bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lepidoptera genomics based on 88 chromosomal reference sequences informs population genetic parameters for conservation
Authors: Bortoluzzi Chiara , Wright Charlotte J. , Lee Sangjin , Cousins Trevor , Genez Thiago A. L. , Thybert David , Martin Fergal J. , Haggerty Leanne ,   The Darwin Tree of Life Project Consortium, Blaxter Mark , Durbin Richard 
Published: April 2023

SummaryButterflies and moths (Lepidoptera) are one of the most ecologically diverse and speciose insect orders, with more than 157,000 described species. However, the abundance and diversity of Lepidoptera are declining worldwide at an alarming rate. As few Lepidoptera are explicitly recognised as at risk globally, the need for conservation is neither mandated nor well-evidenced. Large-scale biodiversity genomics projects that take advantage of the latest developments in long-read sequencing technologies offer a valuable source of information. We here present a comprehensive, reference-free, whole-genome, multiple sequence alignment of 88 species of Lepidoptera. We show that the accuracy and quality of the alignment is influenced by the contiguity of the reference genomes analysed. We explored genomic signatures that might indicate conservation concern in these species. In our dataset, which is largely from Britain, many species, in particular moths, display low heterozygosity and a high level of inbreeding, reflected in medium (0.1 - 1 Mb) and long (> 1 Mb) runs of homozygosity. Many species with low inbreeding display a higher masked load, estimated from the sum of rejected substitution scores at heterozygous sites. Our study shows that the analysis of a single diploid genome in a comparative phylogenetic context can provide relevant genetic information to prioritise species for future conservation investigation, particularly for those with an unknown conservation status.
Signal-amplification for cell-free biosensors, an analog-to-digital converter
Authors: Lopes Franco Rafael Augusto , Brenner Gabriel , Bertolazzi Zocca Vitória Fernanda , de Paiva Gabriela Barbosa , Lima Rayane Nunes , Rech Elibio Leopoldo , Costa Ribeiro Lins Milca Rachel da , Pedrolli Danielle Biscaro 
Published: April 2023

ABSTRACTToehold switches are biosensors useful for the detection of endogenous and environmental RNAs. They have been engineered to detect virus RNAs in cell-free gene expression reactions. Their inherent sequence programmability makes engineering a fast and predictable process. Despite improvements in the design, toehold switches suffer from leaky translation in the OFF state, which compromises the fold change and sensitivity of the biosensor. To address this, we constructed and tested signal amplification circuits for three toehold switches triggered by Dengue and Sars-CoV-2 RNAs and an artificial RNA. The serine integrase circuit efficientl contained leakage, boosted the expression fold-change from OFF to ON, and decreased the detection limit of the switches by three to four orders of magnitude. Ultimately, the integrase circuit converted the analog switches’ signals into digital-like output. The circuit is broadly useful for biosensors and eliminates the hard work of designing and testing multiple switches to find the best possible performer.GRAPHICAL ABSTRACT
Gut microbiome-based prediction of autoimmune neuroinflammation
Authors: Steimle Alex , Neumann Mareike , Grant Erica T. , Willieme Stéphanie , De Sciscio Alessandro , Parrish Amy , Ollert Markus , Miyauchi Eiji , Soga Tomoyoshi , Fukuda Shinji , Ohno Hiroshi , Desai Mahesh S. 
Published: April 2023

AbstractGut commensals are linked to neurodegenerative diseases, yet little is known about causal and functional roles of microbial risk factors in the gut–brain axis. Here, we employed a pre-clinical model of multiple sclerosis in mice harboring distinct complex microbiotas and six defined strain combinations of a functionally-characterized synthetic human microbiota. Discrete microbiota compositions resulted in different probabilities for development of severe autoimmune neuroinflammation. Nevertheless, assessing presence or the relative abundances of a suspected microbial risk factor failed to predict disease courses across different microbiota compositions. Importantly, we found considerable inter-individual disease course variations between mice harboring the same microbiota. Evaluation of multiple microbiome-associated functional characteristics and host immune responses demonstrated that the immunoglobulin A-coating index ofBacteroides ovatusbefore disease onset is a robust individual predictor for disease development. Our study highlights that the “microbial risk factor” concept needs to be seen in the context of a given microbial community network, and host-specific responses to that community must be considered when aiming for predicting disease risk based on microbiota characteristics.
Defining the mechanisms of action and resistance to the anti-PD-1+LAG-3 and anti-PD-1+CTLA-4 combinations in melanoma flank and brain models
Authors: Phadke Manali S. , Li Jiannong , Chen Zhihua , Rodriguez Paulo C. , Mandula J.K. , Karapetyan Lilit , Forsyth Peter A. , Chen Y. Ann , Smalley Keiran S.M. 
Published: April 2023

