bluuebunny/crossref_metadata_2025 huggingface dataset:
Triangulation fails when neither linguistic, genetic, nor archaeological data support the Transeurasian narrative
Authors: Tian Zheng , Tao Yuxin , Zhu Kongyang , Jacques Guillaume , Ryder Robin J. , de la Fuente José Andrés Alonso , Antonov Anton , Xia Ziyang , Zhang Yuxuan , Ji Xiaoyan , Ren Xiaoying , He Guanglin , Guo Jianxin , Wang Rui , Yang Xiaomin , Zhao Jing , Xu Dan , Gray Russell D. , Zhang Menghan , Wen Shaoqing , Wang Chuan-Chao , Pellard Thomas
Published: June 2022

Robbeets et al.1 argue that the dispersal of the so-called “Transeurasian” languages, a highly disputed language superfamily comprising the Turkic, Mongolian, Tungusic, Koreanic, and Japonic language families, was driven by Neolithic farmers in the West Liao River region of China. They adduce evidence from linguistics, archaeology, and genetics to support their claim. An admirable feature of the Robbeets et al.’s paper is that all their datasets can be accessed. However, a closer investigation of all three types of evidence reveals fundamental problems with each of them. Robbeets et al.’s analysis of the linguistic data does not conform to the minimal standards required by traditional scholarship in historical linguistics and contradicts their own stated sound correspondence principles. A reanalysis of the genetic data finds that they do not conclusively support the farming-driven dispersal of Turkic, Mongolian, and Tungusic, nor the two-wave spread of farming to Korea. Their archaeological data contain little phylogenetic signal, and we failed to reproduce the results supporting their core hypotheses about migrations.

Given the severe problems we identify in all three parts of the “triangulation” process, we conclude that there is neither conclusive evidence for a Transeurasian language family nor for associating the five different language families with the spread of Neolithic farmers from the West Liao River region.
Viscoelastic Notch Signaling Hydrogel Induces Liver Bile Duct Organoid Growth and Morphogenesis
Authors: Rizwan Muhammad , Ling Christopher , Guo Chengyu , Liu Tracy , Jiang Jia-Xin , Bear Christine E , Ogawa Shinichiro , Shoichet Molly S.
Published: June 2022

Cholangiocyte organoids can be used to model liver biliary disease; however, both a defined matrix in which to emulate cholangiocyte self-assembly and the mechano-transduction pathways involved therein remain elusive. We designed a series of defined viscoelastic hyaluronan hydrogels in which to culture primary cholangiocytes and found that by mimicking the stress relaxation rate of liver tissue, we could induce cholangiocyte organoid growth and significantly increase expression of Yes-associated protein (YAP) target genes. Strikingly, inhibition of matrix metalloproteinases (MMPs) did not significantly affect organoid growth in 3D culture, suggesting that mechanical remodeling of the viscoelastic microenvironment – and not MMP-mediated degradation – is key to cholangiocyte organoid growth. By immobilizing jagged1 to the hyaluronan, stress relaxing hydrogel, self-assembled bile duct structures formed in organoid culture, indicating the synergistic effects of Notch signaling and viscoelasticity. By uncovering critical roles of hydrogel viscoelasticity, YAP signaling and Notch activation, we controlled cholangiocyte organogenesis, thereby paving the way for their use in disease modeling and/or transplantation.
Innate and adaptive immune basis of mental health effect on Alzheimer’s disease progression
Authors: Feng Yilin , Fan Jiaqi , Cheng Yifan , Dai Qionghai , Ma Shaohua
Published: June 2022

Mental health has long been suspected to be highly associated with neurodegenerative disease, but it lacks experimental evidence to elaborate the link and immunological mechanism between them. In this work, we studied the progression of Alzheimer’s disease (AD) and its associated immune activity by using the transgenic mice under negative (depression) and positive (environmental enrichment, EE) mental health intervention. The tissue pathology, resident and peripheral immunity and behavioral characteristics were investigated. The transgenic mice undergoing depression treatment was featured with aggravated AD pathology, elevated activation of microglia in the brains, more abundance of Treg cells and cytotoxic T cells, and higher ratios of central memory T cells to effector memory T (TCM-to-TEM) cells in the peripheral blood and spleens. The EE treated mice were featured with alleviated AD pathology, reduced activation of microglia, less amounts of Treg and cytotoxic T cells and lower ratios of TCM-to-TEM cells. This study may provide strategies for immunity regulation and mental health intervention that benefit AD therapy.

Significance statement

Mental health is suspected to regulate AD progression, but its validation in histology examination and the regulatory mechanism remains unclear. Here, we prove that both innate and adaptive immunity are playing important roles and mental health-immunity-AD progression forms a triad. More active microglia, Treg, and cytotoxic T cells, and higher TCM-to-TEM feature negative mental health and severer AD progress, and vice versa. The findings in adaptive immunity and the triad may inspire AD regulation.
Invasive genetic rescue: Dispersal following repeated culling reinforces the genetic diversity of an invasive mammal
Authors: Synnott Rebecca , Shuttleworth Craig , Everest David J. , Stevenson-Holt Claire , O’Reilly Catherine , McDevitt Allan D. , O’Meara Denise B
Published: June 2022

