bluuebunny/crossref_metadata_2025 huggingface dataset:
Near real-time monitoring of wading birds using uncrewed aircraft systems and computer vision
Authors: White Ethan P. , Garner Lindsey , Weinstein Ben G. , Senyondo Henry , Ortega Andrew , Steinkraus Ashley , Yenni Glenda M. , Frederick Peter , Ernest S. K. Morgan
Published: May 2024

Wildlife population monitoring over large geographic areas is increasingly feasible due to developments in aerial survey methods coupled with the use of computer vision models for identifying and classifying individual organisms. However, aerial surveys still occur infrequently, and there are often long delays between the acquisition of airborne imagery and its conversion into population monitoring data. Near real-time monitoring is increasingly important for active management decisions and ecological forecasting. Accomplishing this over large scales requires a combination of airborne imagery, computer vision models to process imagery into information on individual organisms, and automated workflows to ensure that imagery is quickly processed into data following acquisition. Here we present our end-to-end workflow for conducting near real-time monitoring of wading birds in the Everglades, Florida, USA. Imagery is acquired as frequently as weekly using uncrewed aircraft systems (aka drones), processed into orthomosaics (using Agisoft metashape), converted into individual level species data using a Retinanet-50 object detector, post-processed, archived, and presented on a web-based visualization platform (using Shiny). The main components of the workflow are automated using Snakemake. The underlying computer vision model provides accurate object detection, species classification, and both total and species-level counts for five out of six target species (White Ibis, Great Egret, Great Blue Heron, Wood Stork, and Roseate Spoonbill). The model performed poorly for Snowy Egrets due to the small number of labels and difficulty distinguishing them from White Ibis (the most abundant species). By automating the post-survey processing, data on the populations of these species is available in near real-time (< 1 week from the date of the survey) providing information at the time-scales needed for ecological forecasting and active management.
“The best home for this paper”: A qualitative study of how authors select where to submit manuscripts
Authors: Maggio Lauren A. , Chtena Natascha , Alperin Juan Pablo , Moorhead Laura , Willinsky John M.
Published: May 2024

Introduction

For academics selecting a target journal to submit a manuscript is a critical decision with career implications. In medical education, research conducted in 2016 found that authors were influenced by multiple factors such as a journal’s prestige and its mission. However, since this research was conducted the publishing landscape has shifted to include a broader variety of journals, an increased threat of predatory journals, and new publishing models. This study updates and expands upon how medical education authors decide which journal to submit to with the aim of describing the motivational factors and journal characteristics that guide authors’ decision making.

Methods

The authors conducted five qualitative focus groups in which twenty-two medical education authors and editors participated. During the focus groups participants were engaged in a discussion about how they select a journal to submit their manuscripts. Audio from all focus groups was transcribed. Transcripts were analyzed using codebook thematic analysis.

Results

Participants considered multiple factors when selecting a target journal. Factors included a journal’s impact, the scope of a journal, journal quality, and technical factors (e.g., word limits). Participants also described how social factors influenced their process and that open access plays a role that could both encourage or deter submission.

Discussion

The findings describe the motivational factors and influential signals that guide authors in their journal selection decision making. These findings confirm, extend, and update journal selection factors reported in medical education and other disciplines. Notably, these findings emphasize the role of social factors, relationships and personal experiences, which were absent from previous work. Additionally, we observed increased consideration of OA and a shift away from an emphasis on journal prestige.
CD4 T cells and CD8α+ lymphocytes are necessary for intravenous BCG-induced protection against tuberculosis in macaques
Authors: Simonson Andrew W. , Zeppa Joseph J. , Bucsan Allison N. , Chao Michael C. , Pokkali Supriya , Hopkins Forrest , Chase Michael R. , Vickers Andrew J. , Sutton Matthew S. , Winchell Caylin G. , Myers Amy J. , Ameel Cassaundra L. , Kelly Ryan , Krouse Ben , Hood Luke E. , Li Jiaxiang , Lehman Chelsea C. , Kamath Megha , Tomko Jaime , Rodgers Mark A. , Donlan Rachel , Chishti Harris , Borish H. Jacob , Klein Edwin , Scanga Charles A. , Fortune Sarah , Lin Philana Ling , Maiello Pauline , Roederer Mario , Darrah Patricia A. , Seder Robert A. , Flynn JoAnne L.
Published: May 2024

Tuberculosis (TB) is a major cause of morbidity and mortality worldwide despite widespread intradermal (ID) BCG vaccination in newborns. We previously demonstrated that changing the route and dose of BCG vaccination from 5ξ105CFU ID to 5ξ107CFU intravenous (IV) resulted in prevention of infection and disease in a rigorous, highly susceptible non-human primate model of TB. Identifying the immune mechanisms of protection for IV BCG will facilitate development of more effective vaccines against TB. Here, we depleted select lymphocyte subsets in IV BCG vaccinated macaques prior to Mtb challenge to determine the cell types necessary for that protection. Depletion of CD4 T cells or all CD8α expressing lymphoycytes (both innate and adaptive) resulted in loss of protection in most macaques, concomitant with increased bacterial burdens (∼4-5 log10 thoracic CFU) and dissemination of infection. In contrast, depletion of only adaptive CD8αβ+ T cells did not significantly reduce protection against disease. Our results demonstrate that CD4 T cells and innate CD8α+ lymphocytes are critical for IV BCG-induced protection, supporting investigation of how eliciting these cells and their functions can improve future TB vaccines.

