bluuebunny/crossref_metadata_2025_split huggingface dataset:
What mycologists should talk about when they are talking about the International Code of Nomenclature for algae, fungi, and plants
Authors: Nilsson R. Henrik , Ryberg Martin , Wurzbacher Christian , Tedersoo Leho , Anslan Sten , Põlme Sergei , Spirin Viacheslav , Mikryukov Vladimir , Svantesson Sten , Hartmann Martin , Lennartsdotter Charlotte , Belford Pauline , Khomich Maryia , Retter Alice , Corcoll Natàlia , Martinez Daniela Gómez , Jansson Tobias , Ghobad-Nejhad Masoomeh , Vu Duong , Sanchez-Garcia Marisol , Kristiansson Erik , Abarenkov Kessy 
Published: February 2023

AbstractFungal metabarcoding of substrates such as soil, wood, and water are uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside of the ambit of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of the mycological community – that “the code” works fine and that these complications will somehow sort themselves out given enough time and a following wind – and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. However, the present authors fear that no waves of change will be lapping the shores of mycology for the foreseeable future, leaving the overwhelming majority of extant fungi without formal names and thus scientific and environmental agency. It is not clear to us who benefits from that, but neither fungi nor mycology are likely to be on the winning side.
Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context
Authors: Cai Leon Y. , Lee Ho Hin , Newlin Nancy R. , Kerley Cailey I. , Kanakaraj Praitayini , Yang Qi , Johnson Graham W. , Moyer Daniel , Schilling Kurt G. , Rheault François , Landman Bennett A. 
Published: February 2023

AbstractDiffusion MRI (dMRI) streamline tractography is the gold-standard forin vivoestimation of white matter (WM) pathways in the brain. However, the high angular resolution dMRI acquisitions capable of fitting the microstructural models needed for tractography are often time-consuming and not routinely collected clinically, restricting the scope of tractography analyses. To address this limitation, we build on recent advances in deep learning which have demonstrated that streamline propagation can be learned from dMRI directly without traditional model fitting. Specifically, we propose learning the streamline propagator from T1w MRI to facilitate arbitrary tractography analyses when dMRI is unavailable. To do so, we present a novel convolutional-recurrent neural network (CoRNN) trained in a teacher-student framework that leverages T1w MRI, associated anatomical context, and streamline memory from data acquired for the Human Connectome Project. We characterize our approach under two common tractography paradigms, WM bundle analysis and structural connectomics, and find approximately a 5-15% difference between measures computed from streamlines generated with our approach and those generated using traditional dMRI tractography. When placed in the literature, these results suggest that the accuracy of WM measures computed from T1w MRI with our method is on the level of scan-rescan dMRI variability and raise an important question: is tractography truly a microstructural phenomenon, or has dMRI merely facilitated its discovery and implementation?
Secretory IgM (sIgM) is an ancient master regulator of microbiota homeostasis and metabolism
Authors: Ding Yang , Fernández-Montero Alvaro , Mani Amir , Casadei Elisa , Shibasaki Yasuhiro , Takizawa Fumio , Miyazawa Ryuichiro , Salinas Irene , Sunyer J. Oriol 
Published: February 2023

AbstractThe co-evolution between secretory immunoglobulins (sIgs) and microbiota began with the emergence of IgM over half a billion years ago. Yet, IgM function in vertebrates is mostly associated with systemic immunity against pathogens. sIgA and sIgT are the only sIgs known to be required in the control of microbiota homeostasis in warm- and cold-blooded vertebrates respectively. Recent studies have shown that sIgM coats a large proportion of the gut microbiota of humans and teleost fish, thus suggesting an ancient and conserved relationship between sIgM and microbiota early in vertebrate evolution. To test this hypothesis, we temporarily and selectively depleted IgM from rainbow trout, an old bony fish species. IgM depletion resulted in a drastic reduction in microbiota IgM coating levels and losses in gutassociated bacteria. These were accompanied by bacterial translocation, severe gut tissue damage, inflammation and dysbiosis predictive of metabolic shifts. Furthermore, depletion of IgM resulted in body weight loss and lethality in an experimental colitis model. Recovery of sIgM to physiological levels restores tissue barrier integrity, while microbiome homeostasis and their predictive metabolic capabilities are not fully restituted. Our findings uncover a previously unrecognized role of sIgM as an ancient master regulator of microbiota homeostasis and metabolism and challenge the current paradigm that sIgA and sIgT are the key vertebrate sIgs regulating microbiome homeostasis.One-Sentence SummaryIgM, the most ancient and conserved immunoglobulin in jawed vertebrates, is required for successful symbiosis with the gut microbiota.
EiDA: A lossless approach for the dynamic analysis of connectivity patterns in signals; application to resting state fMRI of a model of ageing
Authors: de Alteriis Giuseppe , MacNicol Eilidh , Hancock Fran , Ciaramella Alessandro , Cash Diana , Expert Paul , Turkheimer Federico E. 
Published: February 2023

