bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Evaluating the Benefits and Limits of Multiple Displacement Amplification with Whole-Genome Oxford Nanopore Sequencing”
Authors: Dadzie Fiifi A. , Beaudry Megan S. , Deyanov Alex , Slanis Haley , Duong Minh Q. , Turner Randi , Khan Asis , Arias Cesar A. , Kissinger Jessica C. , Glenn Travis C. , de Paula Baptista Rodrigo 
Published: February 2024

ABSTRACTMultiple Displacement Amplification (MDA) outperforms conventional PCR in long fragment and whole genome amplification which makes it attractive to couple with long-read sequencing of samples with limited quantities of DNA to obtain improved genome assemblies. Here, we explore the efficacy and limits of MDA for genome sequence assembly using Oxford Nanopore Technologies (ONT) rapid library preparations and minION sequencing. We successfully generated almost complete genome sequences for all organisms examined, includingCryptosporidium meleagridis,Staphylococcus aureus,Enterococcus faecium, andEscherichia coli,with the ability to generate high-quality data from samples starting with only 0.025 ng of total DNA. Controlled sheared DNA samples exhibited a distinct pattern of size-increase after MDA, which may be associated with the amplification of long, low-abundance fragments present in the assay, as well as generating concatemeric sequences during amplification. To address concatemers, we developed a computational pipeline (CADECT: Concatemer Detection Tool) to identify and remove putative concatemeric sequences. This study highlights the efficacy of MDA in generating high-quality genome assemblies from limited amounts of input DNA. Also, the CADECT pipeline effectively mitigated the impact of concatemeric sequences, enabling the assembly of contiguous sequences even in cases where the input genomic DNA was degraded. These results have significant implications for the study of organisms that are challenging to culturein vitro, such asCryptosporidium, and for expediting critical results in clinical settings with limited quantities of available genomic DNA.
Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes
Authors: Braakman Rogier , Satinsky Brandon , O’Keefe Tyler J. , Longnecker Krista , Hogle Shane L. , Becker Jamie W. , Li Robert C. , Dooley Keven , Arellano Aldo , Soule Melissa C. Kido , Kujawinski Elizabeth B. , Chisholm Sallie W. 
Published: February 2024

AbstractCross-feeding involves microbes consuming the exudates of other surrounding microbes, mediating elemental cycling. Characterizing the diversity of cross-feeding pathways in ocean microbes illuminates evolutionary forces driving self-organization of ocean ecosystems. Here, we uncover a purine and pyrimidine cross-feeding network in globally abundant groups. The cyanobacteriumProchlorococcusexudes both compound classes, which metabolic reconstructions suggest follows synchronous daily genome replication. Co-occurring heterotrophs differentiate into purine– and pyrimidine-using generalists, or specialists that use compounds for different purposes. The most abundant heterotroph, SAR11, is a specialist that uses purines as sources of energy, carbon and/or nitrogen, with subgroups differentiating along ocean-scale gradients in the supply of energy and nitrogen, in turn producing putative cryptic nitrogen cycles that link many microbes. Finally, in a SAR11 subgroup that dominates whereProchlorococcusis abundant, adenine additions to cultures inhibit DNA synthesis, poising cells for replication. We argue this subgroup uses inferred daily adenine pulses fromProchlorococcusto synchronize to the daily photosynthate supply from surrounding phytoplankton.
High-throughput phenotyping reveals multiple drought responses of wild and cultivated Phaseolinae beans
Authors: Verheyen Jon , Dhondt Stijn , Abbeloos Rafael , Eeckhout Joris , Janssens Steven , Leyns Frederik , Scheldeman Xavier , Storme Veronique , Vandelook Filip 
Published: February 2024

AbstractCrop production worldwide is increasingly affected by drought stress. Although drought tolerance of a plant may be achieved through morphological, structural, physiological, cellular, and molecular adaptations, most studies remain limited to quantifying the effect of drought on biomass yield. Using a high-throughput phenotypic imaging system, we evaluated the drought tolerance of 151 bean accessions (Phaseolinae; Fabaceae) by quantifying five different traits simultaneously: biomass, water use efficiency, relative water content, chlorophyll content, and root/shoot ratio. Since crop wild relatives are important resources for breeding programmes, both wild and cultivated accessions were analyzed, the majority never evaluated for drought tolerance before. We demonstrate that the five traits are affected very differently by drought in the studied accessions, although a cluster analysis grouped the accessions into five distinct clusters with similar responses. We correlated the results for each accession to local climate variables at their original collection sites. Except for the root/shoot ratio, the results of all indicators were related to precipitation data, confirming that drought tolerant accessions grow in arid environments. This broader knowledge on the complex responses of plants to drought stress may prove an invaluable resource for future crop production.HighlightThis study presents an innovative approach for the fast evaluation of different drought tolerance traits of legumes. Multiple responses to drought were observed in the economically important Phaseolinae beans.
Age-Related Dynamics of Methanogenic Archaea in the Human Gut Microbiome: Implications for Longevity and Health
Authors: Mohammadzadeh Rokhsareh , Mahnert Alexander , Shinde Tejus , Kumpitsch Christina , Weinberger Viktoria , Schmidt Helena , Moissl-Eichinger Christine 
Published: February 2024

AbstractThe reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. To address these questions, we analyzed metagenomic data from the stool samples of young adults (n=127, Age: 19-59 y), older adults (n=86), and centenarians (n=34, age: 100-109 years).Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase inMethanobrevibacter smithii, rather thanCa.M. intestini. Remarkably,Ca.M. intestini emerged as a central player in the network stability of adults, paving the way forM. smithiiin older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. Furthermore, the mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with butyrate-producing Oscillospiraceae.This study underscores the crucial role of the archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance ofCa.M. intestini and the partnership between methanogens and specific butyrate-producing bacteria for enhanced health and potential longevity.
NCLX controls hepatic mitochondrial Ca2+extrusion and couples hormone-mediated mitochondrial Ca2+oscillations with gluconeogenesis
Authors: Taha Mahmoud , Assali Essam A. , Stuzmann Grace E. , Shirihai Orian S. , Hershfinkel Michal , Sekler Israel 
Published: February 2024

AbstractHepatic Ca2+signaling is emerging as a key factor in mediating gluconeogenesis. However, the identity of the hepatic mitochondrial Ca2+transporter is controversial and the role of mitochondria in controlling hormonal Ca2+signaling and linking them to metabolic activity is poorly understood. We first interrogated the role of the mitochondrial Na+/Ca2+exchanger NCLX by triggering cytosolic Ca2+purinergic signaling in primary hepatocytes, and Ca2+responses in isolated mitochondria from WT, global NCLX KO, and conditional hepatic NCLX KO mice models. We monitored a higher rate of Na+-dependent mitochondrial Ca2+efflux in NCLX-expressing hepatocytes, indicating that it constitutes the major Ca2+efflux pathway. We then asked if NCLX is controlling the hormone-dependent mitochondrial Ca2+oscillations by employing physiological concentrations of glucagon and vasopressin. Consistent with previous studies, hormone applications triggered mitochondrial Ca2+oscillations in WT hepatocytes. In NCLX KO hepatocytes the cytosolic oscillations persisted, however, the mitochondrial Ca2+oscillations were suppressed. To further understand the metabolic role of NCLX in the hepatic system, we examined gluconeogenic function in vivo and ex vitro by monitoring hepatic glucose production. We found that blood glucose dropped faster in the conditional KO mice and their hepatic glucagon-dependent glucose production was reduced, indicating that gluconeogenesis was impaired in hepatic conditional NCLX KO mice. Taken together, our results indicate that NCLX is the primary Ca2+extruder in hepatocytes and is required for mediating the hormone-dependent mitochondrial Ca2+oscillations and gluconeogenesis.SignificanceHepatic Ca2+signaling is crucial for gluconeogenesis, but the mitochondrial control of this process is not resolved. This study identifies the mitochondrial transporter, NCLX, as a critical link between hormonal-dependent mitochondrial Ca2+oscillations and gluconeogenesis. We first show that NCLX is the major hepatic mitochondrial efflux pathway. We then demonstrate that NCLX is required for glucagon-dependent mitochondrial Ca2+oscillations and the acceleration of mitochondrial oxidative function. Using a conditional hepatic NCLX-null mouse model, we show that NCLX is required for maintaining hepatic glucose production during fasting and in response to glucagon stimulation. Overall, the study identifies NCLX as the integrator of hepatic mitochondrial Ca2+signaling, required for gluconeogenesis.
Spatial transcriptomics reveals focal induction of molecular responses and cellular interactions in the small intestine duringHeligmosomoides polygyrusInfection
Authors: Campillo Poveda Marta , Laidlaw Ross F , Hardy Olympia , Otto Thomas D , Maizels Rick M 
Published: February 2024

AbstractThe infective L3 larvae ofHeligmosomoides polygyrusmigrate to the small intestine where they take up residence in the submucosa, triggering the formation of complex granulomas around the parasite. Here, we employ spatial transcriptomics to elucidate the transcriptional intricacies and cell-cell interactions of the murine small intestine under both steady-state conditions and in response toH. polygyrusinfection. Our findings unveil distinct transcriptional signatures in the crypt zone, villi, and granulomas, providing nuanced insights into the molecular dynamics of the host response to parasitic infection. Molecular characterization ofH. polygyrusgranulomas reveals unique cellular compositions within distinct clusters, shedding light on localized immune activation and cellular dynamics. Utilizing deconvolution techniques, we uncovered common and infection-specific signatures of cell type colocalization, and identified potential ligand-receptor pairs that may mediate communication between the granuloma tissue and the epithelial crypt cells. Additionally, our study highlights the upregulation of genes such asCcl9, Fcer1gandTmsb4xwithin granulomas, suggesting roles in type 2 inflammation, and genes (e.gReg3bandMxra7) associated with wound healing and tissue repair. These results not only enhance our understanding of the murine small intestine’s transcriptional landscape but also provide a platform for exploring host-pathogen interactions. The comprehensive analysis presented here contributes to a holistic comprehension of tissue-specific responses during parasitic infections, offering valuable insights for targeted therapeutic interventions.
Insights from Genetic Studies: SNP Analyses Confirm White Clover Naturalization in Brazil
Authors: Alencar Amanda S , Suyama Yoshishisa , Takahashi Daiki , Mansano Vidal de F , Lira Catarina da F 
Published: February 2024

AbstractWhite clover (Trifolium repens) is a stoloniferous legume herb native to Eurasia, which had been introduced and spread globally. In Brazil, it was introduced as forage crop. While previous studies focused mainly on its agricultural benefits, much remains unclear about its territorial dynamics, introduction process and potential threats in Brazil. This study aims to estimate the genetic diversity of naturalized white clover populations in Brazil and assess the influence of cultivars into these populations’ diversity. Through MIG-Seq analysis, 1097 SNPs show that Brazilian populations have 94% within-population variation. Additionally, two mountainous areas clustered together, while rural and urban areas formed a second cluster. Cultivars are less diverse and have 27% of their genetic variability between them. We found that some populations admixture with cultivated varieties, while more isolated mountainous populations were singular in their genetic background. We can conclude that it is possible that parts of the populations are originally native, brought during European immigration, while others appear to have similar cultivar ancestry, indicating possible biological escapes from cultivars into naturalized populations. Considering ecological data and our genetic findings, it is confirmed that white clover is indeed naturalized in Brazil.
Investigating the performance of foundation models on human 3’UTR sequences
Authors: Vilov Sergey , Heinig Matthias 
Published: February 2024

AbstractFoundation models, such as DNABERT and Nucleotide Transformer have recently shaped a new direction in DNA research. Trained in an unsupervised manner on a vast quantity of genomic data, they can be used for a variety of downstream tasks, such as promoter prediction, DNA methylation prediction, gene network prediction or functional variant prioritization. However, these models are often trained and evaluated on entire genomes, neglecting genome partitioning into different functional regions. In our study, we investigate the efficacy of various unsupervised approaches, including genome-wide and 3’UTR-specific foundation models on human 3’UTR regions. Our evaluation includes downstream tasks specific for RNA biology, such as recognition of binding motifs of RNA binding proteins, detection of functional genetic variants, prediction of expression levels in massively parallel reporter assays, and estimation of mRNA half-life. Remarkably, models specifically trained on 3’UTR sequences demonstrate superior performance when compared to the established genome-wide foundation models in three out of four downstream tasks. Our results underscore the importance of considering genome partitioning into functional regions when training and evaluating foundation models.
The genome ofPasteuria ramosareveals a high turnover rate of collagen-like genes
Authors: Thivolle Alix , Paljakka Marjut , Ebert Dieter , Fields Peter D. 
Published: February 2024

AbstractCollagen-like proteins (CLP) are commonly found in many pathogenic bacteria where they serve as adhesins to attach to host tissue. The repetition of the amino-acid pattern (Gly-Xaa-Yaa)nis the major feature of collagen and is essential to the formation of its stable triple helical structure. In theDaphnia magna–Pasteuria ramosasystem, a model system for studying antagonistic coevolution, a specific CLP in the virulent parasiteP. ramosaplays a pivotal role in host attachment, regulated by matching allele model. Recognizing the crucial role of CLPs in the infection process, we aimed to enhance our understanding ofP. ramosa-CLPs by sequencing high-quality genomes of two isolates, using long-read technology. An analysis of a CLP gene tree of representativeBacillotaspecies revealed a clear radiation of these genes inP. ramosa, which was not found in the closely relatedPasteuria penetrans. A comparison of the isolates reveals a high synteny, with the exception of a few duplications and inversions, mainly involving CLPs or transposases. Across isolates, we observed a recent burst of transposases as well as duplications of CLP genes. On average, CLP genes are well conserved between isolates, but the presence/absence of individual CLP genes is not fully shared, with 39 and 43 genes in the two isolates. Our findings suggest a rapid radiation of CLP genes combined with a birth and death process of the largeP. ramosa-CLP gene family, possibly driven by transposition and coevolution.ImportanceAlthough the host–pathogenDaphnia magna–Pasteuria ramosasystem has served as a model for coevolution, we have, to date, lacked high-quality genomic resources for the parasite, as is the case for many such systems. By presenting a complete assembly of two distinctP. ramosaisolates, our study addresses this lack and provides deeper insights into theP. ramosaCollagen Like Protein (CLP) family, essential proteins involved in attachment to the host. We discover that the rapid radiation of CLP genes inP. ramosaappears to be driven by transposition and coevolution, enabling the parasite to adapt to host resistance mechanisms. These insights improve our understanding of host–parasite interactions and pave the way for comparative genomic analyses to better understand the evolution of these genes. They also have broader implications for disease control and therapeutic development targeting pathogenic bacteria adhesion mechanisms.
Automated 3D Landmarking of the Skull: A Novel Approach for Craniofacial Analysis
Authors: Wilke Franziska , Matthews Harold , Herrick Noah , Dopkins Nichole , Claes Peter , Walsh Susan 
Published: February 2024