Since its introduction from the United States in 1876 the invasive North American Eastern grey squirrel (Sciurus carolinensis) has contributed to the decline of the native Eurasian red squirrel (Sciurus vulgaris) in Britain. Consequently, grey squirrel populations are often subjected to extensive control efforts in order to reduce local abundance and prevent spread, particularly within habitats containing red squirrels. Grey squirrel removal from the island of Anglesey off the coast of north Wales began in 1998 and was completed in 2013. A parallel successful red squirrel reinforcement translocation project also took place. The narrow sea-channel, road and rail bridge connection has meant that the adjacent mainland grey squirrel population has been controlled in subsequent years to reduce the probability of re-invasion. The aim of this study was to assess the overall impact of repeated culling efforts carried out between 2011 and 2020 on the genetic diversity of the grey squirrel population in north Wales to inform future adaptive management plans. Using a combination of mitochondrial DNA (mtDNA) and microsatellite DNA analysis, we found high genetic diversity in both marker types, with six diverse mtDNA haplotypes found and relatively high levels of nuclear genetic diversity, even after repeated culling efforts. Our results suggest that ongoing culling efforts may not adequately reduce genetic diversity to a level where it contributes to a long-term population decline.
Masked target visibility is selectively impaired by 20 Hz transcranial alternating current stimulation
Authors: Ilkson Yayla , de la Fuente Alethia , Tagliazucchi Enzo , Pallavicini Carla
Published: June 2022

It has been proposed that both conscious and unconscious perception are associated with a feedforward sweep of oscillatory activity in the gamma band (>40 Hz), while conscious perception also requires recurrent feedback via beta band (~20 Hz) oscillations. To investigate the causal relationship between these oscillations and (un)conscious visual perception, we assessed the effect of transcranial alternating current stimulation (tACS) in the gamma (40 Hz) and beta (20 Hz) bands on the objective and subjective visibility of targets in a metacontrast backward masking task. We expected that 40hz-tACS would affect both the correct categorization of the target (i.e. objective visibility) and the reports of conscious perception (i.e. subjective visibility). Moreover, we expected that 20Hz-tACS would selectively affect the subjective visibility. Our results showed that target visibility was selectively compromised by 20Hz-tACS but, in contrast to our hypothesis, this effect was specific to objective visibility. Although the power of local beta oscillations increased after 20Hz-tACS, inter-areal beta synchrony could have nevertheless been impaired, a possibility that should be investigated in the future by means of source reconstructed high density electroencephalography recordings. In summary, we provided evidence supporting that 20Hz-tACS is capable of modulating target visibility, suggesting a possible a causal link between synchrony in this frequency band and visual perception. Future studies could build upon this result by investigating other forms of stimulation and other model organisms, further contributing to our knowledge of how conscious access causally depends on brain oscillations.
Effects of Aversive Classical Conditioning on Pupil Dilation and Microsaccades
Authors: Friedl W.M. , Keil Andreas
Published: June 2022

Unintentional shifts of gaze and the modulation of pupil size are both highly automated processes that serve to regulate the initial influx of visual information. The present work investigated these mechanisms as they came to differentially respond to initially unthreatening stimuli following aversive conditioning. The classical conditioning experimental paradigm employed simple grating stimuli (Gabor patches) shown individually at various (5) on-screen locations, one of which was paired with a noxious auditory unconditioned stimulus (US). Aversively paired Gabor patches elicited an attenuated initial constriction of the pupil (pupillary light response; PLR) along with more rapid re-dilation compared to otherwise identical but unpaired gratings. Modulation of both the PLR and the rate of re-dilation following conditioning showed pronounced individual differences. Rapid eye movements away from fixation (microsaccades) were suppressed for the aversively associated compared to unassociated stimulus locations at several post-stimulus latencies. Mutual information between pupil dilation and microsaccade rate, meanwhile, did not differ between the aversively associated and unassociated visual on-screen locations. Together, these results suggest that measures of pupil diameter and microsaccade rate supply complementary information on early-stage processes of associative learning through experience.
Starvation Decreases Immunity and Immune Regulatory Factor NF-κB in the Starlet Sea Anemone Nematostella vectensis
Authors: Carrión Pablo J. Aguirre , Desai Niharika , Brennan Joseph J. , Fifer James E. , Davies Sarah W. , Gilmore Thomas D.
Published: June 2022

Lack of proper nutrition (malnutrition) or the complete absence of all food (starvation) have important consequences on the physiology of all organisms. In many cases, nutritional status affects immunity, but, for the most part, the relationship between nutrition and immunity has been limited to studies in vertebrates and terrestrial invertebrates. Herein, we describe a positive correlation between nutrition and immunity in the sea anemone Nematostella vectensis. Gene expression profiling of adult fed and starved anemones showed downregulation of many genes involved in nutrient metabolism and cellular respiration, as well as immune-related genes, in starved animals. Starved adult anemones also had reduced protein levels and DNA-binding activity of immunity-related transcription factor NF-κB. Starved juvenile anemones had increased sensitivity to bacterial infection and also had lower NF-κB protein levels, as compared to fed controls. Weighted Gene Correlation Network Analysis (WGCNA) revealed significantly correlated gene networks that were inversely associated with starvation. Based on the WGCNA and a reporter gene assay, we identified TRAF3 as a likely NF-κB target gene in N. vectensis. Overall, these experiments demonstrate a correlation between nutrition and immunity in a basal marine metazoan, and the results have implications for the survival of marine organisms as they encounter changing environments.

