bluuebunny/crossref_metadata_2025_split huggingface dataset:
nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling
Authors: Stamouli Sofia , Beber Moritz E. , Normark Tanja , Christensen Thomas A. , Andersson-Li Lili , Borry Maxime , Jamy Mahwash ,   nf-core community, Fellows Yates James A. 
Published: October 2023

1 AbstractMetagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases. This, however, is a very time-consuming task when performed manually - particularly when combined with the appropriate preprocessing of sequencing reads before the classification.Here we present nf-core/taxprofiler, a highly parallelised read-processing and taxonomic classification pipeline. It is designed for the automated and simultaneous classification and/or profiling of both short- and long-read metagenomic sequencing libraries against a 11 taxonomic classifiers and profilers as well as databases within a single pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the pipeline benefits from high levels of scalability and portability, accommodating from small to extremely large projects on a wide range of computing infrastructure. It has been developed following best-practise software development practises and community support to ensure longevity and adaptability of the pipeline, to help keep it up to date with the field of metagenomics.
Synergistic phenotypic shifts during domestication promote plankton-to-biofilm transition in purple sulfur bacteriumChromatium okenii
Authors: Di Nezio Francesco , Ong Irvine Lian Hao , Riedel René , Goshal Arkajyoti , Dhar Jayabrata , Roman Samuele , Storelli Nicola , Sengupta Anupam 
Published: October 2023

AbstractThe ability to isolate microorganisms from natural environments to pure cultures under optimized laboratory settings has markedly improved our understanding of microbial ecology. Laboratory-induced artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into selective pressures which are distinct compared to those in nature. Consequently, fresh isolates undergo diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms, we still lack a biophysical understanding of the relevant traits which emerge during domestication, and possible mechanistic interrelations between them which could ultimately drive short-to-long term microbial adaptation under laboratory conditions. Here, using microfluidics, atomic force microscopy (AFM), quantitative imaging, and mathematical modelling, we study phenotypic adaptation of natural isolates ofChromatium okenii, a motile phototrophic purple sulfur bacterium (PSB) common to meromictic settings, grown under ecologically-relevant laboratory conditions over multiple generations. Our results indicate that the naturally planktonicC. okeniipopulations leverage synergistic shifts in cell-surface adhesive interactions, together with changes in their cell morphology, mass density, and distribution of intracellular sulfur globules, to supress their swimming traits, ultimately switching to a sessile lifeform under laboratory conditions. A computational model of cell mechanics confirms the role of the synergistic phenotypic shifts in suppressing the planktonic lifeform. Over longer domestication periods (∼10 generations), the switch from planktonic to sessile lifeform is driven by loss of flagella and enhanced adhesion. By investigating key phenotypic traits across different physiological stages of lab-grownC. okenii, we uncover a progressive loss of motility via synergistic phenotypic shifts during the early stages of domestication, which is followed by concomitant deflagellation and enhanced surface attachment that ultimately drive the transition of motile sulphur bacteria to a sessile biofilm state. Our results establish a mechanistic link between suppression of motility and surface attachment via synergistic phenotypic changes, underscoring the emergence of adaptive fitness under felicitous laboratory conditions that comes at a cost of lost ecophysiological traits tailored for natural environments.Graphical abstract
Local sleep in songbirds: Different simultaneous sleep states across the avian pallium
Authors: Yeganegi Hamed , Ondracek Janie M. 
Published: October 2023

SummaryWakefulness and sleep have often been treated as distinct and global brain states. However, an emerging body of evidence on the local regulation of sleep stages challenges this conventional view. Apart from unihemispheric sleep, the current data that support local variations of neural oscillations during sleep are focused on the homeostatic regulation of local sleep, i.e., the role preceding awake activity. Here, to examine local differences in brain activity during natural sleep, we recorded the electroencephalogram (EEG) and the local field potential (LFP) across multiple sites within the avian pallium of zebra finches without perturbing the previous awake state. We scored the sleep stages independently in each pallial site and found that the sleep stages are not pallium-wide phenomena but rather deviate widely across electrode sites. Importantly, deeper electrode sites had a dominant role in defining the temporal aspects of sleep state congruence. Altogether, these findings show that local regulation of sleep oscillations also occurs in the avian brain without prior awake recruitment of specific pallial circuits and in the absence of mammalian cortical neural architecture.
Conformations of a highly expressed Z19 α-zein studied with AlphaFold2 and MD simulations
Authors: Christensen Niels Johan 
Published: October 2023