One Sentence Summary

Antibody depletion of lymphocytes in rhesus macques demonstrates key roles for CD4 T cells and innate-like CD8α+ lymphocytes in conferring sterilizing immunity against tuberculosis following intravenous BCG vaccination.
ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Authors: Wang Mukai , Fontaine Simon , Jiang Hui , Li Gen
Published: May 2024

Microbiome differential abundance analysis remains a challenging problem despite multiple methods proposed in the literature. The excessive zeros and compositionality of metagenomics data are two main challenges for differential abundance analysis. We propose a novel method called “analysis of differential abundance by pooling Tobit models” (ADAPT) to overcome these two challenges. ADAPT uniquely treats zero counts as left-censored observations to facilitate computation and enhance interpretation. ADAPT also encompasses a theoretically justified way of selecting non-differentially abundant microbiome taxa as a reference for hypothesis testing. We generate synthetic data using independent simulation frameworks to show that ADAPT has more consistent false discovery rate control and higher statistical power than competitors. We use ADAPT to analyze 16S rRNA sequencing of saliva samples and shotgun metagenomics sequencing of plaque samples collected from infants in the COHRA2 study. The results provide novel insights into the association between the oral microbiome and early childhood dental caries.
Melanoma antigens in pediatric medulloblastoma contribute to tumor heterogeneity and species-specificity of group 3 tumors
Authors: Collins Rebecca R.J. , Gee Rebecca R. Florke , Sanchez Maria Camila Hoyos , Tozandehjani Sima , Bayat Tara , Breznik Barbara , Lee Anna K. , Peters Samuel T. , Connelly Jon P. , Pruett-Miller Shondra M. , Roussel Martine F. , Rakheja Dinesh , Tillman Heather S. , Potts Patrick Ryan , Fon Tacer Klementina
Published: May 2024

Background

Medulloblastoma (MB) is the most malignant childhood brain cancer. Group 3 MB subtype accounts for about 25% of MB diagnoses and is associated with the most unfavorable outcomes. Herein, we report that more than half of group 3 MB tumors express melanoma antigens (MAGEs), which are potential prognostic and therapeutic markers. MAGEs are tumor antigens, expressed in several types of adult cancers and associated with poorer prognosis and therapy resistance; however, their expression in pediatric cancers is mostly unknown. The aim of this study was to determine whetherMAGEsare activated in pediatric MB.

Methods

To determineMAGEfrequency in pediatric MB, we obtained formalin-fixed paraffin-embedded tissue (FFPE) samples of 34 patients, collected between 2008 – 2015, from the Children’s Medical Center Dallas pathology archives and applied our validated reverse transcription quantitative PCR (RT-qPCR) assay to measure the relative expression of 23MAGEcancer-testis antigen genes. To validate our data, we analyzed several published datasets from pediatric MB patients and patient-derived orthotopic xenografts, totaling 860 patients. We then examined howMAGEexpression affects the growth and oncogenic potential of medulloblastoma cells by CRISPR-Cas9- and siRNA-mediated gene depletion.

Results

Our RT-qPCR analysis suggested thatMAGEswere expressed in group 3/4 medulloblastoma. Further mining of bulk and single-cell RNA-sequencing datasets confirmed that 50-75% of group 3 tumors activate a subset ofMAGEgenes. Depletion of MAGEAs, B2, and Cs alter MB cell survival, viability, and clonogenic growth due to decreased proliferation and increased apoptosis.

Conclusions

These results indicate that targeting MAGEs in medulloblastoma may be a potential therapeutic option for group 3 medulloblastomas.

Key Points

Several Type IMAGECTAs are expressed in >60% of group 3 MBs.

Type I MAGEs affect MB cell proliferation and apoptosis.

MAGEsare potential biomarkers and therapeutic targets for group 3 MBs.

Importance of the Study

This study is the first comprehensive analysis of all Type IMAGECTAs (MAGEA,-B, and-Csubfamily members) in pediatric MBs. Our results show that more than 60% of group 3 MBs expressMAGEgenes, which are required for the viability and growth of cells in which they are expressed. Collectively, these data provide novel insights into the antigen landscape of pediatric MBs. The activation ofMAGEgenes in group 3 MBs presents potential stratifying and therapeutic options.

Abstract Figure
Mass mortality associated with Carpione Rhabdovirus in golden pompano (Trachinotus ovatus) in China: First report
Authors: Sun Heng , Huang Jie , Wang Haoyu , Zhang Yule , Fei Qing , Zhou Jie , Yang Lindi , Li Yanping , Cai Shuanghu , Huang Yucong
Published: May 2024