Significance Statement

Adequate nutrition is required to sustain proper biological function. One factor threatening many marine organisms, as a result of modern day anthropogenic environmental changes, is nutrient availability. Here, we characterize transcriptional changes following food deprivation in the cnidarian model sea anemone Nematostella vectensis. We show that starvation is correlated with decreased expression of genes associated with nutrient metabolism and immunity, among others. Moreover, starvation reduces the level of expression and activity of immune regulatory transcription factor NF-κB and causes anemones to have increased susceptibility to bacterial infection. These results demonstrate that this basal organism responds at the transcriptional level to the absence of food, and that, in addition to changes in metabolic factors, starvation leads to a reduction in immunity.
Diffusion on PCA-UMAP manifold captures a well-balance of local, global, and continuum structure to denoise single-cell RNA sequencing data
Authors: Padron-Manrique Cristian , Vázquez-Jiménez Aarón , Esquivel-Hernandez Diego Armando , Martinez Lopez Yoscelina Estrella , Neri-Rosario Daniel , Sánchez-Castañeda Jean Paul , Giron-Villalobos David , Resendis-Antonio Osbaldo
Published: June 2022

Single-cell transcriptomics (scRNA-seq) is becoming a technology that is transforming biological discovery in many fields of medicine. Despite its impact in many areas, scRNASeq is technologically and experimentally limited by the inefficient transcript capture and the high rise of noise sources. For that reason, imputation methods were designed to denoise and recover missing values. Many imputation methods (e.g., neighbor averaging or graph diffusion) rely on k nearest neighbor graph construction derived from a mathematical space as a low-dimensional manifold. Nevertheless, the construction of mathematical spaces could be misleading the representation of densities of the distinct cell phenotypes due to the negative effects of the curse of dimensionality. In this work, we demonstrated that the imputation of data through diffusion approach on PCA space favor over-smoothing when increases the dimension of PCA and the diffusion parameters, such k-NN (k-nearest neighbors) and t (value of the exponentiation of the Markov matrix) parameters. In this case, the diffusion on PCA space distorts the cell neighborhood captured in the Markovian matrix creating an artifact by connecting densities of distinct cell phenotypes, even though these are not related phenotypically. In this situation, over-smoothing of data is due to the fact of shared information among spurious cell neighbors. Therefore, it can not account for more information on the variability (from principal components) or nearest neighbors for a well construction of a cell-neighborhood. To solve above mentioned issues, we propose a new approach called sc-PHENIX( single cell-PHEnotype recovery by Non-linear Imputation of gene eXpression) which uses PCA-UMAP initialization for revealing new insights into the recovered gene expression that are masked by diffusion on PCA space. sc-PHENIX is an open free algorithm whose code and some examples are shown at https://github.com/resendislab/sc-PHENIX.
Glioma-BioDP: Database for Visualization of Molecular Profiles to Improve Prognosis of Brain Cancer
Authors: Das Shaoli , Deng Xiang , Kaur Harpreet , Wilson Evan , Camphausen Kevin , Shankavaram Uma
Published: June 2022

Cancer researchers often seek user-friendly interactive tools for validation, exploration, analysis, and visualization of molecular profiles in cancer patient samples. To aid researchers working on both low-and high-grade gliomas, we developed Glioma-BioDP, a web tool for exploration and visualization of RNA and protein expression profiles of interest in these tumor types. Glioma-BioDP is an extended version of our earlier published tool GBM-BioDP. In this version we have included expression data from both the low-and high-grade glioma patient samples from The Cancer Genome Atlas and enabled querying by mRNA, microRNA, and protein level expression data from Illumina HiSeq and RPPA platforms respectively. Glioma-BioDP enables users to explore the association of genes, proteins, and miRNA expression with molecular and/or histological subtypes of gliomas, surgical resection status and survival. The prognostic significance and visualization of the selected expression profiles can be explored using interactive utilities provided. This tool also enables potential validation and generation of new hypotheses of novel therapies impacting gliomas that aid in personalization of treatment for optimum outcomes.

Availability

Glioma-BioDP web tool with user manual is available from: https://glioma-biodp.nci.nih.gov Contact: uma@mail.nih.gov
Gait Abnormalities and Aberrant D2 Receptor Expression and Signaling in a Mouse Model of the Human Pathogenic Mutation DRD2I212F
Authors: Rodriguez-Contreras Dayana , Gong Sheng , Lebowitz Joseph J , Fedorov Lev M , Asad Naeem , Dore Timothy M , Ford Christopher P , Williams John T , Neve Kim A
Published: June 2022

A dopamine D2 receptor mutation was recently identified in a family with a novel hyperkinetic movement disorder (Mov Disord 36: 729-739, 2021). That allelic variant D2-I212F is a constitutively active and G protein-biased receptor. We now describe mice engineered to carry the D2-I212F variant, Drd2I212F. The mice exhibited gait abnormalities resembling those in other mouse models of chorea and/or dystonia, and had decreased striatal D2 receptor expression. Electrically evoked IPSCs in midbrain dopamine neurons and striatum from Drd2I212F mice exhibited slow onset and decay compared to wild type mice. In the presence of dopamine, current decay initiated by photolytic release of sulpiride from CyHQ-sulpiride was slower in midbrain slices from Drd2I212F mice than Drd2+/+ mice. Furthermore, in contrast to wild type mice in which dopamine is more potent at neurons in the nucleus accumbens than in the dorsal striatum, reflecting activation of Gαo vs. Gαi1, dopamine had similar potencies in those two brain regions of Drd2I212F mice. Repeated cocaine treatment, which decreases dopamine potency in the nucleus accumbens of wild type mice, had no effect on dopamine potency in Drd2I212F mice. The results demonstrate the utility of this mouse model for investigating the role of pathogenic DRD2 variants in early-onset hyperkinetic movement disorders.
Fine temporal brain network structure modularizes and localizes differently in men and women: Insights from a novel explainability framework
Authors: Lewis Noah , Miller Robyn , Gazula Harshvardhan , Calhoun Vince
Published: June 2022

