bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL
Authors: Lagou Loudmila Jelinscaia , Kadereit Gudrun , Morales-Briones Diego F. 
Published: January 2024

Background and AimsCypripediumis the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny ofCypripediumand explore its evolutionary history using target capture data for the first time.MethodsWe used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny ofCypripediumbased on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events.Key ResultsAll sections were recovered as monophyletic, contrary to the two subsections within sect.Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect.Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene (∼30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene (∼22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (∼15–13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution withinCypripedium.ConclusionsOur study provided novel insights into the evolutionary history ofCypripediumbased on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.
A microRNA that controls the emergence of embryonic movement
Authors: Menzies Jonathan A. C. , Chagas Andre M. , Baden Tom , Alonso Claudio R. 
Published: January 2024

SUMMARYMovement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here we investigate the genetic basis underlying the embryonic onset of movement inDrosophilafocusing on the role played by small non-coding RNAs (microRNAs, miRNAs). To this end, we first develop a quantitative behavioural pipeline capable of tracking embryonic movement in large populations of fly embryos, and using this system, discover that theDrosophilamiRNAmiR-2b-1plays a role in the emergence of movement. Through the combination of spectral analysis of embryonic motor patterns, cell sorting and RNAin situs, genetic reconstitution tests, and neural optical imaging we define thatmiR-2b-1influences the emergence of embryonic movement by exerting actions in the developing nervous system. Furthermore, through the combination of bioinformatics coupled to genetic manipulation of miRNA expression and phenocopy tests we identify a previously uncharacterised (but evolutionarily conserved) chloride channel encoding gene – which we termMovement Modulator(Motor)– as a genetic target that mechanistically linksmiR-2b-1to the onset of movement. Cell-specific genetic reconstitution ofmiR-2b-1expression in a null miRNA mutant background, followed by behavioural assays and target gene analyses, suggest thatmiR-2b-1affects the emergence of movement through effects in sensory elements of the embryonic circuitry, rather than in the motor domain. Our work thus reports the first miRNA system capable of regulating embryonic movement, suggesting that other miRNAs are likely to play a role in this key developmental process inDrosophilaas well as in other species.
Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities
Authors: Chen Molly , Grégoire Daniel S. , Bain Jeffrey G. , Blowes David W. , Hug Laura A. 
Published: January 2024

ABSTRACTThe oxidation of sulfide-bearing mine tailings catalysed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of endogenous microbes living in tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.
IgG hexamers initiate acute lung injury
Authors: Cleary Simon J. , Seo Yurim , Tian Jennifer J. , Kwaan Nicholas , Bulkley David P. , Bentlage Arthur E. H. , Vidarsson Gestur , Boilard Éric , Spirig Rolf , Zimring James C. , Looney Mark R. 
Published: January 2024

AbstractAntibodies can initiate lung injury in a variety of disease states such as autoimmunity, transfusion reactions, or after organ transplantation, but the key factors determining in vivo pathogenicity of injury-inducing antibodies are unclear. A previously overlooked step in complement activation by IgG antibodies has been elucidated involving interactions between IgG Fc domains that enable assembly of IgG hexamers, which can optimally activate the complement cascade. Here, we tested the in vivo relevance of IgG hexamers in a complement-dependent alloantibody model of acute lung injury. We used three approaches to block alloantibody hexamerization (antibody carbamylation, the K439E Fc mutation, or treatment with domain B from Staphylococcal protein A), all of which reduced acute lung injury. Conversely, Fc mutations promoting spontaneous hexamerization made a harmful alloantibody into a more potent inducer of acute lung injury and rendered an innocuous alloantibody pathogenic. Treatment with a recombinant Fc hexamer ‘decoy’ therapeutic protected mice from lung injury, including in a model with transgenic human FCGR2A expression that exacerbated pathology. These results indicate a direct in vivo role of IgG hexamerization in initiating acute lung injury and the potential for therapeutics that inhibit or mimic hexamerization to treat antibody-mediated diseases.Brief summaryIgG antibodies can form hexamers. This study shows that hexamer assembly is an important event determining the ability of IgG to trigger acute lung injury.Graphical abstract
Cell morphology as a quantifier for functional states of resident tissue macrophages
Authors: Schnitzerlein Miriam , Wegner Anja , Brahim Oumaima Ben , Uderhardt Stefan , Zaburdaev Vasily 
Published: January 2024

