungal species, including several other members of the Onygenales order, that co-occurred withCoccidioidesmore frequently than expected by chance.Coccidioides-positive samples were significantly higher in microbial diversity than negative samples, an association partly driven by higherCoccidioidespresence within rodent burrows compared to surface soils. Soil source (i.e.,rodent burrow versus surface soil) explained the largest amount of variation in bacterial and fungal community diversity and composition, with soils collected from rodent burrows having higher microbial diversity than those collected from adjacent surface soils. While prior evidence is mixed regarding associations betweenCoccidioidesand microbial diversity, our study suggests that favorable microhabitats such as rodent burrows can lead to a positive association between soil diversity andCoccidioidespresence, particularly in otherwise resource-limited natural environments.
HU promotes higher-order chromosome organisation and influences DNA replication rates inStreptococcus pneumoniae
Authors: Mazzuoli Maria-Vittoria , van Raaphorst Renske , Martin Louise , Bock Florian , Thierry Agnès , Marbouty Martial , Waclawikova Barbora , Stinenbosch Jasper , Koszul Romain , Veening Jan-Willem
Published: September 2024

Nucleoid-associated proteins (NAPs) are crucial for maintaining chromosomal compaction and architecture and are actively involved in DNA replication, recombination, repair, and gene regulation. In the opportunistic pathogenStreptococcus pneumoniae,HU is the only identified NAP, and its role in chromosome conformation and other essential processes has not yet been investigated. Here, we use a multi-scale approach to explore the role of HU in chromosome conformation and segregation dynamics. By combining superresolution microscopy and whole-genome binding analysis, we describe the nucleoid as a dynamic structure where HU binds transiently across the entire nucleoid, with a preference for the origin of replication over the terminus. Reducing cellular HU levels impacts nucleoid maintenance and disrupts robust nucleoid scaling with cell size. This effect is similar to the distortion caused by fluoroquinolone-antibiotics, supporting earlier observations that HU is essential for maintaining DNA supercoiling. Furthermore, in cells lacking HU, the replication machinery is misplaced, and cells are unable to initiate and proceed with on-going replication. Chromosome conformation capture (Hi-C) experiments revealed that HU is required to maintain cohesion between the two chromosomal arms, in a similar way to the structural maintenance of the chromosome complex SMC. Together, we show that by promoting long-range chromosome interactions and supporting the architecture of the domain encompassing the origin, HU is fundamental for chromosome integrity and the intimately related processes of chromosome replication and segregation.

Graphical abstract
Interaction between climatic variation and pathogen diversity shape endemic disease dynamics in the agricultural settings
Authors: Bhandari Rishi , Kaur Amanpreet , Russell Ivory , Romanus Ogonnaya Michael , Brokaw Destiny , Keinath Anthony P , Snipes Zachary , Rollins Philip , Baugher Nettie , Meadows Inga , Torrance Ty Nicholas , Dutta Bhabesh , Sikora Edward , Molinari Roberto , Soubeyrand Samuel , Potnis Neha
Published: September 2024

Recurring outbreaks caused by endemic pathogens continue to pose problems in managing plant, wildlife, livestock and human health. Understanding how these outbreaks unfold and what drives the variability in disease epidemics across space and time is less understood, especially in the agricultural settings. In this study, we investigated the contribution of pathogen genetic diversity, climatic variation and their interaction towards disease dynamics, with an integrative approach grounded on multitype, high resolution sequencing data and analysis techniques. This investigation was carried out for bacterial spot disease epidemic by surveying tomato fields for bacterial pathogen (Xanthomonas perforans) across southeastern US over a span of three years. The strength of epidemic severity varied across space and time in the agricultural fields. Disease severity was positively associated with strain diversity, and was linked to environmental fluctuations, specifically, large variation and extreme changes in certain climatic factors. Strain-resolved metagenomics approach revealed that co-existence of multiple pathogen lineages was common in the individual fields, although accompanied by differential lineage dynamics. The co-occurring lineages displayed environmentally dependent fitness contributions. By tracing allelic frequencies in pathogen populations across temporal scales, we find evidence for asynchronous allele cycling across seasons, hinting at the presence of adaptive single-nucleotide polymorphisms (SNPs) being polymorphic in space in response to seasonality. Despite this pathogen heterogeneity, we identified positively selected loci under parallel evolution, which may explain the nature of selection pressures experienced by the pathogen. While single pathogen lineage is assumed to dominate the host in the agricultural settings, our findings challenge this notion by demonstrating genetic diversity in the pathogen population observed within a single field and linking it to the disease dynamics. Our results explain the role of pathogen genetic diversity, climate-dependent compositional dynamics, and differential fitness contributions in dictating the variability of disease epidemics in the agricultural settings. Such findings will be invaluable for building predictive models in disease epidemiology. Our high-resolution combinatorial approach exploiting high- resolution sequence data, metadata types and analysis tools, is general enough to finely investigate disease epidemics at large scales in diverse case-studies concerning plant, animal and human health.
Evaluation of the antimicrobial activity of the alcoholic extract ofTagetes erectaagainst bacteria and fungi of clinical importance
Authors: Martínez González Gabriel , Suárez González Frida , Chávez Alanuza Alejandro , Montes de Oca Cuenca Sandra Stephanie , Cuarto Hernández Angélica Guadalupe , de Jesús Olvera Lidia , Almeida Villegas Jorge Angel
Published: September 2024