Abstract

Deep learning has become an effective tool for classifying biological sex based on functional magnetic resonance imaging (fMRI), but research on what features within the brain are most relevant to this classification is still lacking. Model interpretability has become a powerful way to understand “black box” deep-learning models and select features within the input data that are most relevant to the correct classification. However, very little work has been done employing these methods to understand the relationship between the temporal dimension of functional imaging signals and classification of biological sex, nor has there been attention paid to rectifying problems and limitations associated with feature explanation models, e.g. underspecification and instability. We provide a methodology to limit the impact of underspecification on the stability of the measured feature importance, and then, using intrinsic connectivity networks (ICNs) from fMRI data, we provide a deep exploration of sex differences among functional brain networks. We report numerous conclusions, including activity differences in the visual and cognitive domains, as well as major connectivity differences.
Single-cell transcriptomics identifies regulation of invasive behavior in Drosophila follicle cells with polarity loss
Authors: Chatterjee Deeptiman , Wang Xian-Feng , Jevitt Allison , Machado Costa Caique Almeida , Huang Yi- Chun , Deng Wu-Min
Published: June 2022

Apicobasal cell-polarity loss is a founding event in Epithelial-Mesenchymal Transition (EMT) and epithelial tumorigenesis, yet how pathological polarity loss induces plasticity changes remains largely unknown. To understand the mechanisms and mediators regulating plasticity upon polarity loss, we performed single-cell (sc) RNA sequencing of Drosophila ovaries, where inducing polarity-gene l(2)gl knockdown (Lgl-KD) causes invasive delamination of the follicular epithelia. Integrating Lgl-KD with the corresponding wild-type sc-transcriptome, we discovered clusters specific to various discernible phenotype-specific cell types and further characterized the regulons active in those cells. A genetic requirement of Keap1-Nrf2 signaling in promoting multilayer formation of Lgl-KD cells was further identified. Elevated expression of Keap1 increased the volume of delaminated follicle cells that undergo enhanced collective invasion via cytoskeletal remodeling. Overall, our findings describe the comprehensive transcriptome of the follicle-cell tumor model at the single-cell resolution and identify a previously unappreciated link between stress signaling and cell plasticity in early tumorigenesis.
Prediction of HLA genotypes from single-cell transcriptome data
Authors: Solomon Benjamin D , Zheng Hong , Dillon Laura W , Goldman Jason D. , Hourigan Christopher S , Heath James R. , Khatri Purvesh
Published: June 2022

The human leukocyte antigen (HLA) locus plays a central role in adaptive immune function and has significant clinical implications for tissue transplant compatibility and allelic disease associations. Studies using bulk-cell RNA sequencing have demonstrated that HLA transcription may be regulated in an allele-specific manner and single-cell RNA sequencing (scRNA-seq) has the potential to better characterize these expression patterns. However, quantification of allele-specific expression (ASE) for HLA loci requires sample-specific reference genotyping due to extensive polymorphism. While genotype prediction from bulk RNA sequencing is well described, the feasibility of predicting HLA genotypes directly from single-cell data is unknown. Here we evaluate and expand upon several computational HLA genotyping tools by comparing predictions from human single-cell data to gold-standard, molecular genotyping. The highest 2-field accuracy averaged across all loci was 76% by arcasHLA and increased to 86% using a composite model of multiple genotyping tools. We also developed a highly accurate model (AUC 0.93) for predicting HLA-DRB345 copy number in order to improve genotyping accuracy of the HLA-DRB locus. Genotyping accuracy improved with read depth and was reproducible at repeat sampling. Using a metanalytic approach, we also show that HLA genotypes from PHLAT and OptiType can generate ASE ratios that are highly correlated (R2 = 0.8 and 0.94, respectively) with those derived from gold-standard genotyping.

Highlights

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Benchmarking of HLA genotype prediction accuracy from 5’- and 3’-based single-cell RNA-seq data compared to molecular HLA genotyping

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Quantification of transcript coverage by 5’- and 3’-based single cell sequencing methods

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Accurate prediction of complex HLA-DRB345 copy numbers using supervised learning

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Balancing accuracy and performance through composite HLA genotyping

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Meta-analytic approach to summarizing allele-specific expression of HLA genotypes at single-cell level
The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation
Authors: Jabłońska Jagoda , Chun-Chen Yao , Longo Liam M. , Tawfik Dan S. , Gruic-Sovulj Ita
Published: June 2022

