bluuebunny/crossref_metadata_2025 huggingface dataset:
A workflow for clinical profiling of BRCA genes in Chilean breast cancer patients via targeted sequencing
Authors: González Evelin , Moreno Salinas Rodrigo , Muñoz Manuel , Lantadilla Herrera Soledad , Cabrera Morales Mylene , Jullian Pastor , Ebner Durrels Waleska , Vigueras Stari Gonzalo , Anabalón Ramos Javier , Miquel Juan Francisco , Jara Lilian , Moraga Carol , Di Genova Alex
Published: September 2024

Background

Breast cancer (BC) is the leading cause of cancer-related deaths among women globally and in Chile. Mutations in the tumor-suppressor genes BRCA1 and BRCA2 significantly increase the risk of developing cancer, with the probability rising by more than 50%. Identifying pathogenic variants in BRCA1 and BRCA2 is crucial for both diagnosis and treatment. Targeted panels, which focus on medically relevant subsets of genes, have become essential tools in precision oncology. Beyond technical and human resource factors, standardized bioinformatics workflows are essential for the accurate interpretation of results. We developed a robust bioinformatics pipeline, implemented with Nextflow, to process sequencing data from targeted panels to identify germline variants.

Results

We developed an automated and reproducible pipeline using Nextflow for the targeted sequencing of BRCA1/2 genes. The pipeline incorporates two variant callers, Strelka and DeepVariant, both of which have demonstrated high performance in detecting germline SNVs and indels. The runtime is efficient, with a median execution time of less than 3 minutes per task. We sequenced and processed 16 samples from breast cancer patients. In our analysis, we identified 8 nonsynonymous mutations inBRCA1and 9 inBRCA2. Of the total reported germline mutations, 97% were classified as benign, 1% as pathogenic, 1% as of uncertain significance, and 1% as unknown. The allelic frequencies observed in our cohort closely resemble those of Admixed American and South Asian populations, with the greatest divergence observed in comparison to African individuals.

Conclusion

We successfully analyzed theBRCA1andBRCA2genes in 16 breast cancer patients at a public hospital in Chile. A custom Nextflow pipeline was developed to process the sequencing data and evaluate the pathological significance of the identified genetic variants. By employing multiple variant-calling methodologies, we were able to detect and mitigate potential false positives, thereby enhancing the accuracy and reliability of variant detection through cross-verification. A pathogenic variant was identified in one patient, while benign or likely benign variants were found in the remaining 15. Expanding the number of oncogenes sequenced per patient could improve the detection of actionable variants.
Demographic and Historical Processes InfluencingCochliomyia hominivorax(Diptera: Calliphoridae) Population Structure across South America
Authors: Souza Kelly da Silva e , de Paula Letícia Chiara Baldassio , Azeredo-Espin Ana Maria Lima de , Torres Tatiana Teixeira
Published: September 2024

Background

This study investigates the genetic variability and population structure ofCochliomyia hominivorax, the New World screwworm fly. This study tested the hypothesis that the species exhibits a center-periphery distribution of genetic variability, with higher genetic diversity in central populations (e.g., Brazil) and lower diversity in peripheral populations.

Methods

Utilizing microsatellite markers, we analyzed larvae collected from infested livestock across South America. Larvae were collected directly from various wound sites to ensure a broad representation of genetic diversity.

Results

Contrary to our initial hypothesis, the results revealed consistent genetic variability across the species’ distribution, low population differentiation, and no evidence of isolation-by-distance patterns among subpopulations. The genetic analysis indicated an excess of homozygotes, potentially due to the Wahlund effect, null alleles, or selection pressure.

Conclusions

These findings suggest a complex metapopulation structure forCo. hominivorax, challenging classical population genetics models. This complexity likely arises from the species’ high dispersal capability and frequent local extinctions followed by recolonization. These results have important implications for the design and implementation of control programs, emphasizing the need for coordinated and large-scale actions rather than isolated initiatives.
Galar- a large multi-label video capsule endoscopy dataset
Authors: Le Floch Maxime , Wolf Fabian , McIntyre Lucian , Weinert Christoph , Palm Albrecht , Volk Konrad , Herzog Paul , Kirk Sophie Helene , Steinhäuser Jonas L. , Stopp Catrein , Geissler Mark Enrik , Herzog Moritz , Sulk Stefan , Kather Jakob Nikolas , Meining Alexander , Hann Alexander , Palm Steffen , Hampe Jochen , Herzog Nora , Brinkmann Franz
Published: September 2024

Video capsule endoscopy (VCE) is an important technology with many advantages (non-invasive, representation of small bowel), but faces many limitations as well (time-consuming analysis, short battery lifetime, and poor image quality). Artificial intelligence (AI) holds potential to address every one of these challenges, however the progression of machine learning methods is limited by the avaibility of extensive data. We proposeGalar, the most comprehensive dataset of VCE to date.Galarconsists of 80 videos, culminating in 3,513,539 annotated frames covering functional, anatomical, and pathological aspects and introducing a selection of 29 distinct labels. The multisystem and multicenter VCE data from two centers in Saxony (Germany), was annotated framewise and cross-validated by five annotators. The vast scope of annotation and size ofGalarmake the dataset a valuable resource for the use of AI models in VCE, thereby facilitating research in diagnostic methods, patient care workflow, and the development of predictive analytics in the field.
Screening for avoidant restrictive food intake disorder (ARFID) in primary care: clinical presentation and validation of the ARFID-Brief Screener in Swedish preschoolers
Authors: Dinkler Lisa , Brimo Katarzyna , Holmäng Helena , Yasumitsu-Lovell Kahoko , Kuja-Halkola Ralf , Kantzer Anne-Katrin , Omanovic Zerina , Suganuma Narufumi , Eitoku Masamitsu , Fujieda Mikiya , Fernell Elisabeth , Möllborg Per , Bryant-Waugh Rachel , Gillberg Christopher , Råstam Maria
Published: September 2024