Abstractα-zeins are amphiphilic maize proteins with interesting material properties suitable for numerous applications, e.g., in renewable plastics, foods, therapeutics and additive manufacturing (3D-printing). To exploit their full potential, molecular-level insights are essential. Since α-zeins have resisted experimental atomic-resolution characterization, molecular models have been central to elucidating their structure, but deep-learning α-zein models are largely unexplored. Therefore, this work studies an AlphaFold2 model of a highly expressed zein with molecular dynamics (MD) simulations. The mature protein sequence of the α-zein cZ19C2 gave a loosely packed model with 7 α-helical segments connected by turns/loops and 68% total α-helicity. Compact tertiary structure was limited to a C-terminal bundle of three α-helices, each aligning well with the published repeat sequence NPAAYLQQQQLLPFNQLA(V/A)(L/A). The model was subjected to MD simulations in water containing 0, 3, 23, 50, and 100 mol% ethanol for 400 ns, with extension of selected simulations to the μs timescale. Although the simulations gave structurally diverse endpoints, several patterns were observed: In water and ≤ 2 mol% ethanol, the model rapidly formed compact globular structures, largely preserving the C-terminal bundle. At ≥ 50 mol% ethanol, extended conformations prevailed, consistent with previous SAXS studies. Tertiary structure was partially stabilized in water and in 2 mol% and 23 mol% ethanol, but was disrupted in ≥ 50 mol% ethanol. Averaged results indicated slightly increased helicity with ethanol concentration. Multiple copies of a globular model conformation rapidly formed branched aggregates in aqueous all-atom and coarse-grained MD simulations. β-sheet content was typically <1% across all simulations. In aqueous simulations with glycidyl methacrylate (GMA), 55% of GMA was found within 4 Å of the model. Pre-reaction complexes for methacrylation were indicated by GMA epoxide carbons within 2.9 – 3.3 Å of side chain hydroxyl oxygens, suggesting accessibility of reactive sites in compact α-zein conformations.
A dynamic humidity arena to explore humidity related behaviours in insects
Authors: Giri Ganesh , Nagloo Nicolas , Enjin Anders 
Published: October 2023

AbstractHumidity is a critical environmental factor influencing the behaviour of terrestrial organisms. Despite its significance, the neural mechanisms and behavioural algorithms governing humidity sensation in insects remain elusive. In this study, we introduce a novel dynamic humidity arena to investigate humidity-guided behaviour in the vinegar flyDrosophila melanogaster. The arena allows precise humidity control, low error rates, and fast settling times, making it a robust tool for studying humidity-related behaviours. Our results reveal that desiccated and starved flies (DS flies) search for higher relative humidity environments (65-75%) while sated flies tend to stay within their initial environments. In contrast, Ionotropic receptor (Ir)93a mutant flies with impaired humidity sensing show no preference to relative humidity. The search for higher humidity in DS flies is reflected in their relatively high displacement and walking speed compared to control and mutant flies. Our novel method manipulates humidity cues to create complex humidity landscapes that respond in real-time to insect movement. This will help us shed light on how humidity shapes behaviour and offers a foundation for further research in the field of hygrosensation.
Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad
Authors: Karami Yasaman , Bignon Emmanuelle 
Published: October 2023