A severe epizootic outbreak occurred in a deep-water cultured golden pompano (Trachinotus ovatus) in Guangdong Province, China (August–November 2023); the cumulative mortality was 65–82%. The diseased fish showed clinical signs of lethargy, anorexia, whirling movements, and hemorrhage at the base of the fins and in the upper and lower jaws before mass mortality. A Rhabdovirus strain, CARPV2023, was successfully isolated using FHM cells. Cytopathic effects of the tissue filtrate of the diseased golden pompano on FHM and EPC cell monolayers were characterized by rounded cells, grape-like cluster formation, detachment, and lysis. Histopathology revealed congestion, hemorrhage, and necrosis in the spleen, liver, kidney, and intestinal tissues of naturally and experimentally infected golden pompanos. Electron microscopy showed that bullet-shaped viral particles 183.5–201.6-nm long and 57.3–82.7-nm wide budded from cell membrane or aggregated around the infected FHM cells. The virus remained stable for 7 days at 4–33°C and grew optimally at 28°C. Whole-genome sequencing and phylogenetic analysis based on the full genome further indicated that the CARPV2023 strain is a member of Carpione Rhabdovirus, which is related toNovirhabdoviruswith unclassification. A specific nested reverse transcriptase-polymerase chain reaction confirmed the presence of CARPV in the affected golden pompano. Much higher mortality was observed in challenged golden pompanos than in the controls through intraperitoneal injection and immersion infection. In situ hybridization showed positive reactions in the fish tissues. This is the first study to report natural CARPV infections in marine fish in the world.
scAI-SNP: a method for inferring ancestry from single-cell data
Authors: Hong Sung Chul , Muyas Francesc , Cortés-Ciriano Isidro , Hormoz Sahand
Published: May 2024

Collaborative efforts, such as the Human Cell Atlas, are rapidly accumulating large amounts of single-cell data. To ensure that single-cell atlases are representative of human genetic diversity, we need to determine the ancestry of the donors from whom single-cell data are generated. Self-reporting of race and ethnicity, although important, can be biased and is not always available for the datasets already collected. Here, we introduce scAI-SNP, a tool to infer ancestry directly from single-cell genomics data. To train scAI-SNP, we identified 4.5 million ancestry-informative single-nucleotide polymorphisms (SNPs) in the 1000 Genomes Project dataset across 3201 individuals from 26 population groups. For a query single-cell data set, scAI-SNP uses these ancestry-informative SNPs to compute the contribution of each of the 26 population groups to the ancestry of the donor from whom the cells were obtained. Using diverse single-cell data sets with matched whole-genome sequencing data, we show that scAI-SNP is robust to the sparsity of single-cell data, can accurately and consistently infer ancestry from samples derived from diverse types of tissues and cancer cells, and can be applied to different modalities of single-cell profiling assays, such as single-cell RNA-seq and single-cell ATAC-seq. Finally, we argue that ensuring that single-cell atlases represent diverse ancestry, ideally alongside race and ethnicity, is ultimately important for improved and equitable health outcomes by accounting for human diversity.
ProteinCLIP: enhancing protein language models with natural language
Authors: Wu Kevin E. , Chang Howard , Zou James
Published: May 2024

Language models have enabled a new era of biological sequence modeling. However, extracting meaningful sequence-level embeddings from these models remains challenging. In this work, we introduce ProteinCLIP, which applies contrastive learning between a protein’s amino acid sequence and curated text describing its function. ProteinCLIP thus learns to take a pre-trained protein language model’s sequence embedding and refines it produce a function-centric embedding. We show that this embedding space yields sequence representations that enable state-of-the-art performance across a variety of important yet challenging tasks in the study of proteins – from predicting protein protein interactions to accurately detecting homologous proteins despite low sequence similarity. More broadly, ProteinCLIP demonstrates the effectiveness of multi-modal learning in biological contexts, and how such strategies can help isolate key signals from large models and further improve their utility.
Spatiotemporal dynamic models ofAmblyomma americanumquesting activity in the Central Great Plains
Authors: Cobos Marlon E. , Winters Taylor , Martinez Ismari , Yao Yuan , Xiao Xiangming , Ghosh Anuradha , Sundstrom Kellee , Duncan Kathryn , Brennan Robert E. , Little Susan E. , Peterson A. Townsend
Published: May 2024

Ticks represent important vectors of a number of bacterial and viral disease agents, owing to their hematophagous nature and their questing behavior (the process in which they seek new hosts). Questing activity is notably seasonal with spatiotemporal dynamics that needs to be understood in detail as part of mediating and mitigating tick-borne disease risk. Models of the geography of tick questing activity developed to date, however, have ignored the temporal dimensions of that behavior; more fundamentally, they have often not considered the sampling underlying available occurrence data. Here, we have addressed these shortfalls forAmblyomma americanum, the most commonly encountered tick in the central Great Plains, via (1) detailed, longitudinal sampling to characterize the spatiotemporal dimensions of tick questing activity; (2) randomization tests to establish in which environmental dimensions a species is manifesting selective use; and (3) modeling methods that include both presence data and absence data, taking fullest advantage of the information available in the data resource. The outcome was a detailed picture of geographic and temporal variation in suitability for the species through the two-year course of this study. Such models that take full advantage of available information will be crucial in understanding the risk of tick-borne disease into the future.
Pilot study of a ketogenic diet in bipolar disorder: a process evaluation
Authors: Rigby Benjamin P. , Needham Nicole , Grossi Helen , Kamenska Ivana , Campbell Iain H. , Meadowcroft Ben , Creasy Frances , Fisher Cheryl , Bahuguna Pankaj , Norrie John , Thompson Gerard , Gibbs Melissa C. , Mitchell-Grigorjeva Maja , McLellan Ailsa , Moses Tessa , Burgess Karl , Brown Rachel , Thrippleton Michael J. , Campbell Harry , Smith Daniel J. , Simpson Sharon A.
Published: May 2024

Background

Bipolar disorder is a serious mental illness, which requires new strategies for prevention and management. Recent evidence suggests that a ketogenic diet may be an effective intervention. This research aimed to explore the feasibility and acceptability of a ketogenic diet intervention for bipolar disorder, fidelity to its behavioural components and the experiences of the participants and research clinicians involved.