AbstractResident tissue macrophages (RTMs) are essential for maintaining homeostasis in a physiological tissue state. They monitor interstitial fluids, contain acute damage while actively preventing inflammation, and remove dead cells and debris. All these cellular functions are accompanied by characteristic changes in cell morphology, the expression of which can provide information about the functional status of the cells. What is currently known about morphological patterns and dynamic behavior of macrophages is derived primarily from experimentalex vivocell cultures. However, how macrophages operate in living organisms is in many ways fundamentally different from how they do in a cell culture system. In this work, we employed an intravital imaging platform to generate dynamic data from peritoneal RTMsin vivoin mice under various conditions induced either chemically or physically. Using this data, we built an image processing pipeline and defined a set of human-interpretable cell size and shape features which allowed us to quantify RTM morphodynamics over time. We used those features to quantitatively differentiate cells in various functional states - when macrophages are activated, for instance, or when they “shut down” due to detrimental changes in the environment. The qualitative morphology changes associated with these functional states could be inferred directly from the quantitative measurements. Finally we used the set of cell morphology features monitoring the health of RTMs to improve a setup for explanted tissues. Thus, the proposed method is a versatile tool to provide insights into the dynamic behavior ofbona fidemacrophagesin vivoand helps distinguish between physiological and pathological cell states.Author summaryMammalian tissues are constantly subjected to various stresses - due to pathogens, cell death and molecular waste products - which have to be resolved properly to prevent unwanted inflammatory processes and thus maintain tissue homeostasis. To find such incidents, resident tissue macrophages (RTMs)in vivodisplay constant sampling behavior which is accompanied by dynamic changes to their morphology. These changes of cellular features are not yet fully understood and were even not yet quantified for RTMs in living organisms. To fill this knowledge gap, we have used an intravital imaging platform to generate time-lapse images of RTMs over time in the peritoneal serosa of a living mouse. Subsequently we have built a custom image processing pipeline to assess the morphology and dynamics of the cells. We could use these measurements to recover the qualitative cell morphology changes over time and even differentiate cells in distinct physiological and pathological states. Thus this analysis lays the basis to the further development of a mathematical model or RTM sampling dynamics or may even be the first step to diagnose macrophages in disease contexts.
10x Genomics Gene Expression Flex is a powerful tool for single-cell transcriptomics of xenograft models
Authors: Llora-Batlle Oriol , Farcas Anca , Fransen Doreth , Floc’h Nicolas , Talbot Sara , Schwiening Alix , Bojko Laura , Calver John , Josipovic Natasa , Lashuk Kanstantsin , Schueler Julia , Prodan Andrei , Mooijman Dylan , McDermott Ultan 
Published: January 2024

ABSTRACTThe 10x Genomics Gene Expression Flex protocol allows profiling of fixed or frozen material, greatly simplifying the logistics of sample collection, storage and transfer prior to single -cell sequencing. The method makes single-cell transcriptomics possible for existing fresh-frozen or FFPE tissue samples, but also facilitates the logistics of the sampling process, allowing instant preservation of samples. The technology relies on species-specific probes available for human and mouse. Nevertheless, processing of patient-derived (PDX) or cell line (CDX) xenografts, which contain mixed human and mouse cells, is currently not supported by this protocol due to the high degree of homology between the probe sets. Here we show that it is feasible to simultaneously profile populations containing both human and mouse cells by mixing the transcriptome probe sets of both species.Cellrangeroutputs a count table for each of the species allowing evaluation of the performance of the different probe sets. Cross-reactive probes are greatly outperformed by the specific probe hybridizations leading to a clear difference in the recovery of UMIs and unique genes per cell. Furthermore, we developed a pipeline that removes cross-reactive signal from the data and provides species-specific count tables for further downstream analysis. Hence, the 10x Genomics Gene Expression Flex protocol can be used to process xenograft samples without the need for separation of human and mouse cells by flow sorting and allows analysis of the human and mouse single-cell transcriptome from each sample. We anticipate it will be increasingly used for single-cell sequencing of cancer cell line and patient-derived xenografts, facilitating the preservation of the samples and allowing the interrogation of both the (human) xenograft and the (mouse) tumor microenvironment at single-cell resolution.
The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo
Authors: Echterhof Arne , Dharmaraj Tejas , McBride Robert , Berry Joel , Hopkins Max , Selvakumar Hemaa , Miesel Lynn , Chia Ju-Hsin , Lin Kun-Yuan , Shen Chien-Chang , Lee Yu-Ling , Yeh Yu-Chuan , Liao Wei Ting , Suh Gina , Blankenberg Francis G. , Frymoyer Adam R. , Bollyky Paul L. 
Published: January 2024