ABSTRACTGene activity is tightly controlled by reversible chemical modifications called epigenetic marks, which are of various types and modulate gene accessibility without affecting the DNA sequence. Despite an increasing body of evidence demonstrating the role of oxidative-type modifications of histones in gene expression regulation, there remains a complete absence of structural data at the atomistic level to understand the molecular mechanisms behind their regulatory action. Owing toμs time-scale MD simulations and protein communication networks analysis, we describe the impact of histone H3 hyperoxidation (i.e., S-sulfonylation) on the nucleosome dynamics. Our results reveal the atomic-scale details of the intrinsic structural networks within the canonical histone core and their perturbation by hyperoxidation of the histone H3 C110. We show that this modification involves local rearrangement of the communication networks and destabilizes the dyad, which could be important for nucleosome disassembly.
Novel diagnosis- and progression-related microRNA signatures in melanoma
Authors: Gómez-Martínez Helena , Gómez-Cabañes Borja , Galiana-Roselló Cristina , Morales Alejandro Virués , Rabinad Beatriz Dolader , Rey Díez Natalia del , López Adolfo , Hernando Eva , García-García Francisco 
Published: October 2023

ABSTRACTMelanoma, an aggressive form of skin cancer with a high mortality rate, has recently experienced an increase in incidence. Consequently, the search for biomarkers, such as microRNAs (miRNAs), to facilitate the early detection and management of cancer patients represents a significant current concern.To identify these potential biomarkers, we developed a novel and integrative strategy. This involved conducting a systematic review of melanoma studies in accordance with PRISMA guidelines, followed by the performance of exploratory analysis and data normalization. Subsequently, individual analyses were conducted for each study, followed by a meta-analysis of miRNAs that integrated all results while considering patient information.In the diagnostic scenario, we identified twenty-four differentially expressed miRNAs, with eleven being upregulated and thirteen being downregulated. In the severity scenario, a total of twenty-three differentially expressed miRNAs were identified, comprising seven that were upregulated and sixteen that were downregulated. An extensive functional characterization of these miRNA signatures was conducted, providing insight into their biological role and impact on melanoma diagnosis and prognosis.Our findings contribute to a more comprehensive understanding of the molecular mechanisms and developmental processes involved in melanoma, particularly in early-stage development and ulceration. This, in turn, provides a foundation for the development of novel resources for the precise detection and treatment of melanoma.
Socioecological drivers of injuries in female and male rhesus macaques (Macaca mulatta)
Authors: Pavez-Fox Melissa A. , Siracusa Erin R. , Ellis Samuel , Kimock Clare M. , Rivera-Barreto Nahiri , Negron-Del Valle Josue E. , Phillips Daniel , Ruiz-Lambides Angelina , Snyder-Mackler Noah , Higham James P. , Brent Lauren J.N. , De Moor Delphine 
Published: October 2023

AbstractCompetition over access to resources, such as food and mates, is believed to be one of the major costs associated with group living. Two socioecological factors suggested to predict the intensity of competition are group size and the relative abundance of sexually active individuals. However, empirical evidence linking these factors to injuries and survival costs is scarce. Here, we leveraged 10 years of data from free-ranging rhesus macaques where injuries inflicted by conspecifics are associated with a high mortality risk. We tested if group size and adult sex ratio predicted the occurrence of injuries and used data on physical aggression to contextualise these results. We found that males were less likely to be injured when living in larger groups, potentially due to advantages in intergroup encounters. Females, instead, had higher injury risk when living in larger groups but this was not explained by within-group aggression among females. Further, male-biased sex ratios predicted a weak increase in injury risk in females and were positively related to male-female aggression, indicating that male coercion during mating competition may be a cause of injuries in females. Overall, our results provide insights into sex differences in the fitness-related costs of competition and empirical evidence for long-standing predictions on the evolution of group living.
Matrix architecture and mechanics regulate myofibril organization, costamere assembly, and contractility of engineered myocardial microtissues
Authors: DePalma Samuel J. , Jillberto Javiera , Stis Austin E. , Huang Darcy D. , Lo Jason , Davidson Christopher D. , Chowdhury Aamilah , Jewett Maggie E. , Kobeissi Hiba , Chen Christopher S. , Lejeune Emma , Helms Adam S. , Nordsletten David A. , Baker Brendon M. 
Published: October 2023