How protein translation evolved from a simple beginning to its complex and accurate contemporary state is unknown. Aminoacyl-tRNA synthetases (AARSs) define the genetic code by activating amino acids and loading them onto cognate tRNAs. As such, their evolutionary history can shed light on early translation. Using structure-based alignments of the conserved core of Class I AARSs, we reconstructed their phylogenetic tree and ancestral states. Unexpectedly, AARSs charging amino acids that are assumed to have emerged later – such as TrpRS and TyrRS or LysRS and CysRS – appear as the earliest splits in the tree; conversely, those AARSs charging abiotic, early-emerging amino acids, e.g. ValRS, seem to have diverged most recently. Furthermore, the inferred Class I ancestor (excluding TrpRS and TyrRS) lacks the residues that mediate selectivity in contemporary AARSs, and appears to be a generalist that could charge a wide range of amino acids. This ancestor subsequently diverged to two clades: “charged” (which gave rise to ArgRS, GluRS, and GlnRS) and “hydrophobics”, which includes CysRS and LysRS as its outgroups. The ancestors of both clades maintain a wide-accepting pocket that could readily diverge to the contemporary, specialized families. Overall, our findings suggest a “generalist-maintaining” model of class I AARS evolution, in which early statistical translation was kept active by a generalist AARS while the evolution of a specialized, accurate translation system took place.

Significance

Aminoacyl-tRNA synthetases (AARS) define the genetic code by linking amino acids with their cognate tRNAs. While contemporary AARSs leverage exquisite molecular recognition and proofreading to ensure translational fidelity, early translation was likely less stringent and operated on a different pool of amino acids. The co-emergence of translational fidelity and the amino acid alphabet, however, is poorly understood. By inferring the evolutionary history of Class I AARSs we found seemingly conflicting signals: Namely, the oldest AARSs apparently operate on the youngest amino acids. We also observed that the early ancestors had broad amino acid specificities, consistent with a model of statistical translation. Our data suggests that a generalist AARS was actively maintained until complete specialization, thereby resolving the age paradox.
Increased paternal corticosterone exposure preconception shifts offspring social behaviours and expression of urinary pheromones
Authors: Hoffmann Lucas B. , McVicar Evangeline A. , Harris Rebekah V. , Collar-Fernández Coralina , Clark Michael B. , Hannan Anthony J. , Pang Terence Y.
Published: June 2022

Studies have shown that paternal stress prior to conception can influence the innate behaviours of their offspring. The evolutionary impacts of such intergenerational effects are therefore of considerable interest. Our group previously showed that glucocorticoid treatment of adult male mouse breeders prior to conception leads to increased anxiety-related behaviours in male offspring. Here, we aimed to understand the transgenerational effects of paternal stress exposure on the social behaviour of progeny and its potential influence on reproductive success. We assessed social parameters including social reward, male attractiveness and social dominance, in the offspring (F1) and grand-offspring (F2). We report that paternal corticosterone-treatment was associated with increased display of subordination towards other male mice. Those mice were unexpectedly more attractive to female mice while expressing reduced levels of the key rodent pheromone Darcin, contrary to its conventional purpose. We investigated the epigenetic regulation of major urinary protein (Mup) expression by performing the first Oxford Nanopore direct methylation of sperm DNA in a mouse model of stress, but found no differences inMupgenes that could be attributed to corticosterone-treatment. Furthermore, no overt differences of the prefrontal cortex transcriptome were found in F1offspring, implying that peripheral mechanisms are likely contributing to the phenotypic differences. Interestingly, no phenotypic differences were observed in the F2grand-offspring. Overall, our findings highlight the potential of moderate paternal stress to affect intergenerational (mal)adaptive responses, informing future studies of adaptiveness in rodents, humans and other species.
Mathematical Modeling of Fluconazole Resistance in the Ergosterol Pathway of Candida albicans
Authors: Yu Paul K. , Moron Llewelyn S. , Lao Angelyn R.
Published: June 2022

Candidiasis is reported as the most common fungal infection in the critical care setting. The causative agent of this infection is a commensal pathogen belonging to the genus Candida, most common species of which is the Candida albicans. The ergosterol pathway in yeast is a common target by many antifungal agents since ergosterol is an essential component of the cell membrane. The current antifungal agent of choice for the treatment of Candidiasis is fluconazole, which is classified under the azole antifungals. In recent years, the significant increase of fluconazole-resistant C. albicans in clinical samples calls for a need to search for other possible drug targets. In this study, we constructed a mathematical model of the ergosterol pathway of C. albicans using ordinary differential equations with mass action kinetics. From the model simulations, we found the following results: (1) a partial inhibition of the sterol-methyltransferase enzyme yields a fair amount of fluconazole resistance, (2) an overexpression of the ERG6 gene, leading to increased sterol-methyltransferase enzyme, is a good target of antifungals as an adjunct to fluconazole, (3) a partial inhibition of lanosterol yields a fair amount of fluconazole resistance, (4) the C5-desaturase enzyme is not a good target of antifungals as an adjunct to fluconazole, (5) the C14α-demethylase enzyme is confirmed to be a good target of fluconazole, and (6) the dose-dependent effect of fluconazole is confirmed. This study hopes to aid experimenters narrow down the possible drug targets prior to doing costly and time-consuming experiments, and to serve as a cross-validation tool for experimental data.
Reconstruction of visual images from mouse retinal ganglion cell spiking activity using convolutional neural networks
Authors: Benster Tyler , Babino Darwin , Thickstun John , Hunt Matthew , Liu Xiyang , Harchaoui Zaid , Oh Sewoong , Van Gelder Russell N.
Published: June 2022

All visual information in mammals is encoded in the aggregate pattern of retinal ganglion cell (RGC) firing. How this information is decoded to yield percepts remains incompletely understood. We have trained convolutional neural networks with multielectrode array-recorded murine RGC responses to projected images. The trained model accurately reconstructed novel facial images solely from RGC firing data. In this model, subpopulations of cells with faster firing rates are largely sufficient for accurate reconstruction, and ON- and OFF-cells contribute complementary and overlapping information to image reconstruction. Information content for reconstruction correlates with overall firing rate, and locality of information contributing to reconstruction varies substantially across the image and retina. This model demonstrates that artificial neural networks are capable of learning multicellular sensory neural encoding, and provides a viable model for understanding visual information encoding.

