bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures
Authors: Charon Justine , Kahlke Tim , Larsson Michaela E. , Abbriano Raffaela , Commault Audrey , Burke Joel , Ralph Peter , Holmes Edward C. 
Published: May 2022

AbstractUnicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions on virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimised to detect highly divergent RNA viruses, we identified ten RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a great diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterisation and to investigate the effects of viral infections on microalgal physiology, biology and growth, considering their environmental and industrial roles.ImportanceIn comparison to animals or plants, our knowledge of the diversity of RNA viruses infecting microbial algae – the microalgae – is minimal. Yet describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economical levels because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte and euglena major clades of algae. This work identified ten new divergent RNA virus species, belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation
Authors: Shukla Harsh , Suryamohan Kushal , Khan Anubhab , Mohan Krishna , Perumal Rajadurai C. , Mathew Oommen K. , Menon Ramesh , Dixon Mandumpala Davis , Muraleedharan Megha , Kuriakose Boney , Michael Saju , Krishnankutty Sajesh P. , Zachariah Arun , Seshagiri Somasekar , Ramakrishnan Uma 
Published: May 2022

AbstractThe tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of their genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140□Mb, with 19□scaffolds, corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies which will improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 tRNAs and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to tiger’s apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of non-invasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics
Authors: Bittremieux Wout , Avalon Nicole E. , Thomas Sydney P. , Kakhkhorov Sarvar A. , Aksenov Alexander A. , P. Gomes Paulo Wender , Aceves Christine M. , Caraballo-Rodríguez Andrés Mauricio , Gauglitz Julia M. , Gerwick William H. , Huan Tao , Jarmusch Alan K. , Kaddurah-Daouk Rima F. , Kang Kyo Bin , Kim Hyun Woo , Kondić Todor , Mannochio-Russo Helena , Meehan Michael J. , Melnik Alexey V. , Nothias Louis-Felix , O’Donovan Claire , Panitchpakdi Morgan , Petras Daniel , Schmid Robin , Schymanski Emma L. , van der Hooft Justin J. J. , Weldon Kelly C. , Yang Heejung , Xing Shipei , Zemlin Jasmine , Wang Mingxun , Dorrestein Pieter C. 
Published: May 2022

AbstractDespite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
Evolution of personality and locomotory performance traits during a late Pleistocene island colonization in a treefrog
Authors: Bisconti Roberta , Carere Claudio , Costantini David , Liparoto Anita , Chiocchio Andrea , Canestrelli Daniele 
Published: May 2022

AbstractRecent empirical and theoretical studies suggest that personality and locomotory performance traits are crucial components of the dispersal syndromes, and that they can evolve during a dispersal process. Island colonisation is one the best characterized processes in dispersal biogeography, and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales. However, the effect of island colonization on personality and performance traits of natural populations has been little explored, and no studies have addressed these processes in the context of late-Pleistocene range expansions. Here, we investigated the contribution of island colonisations triggered by post-glacial range expansions to intraspecific variation in personality and locomotory performance traits. We compared boldness, exploration, jumping performance, and stickiness abilities, in three equidistant populations of the Tyrrhenian tree frogHyla sarda, two from the source area and one from the colonised island. Individuals from the colonised population were significantly bolder than individuals from the source area, as they emerged sooner from a shelter (p=0.028), while individuals from the source area showed markedly higher jumping and stickiness performance (both p<0.001). We discuss these results in the context of the major microevolutionary processes at play during range expansion, including selection, spatial sorting, and founder effects. However, irrespective of the processes contributing the most, our results clearly indicate that late Pleistocene climatic changes have had major consequences not just on species’ range dynamics, but also on the spatial patterns of phenotypic variation within species, including personality and locomotory traits variation.
Recapitulation of the embryonic transcriptional program in insect pupae
Authors: Ozerova Alexandra M , Gelfand Mikhail S. 
Published: May 2022