ABSTRACTThe mechanical function of the myocardium is defined by cardiomyocyte contractility and the biomechanics of the extracellular matrix (ECM). Understanding this relationship remains an important unmet challenge due to limitations in existing approaches for engineering myocardial tissue. Here, we established arrays of cardiac microtissues with tunable mechanics and architecture by integrating ECM-mimetic synthetic, fiber matrices and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), enabling real-time contractility readouts, in-depth structural assessment, and tissue-specific computational modeling. We find that the stiffness and alignment of matrix fibers distinctly affect the structural development and contractile function of pure iPSC-CM tissues. Further examination into the impact of fibrous matrix stiffness enabled by computational models and quantitative immunofluorescence implicates cell-ECM interactions in myofibril assembly and notably costamere assembly, which correlates with improved contractile function of tissues. These results highlight how iPSC-CM tissue models with controllable architecture and mechanics can inform the design of translatable regenerative cardiac therapies.
Personalised metabolic whole-body models for newborns and infants predict growth and biomarkers of inherited metabolic diseases
Authors: Zaunseder Elaine , Mütze Ulrike , Okun Jürgen G. , Hoffmann Georg F. , Kölker Stefan , Heuveline Vincent , Thiele Ines 
Published: October 2023

AbstractExtensive whole-body models (WBMs) accounting for organ-specific dynamics have been developed to simulate adult metabolism. However, there is currently a lack of models representing infant metabolism taking into consideration its special requirements in energy balance, nutrition, and growth. Here, we present a resource of organ-resolved, sex-specific, anatomically accurate models of newborn and infant metabolism, referred to as infant-whole-body models (infant-WBMs), spanning the first 180 days of life. These infant-WBMs were parameterised to represent the distinct metabolic characteristics of newborns and infants accurately. In particular, we adjusted the changes in organ weights, the energy requirements of brain development, heart function, and thermoregulation, as well as dietary requirements and energy requirements for physical activity. Subsequently, we validated the accuracy of the infant-WBMs by showing that the predicted neonatal and infant growth was consistent with the recommended growth by the World Health Organisation. We assessed the infant-WBMs’ reliability and capabilities for personalisation by simulating 10,000 newborn models, personalised with blood concentration measurements from newborn screening and birth weight. Moreover, we demonstrate that the models can accurately predict changes over time in known blood biomarkers in inherited metabolic diseases. By this, the infant-WBM resource can provide valuable insights into infant metabolism on an organ-resolved level and enable a holistic view of the metabolic processes occurring in infants, considering the unique energy and dietary requirements as well as growth patterns specific to this population. As such, the infant-WBM resource holds promise for personalised medicine, as the infant-WBMs could be a first step to digital metabolic twins for newborn and infant metabolism for personalised systematic simulations and treatment planning.
Do bed bugs transmit human viruses, or do humans transmit bed bug viruses? A worldwide survey of the bed bug RNA virosphere
Authors: Walt Hunter K. , King Jonas G. , Sheele Johnathan M. , Meyer Florencia , Pietri Jose E. , Hoffmann Federico G. 
Published: October 2023

ABSTRACTBed bugs (Hemiptera:Cimicidae) are a globally distributed hematophagous pest that routinely feed on humans. Unlike many blood-sucking arthropods, they have never been linked to disease transmission in a natural setting, and despite interest in their role as disease vectors, little is known about the viruses that bed bugs naturally harbor. Here, we present a global-scale survey of the bed bug RNA virosphere. We sequenced the metatranscriptomes of 22 individual bed bugs (Cimex lectulariusandCimex hemipterus) from 8 locations around the world. We detected sequences from two known bed bug viruses (Shuangao bedbug virus 1 and Shuangao bedbug virus 2) which extends their geographical range and the host range of Shuangao bedbug virus 1 toCimex lectularius. We identified three novel bed bug virus sequences from a tenui-like virus (Bunyavirales), a toti-like virus (Ghabrivirales), and a luteo-like virus (Tolivirales).Interestingly, some of the bed bug viruses branch near to insect-transmitted plant-infecting viruses, opening questions regarding the evolution of plant virus infection. When we analyzed the putative viral sequences by their host’s collection location, we found unexpected patterns of geographical diversity that may reflect humans’ role in bed bug dispersal. Additionally, we investigated the effect thatWolbachia,the primary bed bug endosymbiont, may have on viral abundance and found thatWolbachiainfection neither promotes nor inhibits viral infection. Finally, our results provide no evidence that bed bugs transmit any known human pathogenic viruses.
Y chromosome damage underlies testicular abnormalities in ATR-X syndrome
Authors: Carlos Nayla Leon , Le Thanh Nha Uyen , Garvie Andrew , Wong Lee H , Bagheri-Fam Stefan , Harley Vincent R 
Published: October 2023