Significance Statement

Convolutional neural networks can be trained on high-density neuronal firing data from the optic nerve to reconstruct complicated images within a defined image space.
Formal Recognition and Classification of Gene Transfer Agents as Viriforms
Authors: Kogay Roman , Koppenhöfer Sonja , Beatty J. Thomas , Kuhn Jens H. , Lang Andrew S. , Zhaxybayeva Olga
Published: June 2022

Morphological and genetic features strongly suggest that gene transfer agents (GTAs) are caudoviricete-derived entities that have evolved in concert with cellular genomes to such a degree that they should not be considered viruses. Indeed, GTA particles resemble caudoviricete virions but, in contrast to caudoviricetes (or any viruses), GTAs can encapsidate at best only part of their own genomes, are induced solely in small subpopulations of prokaryotic host cells and are transmitted vertically as part of cellular genomes during replication and division. Therefore, the lifecycles of GTAs are analogous to virus-derived entities found in parasitoid wasps, which have recently been recognized as non-virus entities and therefore reclassified as viriforms. We evaluated three distinct, independently exapted GTA groups for which the genetic basis for GTA particle production has been established. Based on the evidence, we outline a classification scheme for these viriforms.
Galantamine Attenuates Autoinflammation in a Mouse Model of Familial Mediterranean Fever
Authors: Mughrabi Ibrahim T. , Ochani Mahendar , Tanovic Mirza , Wang Ping , Diamond Betty , Sherry Barbara , Pavlov Valentin A. , Ozen Seza , Kastner Daniel L. , Chae Jae Jin , Al-Abed Yousef
Published: June 2022

Autoinflammatory diseases, a diverse group of inherited conditions characterized by excessive innate immune activation, have limited therapeutic options. Neuroimmune circuits of the inflammatory reflex control innate immune overactivation and can be stimulated to treat disease using the acetylcholinesterase inhibitor galantamine. Here, we tested the efficacy of galantamine in a rodent model of the prototypical autoinflammatory disease familial Mediterranean fever (FMF). Long-term treatment with galantamine attenuated the associated splenomegaly, amyloidosis, and anemia that are characteristic features of this disease. Further, treatment reduced inflammatory cell infiltration into affected organs and a subcutaneous air pouch. These findings suggest that galantamine attenuates chronic inflammation in this mouse model of FMF. Further research is warranted to explore the therapeutic potential of galantamine in FMF and other autoinflammatory diseases.
Identification, expression, and purification of DNA cytosine 5-methyltransferases with short recognition sequences
Authors: Miura Fumihito , Miura Miki , Shibata Yukiko , Furuta Yoshikazu , Miyamura Keisuke , Ino Yuki , Bayoumi Asmaa M.A. , Oba Utako , Ito Takashi
Published: June 2022

Background

DNA methyltransferases (MTases) are enzymes that induce methylation, one of the representative epigenetic modifications of DNA, and are also useful tools for analyzing epigenomes. However, regarding DNA cytosine 5-methylation, MTases identified so far have drawbacks in that their recognition sequences overlap with those for intrinsic DNA methylation in mammalian cells and/or that the recognition sequence is too long for fine epigenetic mapping. To identify MTases with short recognition sequences that never overlap with the CG dinucleotide, we systematically investigated the 25 candidate enzymes identified using a database search, which showed high similarity to known cytosine 5-MTases recognizing short sequences.

Results

We identified MTases with six new recognition sequences, including TCTG, CC, CNG, TCG, GCY, and GGCA. Because the recognition sequence never overlapped with the CG dinucleotide, MTases recognizing the CC dinucleotide were promising.

Conclusions

In the current study, we established a procedure for producing active CC-methylating MTases and applied it to nucleosome occupancy and methylome sequencing to prove the usefulness of the enzyme for fine epigenetic mapping. MTases that never overlap with CG dinucleotides would allow us to profile multiple epigenomes simultaneously.
Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family
Authors: Putta Sivasankar , Alvarez Lucia , Lüdtke Stephan , Sehr Peter , Müller Gerd A. , Fernandez Samantha M. , Tripathi Sarvind , Lewis Joe , Gibson Toby J. , Chemes Lucia B. , Rubin Seth M.
Published: June 2022