Antibiotic resistance is a significant global health concern, putting at risk treatment options for infectious diseases. As a result, treatments can be expensive and ineffective, so it is essential to look for new options such as the use of plant extracts with antimicrobial properties to combat these diseases.Tagetessp is a plant species that is used in folk medicine to cure various diseases and has several properties among which the antimicrobial, for this reason, the aim of this research was to evaluate the antimicrobial activity of the ethanolic extract ofTagetes erectaL against various bacteria and yeasts. The antimicrobial activity of the extract was analyzed by the Kirby-Bauer method at different concentrations. The extract showed antimicrobial activity by presenting inhibition halos mainly againstStaphylococcus, obtaining the following results:S. aureusATCC 43300 (19,400 ± 0.435 mm to 500 mg/mL);S. aureusATCC 6538 (11,206 ± 0.342 mm to 750 mg/mL);A. baumanniiATCC 19606 (10.570 ± 0.535 mm a 250 mg/mL);P. mirabilis(7.636 ± 0.196 mm a 250 mg/mL) eI. orientalisATCC 6258 (7.400 ± 0.190 mm a 250 mg/mL). Secondary metabolites such as tannins, quinones, coumarins, phenolic compounds and flavonoids were determined.Tagetes erectaL alcoholic extract has antimicrobial activity against clinically relevant strains and may be considered for further studies against multi-resistant microorganisms in the future.
The role of ERFVIIs as oxygen-sensing transducers in the evolution of land plant response to hypoxia
Authors: Carbonare Laura Dalle , van Veen Hans , Shukla Vinay , Perri Monica , Bui Liem , Holdsworth Michael J. , Licausi Francesco
Published: September 2024

The transcriptional response to low oxygen (hypoxia) in the flowering plantArabidopsis thalianais transduced through group VII Ethylene Response Factor (ERFVII) transcription factors, whose proteolysis is oxygen-dependent via the PLANT CYSTEINE OXIDASE (PCO) N-degron pathway. When and how this response to hypoxia evolved in land plants remains unknown. Here we investigated the conservation and divergence of transcriptional responses to hypoxia in major land plant clades. We identified induction of gene functions associated with glycolysis and fermentation as part of a conserved response across all land plant divisions. Our results indicate that ERFVIIs appeared in the last common ancestor of vascular plants with true roots, concurrently with oxygen-dependent destabilisation, to regulate hypoxia-adaptive genes. Proteins from other ERF groups have been recruited multiple times in different clades as substrates of the PCO N-degron pathway. Our results demonstrate that the response of land plants to hypoxia has been refined in derived clades through the evolution of ERFVIIs as transcriptional transducers, that occurred concomitantly with the appearance of vascular systems and roots as foraging systems through hypoxic soil.
Identification of novel components of the Ced and Ups systems inSaccharolobus islandicusREY15A
Authors: Wu Pengju , Zhang Mengqi , Kou Yanlu , Liang Shikuan , Ni Jinfeng , Huang Qihong , Shen Yulong
Published: September 2024

In the cells ofSulfolobales, the Ced (Crenarchaeal system for exchange of DNA) and Ups (UV-inducible pili ofSulfolobus) systems are highly induced by DNA damages and function in chromosomal DNA exchange by mediating DNA import and cell aggregation, respectively. The Ced system is composed of CedA, CedA1, CedA2, and CedB. The Ups is composed of UpsA, UpsB, UpsE and UpsF. However, how the DNA is transported by these systems is far from clear. Here, we report two novel components of the Ced system, CedD (SiRe_1715) and CedE (SiRe_2100), which are paralogs of CedB and CedA, respectively, and one new component of the Ups system, UpsC (SiRe_1957), which is a paralog of UpsA and UpsB, inSaccharolobus islandicusREY15A. DNA exchange assay revealed thatcedD,cedE, andupsCare essential for DNA import whilecedEandupsCare also important for DNA export. Further microscopy analysis revealed thatupsCis involved in cell aggregation like other Ups genes. Besides, we found thatcedBandcedDco-occur in the genomes of crenarchaea which lackvirB4and the presence ofcedBandcedD, andvirB4is complementary. Both proteins show homology to different parts of the N-terminal domain of VirB4 in a complementary manner and form stable homo-oligomersin vitro. Collectively, our results indicate that CedD and CedE, and UpsC are essential components of the Ced and Ups systems, respectively.
Organ-specific electrophile responsivity mapping in liveC. elegans
Authors: Liu Jinmin , Kulkarni Amogh , Gao Yong-Qi , Urul Daniel A. , Hamelin Romain , Novotny Balázs Á. , Long Marcus J. C. , Aye Yimon
Published: September 2024

Proximity labeling technologies are limited to indexing localized protein residents. Such data— although valuable—cannot inform on small-molecule responsivity of local residents. We here bridge this gap by demonstrating in liveC. eleganshow electrophile-sensing propensity in specific organs can be quantitatively mapped and ranked. Using this method, >70% of tissue-specific responders exhibit novel responsivity,independentof tissue-specific abundance. One responder, cyp-33e1—for which both human and worm orthologs are electrophile responsive—marshals stress-dependent gut functions, despite manifesting uniform abundance across all tissues studied. Cyp-33e1’s localized electrophile responsivity operates site-specifically, triggering multifaceted responses: electrophile sensing through the catalytic-site cysteine results in partitioning between enzyme inhibition and localized production of a critical metabolite that governs global lipid availability, whereas a rapid dual-cysteine site-specific sensing modulates gut homeostasis. Beyond pinpointing chemical actionability within local proteomes, tissue-specific electrophile responsivity mapping illuminates otherwise intractable locale-specific metabolite signaling and stress response programs influencing organ-specific decision-making.

IN BRIEF

Context-specific protein reactivity is a cornerstone of biological stress responsivity, and thus has important ramifications for drug discovery; no current method can inform on these parameters. Here we debut a method that cartographs locale-specific actionability to reactive metabolites; Cyp-33e1, a gut-specific responder, emerged to partition between electrophile-driven localized enzymatic turnover that triggers gut-specific metabolite production shaping global lipid storage, and localized electrophile sensing that marshals global stress response.

HIGHLIGHTS

Localis-REX maps organ-specific electrophile-responsive proteins in worms

Hits are neither identified by organ-specific Ultra-ID nor biased by localized expression

Hits are enriched in proteins functionally relevant to stress-related phenotypes

Localized responsivity of gut-specific hit, cyp-33e1, shapes global lipid availability
Recurrent introgression and geographical stratification shapeSaccharomyces cerevisiaein the Neotropics
Authors: Avelar-Rivas J. Abraham , Sedeño Iván , García-Ortega Luis Fernando , Urban Aragon Jose A , Mancera Eugenio , DeLuna Alexander , Morales Lucía
Published: September 2024

From yeasts to humans, introgressive hybridization significantly influences the evolutionary history of living organisms by introducing new genetic diversity. Strains of Saccharomyces cerevisiae worldwide exhibit introgressions from the sister species S. paradoxus, despite the average sequence identity between these species being lower than 90%. While S. cerevisiae isolates from the Neotropics are known for their high levels of introgression, the evolutionary events leading to the unusually high prevalence of them remain unclear. Here, we sequenced 216 S. cerevisiae isolates living in open agave fermentation across Mexico, a habitat at the interface of natural and industrial environments. The genomes of these strains revealed considerable genetic diversity and population structure linked to geographic distribution, which had been overlooked due to undersampling of this megadiverse region. These strains, along with those from French Guiana, Ecuador, and Brazil, form a broader Neotropical phylogenetic cluster that is notably enriched in introgressed DNA. Surprisingly, the origins and conservation patterns of introgressions indicate multiple hybridization events, suggesting an unprecedented scenario of flexible species barriers in this region. Our findings underscore concurrent evolutionary processes—geographical stratification and multiple introgressions—that shape the genomes of a diverse lineage of S. cerevisiae. Neotropical yeasts thus provide a natural laboratory for exploring the mechanisms and adaptive significance of introgressive hybridization in eukaryotic genome evolution.
Profiling proteins involved in peroxynitrite homeostasis using ROS/RNS conditional proteomics
Authors: Zhu Hao , Uno Hiroaki , Matsuba Kyoichi , Hamachi Itaru
Published: September 2024

Peroxynitrite (ONOO−), the product of the diffusion-controlled reaction of superoxide (O2•−) with nitric oxide (NO•), plays a crucial role in oxidative and nitrative stress and modulates key physiological processes such as redox signaling. While biological ONOO−is conventionally analyzed using 3-nitrotyrosine antibodies and fluorescent sensors, such probes lack specificity and sensitivity, making high-throughput and comprehensive profiling of ONOO−-associated proteins challenging. In this study, we used a conditional proteomics approach to investigate ONOO−homeostasis by identifying its protein neighbors in cells. We developedPeroxynitrite-responsiveproteinLabeling reagents (Porp-L) and, for the first time, discovered 2,6-dichlorophenol as an ideal moiety that can be selectively and rapidly activated by ONOO−for labeling of proximal proteins. The reaction ofPorp-Lwith ONOO−generated several short-lived reactive intermediates that can modify Tyr, His, and Lys residues on the protein surface. We have demonstrated thePorp-L-based conditional proteomics in immune-stimulated macrophages, which indeed identified proteins known to be involved in the generation and modification of ONOO−and revealed the endoplasmic reticulum (ER) as a ONOO−hot spot. Moreover, we discovered a previously unknown role for Ero1a, an ER-resident protein, in the formation of ONOO−. Overall,Porp-Lrepresent a promising research tool for advancing our understanding of the biological roles of ONOO−.