AbstractATR-X (alphathalassemia,mentalretardation,X-linked) syndrome is a severe developmental disorder affecting males caused by mutations in the chromatin remodelling geneATRX. Genital abnormalities in affected boys include hypospadias and ambiguous genitalia, and patients show small poorly formed testes with only a few seminiferous tubules. Our mouse model recapitulated these testicular defects whenAtrxwas specifically deleted in Sertoli cells (ScAtrxKO). ScAtrxKO mice develop small testes with fewer and discontinuous tubules due to G2/M arrest and apoptosis of Sertoli cells.Here, we investigated the mechanism underlying the Sertoli cell defects in ATR-X syndrome. In healthy male control mice, Sertoli cell nuclei contain a single novel “GATA4 PML nuclear body (NB)” that strongly expresses the transcription factor GATA4, as well as ATRX and its binding partner DAXX. The GATA4 PML NB co-localizes with heterochromatin protein HP1α and PH3 (a marker of chromosome condensation), and with the short arm of the Y chromosome (Yp). In contrast, ScAtrxKO Sertoli cells contain a single giant GATA4 PML NB, frequently associated with DNA double-strand breaks in G2/M-arrested Sertoli cells that underwent apoptosis. HP1α and PH3 were absent from the giant GATA4 foci suggesting a local failure in heterochromatin formation and chromosome condensation. Our data indicate that in Sertoli cells, ATRX protects a chromosomal region of Yp from DNA damage, probably during replication stress, and thus protects Sertoli cells from cell death. We discuss Y chromosome damage as a novel mechanism for testicular failure and the potential role of GATA4 during this process.Disclosure SummaryThe authors have nothing to disclose.
A 50-gene high-risk profile predictive of COVID-19 and Idiopathic Pulmonary Fibrosis mortality originates from a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease
Authors: Tourki Bochra , Jia Minxue , Karampitsakos Theodoros , Vera Iset M , Arsenault Alyssa , Marlin Krystin , Perrot Carole Y , Allen Dylan , Farsaei Forouzandeh , Rutenberg David , Bandyopadhyay Debabrata , Restrepo Ricardo , Qureshi Muhammad R. , Patel Kapilkumar , Tzouvelekis Argyrios , Kapetanaki Maria , Juan-Guardela Brenda , Kim Kami , Benos Panayiotis V , Herazo-Maya Jose D. 
Published: October 2023

AbstractBackgroundWe aim to study the source of circulating immune cells expressing a 50-gene signature predictive of COVID-19 and IPF mortality.MethodsWhole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 231 subjects with COVID-19, post-COVID-19-ILD, IPF and controls. We measured the 50-gene signature (nCounter, Nanostring), interleukin 6 (IL6), interferon γ-induced protein (IP10), secreted phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-β) by Luminex. PCR was used to validate COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Controller (10X Genomics). For analysis we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger, Seurat, Propeller, Kaplan-Meier curves, CoxPH models, Two-way ANOVA, T-test, and Fisher’s exact.ResultsWe identified three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19 with significant differences in IL6, IP10, SPP1 and TGFβ-1. scRNA-seq identified Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+and high levels of the 7-gene signature (7Gene-M-MDSC) in COVID-19. These cells were not observed in post-COVID-19-ILD or IPF. The 43-gene signature was mostly expressed in CD4 T and CD8 T cell subsets. Increased expression of the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19-ILD. The expression of these genes remained low in IPF.ConclusionA 50-gene, high-risk profile in COVID-19 is characterized by a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease