bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted nanopore resequencing and methylation analysis of LINE-1 retrotransposons
Authors: Sarkar Arpita , Lanciano Sophie , Cristofari Gael 
Published: June 2022

SummaryRetrotransposition of LINE-1 (L1) elements represent a major source of insertional polymorphisms in mammals and their mutagenic activity is restricted by silencing mechanisms, such as DNA methylation. Despite a very high level of sequence identity between copies, their internal sequence contains small nucleotide polymorphisms (SNPs) that can alter their activity. Such internal SNPs can also appear in different alleles of a given L1 locus. Given their repetitive nature and relatively long size, short-read sequencing approaches have limited access to L1 internal sequence or DNA methylation state. Here we describe a targeted method to specifically sequence more than a hundred L1-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (∼45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. Our protocol, modified from the nanopore Cas9 targeted sequencing (nCATS) strategy, provides a full and haplotype-resolved L1 sequence and DNA methylation levels. It introduces a streamlined and multiplex approach to synthesize guide RNAs and a quantitative PCR (qPCR)-based quality check during library preparation for cost-effective L1 sequencing. More generally, this method can be applied to any type of transposable elements and organisms.
Disruptive selection via pollinators and seed predators on the height of flowers in a wind-dispersed alpine herb
Authors: Chen Kai-Hsiu , Pannell John R. 
Published: June 2022

ABSTRACTPremise of the studyFloral stalk height is known to affect pollination and seed dispersal in wind-dispersed grassland species, but it may also affect the attractiveness of flowers and fruits in animal-pollinated and animal-dispersed plants. Stalk height may thus be responsive to selection via interactions with both mutualist pollinators and seed dispersers, but also antagonist florivors and seed predators. In this study, we aimed to determine the effect of pollinators and seed predators on selection on floral stalk height in the insect-pollinated and wind-dispersed alpine andromonoecious herbPulsatilla alpina, whose flowers also vary in their sex allocation and thus in the resources available to both mutualists and antagonists.MethodsWe measured the resource status of individuals in terms of their size and the height of the vegetation surrounding plants ofP. alpinaat eleven sites. In one population, we recorded the dynamics of floral stalk height over the course of an entire growing season and its association with floral morphology and floral sex allocation (pistil and stamen number), and we used leaf-removal manipulations to assess the effect of herbivory on floral stalk height. Finally, in four populations we studied phenotypic selection on floral stalk height in four female components of reproductive success before seed dispersal.Key resultsStalk height was positively associated with female allocation of the respective flower, the resource status of the individual, and the height of the surrounding vegetation, and negatively affected by leaf removal. Our results point to disruptive selection on stalk height in terms of both selection differentials and selection gradients for fertilization, seed predation, and seed maturation rates, and to positive selection on stalk height in terms of a selection differential for mature seed number.ConclusionsStalk height inP. alpinais a costly trait that affects female reproductive success via interactions with both mutualists and antagonists. We discuss the interplay between the resource status and selection imposed on female reproductive success and its likely role in the evolution of sex-allocation strategies, especially andromonoecy.
TREE-QMC: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
Authors: Han Yunheng , Molloy Erin K. 
Published: June 2022

AbstractSummary methods are one of the dominant approaches for estimating species trees from genome-scale data. However, they can fail to produce accurate species trees when the input gene trees are highly discordant due to gene tree estimation error as well as biological processes, like incomplete lineage sorting. Here, we introduce a new summary method TREE-QMC that offers improved accuracy and scalability under these challenging scenarios. TREE-QMC builds upon the algorithmic framework of QMC (Snir and Rao 2010) and its weighted version wQMC (Avni et al. 2014). Their approach takes weighted quartets (four-leaf trees) as input and builds a species tree in a divide-and-conquer fashion, at each step constructing a graph and seeking its max cut. We improve upon this methodology in two ways. First, we address scalability by providing an algorithm to construct the graph directly from the input gene trees. By skipping the quartet weighting step, TREE-QMC has a time complexity ofO(n3k) with some assumptions on subproblem sizes, wherenis the number of species andkis the number of gene trees. Second, we address accuracy by normalizing the quartet weights to account for “artificial taxa,” which are introduced during the divide phase so that solutions on subproblems can be combined during the conquer phase. Together, these contributions enable TREE-QMC to outperform the leading methods (ASTRAL-III, FASTRAL, wQFM) in an extensive simulation study. We also present the application of these methods to an avian phylogenomics data set.
Insulin signaling and extended longevity in ants
Authors: Yan Hua , Opachaloemphan Comzit , Carmona-Aldana Francisco , Mancini Giacomo , Mlejnek Jakub , Descostes Nicolas , Sieriebriennikov Bogdan , Leibholz Alexandra , Zhou Xiaofan , Ding Long , Traficante Maria , Desplan Claude , Reinberg Danny 
Published: June 2022