Objective

Little is known about the prevalence and clinical presentation of avoidant restrictive food intake disorder (ARFID) in preschool children, and well-validated, parent-reported screening tools are lacking. This study evaluated the diagnostic validity of the parent-reported ARFID-Brief Screener in preschool children and examined prevalence and clinical characteristics of ARFID.

Method

Parents of 645 children (50.5% male, mean age 3.2 years) completed the ARFID-Brief Screener in connection with the 2.5- and 4-year routine check-ups at 21 child health services centers in West Sweden. Parents of all screen-positive and of randomly selected screen-negative children were invited to a clinical follow-up interview via phone. Co-occurring neurodevelopmental problems were assessed via questionnaire, clinical examination, and health care records.

Results

Of 42 (6.5%) children screening positive for ARFID, 29 were followed up via interview, and ARFID diagnosis was confirmed in 21 (positive predicted value 72%; other diagnostic metrics: negative predictive value 94%, sensitivity 91%, specificity 79%, and overall accuracy 84%. The adjusted prevalence of ARFID was 5.9%. All children with ARFID presented with both sensory-based avoidance and low interest, and the majority (65.2%) met criteria solely through DSM-5 criterion A4 (marked interference with psychosocial functioning). The ARFID group had significantly more co-occurring neurodevelopmental problems.

Discussion

ARFID is not rare among preschoolers, although prevalence might have been slightly overestimated here. The ARFID–Brief Screener showed high diagnostic validity, but follow-up assessments are necessary to confirm diagnoses and reduce false positives. Co-occurring neurodevelopmental problems were common in ARFID and may serve as early markers of increased ARFID risk.

Public Significance Statement

This study provides valuable insights into the occurrence of avoidant restrictive food intake disorder (ARFID) in preschool children, a group previously underrepresented in research. Our findings support the effectiveness of the ARFID-Brief Screener in identifying at-risk children, potentially enabling timely interventions and improving long-term outcomes. The higher prevalence of early-onset neurodevelopmental problems in children with ARFID suggest that they may serve as early markers of increased risk of ARFID.
Genetic Risk of Reticular Pseudodrusen in Age-Related Macular Degeneration:HTRA1/lncRNABX842242.1dominates, with no evidence for Complement Cascade involvement
Authors: Farashi Samaneh , Abbott Carla J , Ansell Brendan RE , Wu Zhichao , Altay Lebriz , Arnon Ella , Arnould Louis , Bagdasarova Yelena , Balaskas Konstantinos , Chen Fred K , Chew Emily , Chowers Itay , Clarke Steven , Cukras Catherine , Delcourt Cécile , Delyfer Marie-Noëlle , den Hollander Anneke I. , Fauser Sascha , Finger Robert P. , Gabrielle Pierre-Henry , Han Jiru , Hodgson Lauren AB , Hogg Ruth , Holz Frank G , Hoyng Carel , Kumar Himeesh , Lad Eleonora M , Lee Aaron , Luhmann Ulrich FO , Mauschitz Matthias M , McKnight Amy J , McLenachan Samuel , Mishra Aniket , Moghul Ismail , Orozco Luz D , Sampson Danuta M , Scott Liam W , Sitnilska Vasilena , Song Scott , Stockwell Amy , Swaroop Anand , Terheyden Jan H , Tiosano Liran , Tufail Adnan , Yaspan Brian L ,   MACUSTAR consortium,   NICOLA consortium, Pébay Alice , Fletcher Erica L , Guymer Robyn H , Bahlo Melanie
Published: September 2024

Age-related macular degeneration (AMD) is a multifactorial retinal disease with a large genetic risk contribution. Reticular pseudodrusen (RPD) is a sub-phenotype of AMD with a high risk of progression to late vision threatening AMD. In a genome-wide association study of 2,165 AMD+/RPD+ and 4,181 AMD+/RPD-compared to 7,660 control participants, both chromosomes 1 (CFH) and 10 (ARMS2/HTRA1) major AMD risk loci were reidentified. However association was only detected for the chromosome 10 locus when comparing AMD+/RPD+ to AMD+/RPD-cases. The chromosome 1 locus was notably absent. The chromosome 10 RPD risk region contains a long non-coding RNA (ENSG00000285955/BX842242.1) which colocalizes with genetic markers of retinal thickness.BX842242.1has a strong retinal eQTL signal, pinpointing the parafoveal photoreceptor outer segment layer. Whole genome sequencing of phenotypically extreme RPD cases identified even stronger enrichment for the chromosome 10 risk genotype.
A Tear-Based Approach for Rapid Identification of Bacterial Pathogens in Corneal Ulcers Using Nanopore Sequencing
Authors: Dibbs Mark , Matesva Mitchelle , Theotoka Despoina , Jayaraj Christina , Metiku Beruk , Demkowicz Patrick , Heng Jacob S. , Wang Yvonne , Bakhoum Christine Y. , Chow Jessica , Bakhoum Mathieu F.
Published: September 2024

Purpose

Corneal ulcers pose a significant threat to vision, with the need for prompt and precise pathogen identification being critical to effective treatment. This study assesses the efficacy of using next-generation portable sequencing (Nanopore Technology) to detect and identify bacterial pathogens directly from tear samples, providing a non-invasive alternative to traditional corneal scraping and culture, which are limited by high false-negative rates.