AbstractDynamic Functional Connectivity (dFC) is the study of the dynamical patterns emerging from brain function. We introduce EiDA (Eigenvector Dynamic Analysis), a method that losslessly reduces the dimension of the instantaneous connectivity patterns of a time series to characterise dynamic Functional Connectivity (dFC). We apply EiDA to investigate the signatures of ageing on brain network dynamics in a longitudinal dataset of resting-state fMRI in ageing rats.Previous dFC approaches have relied on the concept of the instantaneous phase of signals, computing the instantaneous phase-locking matrix (iPL) and its eigenvector decomposition. In this work, we fully characterise the eigenstructure of theiPLanalytically, which provides a 1000 fold speed up in dFC computations.The analytical characterization of theiPLmatrix allows us to introduce two methods for its dynamic analysis. 1) Discrete EiDA identifies a discrete set of phase locking modes using k-means clustering on the decomposediPLmatrices. 2) Continuous EiDA provides a 2-dimensional “position” and “speed” embedding of the matrix; here, dFC is conceived as a continuous exploration of this 2-D space rather than assuming the existence of discrete brain states.We apply EiDA to a cohort of 48 rats that underwent functional magnetic resonance imaging (fMRI) at four stages during the course of their lifetime. Using Continuous and Discrete EiDA we found that brain phase-locking patterns become less intense and less structured with ageing. Using information theory and metastability measures derived from the properties of theiPLmatrix, we see that ageing reduces the available functional repertoire postulated to be responsible for flexible cognitive functions and overt behaviours, and reduces the area explored in the embedding space.
Single-cell analysis of CX3CR1+cells reveal a pathogenic role for BIRC5+myeloid proliferating cells driven byStaphylococcus aureusleukotoxins
Authors: Loredan Denis G. , Devlin Joseph C. , Lacey Keenan A. , Howard Nina , Chen Ze , Zwack Erin E. , Lin Jian-Da , Ruggles Kelly V. , Khanna Kamal M. , Torres Victor J. , Loke P’ng 
Published: February 2023

AbstractOur previous studies identified a population of stem cell-like proliferating myeloid cells within inflamed tissues that could serve as a reservoir for tissue macrophages to adopt different activation states depending on the microenvironment. By lineage tracing cells derived from CX3CR1+precursors in mice during infection and profiling by scRNA-seq, here we identify a cluster of BIRC5+myeloid cells that expanded in the liver during either chronic infection with the parasiteSchistosoma mansonior the bacterial pathogenStaphylococcus aureus. In the absence of tissue damaging toxins,S. aureusinfection does not elicit these BIRC5+cells. Moreover, deletion of BIRC5 from CX3CR1 expressing cells results in improved survival duringS. aureusinfection. Hence, the combination of scRNA-Seq and genetic fate mapping CX3CR1+cells revealed a toxin dependent pathogenic role for BIRC5 in myeloid cells duringS. aureusinfection.
Climatic factors and host species composition at hibernation sites drive the incidence of bat fungal disease
Authors: Blomberg AS , Lilley TM , Fritze M , Puechmaille SJ 
Published: February 2023

