bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatomy of a mega-radiation: Biogeography and niche evolution inAstragalus
Authors: Folk R.A. , Charboneau J.L.M. , Belitz M. , Singh T. , Kates H.R. , Soltis D.E. , Soltis P.S. , Guralnick R.P. , Siniscalchi C.M. 
Published: June 2023

AbstractAstragalus(Fabaceae), with more than 3,000 species, represents a successful radiation of morphologically highly similar species found across the Northern Hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. Here, for the first time using extensive taxonomic sampling in a phylogenetic analysis, we ask whether (1)Astragalusis uniquely characterized by bursts of radiation or is instead similar to related taxa. Then we test whether the species diversity ofAstragalusis attributable specifically to its predilection for (2) cold and arid habitats or (3) particular soils. Finally, we test (4) whetherAstragalusoriginated in central Asia as proposed and (5) whether niche evolutionary shifts were associated with the colonization of other continents. Our results point to the importance of heterogeneity in the diversification ofAstragalus, with upshifts associated with the earliest divergences but attributable to no abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. We find strong evidence for a central Asian origin and direct dispersals from this region responsible for much of the present-day distribution, highlighting the importance of central Asia as a biogeographic gateway. In contrast to diversification shifts, biogeographic shifts have a strong association with the abiotic environment. Our most important result was a fundamental divide in soil types and diurnal temperature variation between the Eastern and Western Hemisphere species; this divergence does not reflect differences in available habitat among these biogeographic domains but may reflect unique local gains of edaphic and abiotic stress adaptations. While large clades are logistically difficult to tackle, our investigation shows the importance of phylogenetic and evolutionary studies of “mega-radiations.” Our findings reject any simple key innovation behind the dominance and richness ofAstragalusand underline the often nuanced, multifactorial processes leading to species-rich clades.
Disentangling the biotic and abiotic drivers of bird-building collisions in a tropical Asian city using ecological niche modeling
Authors: Tan David J. X. , Freymueller Nicholas A. , Teo Kah Ming , Symes William S. , Lum Shawn K.Y. , Rheindt Frank E. 
Published: June 2023

AbstractBird-building collisions are responsible for a large number of bird deaths in cities around the world, yet they remain poorly studied outside of North America. This study presents one of the first city-wide fine-scale and landscape-scale analyses of bird-building collisions from Asia and represents a novel application of maximum entropy modeling (as commonly applied to species distribution modeling) to assess the drivers of bird-building collisions in the tropical city-state of Singapore. Our results show that the drivers of bird-building collisions often vary among taxa, with several migratory taxa having a higher relative collision risk linked to areas with high building densities and high levels of nocturnal blue light pollution. In contrast, non-migratory taxa had a higher collision risk in areas proximate to woodland cover. Projecting these models onto high-fidelity long-term government land-use plans, we demonstrate that our approach can be applied to predict future changes in bird-building collision risk stemming from future increases in blue light pollution and encroachment of buildings into forested areas. Our results suggest that bird-building collision mitigation measures need to account for the differential drivers of collision across both resident and migratory species, and show that combining community science and ecological modeling can be a powerful approach for analyzing bird-building collision data.Article impact statementInferring the drivers and distribution patterns of bird-building collision hotspots in Singapore using community science and maximum entropy modeling
VARIATIONS IN THE ULTRAVIOLET FLORAL PATTERNS AND POLLINATOR PREFERENCE AMONG SELECTED NON-INVASIVE AND INVASIVE PLANTS OF TAMIL NADU, INDIA
Authors: Ravichandran Indhar Saidanyan , Balasingam Parthiban , Rajasekaran Mohan Raj , Ananthapadmanabhan Karthikeyan , Muthuvel Manojkumar , Ramalingam Kottaimuthu , M Vigneshwaran , Nalluchamy Kamaladhasan , Soorangkattan Saravanan , MR Anbarasan , Sivagnanam Chandrasekaran 
Published: June 2023