Design

Prospective observational study.

Participants

Ten participants diagnosed with corneal ulcers.

Methods

Tear samples were collected from the ocular surface using Schirmer strips. Corneal scrapings and cultures were performed as medically indicated. The 16S rRNA gene was amplified directly from the tear samples using polymerase chain reaction (PCR), and Nanopore sequencing was used for bacterial species identification and taxonomic classification. Comparative analysis was conducted to evaluate the concordance between Nanopore sequencing results and traditional culture methods.

Main Outcome Measures

Comparison of bacterial species detected via Nanopore sequencing with those identified through traditional culture methods.

Results

Bacterial DNA was identified in 8 of the 10 samples analyzed using the tear-based sequencing method. Notably, Nanopore sequencing accurately identified the causative bacteria in all 4 samples that exhibited bacterial growth on culture. Additionally, it detected bacterial pathogens in 2 of the 4 ulcers that did not show bacterial growth on culture. In 2 cases where cultures could not be obtained due to the small size of the ulcer, tear sequencing successfully identified bacterial species, highlighting potentially overlooked pathogens in corneal ulcers.

Conclusions

PCR amplification of 16S RNA directly from tears followed by Nanopore sequencing is an effective, non-invasive method to identify bacterial pathogens in corneal ulcers, offering non-inferior results to traditional culture methods. This technique not only allows for the detection of traditionally hard-to-culture organisms, providing immediate diagnostic value to guide treatment, but also enhances our understanding of the microbiological landscape of corneal ulcers, thereby informing more effective treatment strategies.
Stakeholder Perspectives on an Adult Cerebral Palsy Community Registry: A Qualitative Study
Authors: Sarmiento Cristina A. , Hurvitz Edward , Cohen Jocelyn , Gannotti Mary
Published: September 2024

Background

The Cerebral Palsy Research Network (CPRN) community registry has yielded valuable information about changes in function and pain in adults with cerebral palsy (CP) through a patient-reported outcomes registry. However, it requires increased enrollment and diversity of participants to produce more generalizable conclusions.

Objective

To identify stakeholder perspectives about the barriers and facilitators to enrollment in the CPRN Community Registry, strategies to enhance recruitment efforts, and important questions for the registry.

Methods

Qualitative descriptive study using iterative focus groups, followed by inductive thematic analysis. Participants included adults with CP and caregivers, clinical investigators, and community leaders in the CP and disability spaces. We explored perspectives about motivations for registry participation, barriers and facilitators to participation, and strategies for increasing and enhancing diversity of enrollment.

Results

We conducted four focus groups (20 participants with lived experience; 10 clinical investigators; 9 community leaders). All participants valued the information provided by the registry and felt that ongoing data collection was important. Barriers and related facilitators to participation include benefits of participation, awareness, accessibility, and collaboration with community and clinical partners. Adults with lived experience seek more precisely defined health and function outcomes for adults with CP.

Conclusions

Adults with lived experience, clinical investigators, and community leaders identified barriers and facilitators to participation in a patient-reported registry and important questions. Our study revealed that communicating a direct benefit to the participant, improved visibility and accessibility, leveraging collaboration with clinical and community partners and answering more precise research questions could promote enrollment.
Predictive Time Series Modeling of Malaria Incidence in India: A 20-Year Retrospective and 5-Year Forecast
Authors: Soni Ami
Published: September 2024

Background

Malaria poses a significant health challenge in India, with notable contributions to the global malaria burden. This study aims to analyze trends in malaria incidence in India over the past two decades, evaluating the effectiveness of public health interventions.

Objective

The objective of this study is to analyze trends in malaria incidence in India over the past decades, evaluate the effectiveness of public health interventions, and project future trends in order to support the country’s goal of malaria elimination by 2030.

Methods

A comprehensive 20-year dataset was utilized to conduct time series analyses, including linear regression and ARIMA modeling. The linear regression model assessed the trend in malaria incidence per 1,000 population at risk, while the ARIMA model was used for forecasting future trends. Residuals were evaluated for adequacy to ensure model reliability.

Results

The linear regression analysis revealed a significant annual decrease in malaria incidence by approximately 0.92 units (p < 0.001), explaining 90.77% of the variability in the data. The ARIMA model forecasts indicate a continued decline, projecting negative incidence values by 2026 and 2027, despite some residual autocorrelation suggesting further model refinement may be necessary.

Discussion

These findings highlight the effectiveness of current public health strategies and the importance of ongoing monitoring to address remaining challenges. The projected downward trend aligns with India’s goal of malaria elimination by 2030, reinforcing the need for sustained interventions in high-burden areas.