The retinoblastoma protein (Rb) and its homologs p107 and p130 are critical regulators of gene expression during the cell cycle. Functional inactivation of Rb family proteins leads to loss of cell-cycle control and promotes genome instability and proliferation, which are hallmarks of cancer. Rb proteins share a structural domain, known as the “pocket domain”, which mediates association with a large number of cellular proteins. A cleft in the pocket domain binds an LxCxE sequence motif in these proteins, many of which function with Rb proteins to co-regulate transcription during quiescence and G1. Proteins from oncogenic DNA viruses also bind this cleft to inactivate Rb family proteins, and the E7 protein from the human papillomavirus has been used as the primary model for understanding LxCxE motif interactions. Evidence presented previously and here demonstrates that the E7 sequence binds tighter and competes with cellular proteins for the LxCxE site, but the molecular basis for the relatively weak affinities of the cellular proteins has been poorly understood. Here, we present binding data and a series of crystal structures of the p107 pocket domain in complex with LxCxE peptides derived from the transcriptional co-repressor proteins HDAC1, ARI4DA, and EID1. The structures reveal determinants of protein binding beyond the L-C-E core that include the N and C-terminal sides of the LxCxE motif and the x (wild card) residues. Our results explain how differences in these interactions outside the L-C-E core result in weaker affinities of pocket protein for cellular LxCxE proteins compared to E7 and result in differences in Rb and p107 affinities for some LxCxE-containing sequences. Our study provides new insights into how Rb proteins bind their myriad of cell partners and lays the foundation for structure-based design of peptides that inhibit oncogenic viral protein interactions.
Metabolic control of histone acetylation for precise and timely regulation of minor ZGA in early mammalian embryos
Authors: Li Jingyu , Zhang Jiaming , Hou Weibo , Yang Xu , Liu Xiaoyu , Zhang Yan , Gao Meiling , Zong Ming , Dong Zhixiong , Liu Zhonghua , Shen Jingling , Cong Weitao , Ding Chunming , Gao Shaorong , Huang Guoning , Kong Qingran
Published: June 2022

Metabolism feeds into the regulation of epigenetics via metabolic enzymes and metabolites. However, metabolic features, and their impact on epigenetic remodeling during mammalian pre-implantation development, remain poorly understood. In this study, we established the metabolic landscape of mouse pre-implantation embryos from zygote to blastocyst, and quantified some absolute carbohydrate metabolites. We integrated these data with transcriptomic and proteomic data, and discovered the metabolic characteristics of the development process, including the activation of methionine cycle from 8-cell embryo to blastocyst, high glutaminolysis metabolism at blastocyst stage, enhanced TCA cycle activity from the 8-cell embryo stage, and active glycolysis in the blastocyst. We further demonstrated that oxidized nicotinamide adenine dinucleotide (NAD+) synthesis is indispensable for mouse pre-implantation development. Mechanistically, in part, NAD+ is required for the exit of minor zygotic gene activation (ZGA) by cooperating with SIRT1 to remove zygotic H3K27ac. In human, NAD+ supplement can promote the removal of zygotic H3K27ac and benefit pre-implantation development. Our findings demonstrate that precise and timely regulation of minor ZGA is controlled by metabolic dynamics, and enhance our understanding of the metabolism of mammalian early embryos.

Highlights

We identified the metabolic features of mouse pre-implantation embryo development.

NAD+ synthesis is indispensable for mouse embryo pre-implantation development.

NAD+-mediated erasure of zygotic H3K27ac is required for the exit of minor ZGA.

NAD+ supplement promotes the removal of zygotic H3K27ac and benefits preimplantation development of human embryos.
Multiple lineages of Monkeypox virus detected in the United States, 2021- 2022
Authors: Gigante Crystal M. , Korber Bette , Seabolt Matthew H. , Wilkins Kimberly , Davidson Whitni , Rao Agam K. , Zhao Hui , Hughes Christine M. , Minhaj Faisal , Waltenburg Michelle A. , Theiler James , Smole Sandra , Gallagher Glen R. , Blythe David , Myers Robert , Schulte Joann , Stringer Joey , Lee Philip , Mendoza Rafael M. , Griffin-Thomas LaToya A. , Crain Jenny , Murray Jade , Atkinson Annette , Gonzalez Anthony H. , Nash June , Batra Dhwani , Damon Inger , McQuiston Jennifer , Hutson Christina L. , McCollum Andrea M. , Li Yu
Published: June 2022

Monkeypox is a viral zoonotic disease endemic in Central and West Africa. In May 2022, dozens of non-endemic countries reported hundreds of monkeypox cases, most with no epidemiological link to Africa. We identified two lineages of Monkeypox virus (MPXV) among nine 2021 and 2022 U.S. monkeypox cases. A 2021 case was highly similar to the 2022 MPXV outbreak variant, suggesting a common ancestor. Analysis of mutations among these two lineages revealed an extreme preference for GA-to-AA mutations indicative of APOBEC3 cytosine deaminase activity that was shared among West African MPXV since 2017 but absent from Congo Basin lineages. Poxviruses are not thought to be subject to APOBEC3 editing; however, these findings suggest APOBEC3 activity has been recurrent and dominant in recent West African MPXV evolution.
Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop
Authors: Cummins Breschine , Vrana Justin , Moseley Robert C. , Eramian Hamed , Deckard Anastasia , Fontanarrosa Pedro , Bryce Daniel , Weston Mark , Zheng George , Nowak Joshua , Motta Francis C. , Eslami Mohammed , Johnson Kara Layne , Goldman Robert P. , Myers Chris J. , Johnson Tessa , Vaughn Matthew W. , Gaffney Niall , Urrutia Joshua , Gopaulakrishnan Shweta , Biggers Vanessa , Higa Trissha R. , Mosqueda Lorraine A. , Gameiro Marcio , Gedeon Tomáš , Mischaikow Konstantin , Beal Jacob , Bartley Bryan , Mitchell Tom , Nguyen Tramy T. , Roehner Nicholas , Haase Steven B.
Published: June 2022