AbstractMetamorphosis of holometabolous insects is predominantly a motionless stage, when no active feeding is observed and the body is enclosed into the pupa. These physiological properties as well as undergoing processes resemble embryogenesis since at the pupal stage organs and systems of the imago are formed. Therefore recapitulation of the embryonic expression program during pupa development could be hypothesized. To assess this hypothesis at the transcriptome level, we have performed a comprehensive analysis of the developmental datasets available in the public domain. Indeed, for most datasets, the pupal gene expression resembles the embryonic rather than the larval pattern, interrupting gradual changes of the transcriptome. Moreover, changes in the transcriptome profile during the pupa-to-imago transition are positively correlated with those at the embryo-to-larvae transition, suggesting that similar expression programs are activated. Gene sets that change their expression level during the larval stage and revert it to the embryonic-like state during the metamorphosis are enriched with genes associated with metabolism and development.
The neurodevelopmental genesalan shepardandNeurogliancontribute to female mate preference in AfricanDrosophila melanogaster
Authors: Roy Paula R. , Castillo Dean M. 
Published: May 2022

AbstractMate choice is a key trait that determines fitness for most sexually reproducing organisms, with females often being the choosy sex. Female preference often results in strong selection on male traits that can drive rapid divergence of traits and preferences between lineages, leading to reproductive isolation. Despite this fundamental property of female mate choice, very few loci have been identified that contribute to mate choice and reproductive isolation. We used a combination of population genetics, quantitative complementation tests, and behavioral assays to demonstrate thatalan shepardandNeurogliancontribute to female mate choice, and could contribute to partial reproductive isolation between populations ofDrosophila melanogaster. Our study is among the first to identify genes that contribute to female mate preference in this historically important system, where female preference is an active premating barrier to reproduction. The identification of loci that are primarily known for their roles in neurodevelopment provides intriguing questions of how female mate preference evolves in populations via changes in sensory system and higher learning brain centers.
MHC-II molecules present RhoC-derived peptides on the surface of tumour cells
Authors: Thomas Pavana , Srivastava Sweta 
Published: May 2022

ABSTRACTRhoC is an important regulator of metastasis and tumour progression across various tumour models. Since RhoC has been found to have no major contribution towards normal embryogenic development, it has emerged as a suitable therapeutic target for effective cancer treatment. Recent evidence has shown that Rho-based peptide vaccines have favourable outcomes in prostate cancer patients, by bringing about activation of CD4+ T-cells. Antigen presentation on the surface of cells is brought about by the MHC-I/MHC-II complex. This work provides conclusive evidence to show that the seemingly cytosolic protein, RhoC, is in fact, present on the surface of tumour cells. This report goes on to prove that the presentation of RhoC peptides is brought about in association with MHC-II, becoming the first piece of scientific evidence to report this phenomenon.
Identification of representative trees in random forests based on a new tree-based distance measure
Authors: von Holt Björn-Hergen Laabs , Westenberger Ana , König Inke R. 
Published: May 2022

AbstractIn life sciences random forests are often used to train predictive models. However, gaining any explanatory insight into the mechanics leading to a specific outcome is rather complex, which impedes the implementation of random forests into clinical practice. By simplifying a complex ensemble of decision trees to a single most representative tree, it is assumed to be possible to observe common tree structures, the importance of specific features and variable interactions. Thus, representative trees could also help to understand interactions between genetic variants. Intuitively, representative trees are those with the minimal distance to all other trees, which requires a proper definition of the distance between two trees. Thus, we developed a new tree-based distance measure, which incorporates more of the underlying tree structure than other metrics. We compared our new method with the existing metrics in an extensive simulation study and applied it to predict the age at onset based on a set of genetic risk factors in a clinical data set. In our simulation study we were able to show the advantages of our weighted splitting variable approach. Our real data application revealed that representative trees are not only able to replicate the results from a recent genome-wide association study, but also can give additional explanations of the genetic mechanisms. Finally, we implemented all compared distance measures in R and made them publicly available in the R package timbR (https://github.com/imbs-hl/timbR).
All Staphylococcus aureus bacteraemia strains have the potential to cause infective endocarditis: results of GWAS and experimental animal studies
Authors: Bastien Sylvère , Meyers Severien , Salgado-Pabón Wilmara , Giulieri Stefano , Rasigade Jean-Phillipe , Liesenborghs Laurens , Kinney Kyle J. , Couzon Florence , Martins-Simoes Patricia , Le Moing Vincent , Duval Xavier , Holmes Natasha E , Bruun Niels Eske , Skov Robert , Howden Benjamin P , Fowler Vance G. , Verhamme Peter , Andersen Paal Skytt , Bouchiat Coralie , Moreau Karen , Vandenesch François 
Published: May 2022