ABSTRACTEmerging infectious diseases pose a remarkable threat to wildlife, and their incidence will likely be further exacerbated due to climate change. Therefore, developing new, preferably minimally invasive yet effective monitoring systems is crucial for conservation. We investigated whether the occurrence of white-nose disease (WND), a fungal disease of hibernating bats, can be predicted using local climatic conditions and host community composition at hibernation sites. In addition, we used our model to predict the current worldwide potential global distribution of white-nose disease, revealing areas that may be under risk if the pathogen is introduced, and further applied our model to a climate change scenario to illuminate how the potential global distribution of the disease may shift in the future. To achieve this, we fitted a logistic regression model using open-source climate data (mean annual surface temperature (MAST), annual precipitation) and hibernation site census data from 441 hibernacula across Europe. We then applied our model to the current global climatic conditions, as well as a climate change scenario for years 2061–2080, to illuminate the current and future potential global distribution of the disease. We discovered a positive association between the occurrence of WND andMyotis emarginatus,M. myotis/blythii, andM.mystacinus/brandtii, whereasRhinolophus ferrumequinumandR. hipposideroswere negatively associated with the disease. In addition, we were able to detect several areas in the southern hemisphere, that are likely to be at risk if the pathogen is introduced, and demonstrate that climate change may cause a remarkable shift in the distribution range of the disease. We further show that MAST can be used to predict the occurrence of WND, with the highest probability in areas where MAST was 8.3 °C. Our results highlight the importance of environmental factors in controlling the manifestation of disease in localities where both the pathogen and suitable hosts are present, and the massive impact climate change could have in reshaping and expanding the geographic range where WND can occur.
Genetic features and genomic targets of human KRAB-Zinc Finger Proteins
Authors: de Tribolet-Hardy Jonas , Thorball Christian W. , Forey Romain , Planet Evarist , Duc Julien , Khubieh Bara , Offner Sandra , Fellay Jacques , Imbeault Michael , Turelli Priscilla , Trono Didier 
Published: February 2023

ABSTRACTKrüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on more than a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
Beyond the Active Site: The addition of a remote loop reveals a new complex biological function for chitinase enzymes
Authors: Kozome Dan , Sljoka Adnan , Laurino Paola 
Published: February 2023

AbstractLoops are small secondary structural elements that play a crucial role in the emergence of new enzyme functions. However, our understanding of loop functions is mainly limited to the catalytic loops. To understand the function of remote loops in enzymes, we studied Glycoside hydrolase family 19 (GH19) chitinase - an essential enzyme family for pathogen degradation in plants. By revealing the evolutionary history and loops appearance of GH19 chitinase, we discovered that one loop which is remote from the catalytic site, is necessary to acquire the new antifungal activity. We demonstrated that this remote loop directly accesses the fungal cell wall, and surprisingly, it needs to adopt a defined structure supported by long-range intramolecular interactions to perform its function. Our findings prove that Nature applies this new strategy at the molecular level to achieve a complex biological function while maintaining the original activity one in the catalytic pocket, suggesting an alternative way to design new enzyme function.
Broad-scale signatures of linked selection under divergent recombination landscapes and mating systems in natural populations of rye and barley
Authors: Waesch Christina , Dreissig Steven 
Published: February 2023

AbstractUnderstanding the interactions between patterns of recombination, mating systems, and signatures of natural selection is a central aim in evolutionary biology. Patterns of recombination shape the evolution of genomes by affecting the efficacy of selection. Within populations, genetic shuffling is achieved through meiotic recombination, random chromosome segregation, and the frequency of outbreeding. Recombination landscapes vary between species and populations, and are further influenced by mating systems. Here, we use populations of two related grass species, rye (Secale cereale) and barley (Hordeum vulgaressp.spontaneum), that differ in their mating system, to analyse signatures of linked selection under divergent recombination landscapes. Rye (outbreeding) and barley (inbreeding) are members of the Poaceae and diverged approximately 15 M years ago. We estimated population recombination rates, analysed patterns of genetic diversity, identified signatures of linked selection, and quantified the fraction and functional class of genes affected by linked selection. In this comparison, we detected signatures of linked selection in low-recombining regions in both species. In inbreeding barley, the low-recombining fraction of the genome was more than 2-fold larger than in outbreeding rye. Furthermore, considering differences in gene density across the genome, approximately 1.5 times more genes were affected by linked selection in barley than in rye. In both species, genomic regions affected by linked selection harbour mostly genes involved in basic cellular processes. We provide empirical evidence for quantitative differences in recombination landscapes between closely related species of divergent mating systems, and discuss the consequences of linked selection and the efficacy of natural selection.Significance statementThe ability of natural selection to disentangle beneficial from deleterious mutations across the genome is shaped by patterns of recombination, yet our understanding of the magnitude of this interaction is incomplete. In our work, we show that patterns of recombination differ between related outbreeding and inbreeding grass species, and that the efficacy of selection differs between them. We provide empirical evidence for quantitative differences in recombination landscapes and patterns of selection.
Robustness of Felsenstein’s versus Transfer Bootstrap Supports with respect to Taxon Sampling
Authors: Zaharias Paul , Lemoine Frédéric , Gascuel Olivier 
Published: February 2023