AbstractIn most organisms, the cost of reproduction is a shorter lifespan. However, the reproductive caste in eusocial insect species (queen) exhibits an extraordinarily longer lifespan than non-reproductive castes (workers) despite having a similar genome, thus contradicting the aging dogma. In the absence of the queen, Harpegnathos saltator ants can undergo a caste switch from workers to reproductive pseudo-queens (gamergates). Gamergates exhibit a dramatically prolonged lifespan. When placed in the presence of a reproductive, they revert to worker status and their lifespan is then shortened accordingly.To understand this unique relationship between reproduction and longevity, we analyzed tissue-specific gene expression between castes. Insulin is upregulated in the gamergate brain that leads to oogenesis, but surprisingly correlates with extended longevity. This correlates with increased lipid synthesis and elevated production of vitellogenin in the fat body, which are both transported to the egg. We show that the production of vitellogenin in the fat body is due to the systemic activation of the MAPK branch of the insulin/IGF signaling (IIS)-pathway. In contrast, reduced expression of insulin receptors in the fat body of gamergates and the production in their developing ovary of an anti-insulin (Imp-L2) lead to the downregulation of the AKT/FOXO branch of the IIS-signaling pathway in the fat body, and to the dramatically extended longevity. This reveals a dual-pathway mechanism that reconciles increased longevity in the context of active reproduction in eusocial insects.One Sentence SummaryInsulin-dependent reproduction in ants correlates with extended longevity through insulin inhibition by anti-insulin Imp-L2.
Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
Authors: Racle Julien , Guillaume Philippe , Schmidt Julien , Michaux Justine , Larabi Amédé , Lau Kelvin , Perez Marta A. S. , Croce Giancarlo , Genolet Raphaël , Coukos George , Zoete Vincent , Pojer Florence , Bassani-Sternberg Michal , Harari Alexandre , Gfeller David 
Published: June 2022

AbstractCD4+ T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on MHC-II molecules. The high polymorphism of MHC-II genes represents an important hurdle towards accurate prediction and identification of CD4+ T-cell epitopes in different individuals and different species. Here we collected and curated a dataset of 627,013 unique MHC-II ligands identified by mass spectrometry. This enabled us to precisely determine the binding motifs of 88 MHC-II alleles across human, mouse, cattle and chicken. Analysis of these binding specificities combined with X-ray crystallography refined our understanding of the molecular determinants of MHC-II motifs and revealed a widespread reverse binding mode in MHC-II ligands. We then developed a machine learning framework to accurately predict binding specificities and ligands of any MHC-II allele. This tool improves and expands predictions of CD4+ T-cell epitopes, and enabled us to discover and characterize several viral and bacterial epitopes following the aforementioned reverse binding mode.
A deep learning approach reveals unexplored landscape of viral expression in cancer
Authors: Elbasir Abdurrahman , Ye Ying , Schäffer Daniel E. , Hao Xue , Wickramasinghe Jayamanna , Tsingas Konstantinos , Lieberman Paul M. , Long Qi , Morris Quaid , Zhang Rugang , Schäffer Alejandro A. , Auslander Noam 
Published: June 2022

AbstractAbout 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
Infection-competent monkeypox virus contamination identified in domestic settings following an imported case of monkeypox into the UK
Authors: Atkinson Barry , Burton Christopher , Pottage Thomas , Thompson Katy-Anne , Ngabo Didier , Crook Ant , Pitman James , Summers Sian , Lewandowski Kuiama , Furneaux Jenna , Davies Katherine , Brooks Timothy , Bennett Allan M , Richards Kevin S. 
Published: June 2022