Conclusion

This study underscores the positive impact of public health initiatives on malaria incidence in India, while emphasizing the necessity for continuous research and adaptive strategies to achieve the ambitious target of malaria eradication by 2030.
Human Glycolysis Isomerases are Inhibited by Weak Metabolite Modulators
Authors: Jónatansdóttir Yiming Yang , Rolfsson Óttar , Hjörleifsson Jens G.
Published: September 2024

Modulation of enzyme activity by metabolites represents the most efficient and rapid way of controlling metabolism. Investigating enzyme-metabolite interactions can deepen our understanding of metabolic control and aid in identifying enzyme modulators with potential therapeutic applications. These interactions vary in strength, with dissociation constants (Kd) ranging from strong (nM) to weak (µM-mM). However, weak interactions are often overlooked due to the challenges in studying them. Despite this, weak modulators can reveal novel binding modes and serve as starting points for compound optimization. In this study, we aim to identify metabolites that weakly modulate the activity of human glucose-6-phosphate isomerase (GPI) and triosephosphate isomerase (TPI), which are potential therapeutic targets in tumor glycolysis. Through a combination of activity and binding assays, the screening revealed multiple weak inhibitors for the two targets, causing partial attenuation of their activity, with Kdand Kiin the low mM range. X-ray crystallography revealed six orthosteric ligands binding to the active sites – four inhibitors of GPI and two of TPI. Our findings underscore the role of weak interactions in enzyme regulation and may provide structural insights that could guide the design of inhibitors targeting human GPI and TPI in cancer intervention.

Abstract Figure
Transcripts with high distal heritability mediate genetic effects on complex metabolic traits
Authors: Tyler Anna L. , Mahoney J. Matthew , Keller Mark P. , Baker Candice N. , Gaca Margaret , Srivastava Anuj , Gerdes Gyuricza Isabela , Braun Madeleine J. , Rosenthal Nadia A. , Attie Alan D. , Churchill Gary A. , Carter Gregory W.
Published: September 2024

Although many genes are subject to local regulation, recent evidence suggests that complex distal regulation may be more important in mediating phenotypic variability. To assess the role of distal gene regulation in complex traits, we combined multi-tissue transcriptomes with physiological outcomes to model diet-induced obesity and metabolic disease in a population of Diversity Outbred mice. Using a novel high-dimensional mediation analysis, we identified a composite transcriptome signature that summarized genetic effects on gene expression and explained 30% of the variation across all metabolic traits. The signature was heritable, interpretable in biological terms, and predicted obesity status from gene expression in an independently derived mouse cohort and multiple human studies. Transcripts contributing most strongly to this composite mediator frequently had complex, distal regulation distributed throughout the genome. These results suggest that trait-relevant variation in transcription is largely distally regulated, but is nonetheless identifiable, interpretable, and translatable across species.
Asymptomatic infection and antibody prevalence to co-occurring avian influenza viruses vary substantially between sympatric seabird species following H5N1 outbreaks
Authors: Greco Fiona , Ravenswater Hannah M. , Ruiz-Raya Francisco , D’Avino Chiara , Newell Mark A. , Hewitt Josie , Taylor Erin , Benninghaus Ella , Daunt Francis , Goodman Gidona , Steel David , Park Jenny , Philip Emma , Thomas Saumya , Slomka Marek J. , Falchieri Marco , Reid Scott M. , James Joe , Banyard Ashley C. , Burthe Sarah J. , Cunningham Emma J.A.
Published: September 2024

Emerging infectious diseases are of major concern to animal and human health. Recent emergence of high pathogenicity avian influenza virus (HPAIV) (H5N1 clade 2.3.4.4b) led to substantial global mortality across a range of host species. Co-occurring species showed marked differences in mortality, generating an urgent need for better epidemiological understanding within affected populations. We therefore tested for antibodies, indicative of previous exposure and recovery, and for active viral infection in apparently healthy individuals (n=350) across five co-occurring seabird species on the Isle of May, Scotland, during 2023, following H5N1 HPAIV associated mortality in the preceding summer. Antibody prevalence to AIV subtypes varied substantially between species, ranging from 1.1% in European shags (Gulosus aristotelis) (to H5) to 78.7% in black-legged kittiwakes (Rissa tridactyla) (to H16 or both H13 and H16), and between 31-41% for three auk species (H5, H16 or both). At least 20.4% of auks had antibodies to an as yet unidentified subtype, suggesting further subtypes circulating in the population. We found low levels of active, but asymptomatic, AIV infection in individuals (1.6-4.5%), but excluded this as H5N1. Our results emphasise the importance of testing healthy individuals to understand the prevalence of co-circulating AIV subtypes in wild populations, and the potential for future reassortment events which could alter virus behaviour and impact.
A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2018-2020
Authors: Daraghmeh Nauras , Exter Katrina , Pagnier Justine , Bałazy Piotr , Cancio Ibon , Chatzigeorgiou Giorgos , Chatzinikolaou Eva , Chełchowski Maciej , Chrismas Nathan Alexis Mitchell , Comtet Thierry , Dailianis Thanos , Deneudt Klaas , Diaz de Cerio Oihane , Digenis Markos , Gerovasileiou Vasilis , González José , Kauppi Laura , Kristoffersen Jon Bent , Kukliński Piotr , Lasota Rafał , Levy Liraz , Małachowicz Magdalena , Mavrič Borut , Mortelmans Jonas , Paredes Estefania , Poćwierz-Kotus Anita , Reiss Henning , Santi Ioulia , Sarafidou Georgia , Skouradakis Grigorios , Solbakken Jostein , Staehr Peter A.U. , Tajadura Javier , Thyrring Jakob , Troncoso Jesus S. , Vernadou Emmanouela , Viard Frederique , Zafeiropoulos Haris , Zbawicka Małgorzata , Pavloudi Christina , Obst Matthias
Published: September 2024