AbstractThe bootstrap method is based on resampling alignments and re-estimating trees. Felsenstein’s bootstrap proportions (FBP) is the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon-sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tends to return low supports for deep branches. The Transfer Bootstrap Expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports, without inducing falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depth, using empirical datasets. Our results show that the main critic of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.
Genome assembly of the deep-sea coralLophelia pertusa
Authors: Herrera Santiago , Cordes Erik E. 
Published: February 2023

AbstractLike their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly ofLophelia pertusafrom the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio CLR data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, andab initiogene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.
Comparative analysis ofSQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL)gene family between bryophytes and seed plants
Authors: Alisha Alisha , Szweykowska-Kulińska Zofia , Sierocka Izabela 
Published: February 2023

AbstractSQUAMOSA-PROMOTER BINDING PROTEIN-LIKE(SPL) genes encode plant-specific transcription factors which have been found to be conserved in green plants lineage. SPL proteins are important regulators of diverse plant developmental processes in bryophytes and vascular plants. In our study, we took advantage of available genome sequences of representatives of each bryophyte clade to investigate the relationships ofSPLgenes between bryophytes and model angiospermArabidopsis thaliana. We have identified fourSPLgenes in each of the two hornworts species,Anthoceros agrestisandAnthoceros punctatus, what is similar to the set ofSPLgenes present in the liverwortMarchantia polymorpha. Thus, the analyzed hornworts and liverwort genomes encode a minimal set ofSPLgenes in comparison to other land plants that may resemble an archetype ofSPLgenes present in the ancestor of land plants. The phylogenetic analysis revealed the presence of fourSPLgroups. Comparative gene structure analysis showed thatSPLsshare similar exon-intron organization within the same phylogenetic group with some exceptions in hornworts. While we have identified conserved protein motifs between bryophytes andArabidopsisin three out of four phylogenetic groups, the motif content differed explicitly in the fourth group. Since current understanding ofSPLgenes mostly arises from seed plants, the presented comparative and phylogenetic analysis will provide better understanding ofSPLgene family from the representatives of the oldest living land plants.
Label-free differential imaging of cellular components in mouse brain tissue by wide-band photoacoustic microscopy
Authors: Liu Yajing , Wong Terence T W , Shi Junhui , He Yun , Nie Liming , Wang Lihong V. 
Published: February 2023

AbstractMapping diverse cellular components with high spatial resolution is important to interrogate biological systems and study disease pathogenesis. Conventional optical imaging techniques for mapping biomolecular profiles with differential staining and labeling methods are cumbersome. Different types of cellular components exhibit distinctive characteristic absorption spectra across a wide wavelength range. By virtue of this property, a lab-made wide-band optical-resolution photoacoustic microscopy (wbOR-PAM) system, which covers wavelengths from the ultraviolet and visible to the shortwave infrared regions, was designed and developed to capture multiple cellular components in 300-μm-thick brain slices at nine different wavelengths without repetitive staining and complicated processing. This wbOR-PAM system provides abundant spectral information. A reflective objective lens with an infinite conjugate design was applied to focus laser beams with different wavelengths, avoiding chromatic aberration. The molecular components of complex brain slices were probed without labeling. The findings of the present study demonstrated a distinctive absorption of phospholipids, a major component of the cell membrane, brain, and nervous system, at 1690 nm and revealed their precise distribution with microscopic resolution in a mouse brain, for the first time. This novel imaging modality provides a new opportunity to investigate important biomolecular components without either labeling or lengthy specimen processing, thus, laying the groundwork for revealing cellular mechanisms involved in disease pathogenesis.