Abstract and KeywordsAimsInfective endocarditis (IE) complicates 10-20% of Staphylococcus aureus bacteraemia (SAB). We aimed to determine whether IE strains of S. aureus are genotypically different or behave differently in experimental endocarditis models as compared to non-IE SAB strains.Methods and ResultsWe conducted a genome wide association study (GWAS) of 924 S. aureus genomes from IE (274) and non-IE (650) SAB patients, and tested a subset of strains in two experimental animal models of IE, one studying the early step of bacterial adhesion to inflamed mice valves, the second evaluating the local and systemic developmental process of IE on mechanically damaged rabbit valves. The genetic profile of S. aureus IE and non-IE SAB strains did not differ when considering single nucleotide polymorphisms, coding sequences and k-mers analyses in GWASs. In the inflammation-induced IE model in mice no difference was observed between IE and non-IE SAB strains both in adhesion to the cardiac valves and in the propensity to cause IE; in the mechanical IE-induced rabbit model, there was no difference between IE and non-IE SAB strains regarding vegetation size and CFU.ConclusionS. aureus isolates from SAB patients with and without IE were indistinguishable, by GWAS and by two in vivo models of IE. Thus, S. aureus strain variation is not the primary determinant of IE. Pending the possible identification of host factors predisposing to IE, all strains of S. aureus must be considered in patients as capable of causing this common, lethal infection once they have accessed the bloodstream.Translational PerspectiveStaphylococcus aureus endocarditis (IE) is a deadly complication of S. aureus bacteraemia (SAB). Beyond well-identified host related IE risk factors, whether bacterial features may influence the occurrence of IE in the course of bacteraemia remain elusive. We analysed the genomes of 924 S. aureus strains from IE and non-IE SAB and compared some in two in vivo IE models. We demonstrated that the propensity of S. aureus to cause IE in the course of bacteraemia does not depend on the intrinsic genetic or virulence factors of S. aureus. These findings are of importance for the management of S. aureus bacteraemia.
SARS-CoV-2 ORF1abA1061S potentiate autoreactive T cell responses via epitope mimicry: an explanation to hepatitis of unknown cause
Authors: Wang Yu , Liu Yuexing 
Published: May 2022