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic, and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to ∼5,500 amplicon sequence variants and ∼1,800 operational taxonomic units, and up to ∼250 and ∼50 species per observatory using the cytochromecoxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least three to six months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programmes and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.
Twist is the key to the gating of mechanosensitive ion channel NOMPC
Authors: Duan Jingze , Song Chen
Published: September 2024

NOMPC, a tethered mechanosensitive ion channel from the transient receptor potential (TRP) family, can convert mechanical stimuli to ionic electric signals to excite neuron cells. Previous investigations revealed that a pushing force exerted on the linker helix domain or the compression of NOMPC’s ankyrin repeat (AR) domain triggers channel opening. In this study, we explored the direct mechanical cause for NOMPC channel opening as well as the torsional properties of the AR domain using all-atom molecular dynamics simulations. Our results demonstrate that a torque pointing toward the extracellular side, exerted on the amphipathic TRP domain, serves as the direct cause of driving the channel open. The coupling between the compression and twisting of the AR domain ensures that both types of deformations can open the channel. Therefore, we propose a twist-to-open model, facilitated by the compression-twist coupling property of the AR domain, to further elucidate the gating mechanism of the NOMPC channel.
WITHDRAWN: New neural-inspired controller generalises modularity over lower limb tasks through internal models
Authors: Muñoz David , Holland Donal , Severini Giacomo
Published: September 2024

Withdraw statement

The authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2023/569887. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: 10.1101/2023.12.04.569887
A qualitative review of Oxford Nanopore Sequencing datasets for RNA modifications
Authors: Pahar Madhurananda , Liu Qian
Published: September 2024

There are many oxford nanopore datasets available to study methylations. Methylations and modifications occur at nucleotides such as adenine (A), cytosine (C), guanine (G) and theanine (T) or uracil (U). Among all these provided datasets, some have the most common m6A methylation and others have m5C etc. using various real organism reference sequences such as human, mouse and artificial reference sequences which are prepared in the laboratory such as curlcake and IVT. These datasets are required to be organized by the methylation types to research ONT datasets. Here we provide a summary of the read qualities, base mapping success rates etc. for these methylation types and reference genomes. We have used minimap2 base mapping and longreadsum results. We find that methylated data have lower success rates than non-methylated data and mapping quality is lower for the real reference genomes such as human and mice. This could be because they contain more than 100,000 transcriptomes whereas artificial reference sequences contain only a few transcriptomes. Datasets which contain artificially created reference sequences have a higher quality than the others, thus they are recommended to be used for methylation or modification classification tasks in the future.

Dataset

All datasets used in this study are the publicly available.

Dataset License

All datasets used in this study are the publicly available.
Small eukaryotic phytoplankton can play an outsized role in carbon export in iron-limited regions
Authors: Meyer Meredith G. , White Vincent J. , Torano Olivia , Hannoush Heidi , Marchetti Adrian
Published: September 2024

Small eukaryotic phytoplankton can account for considerable amounts of biomass and primary production in high nutrient, low chlorophyll (HNLC) regions of the ocean where iron-limitation is pronounced. However, the strategies these cells invoke to cope under low iron conditions and the extent to which they are responsible for new production (i.e., the fraction of primary production supported by nutrients from outside of the euphotic zone) is unclear. Here, we examine how a representative picoeukaryote, the chlorophyteBathycoccus sp., recently isolated from the iron-limited subarctic North Pacific Ocean, responds to iron-limitation and quantify its potential contribution to carbon export. Iron-limitedBathycoccusexhibits reductions in cellular growth rate, volume, and carbon and nitrogen quotas along with a restructuring of cellular metabolism. Gene expression and pathway analyses show evidence of cellular strategies to mitigate iron limitation but constitutive expression of genes related to nitrogen uptake and utilization. Additionally, when grown on nitrate, cellular carbon and nitrogen quotas ranged from 0.02 – 0.17 pmol C cell-1and 3.3 x 10-3– 2.2 x 10-2pmol N cell-1, respectively, as a function of iron status. Based on the measured cellular quotas, we estimate that representative picoeukaryotes, such asBathycoccus,in HNLC North Pacific waters can account for a majority of new production under ambient iron-limited conditions, supporting the need for a paradigm shift in our thinking of the role small eukaryotic phytoplankton play in the global carbon cycle.
Laser Speckle Particle Sizer (SPARSE) Informs the Size Distribution of Tissue Granularities
Authors: Hajjarian Zeinab , Zeng Ziqian , Leartprapun Nichaluk , Nadkarni Seemantini K.
Published: September 2024

Particle sizing of biomaterials and tissues holds profound implications across diverse industrial and clinical disciplines. Conventional approaches such as dynamic light scattering (DLS) are restricted to dilute liquids, and unable to assess particle size distribution in intact, untampered biomaterials and tissues in their native state. Here, we introduce the laser Speckle PARticle SizEr (SPARSE), which leverages the size-dependent attributes of polarized back-scattered laser speckle to characterize the average radius of a continuum of endogenous scattering particles, in the 10nm-10μm range, in biological fluids and soft tissues in their native state. The SPARSE approach exploits cross- and co-polarized attributes of spatial and temporal laser speckle intensity fluctuations to quantify the average particle size in various specimens, including polystyrene microspheres, milk, whole blood specimens, and intact soft tissues, without prior knowledge or explicit account of refractive index and scattering concentrations. Through scanning the laser beam across the tissue surface, we establish the capability of SPARSE to evaluate a spatial map of heterogenous scattering particle sizes with a resolution of a few 10s ofμm that closely mirrors histopathological microstructures in benign and carcinoma breast tissue specimens. By enabling the size characterization of intact tissues and biomaterials across a continuum of granularities, non-destructively in native specimens, SPARSE opens substantial opportunities for quality control in industrial applications, drug development, and advanced clinical diagnostics.
Altered mRNA transport and local translation in iNeurons with RNA binding protein knockdown
Authors: Dargan Rachael , Mikheenko Alla , Johnson Nicholas L. , Packer Benjamin , Li Ziyi , Craig Emma J. , Sarbanes Stephanie L. , Bereda Colleen , Mehta Puja R. , Keuss Matthew , Nalls Mike A. , Qi Yue A. , Weller Cory A. , Fratta Pietro , Ryan Veronica H.
Published: September 2024

Neurons rely on mRNA transport and local translation to facilitate rapid protein synthesis in processes far from the cell body. These processes allow precise spatial and temporal control of translation and are mediated by RNA binding proteins (RBPs), including those known to be associated with neurodegenerative diseases. Here, we use proteomics, transcriptomics, and microscopy to investigate the impact of RBP knockdown on mRNA transport and local translation in iPSC-derived neurons. We find thousands of transcripts enriched in neurites and that many of these transcripts are locally translated, possibly due to the shorter length of transcripts in neurites. Loss of frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS)-associated RBPs TDP- 43 and hnRNPA1 lead to distinct alterations in the neuritic proteome and transcriptome. TDP-43 knockdown (KD) leads to increased neuritic mRNA and translation. In contrast, hnRNPA1 leads to increased neuritic mRNA, but not translation, and more moderate effects on local mRNA profiles, possibly due to compensation by hnRNPA3. These results highlight the crucial role of FTD/ALS-associated RBPs in mRNA transport and local translation in neurons and the importance of these processes in neuron health and disease.
Bimodal cell mass distribution separates CD8+ T cells into two distinct types with divergent differentiation dynamics
Authors: Yu Jiaquan , Zhang Ye , Duquette Sarah M. , Yee Gianfranco L. , Dinter Teresa , Usherwood Thomas R. , Wu Weida , Miettinen Teemu , Spranger Stefani , Manalis Scott R.
Published: September 2024

T cell heterogeneity is a cornerstone of the adaptive immune response, with CD8+ T cells playing a pivotal role in mediating cytotoxic responses to pathogens and tumors. While traditional studies have focused on phenotypic and functional diversity through surface marker expression and functional assays, the significance of biophysical properties in delineating T cell subpopulations remains underexplored. Here, we show that resting T cells exhibit a bimodal distribution in buoyant mass, which is not captured by surface marker based canonical immunophenotypes or physical parameters such as volume, density, dry mass, or light scattering. Functionally, we demonstrate that T cells with lower buoyant mass exhibit reduced proliferation, tend towards effector differentiation, and become more exhausted in the presence of innate tumor-secreted factors. Conversely, T cells with higher buoyant mass show greater memory potential and resistance to exhaustion. Our study not only provides insights into T cell biology but also suggests buoyant mass as a promising label-free biomarker to potentiate T cell-based therapies.
Decoding mEos4b Day-Long Maturation and Engineering Fast Maturing Variants
Authors: Maity Arijit , Glushonkov Oleksandr , Ayala Isabel , Tacnet Pascale , Wulffelé Jip , Frachet Philippe , Brutscher Bernhard , Bourgeois Dominique , Adam Virgile
Published: September 2024

The maturation speed of fluorescent proteins is a crucial parameter that influences cellular brightness, effective labeling efficiency and temporal resolution in fluorescence microscopy. Green-to-red photoconvertible fluorescent proteins (PCFPs) used in pulse-chase experiments and super-resolution techniques such as Photoactivated Localization Microscopy (PALM), single-particle-tracking PALM (sptPALM) and Minimal Fluorescence Photon Fluxes Microscopy (MINFLUX) may be hampered by slow maturation. We systematically characterized the maturation speed of mEos-derived PCFPs inE. coliand found that, in contrast to pcStar and mEosEM, several variants such as mEos2, mEos3.1, mEos3.2 and mEos4b mature extremely slowly. Strikingly, the oxidation step in those PCFPs is fast and not rate-limiting. Through a rational mutagenesis approach, we developed a strategy to reduce the day-long maturation time of mEos4b by nearly two orders of magnitude without significantly impacting its molecular brightness and photophysical performance under single-molecule imaging conditions.
Comparative evaluation of cell-based assay technologies for scoring drug-induced condensation of SARS-CoV-2 nucleocapsid protein
Authors: Quek Rui Tong , Shirazinejad Cyna R. , Young Christina L. , Hardy Kierra S. , Lim Samuel , Elms Phillip J. , McSwiggen David T. , Mitchison Timothy J. , Silver Pamela A.
Published: September 2024

Protein-nucleic acid phase separation has been implicated in many diseases such as viral infections, neurodegeneration, and cancer. There is great interest in identifying condensate modulators (CMODs), which are small molecules that alter the dynamics and functions of phase-separated condensates, as a potential therapeutic modality. Most CMODs were identified in cellular high-content screens (HCS) where micron-scale condensates were characterized by fluorescence microscopy. These approaches lack information on protein dynamics, are limited by microscope resolution, and are insensitive to subtle condensation phenotypes missed by overfit analysis pipelines. Here, we evaluate two alternative cell-based assays: high-throughput single molecule tracking (htSMT) and proximity-based condensate biosensors using NanoBIT (split luciferase) and NanoBRET (bioluminescence resonance energy transfer) technologies. We applied these methods to evaluate condensation of the SARS-CoV-2 nucleocapsid (N) protein under GSK3 inhibitor treatment, which we had previously identified in our HCS campaign to induce condensation with well-defined structure-activity relationships (SAR). Using htSMT, we observed robust changes in N protein diffusion as early as 3 hours post GSK3 inhibition. Proximity-based N biosensors also reliably reported on condensation, enabling the rapid assaying of large compound libraries with a readout independent of imaging. Both htSMT and proximity-based biosensors performed well in a screening format and provided information on CMOD activity that was complementary to HCS. We expect that this expanded toolkit for interrogating phase-separated proteins will accelerate the identification of CMODs for important therapeutic targets.
Tolerance Mechanisms in Polysaccharide Biosynthesis: Implications for Undecaprenol Phosphate Recycling inEscherichia coliandShigella flexneri
Authors: Qin Jilong , Hong Yaoqin , Morona Renato , Totsika Makrina
Published: September 2024

Bacterial polysaccharide synthesis is catalysed on the universal lipid carrier, undecaprenol phosphate (UndP). The cellular UndP pool is shared by other polysaccharide synthesis pathways and in peptidoglycan (PG) biogenesis. Disruptions in cytosolic polysaccharide synthesis steps are detrimental to bacterial survival due to affecting UndP recycling. In contrast, bacteria can survive disruptions in the periplasmic steps, suggesting a tolerance mechanism to mitigate UndP sequestration. Here we investigated tolerance mechanisms to disruptions of polymerases that are involved in UndP-releasing steps in two related polysaccharide synthesis pathways: the enterobacterial common antigen (ECA) and the O antigen (OAg), inEscherichia coliandShigella flexneri. Our study reveals that polysaccharide polymerisation is crucial for efficient UndP recycling. InE. coliK-12, cell survival upon disruptions in OAg polymerase is dependent on a functional ECA synthesis pathway and vice versa. This is because disruptions in OAg synthesis leads to the redirection of the shared lipid-linked sugar substrate UndPP-GlcNAc towards increased ECA production. Conversely, inS. flexneri, the OAg polymerase is essential due to its limited ECA production, which inadequately redirects UndP flow to support cell survival. We propose a model whereby sharing the initial sugar intermediate UndPP-GlcNAc between the ECA and OAg synthesis pathways allows UndP to be redirected towards ECA production, mitigating sequestration issues caused by disruptions in the OAg pathway. These findings suggest an evolutionary buffering mechanism that enhances bacterial survival when UndP sequestration occurs due to stalled polysaccharide biosynthesis, which may allow polysaccharide diversity in the species to increase over time.

Importance

Enzymes involved in bacterial polysaccharide biosynthesis have substrate specificity to ensure the correct polysaccharide is produced at the appropriate place and time. However, this specificity poses a challenge for the diversification of polysaccharide structure and hence function, as the acquisition of a novel oligosaccharide RU would likely disrupt the synthesis pathways, leading to sequestration of the essential universal lipid carrier UndP and ultimately cause cell death. We investigated how cells tolerate disruptions in polysaccharide synthesis pathways and provide evidence that suggests that sharing a common substrate between the synthesis pathways of two common enteric bacterial surface polysaccharides (ECA and OAg), can redirect the flow of UndP. Our study provides insights into the mechanism of how bacteria alleviate sequestration issues, thereby enhancing cell survival which may allow them additional capacity for polysaccharide diversification.
Novel color vision assessment tool: AIM Color Detection and Discrimination
Authors: He Jingyi , Skerswetat Jan , Bex Peter J.
Published: September 2024