Methods

A mixed-methods process evaluation was conducted. Semi-structured telephone interviews were carried out with 15 participants 1-2 months after completing a 6-8 week modified ketogenic diet intervention, and 4 research clinicians from the study team following the completion of data collection. Data were thematically analysed. Fidelity checklists completed by research dietitians were analysed using descriptive count and percentage statistics. Findings are reported post-hoc, following the analysis and publication of the main pilot study findings.

Results

Qualitative data indicated that participants had various motives for taking part in the study, including weight loss. It was important to support people’s motives while facilitating clear and realistic expectations. Despite the challenges of initiating and maintaining a ketogenic diet, including for some its disruptive effects on daily living, many participants perceived physical and psychological benefits (e.g. significant weight loss, mood stability and an enhanced ability to focus). A range of behavioural (e.g.goal setting), social (e.g.family and dietitians) and technological (e.g.apps for monitoring) support mechanisms were generally considered key facilitating factors. Meanwhile, dietary preferences, concerns about the diet and its impact, the testing burden and capacity of the delivery team were perceived as barriers for some. The importance of wider contextual influences (e.g.the cost of living and sociocultural expectations) were highlighted. Overall, descriptive analyses indicated moderate-to-good fidelity to the behaviour change components of the study.

Conclusion

We provide novel insight into the experiences of people living with bipolar disorder initiating and following a ketogenic diet, as well as those of research clinicians who support the intervention. Future trials may benefit from increased clinical research capacity, better-defined entry and exit routes, additional interpersonal support, and greater understanding of how social and societal factors impact participation.

Trial registration

Study registration number:ISRCTN6163198(02 March 2022)
The mutagenic forces shaping the genomic landscape of lung cancer in never smokers
Authors: Díaz-Gay Marcos , Zhang Tongwu , Hoang Phuc H. , Khandekar Azhar , Zhao Wei , Steele Christopher D. , Otlu Burçak , Nandi Shuvro P. , Vangara Raviteja , Bergstrom Erik N. , Kazachkova Mariya , Pich Oriol , Swanton Charles , Hsiung Chao Agnes , Chang I-Shou , Wong Maria Pik , Leung Kin Chung , Sang Jian , McElderry John , Yang Lixing , Nowak Martin A , Shi Jianxin , Rothman Nathaniel , Wedge David C. , Homer Robert , Yang Soo-Ryum , Lan Qing , Zhu Bin , Chanock Stephen J. , Alexandrov Ludmil B. , Landi Maria Teresa
Published: May 2024

Lung cancer in never smokers (LCINS) accounts for up to 25% of all lung cancers and has been associated with exposure to secondhand tobacco smoke and air pollution in observational studies. Here, we evaluate the mutagenic exposures in LCINS by examining deep whole-genome sequencing data from a large international cohort of 871 treatment-naïve LCINS recruited from 28 geographical locations within the Sherlock-Lungstudy.KRASmutations were 3.8-fold more common in adenocarcinomas of never smokers from North America and Europe, while a 1.6-fold higher prevalence ofEGFRandTP53mutations was observed in adenocarcinomas from East Asia. Signature SBS40a, with unknown cause, was found in most samples and accounted for the largest proportion of single base substitutions in adenocarcinomas, being enriched inEGFR-mutated cases. Conversely, the aristolochic acid signature SBS22a was almost exclusively observed in patients from Taipei. Even though LCINS exposed to secondhand smoke had an 8.3% higher mutational burden and 5.4% shorter telomeres, passive smoking was not associated with driver mutations in cancer driver genes or the activities of individual mutational signatures. In contrast, patients from regions with high levels of air pollution were more likely to haveTP53mutations while exhibiting shorter telomeres and an increase in most types of somatic mutations, including a 3.9-fold elevation of signature SBS4 (q-value=3.1 × 10−5), previously linked mainly to tobacco smoking, and a 76% increase of clock-like signature SBS5 (q-value=5.0 × 10−5). A positive dose-response effect was observed with air pollution levels, which correlated with both a decrease in telomere length and an elevation in somatic mutations, notably attributed to signatures SBS4 and SBS5. Our results elucidate the diversity of mutational processes shaping the genomic landscape of lung cancer in never smokers.
Time-Lapse Quantitative Analysis of Drying Patterns and Machine Learning for Classifying Abnormalities in Sessile Blood Droplets
Authors: Pal Anusuya , Yanagisawa Miho , Gope Amalesh
Published: May 2024

When a colloidal droplet dries on a substrate, a unique pattern results from multi-facet phenomena such as Marangoni convection, capillary flow, mass transport, mechanical stress, colloid-colloid, and colloid-substrate interactions. Even under uniform conditions (surface wettability, humidity, and temperature), slight differences in the initial colloidal composition alter the drying pattern. This paper shows how the evolving patterns during drying in the sessile droplets depend on the initial composition and are crucial for assessing any abnormalities in the blood. To do so, texture statistics are derived from time-lapse images acquired during drying, and different traditional machine learning are applied. In addition, a neural network analysis is performed on both images and their texture statistics. As the drying phenomena are correlated with the varying composition, these methods exhibit excellent performance in distinguishing blood abnormalities with an Fl score of over 97%. This indicates that analysis of time-lapse images during drying and their texture statistics, rather than conventional analysis using images at the final dry state, are crucial for classification. Our results highlight the potential of droplet drying as a low-volume, accurate, and simple screening tool for detecting the type and stage of any disease in bio-fluid samples, such as blood, urine, and saliva.
Cell-of-origin epigenome underlies SS18::SSX-mediated transformation
Authors: Hill Lesley A. , Scott R. Wilder , Martin Lauren , Arostegui Martin , Davenport George , Vemon Marcos , Hofvander Jakob , Wang Xue Qi , Li Jinxiu , Nielsen Torsten O. , Jones Kevin B. , Hirst Martin , Underhill T. Michael
Published: May 2024