AbstractThe World Health Organization have recently announced outbreak news of acute, severe hepatitis of unknown cause in children under a Covid-19 pandemic. Whether it is associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is still under debating. Here, we performed genomic sequence alignment analysis of the genome of SARS-Cov-2 (Wuhan-hu-1) to the human genome reference. Sequence analysis revealed that the SARS-CoV-2 ORF1ab1056-1173 presented high identities with the human protein PAPR1453-176(3Q6Z_A). After searching the fully sequenced SARS-CoV-2 genomes deposited in GISAID (https://www.gisaid.org/), we detected 170 SARS-CoV-2 variants with mutation in ORF1ab1061, where alanine (A) was substituted by serine (S). This alteration made a 7-amino acid peptide (VVVNASN) in ORF1ab1056-1062 identical to its counterpart in PARP1453-59(3Q6Z_A). HLA prediction suggested that the peptides with high identities in PARP14 and ORF1ab could be presented by a same globally prevalent HLA-A*11:01 molecule. And in consistent with the first reported case of hepatitis of unknown, SARS-CoV-2 ORF1abVVVNASN variants were mostly identified as Delta lineages in UK by the late 2021, with an overall frequency of 0.00161%. Thus, our preliminary results raised a possibility that infection by SARS-CoV-2 ORF1abVVVNASN variant might elicit an autoimmune T cell response via epitope mimicry and is associated with the outbreak of unknown hepatitis. We anticipated that these findings will alert the human societies to pay more attention to rare mutations beyond the spike proteins.
Retina Gap Junction Networks Facilitate Blind Denoising in the Visual Hierarchy
Authors: Yue Yang , Lun Kehuan , He Liuyuan , He Gan , Zhang Shenjian , Ma Lei , Liu Jian.K. , Tian Yonghong , Du Kai , Huang Tiejun 
Published: May 2022

AbstractGap junctions in the retina are electrical synapses, which strength is regulated byambient light conditions. Such tunable synapses are crucial for the denoising function of the early visual system. However, it is unclear that how the plastic gap junction network processes unknown noise, specifically how this process works synergistically with the brain’s higher visual centers. Inspired by the electrically coupled photoreceptors, we develop a computational model of the gap junction filter (G-filter). We show that G-filter is an effective blind denoiser that converts different noise distributions into a similar form. Next, since deep convolutional neural networks (DCNNs) functionally reflect some intrinsic features of the visual cortex, we combine G-filter with DCNNs as retina and ventral visual pathways to investigate the relationship between retinal denoising processing and the brain’s high-level functions. In the image denoising and reconstruction task, G-filter dramatically improve the classic deep denoising convolutional neural network (DnCNN)’s ability to process blind noise. Further, we find that the gap junction strength of the G-filter modulates the receptive field of DnCNN’s output neurons by the Integrated Gradients method. At last, in the image classification task, G-filter strengthens the defense of state-of-the-arts DCNNs (ResNet50, VGG19 and InceptionV3) against blind noise attacks, far exceeding human performance when noise is large. Our results indicate G-filter significantly enhance DCNNs’ ability on various blind denoising tasks, implying an essential role for retina gap junction networks in high-level visual processing.
Network Topology Metrics Explaining Enrichment of Hybrid Epithelial Mesenchymal Phenotypes in Metastasis
Authors: Rashid Mubasher , Hari Kishore , Thampi John , Santhosh Nived Krishnan , Jolly Mohit Kumar 
Published: May 2022

AbstractEpithelial to mesenchymal transition (EMT) and its reverse mesenchymal to epithelial transition (MET) are hallmarks of metastasis. Cancer cells use this reversible cellular programming to switch among Epithelial (E), Mesenchymal (M), and hybrid Epithelial/Mesenchymal (hybrid E/M) state(s) and seed tumors at distant sites. Hybrid E/M cells are often more aggressive and metastatic than the “pure” E and M cells. Thus, identifying mechanisms to inhibit hybrid E/M cells can be promising in curtailing metastasis. While multiple gene regulatory networks (GRNs) based mathematical models for EMT/MET have been developed recently, identifying topological signatures enriching for hybrid E/M phenotypes remains to be done. Here, we investigate the dynamics of 13 different GRNs and identify which network topologies can enrich for hybrid E/M phenotype(s) across GRNs. We found that increasing negative feedback loops enhances the “hybridness” of these networks, but increasing the number of positive feedback loops or their specific combinations can decrease the frequency of hybrid E/M phenotype. Thus, our analysis identifies network topology based signatures that can give rise to, as well as prevent, the emergence of hybrid E/M phenotype in GRNs underlying EMP. Our results can have implications in terms of targeting specific interactions in GRNs as a potent way to restrict switching to the hybrid E/M phenotype(s) to curtail metastasis.