AbstractBackgroundAlthough the anti-PD-1+LAG-3 and the anti-PD-1+CTLA-4 combinations are effective in advanced melanoma it remains unclear whether their mechanisms of action and resistance overlap.MethodsWe used single cell (sc) RNA-seq, flow cytometry and IHC analysis of responding SM1 and B16 melanoma flank tumors and SM1 brain metastases to explore the mechanism of action of the anti-PD-1+LAG-3 and the anti-PD-1+CTLA-4 combination. CD4+ and CD8+ T cell depletion and ELISPOT assays were used to demonstrate the unique role of CD4+ T cell help in the anti-tumor effects of the anti-PD-1+LAG-3 combination. Tetramer assays confirmed the loss of CD8+ tumor-reactive T cells in brain tumors resistant to the anti-PD-1+LAG-3 combination.ResultsThe anti-PD-1+CTLA-4 combination was associated with the infiltration of FOXP3+ regulatory CD4+ cells (Tregs), fewer activated CD4+ T cells and the accumulation of a subset of IFNγ secreting cytotoxic CD8+ T cells, whereas the anti-PD-1+LAG-3 combination led to the accumulation of CD4+ T helper cells that expressed CXCR4, TNFSF8, IL21R and a subset of CD8+ T cells with reduced expression of cytotoxic markers. T cell depletion studies showed a requirement for CD4+ T cells for the anti-PD-1+LAG-3 combination, but not the PD-1-CTLA-4 combination at both flank and brain tumor sites. In anti-PD-1+LAG-3 treated tumors, CD4+ T cell depletion was associated with fewer activated (CD69+) CD8+ T cells, impaired IFNγ release and increased numbers of myeloid-derived suppressor cells (MDSCs) but, conversely, increased numbers of activated CD8+ T cells and IFNγ release in anti-PD-1+CTLA-4 treated tumors. Analysis of relapsing melanoma brain metastases from anti-PD-1+LAG-3 treated mice showed an increased accumulation of MDSCs and a loss of gp100+ tumor reactive CD8+ T cells. An analysis of the inferred cell-cell interactions from the scRNA-seq data suggested the MDSCs interacted with multiple subsets of T cells in a bi-directional manner.ConclusionsTogether these studies suggest that these two clinically relevant ICI combinations have differential effects upon CD4+ T cell polarization, which in turn, impacted cytotoxic CD8+ T cell function. Further insights into the mechanisms of action/resistance of these clinically-relevant ICI combinations will allow therapy to be further personalized.
An Aging-Susceptible Circadian Rhythm Controls Cutaneous Antiviral Immunity
Authors: Kirchner Stephen , Lei Vivian , Kim Paul , Patel Meera , Shannon Jessica , Corcoran David , Hughes Dalton , Waters Diana , Dzirasa Kafui , Erdmann Detlev , Coers Jörn , MacLeod Amanda , Zhang Jennifer Y. 
Published: April 2023

