bluuebunny/crossref_metadata_2025_split huggingface dataset:
Template switching during DNA replication is a prevalent source of adaptive gene amplification
Authors: Chuong Julie N. , Nun Nadav Ben , Suresh Ina , Matthews Julia Cano , De Titir , Avecilla Grace , Abdul-Rahman Farah , Brandt Nathan , Ram Yoav , Gresham David 
Published: May 2024

AbstractCopy number variants (CNVs)—gains and losses of genomic sequences—are an important source of genetic variation underlying rapid adaptation and genome evolution. However, despite their central role in evolution little is known about the factors that contribute to the structure, size, formation rate, and fitness effects of adaptive CNVs. Local genomic sequences are likely to be an important determinant of these properties. Whereas it is known that point mutation rates vary with genomic location and local DNA sequence features, the role of genome architecture in the formation, selection, and the resulting evolutionary dynamics of CNVs is poorly understood. Previously, we have found that theGAP1gene inSaccharomyces cerevisiaeundergoes frequent and repeated amplification and selection under long-term experimental evolution in glutamine-limiting conditions. TheGAP1gene has a unique genomic architecture consisting of two flanking long terminal repeats (LTRs) and a proximate origin of DNA replication (autonomously replicating sequence, ARS), which are likely to promote rapidGAP1CNV formation. To test the role of these genomic elements on CNV-mediated adaptive evolution, we performed experimental evolution in glutamine-limited chemostats using engineered strains lacking either the adjacent LTRs, ARS, or all elements. Using a CNV reporter system and neural network simulation-based inference (nnSBI) we quantified the formation rate and fitness effect of CNVs for each strain. We find that althoughGAP1CNVs repeatedly form and sweep to high frequency in strains with modified genome architecture, removal of local DNA elements significantly impacts the rate and fitness effect of CNVs and the rate of adaptation. We performed genome sequence analysis to define the molecular mechanisms of CNV formation for 177 CNV lineages. We find that across all four strain backgrounds, between 26% and 80% of allGAP1CNVs are mediated by Origin Dependent Inverted Repeat Amplification (ODIRA) which results from template switching between the leading and lagging strand during DNA synthesis. In the absence of the local ARS, a distal ARS can mediate CNV formation via ODIRA. In the absence of local LTRs, homologous recombination mechanisms still mediate gene amplification followingde novoinsertion of retrotransposon elements at the locus. Our study demonstrates the remarkable plasticity of the genome and reveals that template switching during DNA replication is a frequent source of adaptive CNVs.
Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia
Authors: Watanabe Yusuke , Wakiyama Yoshiki , Waku Daisuke , Valverde Guido , Tanino Akio , Nakamura Yuka , Suzuki Tsubasa , Koganebuchi Kae , Gakuhari Takashi , Katsumura Takafumi , Ogawa Motoyuki , Toyoda Atsushi , Mizushima Soichiro , Nagaoka Tomohito , Hirata Kazuaki , Yoneda Minoru , Nishimura Takayuki , Izuho Masami , Yamada Yasuhiro , Masuyama Tadayuki , Takahashi Ryuzaburo , Ohashi Jun ,   NCBN Controls WGS Consortium, Oota Hiroki 
Published: May 2024

ABSTRACTPrevious genomic studies understanding the dispersal ofHomo sapienshave suggested that present-day East Eurasians and Native Americans can trace their ancestry to migrations from Southeast Asia. However, ineluctable adaptations during the Last Glacial Maximum (LGM) remain unclear. By analyzing 42 genomes of up to 30-fold coverage from prehistoric hunter-gatherers, Jomon, we reveal their descent from Upper Paleolithic (UP) foragers who migrated to and isolated in the Japanese archipelago during Late Pleistocene. We provide compelling evidence suggesting that these UP people underwent positive selection for cold environments, aiding their survival through the LGM facilitated by non-shivering thermogenesis and detecting it polygenically across multiple loci in the Jomon lineage. Our study pioneers the close estimation of the physiological adaptation of ancient humans by the paleogenomic approach.
Seabird and sea duck mortalities were lower during the second breeding season in eastern Canada following the introduction of Highly Pathogenic Avian Influenza A H5Nx viruses
Authors: Cormier Tabatha L. , Barychka Tatsiana , Beaumont Matthieu , Burt Tori V. , English Matthew D , Giacinti Jolene A. , Giroux Jean-François , Guillemette Magella , Hargan Kathryn E. , Jones Megan , Lair Stéphane , Lang Andrew S. , Lepage Christine , Montevecchi William A. , Rahman Ishraq , Rail Jean-François , Robertson Gregory J. , Ronconi Robert A. , Seyer Yannick , Taylor Liam U. , Ward Christopher R. E. , Wight Jordan , Wilhelm Sabina I. , Avery-Gomm Stephanie 
Published: May 2024