Computational tools addressing various components of design-build-test-learn loops (DBTL) for the construction of synthetic genetic networks exist, but do not generally cover the entire DBTL loop. This manuscript introduces an end-to-end sequence of tools that together form a DBTL loop called DART (Design Assemble Round Trip). DART provides rational selection and refinement of genetic parts to construct and test a circuit. Computational support for experimental process, metadata management, standardized data collection, and reproducible data analysis is provided via the previously published Round Trip (RT) test-learn loop. The primary focus of this work is on the Design Assemble (DA) part of the tool chain, which improves on previous techniques by screening up to thousands of network topologies for robust performance using a novel robustness score derived from dynamical behavior based on circuit topology only. In addition, novel experimental support software is introduced for the assembly of genetic circuits. A complete design-through-analysis sequence is presented using several OR and NOR circuit designs, with and without structural redundancy, that are implemented in budding yeast. The execution of DART tested the predictions of the design tools, specifically with regard to robust and reproducible performance under different experimental conditions. The data analysis depended on a novel application of machine learning techniques to segment bimodal flow cytometry distributions. Evidence is presented that, in some cases, a more complex build may impart more robustness and reproducibility across experimental conditions.
LSD1 controls a nuclear checkpoint in Wnt/β-Catenin signaling to regulate muscle stem cell self-renewal
Authors: Mouradian Sandrine , Cicciarello Delia , Lacoste Nicolas , Risson Valérie , Berretta Francesca , Grand Fabien Le , Rose Nicolas , Simonet Thomas , Schaeffer Laurent , Scionti Isabella
Published: June 2022

The Wnt/β-Catenin pathway plays a key role in cell fate determination during development and in adult tissue regeneration by stem cells. These processes involve profound gene expression and epigenome remodeling and linking Wnt/β-Catenin signaling to chromatin modifications has been a challenge over the past decades. Functional studies of the histone demethylase LSD1/KDM1A converge to indicate that this epigenetic regulator is a key regulator of cell fate, although the extracellular cues controlling LSD1 action remain largely unknown. Here we show that β-Catenin is a substrate of LSD1. Demethylation by LSD1 prevents β-Catenin degradation thereby maintaining its nuclear levels. Consistently, in absence of LSD1, β-Catenin transcriptional activity is reduced in both MuSCs and ESCs. Moreover, inactivation of LSD1 in mouse muscle stem cells and embryonic stem cells shows that LSD1 promotes mitotic spindle orientation via β-Catenin protein stabilization. Altogether, by inscribing LSD1 and β-Catenin in the same molecular cascade linking extracellular factors to gene expression, our results provide a mechanistic explanation to the similarity of action of canonical Wnt/β-Catenin signaling and LSD1 on stem cell fate.
The role of diets in maternal vaccinations against typhoid toxin
Authors: Neupane Durga P. , Ahn Changhwan , Yang Yi-An , Lee Gi Young , Song Jeongmin
Published: June 2022

Children are particularly susceptible to typhoid fever caused by the bacterial pathogenSalmonellaTyphi. Typhoid fever is prevalent in developing countries where diets can be less well-balanced. Here, using a murine model, we investigated the role of the macronutrient composition of the diet in maternal vaccination efficacies of two subunit vaccines targeting typhoid toxin: ToxoidVac and PltBVac. We found that maternal vaccinations protected all offspring against a lethal-dose typhoid toxin challenge in a balanced, normal diet (ND) condition, but the declined protection in a malnourished diet (MD) condition was observed in the PltBVac group. Despite the comparable antibody titers in both MD and ND mothers, MD offspring had a significantly lower level of typhoid toxin neutralizing antibodies than their ND counterparts. We observed a lower expression of the neonatal Fc receptor on the yolk sac of MD mothers than in ND mothers, agreeing with the observed lower antibody titers in MD offspring. Protein supplementation to MD diets, but not fat supplementation, increased FcRn expression and protected all MD offspring from the toxin challenge. Similarly, providing additional typhoid toxin-neutralizing antibodies to MD offspring was sufficient to protect all MD offspring from the toxin challenge. These results emphasize the significance of balanced/normal diets for a more effective maternal vaccination transfer to their offspring.

Author summary

Typhoid fever is a life-threatening systemic infectious disease caused bySalmonellaTyphi, which is prevalent in developing countries where diets can be less well-balanced. Here, we used mice to study the role of nutrition in maternal vaccination efficacies of two subunit vaccines targetingSalmonella’s typhoid toxin. We found maternal vaccinations protected all offspring from a lethal-dose typhoid toxin challenge in a balanced/normal diet (ND) condition, but the lack of protection in a malnourished diet (MD) condition was observed in the PltBVac group. Our data indicate that the difference in maternal vaccination outcomes between ND and MD offspring was due to the less effective maternal antibody transfer from MD mothers to their offspring. Providing additional proteins to MD mothers or additional toxin-neutralizing antibodies to MD offspring saved all malnourished offspring from a lethal-dose typhoid toxin challenge, highlighting the importance of balanced/normal diets for effective maternal vaccination outcomes.