ABSTRACTAged skin is prone to viral infections, but the mechanisms responsible for this immunosenescent immune risk are unclear. We observed that aged murine and human skin expressed reduced antiviral proteins (AVPs) and circadian regulators including Bmal1 and Clock. Bmal1 and Clock were found to control rhythmic AVP expression in skin and such circadian-control of AVPs was diminished by disruption of immune cell interleukin 27 signaling and deletion of Bmal1/Clock genes in mouse skins, as well as siRNA-mediated knockdown of CLOCK in human primary keratinocytes. We found that treatment of circadian enhancing agents, nobiletin and SR8278, reduced infection of herpes simplex virus 1 (HSV1) in epidermal explants and human keratinocytes in a Bmal1/Clock-dependent manner. Circadian enhancing treatment also reversed susceptibility of aging murine skin and human primary keratinocytes to viral infection. These findings reveal an evolutionarily conserved and age-sensitive circadian regulation of cutaneous antiviral immunity, underscoring circadian restoration as an antiviral strategy in aging populations.
Scale-free models of chromosome structure, dynamics, and mechanics
Authors: Grosse-Holz Simon , Mirny Leonid , Coulon Antoine 
Published: April 2023

AbstractThe nucleus of a cell contains its genetic information in the form of chromatin: polymers of DNA and associated proteins. The physical nature of this polymer system is yet to be understood. Orthogonal experimental approaches probing chromosome structure, dynamics, and mechanics typically suggest the existence of scaling relationships, leading to the widespread use of scale-free, or fractal, models to represent interphase chromosomes. However, currently, there is no single physical model consistent with all reported scaling exponents. Here, we consider the space of possible scale-free models of chromosome structure, dynamics, and mechanics, and examine the fundamental connections between these physical properties. We demonstrate the existence of two algebraic relationships between the scaling exponents—–connecting structure with dynamics, and dynamics with mechanics, respectively–—outlining the necessary physical conditions for a model to match specific exponent values. Applied to values reported in metazoans, our theory identifies the family of models consistent with all observed scalings, which notably excludes the classical Rouse, Zimm, and fractal globule polymer models. Our theory highlights dynamic correlations between distal genomic loci as necessary to reconnect seemingly contra-dictory measurements. Consequently, we propose new experiments to narrow down the space of possible models. We expect this framework to serve as a guide for understanding past and future measurements, and for building new physical models of interphase chromosomes.
Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes
Authors: Merrill Collin B. , Titos Iris , Pabon Miguel A. , Montgomery Austin B. , Rodan Aylin R. , Rothenfluh Adrian 
Published: April 2023

SummaryTheDrosophilabrain contains tens of thousands of distinct cell types. Thousands of different transgenic lines reproducibly target specific neuron subsets, yet most still express in several cell types. Furthermore, most lines were developed withouta prioriknowledge of where the transgenes would be expressed. To aid in the development of cell type-specific tools for neuronal identification and manipulation, we developed an iterative assay for transposase-accessible chromatin (ATAC) approach. Open chromatin regions (OCRs) enriched in neurons, compared to whole bodies, drove transgene expression preferentially in subsets of neurons. A second round of ATAC-seq from these specific neuron subsets revealed additional enriched OCR2s that further restricted transgene expression within the chosen neuron subset. This approach allows for continued refinement of transgene expression, and we used it to identify neurons relevant for sleep behavior. Furthermore, this approach is widely applicable to other cell types and to other organisms.
RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure
Authors: Rivas Elena 
Published: April 2023

AbstractMany biologically important RNAs fold into specific 3D structures conserved through evolution. Knowing when an RNA sequence includes a conserved RNA structure that could lead to new biology is not trivial and depends on clues left behind by conservation in the form of covariation and variation. For that purpose, the R-scape statistical test was created to identify from alignments of RNA sequences, the base pairs that significantly covary above phylogenetic expectation. R-scape treats base pairs as independent units. However, RNA base pairs do not occur in isolation. The Watson-Crick (WC) base pairs stack together forming helices that constitute the scaffold that facilitates the formation of the non-WC base pairs, and ultimately the complete 3D structure. The helix-forming WC base pairs carry most of the covariation signal in an RNA structure. Here, I introduce a new measure of statistically significant covariation at helix-level by aggregation of the covariation significance and covariation power calculated at base-pair-level resolution. Performance benchmarks show that helix-level aggregated covariation increases sensitivity in the detection of evolutionarily conserved RNA structure without sacrificing specificity. This additional helix-level sensitivity reveals an artifact that results from using covariation to build an alignment for a hypothetical structure and then testing the alignment for whether its covariation significantly supports the structure. Helix-level reanalysis of the evolutionary evidence for a selection of long non-coding RNAs (lncRNAs) reinforces the evidence against these lncRNAs having a conserved secondary structure.AvailabilityHelix aggregated E-values are integrated in the R-scape software package (version 2.0.0.p and higher). The R-scape web servereddylab.org/R-scapeincludes a link to download the source code.Contactelenarivas@fas.harvard.eduSupplementary informationSupplementary data and code are provided with this manuscript atrivaslab.org.
DNA metabarcoding workflow utilizing nanopore long-read sequencing and consensus generation for rapid identification of fungal taxa with high phylogenetic resolution
Authors: Ohta Atsufumi , Nishi Kenichiro , Hirota Kiichi , Matsuo Yoshiyuki 
Published: April 2023