SummaryH5N1 clade 2.3.4.4b viruses have caused significant mortality events in various wild bird species across Europe, North America, South America, and Africa. In North America, the largest impacts on wild birds have been in eastern Canada, where over 40,391 wild birds were reported to have died from highly pathogenic avian influenza (HPAI) between April and September 2022. In the year following, we applied previously established methods to quantify total reported mortality in eastern Canada for a full year October 2022, to September 2023. In this study, we (i) document the spatial, temporal and taxonomic patterns of wild bird mortality in the 12 months that followed the mass mortality event in the summer of 2022 and (ii) quantify the observed differences in mortality across the breeding season (April to September) of 2022 and 2023. In eastern Canada, there was high uncertainty about whether 2023 would bring another year of devastating HPAI-linked mortalities. Mortalities in the breeding season were 93% lower in 2023 compared to 2022 but encompassed a more taxonomically diverse array of species. We found that mortalities in the fall and winter (non-breeding season) were dominated by waterfowl, while mortalities during the spring and summer (breeding season) were dominated by seabirds. Due to a low prevalence of HPAI among the subset of tested birds, we refrained from broadly attributing reported mortalities in 2023 to HPAI. However, our analysis did identify three notable mortality events linked to HPAI, involving at least 1,646 Greater Snow Geese, 232 Canada Geese, and 212 Northern Gannets.This study emphasizes the ongoing need for H5NX surveillance and mortality assessments as the patterns of mortality in wild populations continue to change.
Prediction of KIR3DL1/Human Leukocyte Antigen binding
Authors: Maiers Martin , Louzoun Yoram , Pymm Philip , Vivian Julian P. , Rossjohn Jamie , Brooks Andrew G , Saunders Philippa M. 
Published: May 2024

AbstractKIR3DL1 is a polymorphic inhibitory Natural Killer (NK) cell receptor that recognizes Human Leukocyte Antigen (HLA) class I allotypes that contain the Bw4 motif. Structural analyses have shown that in addition to residues 77-83 that span the Bw4 motif, polymorphism at other sites throughout the HLA molecule can influence the interaction with KIR3DL1. Given the extensive polymorphism of both KIR3DL1 and HLA class I, we built a machine learning prediction model to describe the influence of allotypic variation on the binding of KIR3DL1 to HLA class I. Nine KIR3DL1 tetramers were screened for reactivity against a panel of HLA class I molecules which revealed different patterns of specificity for each KIR3DL1 allotype. Separate models were trained for each of KIR3DL1 allotypes based on the full amino sequence of exons 2 and 3 encoding theα1 andα2 domains of the class I HLA allotypes, the set of polymorphic positions that span the Bw4 motif, or the positions that encodeα1 andα2 but exclude the connecting loops. The Multi-Label-Vector-Optimization (MLVO) model trained on all alpha helix positions performed best with AUC scores ranging from 0.74 to 0.974 for the 9 KIR3DL1 allotype models. We show that a binary division into binder and non-binder is not precise, and that intermediate levels exist. Using the same models, within the binder group, high- and low-binder categories can also be predicted, the regions in HLA affecting the high vs low binder being completely distinct from the classical Bw4 motif. We further show that these positions affect binding affinity in a nonadditive way and induce deviations from linear models used to predict interaction strength. We propose that this approach should be used in lieu of simpler binding models based on a single HLA motif.
miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs
Authors: Baran Andrea M. , Patil Arun H. , Aparicio-Puerta Ernesto , Halushka Marc K. , McCall Matthew N. 
Published: May 2024

AbstractMicroRNA-seq data is produced by aligning small RNA sequencing reads of different miRNA transcript isoforms, called isomiRs, to known microRNAs. Aggregation to microRNA-level counts discards information and violates core assumptions of differential expression (DE) methods developed for mRNA-seq data. We establish miRglmm, a DE method for microRNA-seq data, that uses a generalized linear mixed model of isomiR-level counts, facilitating detection of miRNA with differential expression or differential isomiR usage. We demonstrate that miRglmm outperforms current DE methods in estimating DE for miRNA, whether or not there is significant isomiR variability, and simultaneously provides estimates of isomiR-level DE.
GUIDE deconstructs genetic architectures using association studies
Authors: Lazarev Daniel , Chau Grant , Bloemendal Alex , Churchhouse Claire , Neale Benjamin M 
Published: May 2024

AbstractGenome-wide association studies have revealed that the genetic architecture of most complex traits is characterized by a large number of distinct effects scattered across the genome. Functional enrichment analyses of these results suggest that the associations for any given complex trait are not purely random. Thus, we set out to leverage the genetic association results from many traits with a view to identifying the set of modules, or latent factors, that mediate these associations. The identification of such modules may aid in disease classification as well as the elucidation of complex disease mechanisms. We propose a method, Genetic Unmixing by Independent Decomposition (GUIDE), to estimate a set of statistically independent latent factors that best express the patterns of association across many traits. The resulting latent factors not only have desirable mathematical properties, such as sparsity and a higher variance explained (for both traits and variants), but are also able to single out and prioritize key biological features or pathophysiological mechanisms underlying a given trait or disease. Moreover, we show that these latent factors can index biological pathways as well as epidemiological and environmental influences that compose the genetic architecture of complex traits.
Validating the Target Functions and Synergistic Multi-Target, Multi-Pathway Action Mode of Compound Kushen Injection Using CRISPR/CAS
Authors: Shen Hanyuan , Nourmohammadi Saeed , Zhou Yan , Harata-Lee Yuka , Qu Zhipeng , Wang Wei , Yool Andrea J , Adelson David L. 
Published: May 2024

AbstractBackground and PurposeDue to the complexity of traditional Chinese medicine based on complex mixtures of natural products and their multi-target mechanism of action, the discovery and validation of relevant targets have always been challenging. In previous studies, using transcriptomic methods and Compound Kushen Injection (CKI) as a model drug, we identified multiple pathways and target genes through which CKI exerts its pharmacological effects. Therefore, we wished to verify these targets by perturbing those genetic pathways.Experimental ApproachIn this study, we selected eight key genes from four candidate pathways and used CRISPR/CAS technology to knock out these genes in four cell lines, validating their role in CKI activity.Key ResultsFirstly, we found that although the sensitivity of different cell lines to gene knockout varied, overall, it led to a reduction in various cellular activities. After the addition of CKI, we observed that, except for the minor impact of CDKN1A gene knockout on the effect of CKI, knocking out the other genes significantly affected the pharmacological efficacy of CKI in different assays. Among them, knockout of MYD88 and NFkB genes enhanced the efficacy of CKI. At the same time, we found that the genes IL24 and CYP1B1 play a crucial role in CKI inhibition of tumour cell migration, and the CYP1A1 gene is critical for the cell cycle arrest induced by CKI.Conclusion and ImplicationsThese findings not only validate the results of our previous transcriptomic analysis but also further demonstrate the complexity of pharmacological mechanisms of multi-target synergistic action of natural product mixtures.What is already knownCKI demonstrates antitumor effects in both clinical and pharmacological research. Transcriptomic analysis shows CKI can perturb the expression of numerous genes in pathways related to cancer.What does this study addThe knockout of most selected genes whose expression is altered by CKI can significantly affect the pharmacological effects of CKI.IL24 and CYP1B1genes are essential to CKI’s inhibition of cancer cell migration and CYP1A1 is important for CKI’s G2M cell cycle arrest effect.What is the clinical significanceThe efficacy of CKI is demonstrated to arise from the synergistic action of multiple pathways and targets.
LBFextract: unveiling transcription factor dynamics from liquid biopsy data
Authors: Lazzeri Isaac , Spiegl Benjamin Gernot , Hasenleithner Samantha O. , Speicher Michael R. , Kircher Martin 
Published: May 2024

Structured abstractMotivationThe analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns.ResultsWe introduce LBFextract, a comprehensive package designed to streamline feature extraction from cfDNA data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies. LBFextract facilitates the integration of preprocessing and postprocessing steps through alignment fragment tags and a hook mechanism. It incorporates various methods, including coverage-based and fragment length-based approaches, alongside two novel feature extraction methods: an entropy-based method to infer TF activity from fragmentomics data and a technique to amplify signals from nucleosome dyads. Additionally, it implements a method to extract condition-specific differentially active TFs based on these features for biomarker discovery. We demonstrate the use of LBFextract for the subtype classification of advanced prostate cancer patients using coverage signals at transcription factor binding sites from cfDNA. We show that LBFextract can generate robust and interpretable features that can discriminate between different clinical groups. LBFextract is a versatile and user-friendly package that can facilitate the analysis and interpretation of liquid biopsy data.Data and Code Availability and ImplementationLBFextract is freely accessible athttps://github.com/Isy89/LBF. It is implemented in Python and compatible with Linux and Mac operating systems. Code and data to reproduce these analyses have been uploaded to 10.5281/zenodo.10964406.ContactFor further information, contactisaac.lazzeri@medunigraz.at,samantha.hasenleithner@medunigraz.at,martin.kircher@bih-charite.de.Supplementary InformationFor additional details see Supplementary Information. For usage of the package, refer tohttps://lbf.readthedocs.io/.
Insulin resistance compromises midbrain organoid neural activity and metabolic efficiency predisposing to Parkinson’s disease pathology
Authors: Zagare Alise , Kurlovics Janis , Almeida Catarina , Ferrante Daniele , Frangenberg Daniela , Neises Laura , Vitali Armelle , Gomez-Giro Gemma , Jäger Christian , Antony Paul , Halder Rashi , Krüger Rejko , Glaab Enrico , Meiser Johannes , Stalidzans Egils , Arena Giuseppe , Schwamborn Jens C 
Published: May 2024

SummaryGrowing evidence indicates that Type 2 Diabetes (T2D) is associated with an increased risk of developing Parkinson’s disease through shared disease mechanisms. Studies show that insulin resistance, which is the driving pathophysiological mechanism of T2D plays a major role in neurodegeneration by impairing neuronal functionality, metabolism, and survival. To investigate insulin resistance caused pathological changes in the human midbrain, which could predispose a healthy midbrain to PD development, we exposed iPSC-derived human midbrain organoids from healthy individuals to either high insulin concentrations, promoting insulin resistance, or to more physiological insulin concentrations restoring insulin signalling function. We combined experimental methods with metabolic modelling to identify the most insulin resistance-dependent pathogenic processes. We demonstrate that insulin resistance compromises organoid metabolic efficiency, leading to increased levels of oxidative stress. Additionally, insulin-resistant midbrain organoids showed decreased neural activity and reduced amount of dopaminergic neurons, highlighting insulin resistance as a significant target in PD prevention.
Ancestral role of Pax6 in chordate brain regionalization
Authors: Kozmik Zbynek , Kozmikova Iryna 
Published: May 2024

AbstractThePax6gene is essential for eye and brain development across various animal species. Here, we investigate the function ofPax6in the development of the anterior central nervous system (CNS) of the invertebrate chordate amphioxus using CRISPR/Cas9-induced genome editing. Specifically, we examined Pax6 mutants featuring a 6bp deletion encompassing two invariant amino acids in the conserved paired domain, hypothesized to impair Pax6 DNA-binding capacity and gene regulatory functions. Although this mutation did not result in gross morphological changes in amphioxus larvae, it demonstrated a reduced ability to activate Pax6-responsive reporter gene, suggesting a hypomorphic effect. Expression analysis in mutant larvae revealed changes in gene expression within the anterior CNS, supporting the conserved role ofPax6gene in brain regionalization across chordates. Additionally, our findings lend support to the hypothesis of a zona limitans intrathalamica (ZLI)-like region in amphioxus, suggesting evolutionary continuity in brain patterning mechanisms.
Tuning of Chitosan with Lignin derived Bioactive Properties to develop a Lignin Reinforced and Sustainable Food Packaging Biomaterial
Authors: Garg Sumona , Avanthi Althuri 
Published: May 2024

AbstractThe crucial component of food storage, preservation, and transportation is food packaging. Biodegradable biopolymers are a major area of focus for the future development of food packaging materials due to their ability to mitigate adverse environmental impact by reducing plastic pollution and promoting sustainable waste management practices. Exploring renewable resources is crucial for facilitating the transition from non-renewable practices to sustainability. Chitosan is known for its superior film-forming abilities but has limited antibacterial activity. The inherent properties of lignin, including its high tensile strength, antioxidant, antimicrobial, and UV barrier ability, can contribute to enhance chitosan film performance when added as a co-polymer, making it an active material for food packaging applications. The present work explores the acid-alkali treatment to extract lignin from sugarcane tops, an abundant agricultural waste, and the application of extracted lignin in biopolymer-based hydrogel synthesis for food packaging. The goal is to enhance the hydrogel formulation by incorporation and optimisation of lignin that holds high antioxidant, antimicrobial, UV barrier, and mechanical properties along with significantly low water transmissibility. This study introduces a novel approach by utilizing lignin extracted from sugarcane tops (SCT) rather than commercially derived lignin, thereby expanding the raw material scope of lignin applications. The incorporation of higher proportions of lignin in the hydrogel formulations represents an advancement over reported studies, aimed at improving the bioactivity of the hydrogel by leveraging its advantageous characteristics emanating from lignin. This approach can also reduce the dependency on chitosan which is relatively expensive. Further, the modified synthesis of hydrogels expedited through heating method contributes to shorten the time duration needed for hydrogel film casting and drying.Graphical AbstractHighlightsEnhanced lignin extraction from sugarcane tops using Plackett Burman DesignFormulating green packaging hydrogels through valorisation of sugarcane topsHeating-based short time casting method for Lignin/Chitosan hydrogel synthesisOptimization of lignin content in the hydrogels for balanced mechanical and bioactive properties
Discovery of cyclic peptide natural product inhibitors ofBalamuthia mandrillaris
Authors: Lu Chenyang , Nelson Samantha , Coy Gabriela , Neumann Christopher , Parkinson Elizabeth I. , Rice Christopher A. 
Published: May 2024

AbstractBalamuthia mandrillarisis a pathogenic free-living amoeba that causes infection of central nervous system, calledBalamuthiaamoebic encephalitis (BAE), as well as cutaneous and systemic diseases. Patients infected withB. mandrillarishave a high mortality rate due to the lack of effective treatments. A combination of non-optimized antimicrobial drug regimen is typically recommended; however, they have poor parasite activity and can cause various severe side effects. Cyclic peptides exhibit a broad spectrum of antimicrobial activities and lower cytotoxicity. In this study, we evaluated the anti-B. mandrillariseffect of cyclic peptides. The predicted natural product-43 (pNP-43), identified from the SNaPP (Synthetic Natural Product Inspired Cyclic Peptides) library, and its derivates displayed a significant inhibition forB. mandrillaristrophozoites. Eight pNPs had IC50s <5 μM. Furthermore, all hit pNPs demonstrated minimal hemolytic and cytotoxic effects on human cells. Our study first indicates the anti-B. mandrillariseffect of cyclic peptides, which provides a new direction for drug development. Further studies of the mechanism of action andin vivoeffects will be elucidated to confirm the potency as a treatment forB. mandrillarisinfection in the future.