AbstractFossil evidence shows that pollinator-mediated plant reproduction evolved ∼140 million years ago and bee facilitated pollination evolved ∼70 million years ago. Human vision is limited to the visible color range of 400 to 750 nanometres, whereas most pollinators can perceive the ultraviolet (UV) range in addition to visible colors. Bees have been reported to have highest spectral sensitivity in the ultraviolet spectrum. The main objectives of the study were (1) to assess the prevalence of ultraviolet floral patterns, (2) to analyse floral patterns in relation to plant-pollinator interaction among invasive and non-invasive plants, and (3) to test for intraspecific floral pattern variations among plants with different flower color morphs. A study was conducted on 188 plant species (80 invasive and 108 non-invasive) from parts of Western and Eastern Ghats region of Tamil Nadu, India. The flowers of the studied plant species were imaged in ultraviolet (320-380 nm) and visible spectrums. The mode of pollination for the selected species were documented and confirmed with existing literature. The intraspecific variations in the floral patterns among flower color polymorphic plant species (N=10) were documented in ultraviolet and visible spectrums. Among the studied plant species, around 58% had discernible floral patterns when observed in the UV spectrum, whereas the rest were observed to completely absorb or reflect UV radiation. Whereas 46% of the studied plants exhibited no pattern in the visible spectrum. A significant difference was observed in the pollinator relationship among the ultraviolet floral patterns in invasive plants (χ2= 63.98,df= 32,P< 0.001), whereas no significant variation was evidenced in the pollinator relationship among the ultraviolet floral patterns in non-invasive plants (χ2= 19.50,df= 24,P= 0.724). Analysis of pollinator preference revealed that invasive species were mostly pollinated by bee and butterfly mediated pollination, whereas non-invasive species were mostly pollinated by bees and generalist insects. Intraspecific variations in the floral ultraviolet signal were observed among different morphs in a few flower color polymorphic species, especially inLantana camara. The multispectral analysis of floral patterns revealed that plants utilize both the visible and ultraviolet spectrums to effectively communicate with pollinators. The results from the present study strongly suggest that the variation in the floral ultraviolet signature among invasive species might play a vital role in plant-pollinator interaction and invasion success.
Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection
Authors: Böhne Astrid , Fernández Rosa , Leonard Jennifer A. , McCartney Ann M. , McTaggart Seanna , Melo-Ferreira José , Monteiro Rita , Oomen Rebekah A. , Vinnere Pettersson Olga , Struck Torsten H. 
Published: June 2023

AbstractThe European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe’s eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA’s pan- European network. To demonstrate the community’s capability and capacity to realise ERGA’s ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA’s member base. SSP aims to aid participating researchers through i) establishing standards for and collecting of sample/ specimen metadata; ii) prioritisation of species for genome sequencing; and iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA’s high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.
Fungal phylogeny reconstructed using heterogeneous models reveals new placement of Microsporidia
Authors: Riquelme-Medina Ignacio , McInerney James O. 
Published: June 2023

AbstractFungi have significant impacts on global ecosystems, playing roles in organic matter decomposition, as disease agents, as well as having both positive and negative economic effects. Fungal evolutionary history remains partly unresolved with the presence on manyincertae sedisclades, lacking a robust placement on the fungal phylogenetic tree. Some of the more problematic groups whose placement remains unclear are the intracellular parasitesMicrosporidiaand Cryptomycota, both of whom have accelerated rates of nucleotide substitution and reduced genomes, which makes the resolution of these groups hard. In this project we used tree and data heterogeneous models, that can account for different substitution rates between different protein families as well as different parts of the phylogenetic tree, to reconstruct the phylogeny. We recovered a well-supported topology for much of the fungal phylogeny as well as a robust placement for bothMicrosporidiaand Cryptomycota, the former being rooted deeply within the fungi and the latter a placement on a sister branch to the fungi.
Comparable analysis of multiple DNA double-strand break repair pathways in CRISPR-mediated endogenous tagging
Authors: Tei Chiharu , Hata Shoji , Mabuchi Akira , Okuda Shotaro , Ito Kei K , Genova Mariya , Fukuyama Masamitsu , Yamamoto Shohei , Chinen Takumi , Toyoda Atsushi , Kitagawa Daiju 
Published: June 2023

AbstractCRISPR-mediated endogenous tagging, utilizing the homology-directed repair (HDR) of DNA double-strand breaks (DSBs) with exogenously incorporated donor DNA, is a powerful tool in biological research. Inhibition of the non-homologous end joining (NHEJ) pathway has been proposed as a promising strategy for improving the low efficiency of accurate knock-in via the HDR pathway. However, the influence of alternative DSB repair pathways on gene knock-in remains to be fully explored. In this study, our long-read amplicon sequencing analysis reveals various patterns of imprecise repair in CRISPR/Cas-mediated knock-in, even under conditions where NHEJ is inhibited. Suppression of the microhomology-mediated end joining (MMEJ) or the single strand annealing (SSA) repair mechanisms leads to a reduction in distinct patterns of imprecise repair, thereby elevating the efficiency of accurate knock-in. Furthermore, a novel reporter system shows that the SSA pathway contributes to a specific pattern of imprecise repair, known as asymmetric HDR. Collectively, our study uncovers the involvement of multiple DSB repair pathways in CRISPR/Cas-mediated gene knock-in and proposes alternative approaches to enhance the efficiency of precise gene knock-in.
High-Intensity Interval Training Attenuates Impairment in Regulatory Protein Machinery of Mitochondrial Quality Control in Skeletal Muscle of Diet-Induced Obese Mice
Authors: Tincknell James B. , Kugler Benjamin , Spicuzza Haley , Yan Huimin , You Tongjian , Zou Kai 
Published: June 2023