AbstractThe study of microbiota has been revolutionized by the development of DNA metabarcoding. This sequence-based approach enables the direct detection of microorganisms without the need for culture and isolation, which significantly reduces analysis time and offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there has been an accumulating number of researches on bacteria, molecular phylogenetic analysis of fungi still remains challenging due to the lack of standardized tools and the incompleteness of reference databases limiting the accurate and precise identification of fungal taxa. Here, we present a DNA metabarcoding workflow for characterizing fungal microbiota with high taxonomic resolution. This method involves amplifying longer stretches of ribosomal RNA operons and sequencing them using nanopore long-read sequencing technology. The resulting reads were error-polished to generate consensus sequences with 99.5–100% accuracy, which were then aligned against reference genome assemblies. The efficacy of this method was explored using a polymicrobial mock community and patient-derived specimens, demonstrating the marked potential of long-read sequencing combined with consensus calling for accurate taxonomic classification. Our approach offers a powerful tool for the rapid identification of pathogenic fungi and has the promise to significantly improve our understanding of the role of fungi in health and disease.
Netrin-1 directs vascular patterning and maturity in the developing kidney
Authors: Honeycutt Samuel Emery , N’Guetta Pierre-Emmanuel Yoann , Hardesty Deanna Marie , Xiong Yubin , Cooper Shamus Luke , O’Brien Lori Lynn 
Published: April 2023

AbstractBlood filtering by the kidney requires the establishment of an intricate vascular system that works to support body fluid and organ homeostasis. Despite these critical roles, little is known about how vascular architecture is established during kidney development. More specifically, how signals from the kidney influence vessel maturity and patterning remains poorly understood. Netrin-1 (Ntn1) is a secreted ligand critical for vessel and neuronal guidance. Here, we demonstrate thatNtn1is expressed by stromal progenitors in the developing kidney, and conditional deletion ofNtn1from Foxd1+ stromal progenitors (Foxd1GC/+;Ntn1fl/fl) results in hypoplastic kidneys that display extended nephrogenesis. Despite expression of the netrin-1 receptorUnc5cin the adjacent nephron progenitor niche,Unc5cknockout kidneys develop normally. The netrin-1 receptorUnc5bis expressed by embryonic kidney endothelium and therefore we interrogated the vascular networks ofFoxd1GC/+;Ntn1fl/flkidneys. Wholemount, 3D analyses revealed the loss of a predictable vascular pattern in mutant kidneys. As vascular patterning has been linked to vessel maturity, we investigated arterialization in these mutants. Quantification of the CD31+ endothelium at E15.5 revealed no differences in metrics such as the number of branches or branch points, whereas the arterial vascular smooth muscle metrics were significantly reduced at both E15.5 and P0. In support of these results, whole kidney RNA-seq showed upregulation of angiogenic programs and downregulation of muscle-related programs which included smooth muscle-associated genes. Together, our findings highlight the significance of netrin-1 to proper vascularization and kidney development.
Inference on autoregulation in gene expression with variance-to-mean ratio
Authors: Wang Yue , He Siqi 
Published: April 2023

AbstractSome genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the existence of autoregulation with direct biochemical approaches. Nevertheless, some papers have observed that certain types of autoregulations are linked to noise levels in gene expression. We generalize these results by two propositions on discrete-state continuous-time Markov chains. These two propositions form a simple but robust method to infer the existence of autoregulation from gene expression data. This method only needs to compare the mean and variance of the gene expression level. Compared to other methods for inferring autoregulation, our method only requires non-interventional one-time data, and does not need to estimate parameters. Besides, our method has few restrictions on the model. We apply this method to four groups of experimental data and find some genes that might have autoregulation. Some inferred autoregulations have been verified by experiments or other theoretical works.
Modeling EEG Resting-State Brain Dynamics: A proof of concept for clinical studies
Authors: Kotz Sonja A. , Astudillo Aland , Araya David , Bella Simone Dalla , Trujillo-Barreto Nelson , El-Deredy Wael 
Published: April 2023

AbstractFunctional brain imaging has shown that the awake brain, independent of a task, spontaneously switches between a small set of functional networks. How useful this dynamical view of brain activity is for clinical studies, e.g., as early markers of subsequent structural and/or functional change or for assessing successful training or intervention effects, remains unclear. Core to addressing this question is to assess the robustness and reproducibility of the analysis methods that model, characterize, or infer the features of brain dynamics, and the accuracy by which these features represent and classify specific cognitive or altered cognitive states. This is particularly key given inter- and intra-individual variability and measurement noise. Here we used resting-state EEG from persons with Parkinson’s Disease (PD) and healthy matched controls to systematically assess the reliability, robustness, and sensitivity of Hidden semi-Markov models (HsMM). These models are an example of model-based probabilistic methods for Brain-State allocations that are estimated from observed data. The method estimates model parameters, if the M/EEG recording or observations, over the scale of minutes, are emissions from hidden states that persist over short durations, before switching or transitioning to other states. We introduce an analysis pipeline that leads to sets of reproducible features of neurophysiological dynamics at the individual level. These features can be used as discriminatory variables to classify individuals and to evaluate the effect of non-pharmacological training schemes like in the current example a music-gait exercise program for Parkinson’s Disease. Given the method stochasticity and the data variability, we emphasize the importance of repeating the analysis to reliably identify brain states and their dynamical trajectories that subsequently can be related to individualized variables.
Comparative genomics-based insights into diversification and bio-protection function ofXanthomonas indica, a non-pathogenic species of rice
Authors: Rana Rekha , Madhavan Vishnu Narayanan , Sonti Ramesh V. , Patel Hitendra K. , Patil Prabhu B. 
Published: April 2023

AbstractXanthomonasspecies have been extensively studied as major and model pathogens of plants. However, there is an increasing recognition of the complex and large world of non-pathogenic species ofXanthomonasin the recent decades. One pathogenicXanthomonasspecies has been known in rice for the last hundred years, yet in recent years, three non-pathogenicXanthomonas(NPX) species have been reported. Thus, there is a need to understand the species-level diversity of NPXs like their pathogenic counterparts. In the present study, we report isolation and investigation into the genomic diversity ofXanthomonas indica, a newly discovered NPX species from rice. The study allowed us to establish the relationship ofX. indicastrains within clade I of Xanthomonads. All the strains formed a distinct but diverse clade compared to clades corresponding to other NPX species from rice and other hosts.X. indicalacks major virulence factors found in their pathogenic counterparts. Identification of highly diverse strains and open-pan genome indicates ongoing selection to acquire new functions for adaptation.X. indicaalso harbours large-scale interstrain variations in the lipopolysaccharide O-antigen biosynthetic gene cluster, which hints at the selection at this locus. Interestingly, all the diverse strains ofX. indicawere able to protect rice from bacterial leaf blight pathogen of rice upon leaf clip inoculation. Comparative genomics revealed the association of a RiPP, a metalloprotease and a bacterial-killing type IV secretion system conserved across its related member species, includingX. sontii, in the clade I within-vivoanti-pathogenic properties. Overall the study has provided novel evolutionary insights into an important NPX member species. The findings and genomic resources will allow further systematic molecular studies to understand its interaction with the host plant.