AbstractAn imported case of monkeypox was diagnosed in December 2019 in a traveller returning from Nigeria to the UK. Subsequently, environmental sampling was performed at two adjoining single room residences occupied by the patient and their sibling. Monkeypox virus DNA was identified in multiple locations throughout both properties, and monkeypox virus was isolated from several samples three days after the patient was last in these locations. Positive samples were identified following use of both vacuum and surface sampling techniques; these methodologies allowed for environmental analysis of potentially contaminated porous and non-porous surfaces via real-time quantitative PCR analysis in addition to viral isolation to confirm the presence of infection-competent virus.This report confirms the potential for infection-competent monkeypox virus to be recovered in environmental settings associated with known positive cases and the necessity for rapid environmental assessment to reduce potential exposure to close contacts and the general public. The methods adopted in this investigation may be used for future confirmed cases of monkeypox in order to establish levels of contamination, confirm the presence of infection-competent material, and to identify locations requiring additional cleaning.Originality-Significance StatementSeveral imported cases of human monkeypox infection, an emerging infectious disease with a case fatality rate of up to 10%, have been identified in recent years including importations into the United Kingdom, the United States, Israel, and Singapore. It is likely that this phenomenon relates to decreased immunity against monkeypox infection in endemic regions that was previously provided via the smallpox vaccination programme. It is therefore likely that further imported cases of monkeypox will be reported in future; such occurrences will require significant clinical oversight, including suitable infection control measures. Environmental sampling to identify contaminated sites that may pose a risk can inform infection control guidance. This report documents an environmental sampling response following an imported case detected in late 2019 in the UK. Monkeypox virus DNA was readily identified in numerous locations throughout two domestic residences associated with the infected patient and infectious virus was isolated from several environmental samples confirming that contaminated environmental settings may pose a risk for onward transmission. The methods utilised in this report may advise future environmental responses following cases of this high consequence emerging viral disease in order to prevent secondary cases in close contacts or members of the public.
Digitalization impacts the COVID-19 pandemic and the stringency of government measures
Authors: Heinrichs Helen , Mueller Florian , Rohfleisch Lucia , Schulz Volkmar , Talbot Steven R. , Kiessling Fabian 
Published: June 2022

AbstractCOVID-19 poses a significant burden on populations worldwide. Although the pandemic has accelerated digital transformation, little is known about digitalization’s influence on pandemic developments. Using the Digital Adoption Index (DAI), we examined the effects of digitalization on early COVID-19 cases, deaths, and stringency indices (SI) of government measures. Gradient Tree Boosting pinpointed essential features, such as populations’ smoker fraction, age, poverty, and DAI. Then, regression analyses indicated that higher DAI was associated with significant declines in new cases (β=-362.25/pm;p<0.001) and deaths (β=-5.53/pm;p<0.001) months after the peak. Over the entire range, higher DAI was associated with higher mean SI (β=4.86;p<0.01). Interestingly, however, in countries with high DAI >0.68, the correlation inverted (β=-55.26;p<0.05). Finally, a scoping review identified 70 publications providing valuable arguments for our findings. Thus, digitalization is evident for handling current and future pandemics but can also facilitate stronger government actions restricting individual freedom.
The Effect of Negative Pressure on IOP in the Living Human Eye
Authors: Fazio Massimo A. , Bianco Gianfranco , Karuppanan Udayakumar , Hubbard Meredith , Bruno Luigi , Girkin Christopher A. 
Published: June 2022

PurposeTo quantify the effect of negative pressure applied to the anterior surface of the eye on absolute IOP.SubjectsParticipants, and/or Controls. Three eyes from three research-consented brain-dead organ donors.MethodsAir-tight goggles connected to a negative pressure (NP) pump (Mercury Multi-pressure Dial (MPD); Equinox Ophthalmic, Inc., CA) were tested on three research consented brain-dead organ donors. The MPD was set to generate a vacuum of −20mmHg. A baseline IOP of 10, 20, and 30mmHg was sequentially set by adjusting the height of a balanced salt solution bottle connected to the cornea through a 20G needle. IOP was manually annotated at time = 0s, right before turning on the vacuum pump; after a few seconds with the vacuum pump ON; at 60s; at 120s, right before turning the pump OFF; at 240s with the pump OFF (recovery). Three repetitions per each test at varying baseline IOP were taken for a total of nine series of measures per eye.MainOutcomeMeasuresIOP change with exposure to NP.ResultsEye1 and 3 showed an immediate reduction in IOP at all baselines immediately following activation of the MPD NP pump; Eye2 showed an opposite response to NP. Eye1 and 3 showed a reduction in IOP at all baselines with NP pump ON for 60s and 120s, while Eye 2 showed a consistent increase in IOP. After 120s from turning NP OFF (time=240s), IOP partially recovered to its baseline in all eyes.ConclusionsThis study is the first to evaluate changes in manometrically-measured intracameral IOP due to NP applied to the ocular surface in living conditions. The inconsistent response of IOP following exposure to negative pressure warrants further investigations on the mechanism underlaying IOP lowering by NP.
Pre-existing immunity modulates responses to mRNA boosters
Authors: Dangi Tanushree , Sanchez Sarah , Lew Min Han , Visvabharathy Lavanya , Richner Justin , Koralnik Igor J. , Penaloza-MacMaster Pablo 
Published: June 2022