AbstractWith the increasing prevalence of antimicrobial-resistant bacterial infections, there is great interest in using lytic bacteriophages (phages) to treat such infections. However, the factors that govern bacteriophage pharmacokineticsin vivoremain poorly understood. Here, we have examined the contribution of neutrophils, the most abundant phagocytes in the body, to the pharmacokinetics of intravenously administered bacteriophage in uninfected mice. A single dose of LPS-5, an antipseudomonal bacteriophage recently used in human clinical trials, was administered intravenously to both wild-type BALB/c and neutropenic ICR mice. Phage concentrations were assessed in peripheral blood and spleen at 0.5, 1, 2, 4, 8, 12, and 24 hours after administration by plaque assay and qPCR. We observed that the phage clearance is only minimally affected by neutropenia. Indeed, the half-life of phages in blood in BALB/c and ICR mice is 3.45 and 3.66 hours, respectively. These data suggest that neutrophil-mediated phagocytosis is not a major determinant of phage clearance. Conversely, we observed a substantial discrepancy in circulating phage levels over time when measured by qPCR versus plaque assay, suggesting that substantial functional inactivation of circulating phages occurs over time. These data indicate that circulating factors, but not neutrophils, inactivate intravenously administered phages.
A multi-institutional study to investigate the sparing effect after whole brain electron FLASH in mice: Reproducibility and temporal evolution of functional, electrophysiological, and neurogenic endpoints
Authors: Drayson Olivia GG , Melemenidis Stavros , Katila Nikita , Viswanathan Vignesh , Kramár Enikö A , Zhang Richard , Kim Rachel , Ru Ning , Petit Benoit , Dutt Suparna , Manjappa Rakesh , Ashraf M. Ramish , Lau Brianna , Soto Luis , Skinner Lawrie , Yu Amu S. , Surucu Murat , Maxim Peter , Zebadua-Ballasteros Paola , Wood Marcelo , Baulch Janet E. , Vozenin Marie-Catherine , Loo Billy W , Limoli Charles L. 
Published: January 2024

AbstractPurposeUltra-high dose-rate radiotherapy (FLASH) has been shown to mitigate normal tissue toxicities associated with conventional dose rate radiotherapy (CONV) without compromising tumor killing in preclinical models. A prominent challenge in preclinical radiation research, including FLASH, is validating both the physical dosimetry and the biological effects across multiple institutions.MethodsWe previously demonstrated dosimetric reproducibility of two different electron FLASH devices at separate institutions using standardized phantoms and dosimeters. In this study, we compared the outcome of FLASH and CONV 10 Gy whole brain irradiation on female adult mice at both institutions to evaluate the reproducibility and temporal evolution of multiple endpoints.ResultsFLASH sparing of behavioral performance on novel object recognition (4 months post-irradiation) and electrophysiologic long-term potentiation (LTP, 5-months post-irradiation) was reproduced between institutions. Interestingly, differences between FLASH and CONV on the endpoints of hippocampal neurogenesis (Sox2, doublecortin), neuroinflammation (microglial activation), and electrophysiology (LTP) at late times were not observed at early times.ConclusionsIn summary, we demonstrated reproducible FLASH sparing effects between two beams and two institutions with validated dosimetry. FLASH sparing effects on the endpoints evaluated manifested at late but not early time points.
Assessing the Adequacy of Morphological Models used in Palaeobiology
Authors: Mulvey Laura P. A. , May Michael R. , Brown Jeremy M. , Höhna Sebastian , Wright April M. , Warnock Rachel C. M. 
Published: January 2024

1AbstractReconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this evolutionary history, providing a hypothesis of the events. Within Bayesian phylogenetics a major step in estimating a tree is in choosing an appropriate model of character evolution. In the case of most extinct species, our only source of information to decipher their phylogenetic relationships is through the morphology of fossils. We therefore use a model of morphological character evolution, the most common of which being the Mk Lewis model. While it is frequently used in palaeobiology, it is not known whether the simple Mk substitution model, or any extensions to it, provide a sufficiently good description of the process of morphological evolution. To determine whether or not the Mk model is appropriate for fossil data we used posterior predictive simulations, a model adequacy approach, to estimate absolute fit of the model to morphological data sets. We first investigate the impact that different versions of the Mk model have on key parameter estimates using tetrapod data sets. We show that choice of substitution model has an impact on both topology and branch lengths, highlighting the importance of model choice. Next, we use simulations to investigate the power of posterior predictive simulations for morphology. Having validated this approach we show that current variations of the Mk model are in fact performing adequately in capturing the evolutionary dynamics that generated our data. We do not find any preference for a particular model extension across multiple data sets, indicating that there is no ‘one size fits all’ when it comes to morphological data and that careful consideration should be given to choosing models of discrete character evolution. By using suitable models of character evolution, we can increase our confidence in our phylogenetic estimates, which should in turn allow us to gain more accurate insights into the evolutionary history of both extinct and extant taxa.
DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas: influence of sample type and seasonal variation
Authors: Lavrador Ana S. , Amaral Fábio G. , Moutinho Jorge , Vieira Pedro E. , Costa Filipe O. , Duarte Sofia 
Published: January 2024

AbstractMonitoring of marine invertebrate non-indigenous species (NIS) using DNA metabarcoding can be strongly affected by selected sample type due to life history traits, such as habitat preferences and life cycles. Two marinas in the north of Portugal were sampled to assess the impact of sample type (hard and artificial substrates, water eDNA, and zooplankton) and season (spring, autumn, winter) on species and NIS recovery. Using two molecular markers - the mitochondrial cytochrome c oxidase subunit I (COI) and the small subunit ribosomal RNA (18S) - a total of 636 species and 31 NIS were detected. Species numbers were slightly higher in the marina more exposed to maritime traffic, and the highest percentage of exclusive species was detected in zooplankton (up to 24%), as well as the highest numbers of NIS. Regarding season, the highest numbers of species and NIS were detected in the spring and autumn (varying within each marina). Taxonomic composition analysis revealed differences in species richness and community structure among seasons and sample types, particularly between hard and artificial substratesversuseDNA and zooplankton. Of the 31 NIS detected, six are potential first records for Portugal, which await morphology-based validation. No NIS were detected in all sample types nor in all sampled seasons. This highlights the need to employ different sampling approaches and markers, as well as consider seasonal variation and level of exposure to maritime-driven introductions to guarantee a comprehensive metabarcoding-based surveillance of NIS in recreational marinas.
A fungi hotspot deep down the ocean: explaining the presence ofGjaerumia minorin Equatorial Pacific bathypelagic waters
Authors: Pernice Massimo C. , Forn Irene , Logares Ramiro , Massana Ramon 
Published: January 2024

ABSTRACTA plant parasite associated with the white haze disease in apples, the BasidiomycotaGjaerumia minor,has been found in most samples of the global bathypelagic ocean. An analysis of environmental 18S rDNA sequences on 12 vertical profiles of the Malaspina 2010 expedition shows that the relative abundance of this cultured species actually increases with depth while its distribution is remarkably different between the deep waters of the Pacific and Atlantic oceans, being present in higher concentrations in the former. This is evident from sequence analysis and a microscopic survey with a species-specific newly designed TSA-FISH probe. Several hints point to the hypothesis thatG. minoris transported to the deep ocean attached to particles, and the absence ofG. minorin bathypelagic Atlantic waters could then be explained by the absence of this organism in surface waters of the equatorial Atlantic. The good correlation ofG. minorbiomass with recalcitrant carbon and free-living prokaryotic biomass in South Pacific waters, together with the identification of the observed cells as yeast and not as a resting spore (teliospore), point to the possibility that once arrived at deep layer this species keeps on growing and thriving.