ABSTRACTMitochondrial quality control processes are essential in governing mitochondrial integrity and function. The purpose of the study was to examine the effects of 10 weeks of HIIT on the regulatory protein machinery of skeletal muscle mitochondrial quality control and whole-body glucose homeostasis in diet-induced obese mice. Male C57BL/6 mice were randomly assigned to a low-fat diet (LFD) or high-fat diet (HFD) group. After 10 weeks, HFD-fed mice were divided into sedentary and HIIT (HFD+HIIT) groups and remained on HFD for another 10 weeks (n=9/group). Graded exercise test, glucose and insulin tolerance tests, mitochondrial respiration and regulatory protein markers of mitochondrial quality control processes were determined by immunoblots. Ten weeks of HIIT enhanced ADP-stimulated mitochondrial respiration in diet-induced obese mice (P < 0.05) but did not improve whole-body insulin sensitivity. Importantly, the ratio of Drp1(Ser616) over Drp1(Ser637) phosphorylation, an indicator of mitochondrial fission, was attenuated in HFD-HIIT compared to HFD (−35.7%, P < 0.05). Regarding autophagy, skeletal muscle p62 content was lower in HFD group than LFD group (−35.1%, P < 0.05), however, such reduction was disappeared in HFD+HIIT group. In addition, LC3B II/I ratio was higher in HFD than LFD group (15.5%, P < 0.05) but was ameliorated in HFD+HIIT group (−29.9%, P < 0.05). Overall, our study demonstrated that 10 weeks of HIIT was effective in improving skeletal muscle mitochondrial respiration and the regulatory protein machinery of mitochondrial quality control in diet-induced obese mice through the alterations of mitochondrial fission protein Drp1 activity and p62/LC3B-mediated regulatory machinery of autophagy.
Chromatin compaction and spatial organization in rice interphase nuclei
Authors: Doležalová Alžběta , Beránková Denisa , Koláčková Veronika , Hřibová Eva 
Published: June 2023

AbstractChromatin organization and its interactions are essential for biological processes such as DNA repair, transcription, and DNA replication. Detailed cytogenetics data on chromatin conformation, and the arrangement and mutual positioning of chromosome territories in interphase nuclei are still widely missing in plants. In this study, level of chromatin condensation in interphase nuclei of rice (Oryza sativa) and the distribution of chromosome territories (CTs) were analyzed. Super-resolution, stimulated emission depletion (STED), microscopy showed different level of chromatin condensation in leaf and root interphase nuclei. 3D immuno-FISH experiments with painting probes specific to chromosomes 9 and 2 were conducted to investigate their spatial distribution in root and leaf nuclei. Six different configurations of chromosome territories, including their complete association, weak association, and complete separation, were observed in root meristematic nuclei, and four configurations were observed in leaf nuclei. The volume of CTs and frequency of their association varied between the tissue types. The frequency of association of CTs specific to chromosome 9, containing NOR region, is also affected by the activity of the 45S rDNA locus. Our data suggested that the arrangement of chromosomes in the nucleus is connected to the position and the size of the nucleolus.HighlightSuper-resolution STED microscopy uncovered detailed chromatin ultrastructure; high level of differences in chromatin condensation and mutual positioning of chromosome territories between and within leaf and root meristem G1 were observed.
Discovering Matrix Adducts for Enhanced Metabolite Profiling with Stable Isotope-Labeled MALDI-MSI
Authors: Baquer Gerard , Bernús Miguel , Sementé Lluc , van Zeijl René , García-Altares Maria , Heijs Bram , Boutureira Omar , Correig Xavier , Ràfols Pere 
Published: June 2023

AbstractMatrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) is a widely used technique for spatial metabolomics analysis, but the matrix introduces spectral interferences that impede data processing. In this study, we present an experimental and computational workflow utilizing isotopic labeling to discover and annotate matrix adducts in MALDI-MSI. Our approach enables the removal of matrix-related signals, improving metabolite annotation accuracy, extending metabolome coverage, and facilitating the interpretation of tissue morphology.
AMF-SporeChipprovides new insights into arbuscular mycorrhizal fungal pre-symbiotic hyphal growth dynamics at the cellular level
Authors: Richter Felix , Calonne-Salmon Maryline , van der Heijden Marcel G. A. , Declerck Stéphane , Stanley Claire E. 
Published: June 2023

SummaryArbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants and deliver a wide range of soil-based ecosystem services. Due to their conspicuous belowground lifestyle in a dark environment surrounded by soil particles, much is still to be learned about the influence of environmental (i.e., physical) cues on spore germination, hyphal morphogenesis and hyphopodium formation in AMF.To fill existing gaps in AMF knowledge, we developed a new microfluidic platform – termed theAMF-SporeChip– to immobiliseRhizophagusandGigasporaspores and confront pre-symbiotic hyphae with physical obstacles. In combination with timelapse microscopy, the fungi could be examined at the cellular level and in real-time.TheAMF-SporeChipallowed us to acquire movies with unprecedented visual clarity and therefore identify various exploration strategies of AMF pre-symbiotic hyphae. We witnessed anastomosis formation involving directed hyphal growth in a “stop-and-go” manner, yielding visual evidence of pre-anastomosis signalling and decision-making. Remarkably, we also revealed a so-far undescribed reversible cytoplasmic retraction as part of a highly dynamic space navigation.Our findings demonstrated how AMF employ an intricate mechanism of space searching, involving reversible cytoplasmic retraction, branching and directional changes. In turn, theAMF-SporeChipis expected to open many future frontiers for AMF research.
Global Diversity in Mammalian Life Histories: Environmental Realms and Evolutionary Adaptations
Authors: Beccari E. , Capdevila Lanzaco P. , Salguero-Gómez R. , Pérez Carmona C. 
Published: June 2023

AbstractMammalian life history strategies can be characterized by a few axes of variation, which conform a space where species are positioned according to which life history strategies are favoured in the environment they exploit. Yet, we still lack global descriptions of the diversity of realized mammalian life history and of how this diversity is shaped by the environment. We used six life history traits to build a global life history space and explored how major environmental realms (land, air, water) influence mammalian life history strategies. We demonstrate that realms are tightly linked to distinct life history strategies. Predominantly, aquatic and aerial species adhere to slower life history strategies, while terrestrial species tend to exhibit faster life histories. Highly encephalized terrestrial species are a notable exception to these patterns. In addition, species transitioning between the terrestrial and aquatic realms, such as seals, show intermediate life history strategies. Further, different mode-of-life may play a significant role in allowing to expand the set of strategies exploitable in the terrestrial realm. Our results provide compelling evidence of the link between environmental realms and the diversity of life history strategies among mammals.Statement of authorshipP.C.L., R.S-G., and C.P.C. conceived the core ideas behind this paper, all authors provided fundamental inputs for its final development. E.B collected all data and performed the literature search needed to sort species in environmental realms. E.B. analysed the data with fundamental inputs from C.P.C., P.C.L, and R.G-S. All authors contributed to interpretation of the results. E.B. and C.P.C. led the writing of the manuscript which was edited by all authors.
Theoretical validation of growth curves for quantifying phage-bacteria interactions
Authors: Blazanin Michael , Vasen Emma , Jolis Cèlia Vilaró , An William , Turner Paul E. 
Published: June 2023

AbstractBacteria-infecting viruses, bacteriophages, are the most abundant biological entities on the planet, frequently serving as model systems in basic research and increasingly relevant for medical applications such as phage therapy. A common need is to quantify the infectivity of a phage to a given bacterial host (or the resistance of a host to a phage). However, current methods to quantify infectivity suffer from low-throughput or low-precision. One method that has the potential for high-throughput and high-precision quantification of phage-bacteria interactions is growth curves, where bacterial density is measured over time in the presence and absence of phages. Recent work has proposed several approaches to quantify these curves into a metric of phage infectivity. However, little is known about how these metrics relate to one another or to underlying phage and bacterial traits. To address this gap, we apply ecological modeling of phage and bacterial populations to simulate growth curves across a wide range of trait values. Our findings show that many growth curve metrics provide parallel measures of phage infectivity. Informative metrics include the peak and decline portions of bacterial growth curves, are driven by the interactions between underlying phage and bacterial traits, and correlate with conventional measures of phage fitness. Moreover, we show how intrapopulation trait variation can alter growth curve dynamics. Finally, we test the sensitivity of growth curve metrics to inoculum densities, and assess techniques to compare growth curves across different bacterial hosts. In all, our findings support the use of growth curves for precise high-throughput quantification of phage-bacteria interactions across the microbial sciences.SignificanceBacteriophages are viruses that infect bacteria. Phages have long been laboratory models and are increasingly being explored as antimicrobials. Commonly, we need to quantify how well a phage infects a bacterial strain. Unfortunately, current methods are either laborious or imprecise. One method that could be better is growth curves, where bacterial growth is measured over time in the presence or absence of phages. However, it has remained unclear how to use such data to produce a single metric of phage infectivity. Here, we used simulations to show that many different metrics provide parallel measures of phage infectivity that match conventional measures across a range of conditions. Our work suggests that growth curves can provide rapid, precise measurement of phage infectivity.