Color vision assessment is essential in clinical practice, yet different tests exhibit distinct strengths and limitations. Here we apply a psychophysical paradigm, Angular Indication Measurement (AIM) for color detection and discrimination. AIM is designed to address some of the shortcomings of existing tests, such as prolonged testing time, limited accuracy and sensitivity, and the necessity for clinician oversight. AIM presents adaptively generated charts, each a N×M (here 4×4) grid of stimuli, and participants are instructed to indicate either the orientation of the gap in a cone-isolating Landolt C optotype or the orientation of the edge between two colors in an equiluminant color space. The contrasts or color differences of the stimuli are adaptively selected for each chart based on performance of prior AIM charts. In a group of 23 color-normal and 15 people with color vision deficiency (CVD), we validate AIM color against Hardy-Rand-Rittler (HRR), Farnsworth-Munsell 100 hue test (FM100), and anomaloscope color matching diagnosis and use machine learning techniques to classify the type and severity of CVD. The results show that AIM has classification accuracies comparable to that of the anomaloscope, and while HRR and FM100 are less accurate than AIM and an anomaloscope, HRR is very rapid. We conclude that AIM is a computer-based, self-administered, response-adaptive and rapid tool with high test-retest repeatability that has the potential to be suitable for both clinical and research applications.
Resolution ofSLC6A1variable expressivity in a multi-generational family using deep clinical phenotyping andDrosophilamodels
Authors: Jay Kristy L. , Gogate Nikhita , Ezell Kim , Andrews Jonathan C. , Jangam Sharayu V. , Hall Paige I. , Pan Hongling , Pham Kelvin , German Ryan , Gomez Vanessa , Jellinek-Russo Emily , Storch Eric ,   Brain Gene Registry Consortium,   Undiagnosed Diseases Network, Yamamoto Shinya , Kanca Oguz , Bellen Hugo J. , Dierick Herman , Cogan Joy D. , Phillips John A. , Hamid Rizwan , Cassini Thomas , Rives Lynette , Posey Jennifer E. , Wangler Michael F.
Published: September 2024

Purpose

Variants inSLC6A1result in a rare neurodevelopmental disorder characterized by a variable clinical presentation of symptoms including developmental delay, epilepsy, motor dysfunction, and autism spectrum disorder.SLC6A1haploinsufficiency has been confirmed as the predominant pathway ofSLC6A1-related neurodevelopmental disorders (NDDs), however, the molecular mechanism underlying the variable clinical presentation remains unclear.

Methods

Here, through work of the Undiagnosed Diseases Network, we identify an undiagnosed individual with an inherited p.(A334S) variant of uncertain significance. To resolve this case and better understand the variable expressivity withSLC6A1, we assess the phenotypes of the proband with a cohort of cases diagnosed withSLC6A1-related NDDs. We then create an allelic series in theDrosophila melanogasterto functionally characterize case variants.

Results

We identify significant clinical overlap between the unsolved case and confirmed cases ofSLC6A1-related NDDs and find a mild to severe clinical presentation associated with missense variants. We confirm phenotypes in flies expressingSLC6A1variants consistent with a partial loss-of-function mechanism.

Conclusion

We conclude that the p.(A334S) variant is a hypomorphic allele and begin to elucidate the underlying variability inSLC6A1-related NDDs. These insights will inform clinical diagnosis, prognosis, treatment and inform therapeutic design for those living withSLC6A1-related NDDs.
Consensus guidelines for eligibility assessment of pathogenic variants to antisense oligonucleotide treatments
Authors: Cheerie David , Meserve Margaret , Beijer Danique , Kaiwar Charu , Newton Logan , Tavares Ana Lisa Taylor , Verran Aubrie Soucy , Sherrill Emma , Leonard Stefanie , Sanders Stephan J. , Blake Emily , Elkhateeb Nour , Gandhi Aastha , Liang Nicole S. Y. , Morgan Jack T. , Verwillow Anna , Verheijen Jan , Giles Andrew , Williams Sean , Chopra Maya , Croft Laura , Dafsari Hormos Salimi , Davidson Alice E. , Friedman Jennifer , Gregor Anne , Haque Bushra , Lechner Rosan , Montgomery Kylie-Ann , Ryten Mina , Schober Emil , Siegel Gabriele , Sullivan Patricia , Zardetto Bianca , Yu Timothy , Synofzik Matthis , Aartsma-Rus Annemieke , Costain Gregory , Lauffer Marlen C.
Published: September 2024

Of the around 7,000 known rare diseases worldwide, disease-modifying treatments are available for fewer than 5%, leaving millions of individuals without specialized therapeutic strategies. In recent years, antisense oligonucleotides (ASOs) have shown promise as individualized genetic interventions for rare genetic diseases. However, there is currently no consensus on which disease-causing DNA variants are suitable candidates for this type of genetic therapy. The Patient Identification Working Group of the N=1 Collaborative (N1C), alongside an international group of volunteer assessors, has developed and piloted consensus guidelines for assessing the eligibility of pathogenic variants towards ASO treatments. We herein present the N1C VARIANT (VariantAssessments towards Eligibility forAntisense OligonucleotideTreatment) guidelines, including the guiding scientific principles and our approach to consensus building. Pathogenic, disease-causing variants can be assessed for the three currently best-established ASO treatment approaches: splice correction, exon skipping, and downregulation of RNA transcripts. A genetic variant is classified as either “eligible”, “likely eligible”, “unlikely eligible”, or “not eligible” in relation to the different approaches, or “unable to assess”. We also review key considerations for assessment for upregulation of transcripts from the wildtype allele, an emerging ASO therapeutic strategy. We provide additional tools and training material to enable clinicians and researchers to use these guidelines for their eligibility assessments. With this initial edition of our N1C VARIANT guidelines, we provide the rare genetic disease community with guidance on how to identify suitable candidates for variant-specific ASO-based therapies and the possibility of integrating such assessments into routine clinical practice.