AbstractmRNA vaccines have shown high efficacy in preventing severe COVID-19, but breakthrough infections, emerging variants and waning antibody levels have warranted the use of boosters. Although mRNA boosters have been widely implemented, the extent to which pre-existing immunity influences the efficacy of boosters remains unclear. In a cohort of individuals primed with the mRNA-1273 or BNT162b2 vaccines, we observed that lower antibody levels before boost were associated with higher fold-increase in antibody levels after boost, suggesting that pre-existing antibody modulates the boosting capacity of mRNA vaccines. Mechanistic studies in mice show that pre-existing antibodies significantly limit antigen expression and priming of B cell responses after mRNA vaccination. Furthermore, we demonstrate that the relative superiority of an updated Omicron vaccine over the original vaccine is critically dependent on the serostatus of the host. These data demonstrate that pre-existing immunity dictates responses to mRNA vaccination, elucidating specific circumstances when updated SARS-CoV-2 vaccines confer superior protection to original vaccines.
L-norepinephrine Induces Community Shift, Oxidative Stress Response, Metabolic Reprogramming, and Virulence Potential in Wastewater Microbiomes
Authors: Bains Amrita , Dahal Sanjeev , Manna Bharat , Lyte Mark , Yang Laurence , Singhal Naresh 
Published: June 2022

AbstractNeuroendocrine compounds discharged into wastewater systems represent an emerging challenge at the intersection of human physiology and environmental microbiology. L-norepinephrine (L-NE) L-NE, which has been recognized to potentiate growth of human and animal bacterial pathogens, is discharged in sewage through urine and feces. While extensive pure culture studies have established L-NE’s capacity to modulate bacterial virulence through iron acquisition and quorum sensing pathways, its impact on complex microbial communities, where intricate metabolic networks and interspecies interactions dominate, remains largely unexplored. This knowledge gap is particularly critical as urbanization drives increasing neuroendocrine compound loads in wastewater influents in metropolitan areas. Through parallel treatments of L-NE (1×10□□ to 1×10□□ M), dextrose, and H□O□ in municipal and agricultural wastewater communities, we uncovered sophisticated metabolic and regulatory mechanisms that challenge the conventional understanding of microbial substrate utilization. Despite containing 10-fold less carbon, L-NE treatments achieved superior growth (10□ CFU mL□¹) while maintainingPseudomonadaceae-dominated communities. Targeted metaproteomics revealed coordinated upregulation of oxidative stress genes (oxyR,soxRS) and antioxidant enzymes, while proteome-constrained metabolic modeling demonstrated distinct pathway modulation in central carbon and nitrogen metabolism. Notably, when compared to dextrose-supplemented controls representing typical carbon substrate utilization, L-NE treatments showed similar taxonomic profiles without preferential enrichment of known pathogenic families. However, L-NE significantly enhanced autoinducer gene (luxS,qseC) expression, suggesting increased virulence potential through community-level metabolic reprogramming. These findings reveal L-NE as a potent modulator of microbial community dynamics in engineered ecosystems, with important implications for treatment process stability and downstream environmental impacts.TOC Figure
Crystal structure of the membrane (M) protein from a SARS-COV-2-related coronavirus
Authors: Wang Xiaodong , Yang Yuwei , Sun Ziyi , Zhou Xiaoming 
Published: June 2022

AbstractThe membrane (M) protein is the most abundant structural protein of coronaviruses including SARS-COV-2 and plays a central role in virus assembly through its interaction with various partner proteins. However, mechanistic details about how M protein interacts with others remain elusive due to lack of high-resolution structures. Here, we present the first crystal structure of a coronavirus M protein from Pipistrellus bat coronavirus HKU5 (batCOV5-M), which is closely related to SARS-COV-2 M protein. Furthermore, an interaction analysis indicates that the carboxy-terminus of the batCOV5 nucleocapsid (N) protein mediates its interaction with batCOV5-M. Combined with a computational docking analysis an M-N interaction model is proposed, providing insight into the mechanism of M protein-mediated protein interactions.
Functional unknomics: closing the knowledge gap to accelerate biomedical research
Authors: Rocha Joao , Jayaram Satish Arcot , Stevens Tim J. , Muschalik Nadine , Shah Rajen D. , Emran Sahar , Robles Cristina , Freeman Matthew , Munro Sean 
Published: June 2022

SummaryThe human genome encodes ∼20,000 proteins, many still uncharacterised. Scientific and social factors have resulted in a focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed an “Unknome database” that ranks proteins based on how little is known about them. We applied RNAi inDrosophilato 260 unknown genes that are conserved between flies and humans. About a quarter are required for viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and two genes contributing to male fertility. Our work demonstrates the importance of poorly understood genes, provides a resource for future research acceleration, and highlights a need for our awareness of ignorance to be protected from erosion by automated database annotation.