ABSTRACTAutomatic dense 3D surface registration is a powerful technique for comprehensive 3D shape analysis that has found a successful application in human craniofacial morphology research, particularly within the mandibular and cranial vault regions. However, a notable gap exists when exploring the frontal aspect of the human skull, largely due to the intricate and unique nature of its cranial anatomy. To better examine this region, this study introduces a simplified single-surface craniofacial bone mask comprising 9,999 quasi-landmarks, which can aid in the classification and quantification of variation over human facial bone surfaces.Automatic craniofacial bone phenotyping was conducted on a dataset of 31 skull scans obtained through cone-beam computed tomography (CBCT) imaging. The MeshMonk framework facilitated the non-rigid alignment of the constructed craniofacial bone mask with each individual target mesh. To gauge the accuracy and reliability of this automated process, 20 anatomical facial landmarks were manually placed three times by three independent observers on the same set of images. Intra- and inter-observer error assessments were performed using root mean square (RMS) distances, revealing consistently low scores.Subsequently, the corresponding automatic landmarks were computed and juxtaposed with the manually placed landmarks. The average Euclidean distance between these two landmark sets was 1.5mm, while centroid sizes exhibited noteworthy similarity. Intraclass coefficients (ICC) demonstrated a high level of concordance (>0.988), and automatic landmarking showing significantly lower errors and variation.These results underscore the utility of this newly developed single-surface craniofacial bone mask, in conjunction with the MeshMonk framework, as a highly accurate and reliable method for automated phenotyping of the facial region of human skulls from CBCT and CT imagery. This craniofacial template bone mask expansion of the MeshMonk toolbox not only enhances our capacity to study craniofacial bone variation but also holds significant potential for shedding light on the genetic, developmental, and evolutionary underpinnings of the overall human craniofacial structure.
Advancements in monitoring: a comparison of traditional and application-based tools for measuring outdoor recreation
Authors: Capdevila Talia Vilalta , McLellan Brynn A. , Loosen Annie , Forshner Anne , Pigeon Karine , Jacob Aerin L. , Wright Pamela , Ehlers Libby 
Published: February 2024

ABSTRACTOutdoor recreation has experienced a boom in recent years. While outdoor recreation provides wide-ranging benefits to human well-being and is an important feature of many protected and non-protected areas, there are growing concerns about the sustainability of recreation with the increased pressures placed on ecological systems and visitor experiences. These concerns emphasize the need for managers to access accurate and timely recreation data at scales that match the growing recreation footprint. Here, we compare spatial and temporal patterns of winter and summer recreation use using traditional and application-based tools across the Columbia and Canadian Rocky Mountains of western Canada. We demonstrate how recreation use can be estimated using traditional and application-based tools, although their accuracy and utility varies across space, season and activity type. Cameras and counters captured similar broad-scale patterns in count estimates of pedestrians and all recreation activities. Application-based data provided detailed spatiotemporal information on recreation use, but datasets were biased towards specific recreation types and did not represent the full recreation population. For instance, Strava Metro data was more suited for capturing broad-scale spatial patterns in biking than pedestrian recreation. Traditional tools including aerial surveys and participatory mapping captured coarser information on the intensity and extent of recreation, with the former tool capturing areas with low recreation intensity and the latter tool suited for capturing recreation information across large spatial and temporal scales. Application-based data should be supplemented with data from traditional tools including cameras or trail counters to identify biases in data and fill in data gaps. We provide a comparison of each tool for measuring recreation use, highlight each tools’ strengths and limitations, and suggest how to use these tools to address real-world monitoring and management scenarios. Our research contributes towards a better understanding of what tools are available to measure recreation and can help direct managers in selecting which tool, or combinations of tools, to use that can expand the rigor and scope of recreation research. This information can support decision-making and lead to the protection of ecological systems while allowing for high-quality recreation experiences.GRAPHICAL ABSTRACT