Synovial sarcoma is an aggressive soft-tissue malignancy that is characterized by a pathognomonic t(X;18)(p11.2;q11.2) translocation, which produces the fusion oncogene namedSS18::SSX. Despite recent advancements in our understanding of synovial sarcoma biology, the cell-of-origin remains undefined. A mesenchymal stromal cell (MSC) specific CreERT2 line was employed to expressSS18::SSXin fibroblasts and related cell types, resulting in 100% penetrant synovial sarcoma development in mice, with a median latency period of 16.2 ± 2.5 weeks. Murine tumours exhibited high concordance with human synovial sarcoma sub-types at the histological and molecular levels1. Genetic refinement of the cell-of-origin revealed that synovial sarcomas derive from a rareHic1+Pdgfra+Lgr5+fibroblastic population. Furthermore, longitudinal multi-omic profiling along the transformation continuum revealed the step-wise acquisition of a transformed phenotype initiated by the loss of a mature fibroblastic profile and subsequently, the gradual unmasking of an epigenetically embedded embryonic MSC program. Adult and embryonic MSCs exhibited overlapping H2AK119ub and H3K4me3/H3K27me3 (bivalent) histone marks, while SS18::SSX-mediated transformation culminated in the widespread loss of H3K27me3 at these genes and their consequent transcription. Collectively, these studies define a rare MSC context, conducive for SS18::SSX-mediated transformation, and demonstrate that SS tumorigenesis involves the induction and maintenance of an embryonic-like MSC phenotype.
The role of vocalizations in agonistic interactions during competition for roosts in a solitary bat
Authors: Castillo-Salazar Cristian , Schöner Michael G. , Schöner Caroline R. , Chaverri Gloriana
Published: May 2024

Inter- and intraspecific competition for resources is common among individuals which share ecological niches. To avoid physical confrontations, individuals can use various types of signals to demonstrate their dominance, including vocalizations.Kerivoula hardwickiiis a solitary bat species that lives in highly ephemeral plant structures, which are therefore a limited resource. So far, it is unknown if individuals ofK. hardwickiiuse vocalizations during competitive encounters for roosts, and if the intention of these vocalizations can be deduced by potential rivals. We hypothesized that the calls emitted during roost competition contain information that influences the ability of an individual to defend its roost. We conducted roost competition experiments in a flight cage, where there was an individual roost owner and an intruder who would attempt to evict the owner from the roost. All the vocalizations emitted during these encounters were recorded and analyzed to determine which acoustic parameters, if any, had an influence on the successful defense of the roost. We found that the calls emitted by males can influence their ability to defend the roost, and that entropy is the parameter that most strongly explains a successful defense. High entropy suggests that encounters between individuals ofK. hardwickiiescalate to high levels of aggressiveness and explain whether calls influence an individual’s capacity to defend a roost. We suggest that bat vocalizations contain important information about individual characteristics, which in turn help bats make decisions during resource competition.
SNX10 functions as a modulator of piecemeal mitophagy and mitochondrial bioenergetics
Authors: Trachsel-Moncho Laura , Veroni Chiara , Mathai Benan John , Lapao Ana , Singh Sakshi , Asp Nagham Theres , Schultz Sebastian W. , Pankiv Serhiy , Simonsen Anne
Published: May 2024

We here identify the endosomal protein SNX10 as a negative regulator of piecemeal mitophagy of OXPHOS machinery components. In control conditions, SNX10 localizes to early endocytic compartments in a PtdIns3P-dependent manner and modulates endosomal trafficking but also shows dynamic connections with mitochondria. Upon hypoxia-mimicking conditions, SNX10 localizes to late endosomal structures containing selected mitochondrial proteins, including COX- IV and SAMM50, and the autophagy proteins SQSTM1/p62 and LC3B. The turnover of COX-IV and the ATP synthase subunit pSu9 was enhanced in SNX10-depleted cells, with a corresponding reduced mitochondrial respiration and citrate synthase activity. Importantly, zebrafish larvae lacking Snx10 show reduced levels of COX-IV, as well as elevated ROS levels and ROS-mediated cell death in the brain, demonstrating the in vivo relevance of SNX10-mediated modulation of mitochondrial bioenergetics.

eTOC summary

Trachsel-Moncho et al. identify the endosomal protein SNX10 as a modulator of piecemeal mitophagy of OXPHOS machinery components and mitochondrial homeostasis. They show that loss of SNX10 enhances mitochondrial protein degradation, reduces respiration, and increases ROS levels leading to elevated cell death in vivo.
Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs
Authors: Borniego Lucía , Singla-Rastogi Meenu , Baldrich Patricia , Sampangi-Ramaiah Megha Hastantram , Zand Karimi Hana , McGregor Madison , Meyers Blake C. , Innes Roger W.
Published: May 2024

Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced gene silencing is well-documented, the molecular mechanisms by which RNAs can move from the cytoplasm of plant cells across the plasma membrane of both the host cell and fungal cell are poorly understood. Indirect evidence suggests that this RNA transfer may occur at a very early stage of the infection process, prior to breach of the host cell wall, suggesting that silencing RNAs might be secreted onto leaf surfaces. To assess whether Arabidopsis plants possess a mechanism for secreting RNA onto leaf surfaces, we developed a protocol for isolating leaf surface RNA separately from intercellular (apoplastic) RNA. This protocol yielded abundant leaf surface RNA that displayed an RNA banding pattern distinct from apoplastic RNA, suggesting that it may be secreted directly from the leaf surface rather than exuded through stomata or hydathodes. Notably, this RNA was not associated with either extracellular vesicles or protein complexes; however, RNA species longer than 100 nucleotides could be pelleted by ultracentrifugation. Pelleting was inhibited by the divalent cation chelator EGTA, suggesting that these RNAs may form condensates on the leaf surface. These leaf surface RNAs are derived almost exclusively from Arabidopsis, but come from diverse genomic sources, including rRNA, tRNA, mRNA, intergenic RNA, microRNAs, and small interfering RNAs, with tRNAs especially enriched. We speculate that endogenous leaf surface RNA plays an important role in the assembly of distinct microbial communities on leaf surfaces.

Significance Statement

Plant leaves are colonized by a complex community of microbes that is shaped by host genetics. Although secreted metabolites are thought to mediate this effect, we investigated whether plants might also secrete RNA that could potentially structure microbial communities via cross-kingdom RNA interference. Here we report that Arabidopsis leaves are covered with diverse RNAs of plant origin, including abundant tRNAs and tRNA fragments. This leaf surface RNA is not associated with extracellular vesicles or protein complexes; however, it is less degraded than RNA found inside the extracellular spaces of leaves, suggesting that leaf surface RNA is secreted directly rather than exuded through stomata or hydathodes. We propose that this RNA plays a direct role in shaping the leaf microbiome.
Netrin G1 Ligand is a new stromal immunomodulator that promotes pancreatic cancer
Authors: Vendramini-Costa Débora B. , Francescone Ralph , Franco-Barraza Janusz , Luong Tiffany , Graves Myree , de Aquino Ariana Musa , Steele Nina , Gardiner Jaye C. , dos Santos Sérgio Alexandre Alcantara , Ogier Charline , Malloy Emily , Borghaei Leila , Martinez Esteban , Zhigarev Dmitry I. , Tan Yinfei , Lee Hayan , Zhou Yan , Cai Kathy Q. , Klein-Szanto Andres J. , Wang Huamin , Andrake Mark , Dunbrack Roland L. , Campbell Kerry , Cukierman Edna
Published: May 2024

Understanding pancreatic cancer biology is fundamental for identifying new targets and for developing more effective therapies. In particular, the contribution of the stromal microenvironment to pancreatic cancer tumorigenesis requires further exploration. Here, we report the stromal roles of the synaptic protein Netrin G1 Ligand (NGL-1) in pancreatic cancer, uncovering its pro-tumor functions in cancer-associated fibroblasts and in immune cells. We observed that the stromal expression of NGL-1 inversely correlated with patients’ overall survival. Moreover, germline knockout (KO) mice for NGL-1 presented decreased tumor burden, with a microenvironment that is less supportive of tumor growth. Of note, tumors from NGL-1 KO mice produced less immunosuppressive cytokines and displayed an increased percentage of CD8+T cells than those from control mice, while preserving the physical structure of the tumor microenvironment. These effects were shown to be mediated by NGL-1 in both immune cells and in the local stroma, in a TGF-β-dependent manner. While myeloid cells lacking NGL-1 decreased the production of immunosuppressive cytokines, NGL-1 KO T cells showed increased proliferation rates and overall polyfunctionality compared to control T cells. CAFs lacking NGL-1 were less immunosuppressive than controls, with overall decreased production of pro-tumor cytokines and compromised ability to inhibit CD8+T cells activation. Mechanistically, these CAFs downregulated components of the TGF-β pathway, AP-1 and NFAT transcription factor families, resulting in a less tumor-supportive phenotype. Finally, targeting NGL-1 genetically or using a functionally antagonistic small peptide phenocopied the effects of chemotherapy, while modulating the immunosuppressive tumor microenvironment (TME), rather than eliminating it. We propose NGL-1 as a new local stroma and immunomodulatory molecule, with pro-tumor roles in pancreatic cancer.

Statement of Significance

Here we uncovered the pro-tumor roles of the synaptic protein NGL-1 in the tumor microenvironment of pancreatic cancer, defining a new target that simultaneously modulates tumor cell, fibroblast, and immune cell functions. This study reports a new pathway where NGL-1 controls TGF-β, AP-1 transcription factor members and NFAT1, modulating the immunosuppressive microenvironment in pancreatic cancer. Our findings highlight NGL-1 as a new stromal immunomodulator in pancreatic cancer.
Ecotin protectsSalmonellaTyphimurium against the microbicidal activity of host proteases
Authors: Saposnik L. , Coria L.M. , Bruno L. , Guaimas F.F. , Pandolfi J. , Pol M. , Urga M.E. , Sabbione F. , McClelland M. , Trevani A. , Pasquevich K.A. , Cassataro J.
Published: May 2024

Salmonella entericaserovar Typhimurium causes acute diarrhea upon oral infection in humans. The harsh and proteolytic environment found in the gastrointestinal tract is the first obstacle that these bacteria face after infection. However, the mechanisms that allowSalmonellato survive the hostile conditions of the gut are poorly understood. Theecotingene is found in an extensive range of known phyla of bacteria and it encodes a protein that has been shown to inhibit serine proteases. Thus, in the present work we studied the role ofecotinofSalmonellaTyphimurium in host-pathogen interactions. We found thatSalmonellaTyphimurium Δecotinstrain exhibited lower inflammation in a murine model ofSalmonellainduced colitis. The Δecotinmutant was more susceptible to the action of pancreatin and purified pancreatic elastase. In addition, the lack ofecotinled to impaired adhesion to Caco-2 and HT-29 cell lines, related to the proteolytic activity of brush border enzymes. Besides, Δecotinshowed higher susceptibility to lysosomal proteolytic content and intracellular replication defects in macrophages. In addition, we found Ecotin to have a crucial role inSalmonellaagainst the microbicide action of granules released and neutrophil extracellular traps from human polymorphonuclear leukocytes. Thus, the work presented here highlights the importance ofecotininSalmonellaas countermeasures against the host proteolytic defense system.

IMPORTANCE

The gastrointestinal tract is a very complex and harsh environment.Salmonellais a successful food borne pathogen, but little is known about its capacity to survive against the proteolysis of the gut lumen and intracellular proteases. Here, we show that Ecotin, a serine protease inhibitor, plays an important role in protectingSalmonellaagainst proteases present at different sites encountered during oral infection. Our results indicate that Ecotin is an important virulence factor inSalmonella, adding another tool to the wide range of features this pathogen uses during oral infection.
Controlling lipid droplet dynamics via tether condensates
Authors: Amari Chems , Simon Damien , Bellon Theodore , Plamont Marie-Aude , Thiam Abdou Rachid , Gueroui Zoher
Published: May 2024

Lipid droplets (LDs) exhibit remarkable diversity and functionality within cells, depending on the metabolic needs of cells and the maintenance of lipid homeostasis. Such versatility is acquired through dynamic spatial and temporal positioning, enabling tight communication with other organelles. However, this complexity poses challenges in understanding LD biology. Controlled sequestration and release of LDs within their intracellular environment could offer a method to synchronize their behavior and better understand their function. Here, to advance in this direction, we developed ControLD (Controlled Trapping of Lipid Droplets), a novel approach designed to manipulate LDs and influence their dynamics and life cycle. By orchestrating the assembly/disassembly of engineered condensates, ControLD allows precise sequestration and release of LDs in cells. This technique effectively isolates LDs from the intracellular environment, drastically reducing interactions with other organelles. Notably, our experiments demonstrate that physically isolating LDs impairs their dynamics and remobilization during metabolic needs. ControLD represents a versatile tool for reversible LD trapping, with potential applications in controlling various cellular organelles.
The mitochondrial stress-induced protein carboxyl-terminal alanine and threonine tailing (msiCAT-tailing) promotes glioblastoma tumorigenesis by modulating mitochondrial functions
Authors: Cai Ting , Zhang Bei , Reddy Esha , Wu Yuanna , Tang Yinglu , Mondal Isha , Wang Jerry , Ho Winson S , Lu Rongze Olivia , Wu Zhihao
Published: May 2024

The rapid and sustained proliferation in cancer cells requires accelerated protein synthesis. Accelerated protein synthesis and disordered cell metabolism in cancer cells greatly increase the risk of translation errors. ribosome-associated quality control (RQC) is a recently discovered mechanism for resolving ribosome collisions caused by frequent translation stalls. The role of the RQC pathway in cancer initiation and progression remains controversial and confusing. In this study, we investigated the pathogenic role of mitochondrial stress-induced protein carboxyl-terminal terminal alanine and threonine tailing (msiCAT-tailing) in glioblastoma (GBM), which is a specific RQC response to translational arrest on the outer mitochondrial membrane. We found that msiCAT-tailed mitochondrial proteins frequently exist in glioblastoma stem cells (GSCs). Ectopically expressed msiCAT-tailed mitochondrial ATP synthase F1 subunit alpha (ATP5α) protein increases the mitochondrial membrane potential and blocks mitochondrial permeability transition pore (MPTP) formation/opening. These changes in mitochondrial properties confer resistance to staurosporine (STS)-induced apoptosis in GBM cells. Therefore, msiCAT-tailing can promote cell survival and migration, while genetic and pharmacological inhibition of msiCAT-tailing can prevent the overgrowth of GBM cells.

Highlights

The RQC pathway is disturbed in glioblastoma (GBM) cells

msiCAT-tailing on ATP5α elevates mitochondrial membrane potential and inhibits MPTP opening

msiCAT-tailing on ATP5α inhibits drug-induced apoptosis in GBM cells

Inhibition of msiCAT-tailing impedes overall growth of GBM cells
Comparison of MR coil options for concurrent TMS-fMRI
Authors: Jackson J. B. , Scrivener C. L. , Mada M. , Woolgar A.
Published: May 2024

Concurrent transcranial magnetic stimulation (TMS) with functional magnetic resonance imaging (fMRI) is increasingly being used to study how TMS affects neural processing in local and remote connected brain regions. However, there are many technical challenges that arise when operating this unique combination of techniques. One such challenge is MR head coil compatibility and the image resolution that can be achieved. Here we compare the temporal-signal-to noise-ratio (tSNR) between 3 different MR head coils that can be used with TMS. We show that the 7-channel TMS-dedicated surface coils result in a very high tSNR directly under the TMS and the supplementary coil in comparison to the TxRx and the Magnetica. However, there is low tSNR elsewhere. This field inhomogeneity may not be suitable for all research questions, for example where the aim is to look at distributed neural responses. In these cases, an MR coil with a more homogeneous tSNR such as the Magnetica, may be more appropriate.
Nationwide upsurge in invasive disease in the context of longitudinal surveillance of carriage and invasiveStreptococcus pyogenes2009-2023, the Netherlands: a molecular epidemiological study
Authors: Rümke Lidewij W. , Davies Matthew A. , Vestjens Stefan M.T. , van der Putten Boas C.L. , Bril-Keijzers Wendy C.M. , van Houten Marlies A. , Rots Nynke Y. , Wijmenga-Monsuur Alienke J. , van der Ende Arie , de Gier Brechje , Vlaminckx Bart J.M. , van Sorge Nina M.
Published: May 2024

Background

Since 2022, many countries reported an upsurge in invasive group A streptococcal (iGAS) infections. We explored whether changes inS. pyogenescarriage rates or emergence of more virulent strains, such asemm1 variants M1UKand M1DK, contributed to the 2022/2023 surge in the Netherlands.

Methods

We determinedemm(sub)type distribution for 2,698 invasive and 351S. pyogenescarriage isolates collected between January 2009 - March 2023. Genetic evolution ofemm1 was analyzed by whole-genome sequencing of 497emm1 isolates.

Findings

The nationwide iGAS upsurge coincided with a sharp increase ofemm1.0 from 18% (18/100) of invasive isolates in Q1 2022 to 58% (388/670) in Q1 2023 (Fisher’s exact, p<0.0001). M1UKbecame dominant among invasiveemm1 isolates in 2016 and further expanded from 72% in Q1 2022 to 96% in Q1 2023. Phylogenetic comparison revealed evolution and clonal expansion of four new M1UKclades in 2022/2023. DNase Spd1 and superantigen SpeC were acquired in 9% (46/497) ofemm1 isolates.S. pyogenescarriage rates andemm1 proportions in carriage isolates remained stable during this surge and the expansion of M1UKin iGAS was not reflected in carriage isolates.

Interpretation

During the 2022/2023 iGAS surge in the Netherlands, expansion of four new M1UKclades was observed among invasive isolates but not carriage isolates, suggesting increased virulence and fitness of M1UKcompared to contemporary M1 strains. The emergence of more virulent clades has important implications for public health strategies such as antibiotic prophylaxis for close contacts of iGAS patients.
Characterization of pediatric urinary microbiome at species-level resolution indicates variation due to sex, age, and urologic history
Authors: Kelly Maryellen S , Dahl Erin M , Jeries Layla , Sysoeva Tatyana A , Karstens Lisa
Published: May 2024

Extended Summary

Background

Recently, associations between recurrent urinary tract infections (UTI) and the urinary microbiome (urobiome) composition have been identified in adults. However, little is known about the urobiome in children. We aimed to characterize the urobiome of children with species-level resolution and to identify associations based on UTI history.

Study design

Fifty-four children (31 females and 21 males) from 3 months to 5 years of age participated in the study. Catheterized urine specimens were obtained from children undergoing a clinically indicated voiding cystourethrogram. To improve the analysis of the pediatric urobiome, we used a novel protocol using filters to collect biomass from the urine coupled with synthetic long-read 16S rRNA gene sequencing to obtain culture-independent species-level resolution data. We tested for differences in microbial composition between sex and history of UTIs using non-parametric tests on individual bacteria and alpha diversity measures.

Results

We detected bacteria in 61% of samples from 54 children (mean age 40.7 months, 57% females). Similar to adults, urobiomes were distinct across individuals and varied by sex. The urobiome of females showed higher diversity as measured by the inverse Simpson and Shannon indices but not the Pielou evenness index or number of observed species (p = 0.05, p=0.04, p = 0.35, and p = 0.11, respectively). Additionally, several species were significantly overrepresented in females compared to males, including those from the generaAnaerococcus, Prevotella,andSchaalia(p = 0.03, 0.04, and 0.02, respectively). Urobiome diversity increased with age, driven mainly by males. Comparison of children with a history of 1, 2, or 3+ UTIs revealed that urobiome diversity significantly decreases in the group that experienced 3+ UTIs as measured by the Simpson, Shannon, and Pielou indices (p = 0.03, p = 0.05, p = 0.01). Several bacteria were also found to be reduced in abundance.

Discussion

In this study, we confirm that urobiome can be identified from catheter-collected urine specimens in infants as young as 3 months, providing further evidence that the pediatric bladder is not sterile. In addition to confirming variations in the urobiome related to sex, we identify age-related changes in children under 5 years of age, which conflicts with some prior research. We additionally identify associations with a history of UTIs.

Conclusions

Our study provides additional evidence that the pediatric urobiome exists. The bacteria in the bladder of children appear to be affected by early urologic events and warrants future research.