bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel RNA and DNA analysis after Deep-sequencing (PRDD-seq) reveals cell type specific lineage patterns in human brain
Authors: Huang August Yue , Li Pengpeng , Rodin Rachel E. , Kim Sonia N. , Dou Yanmei , Kenny Connor J. , Akula Shyam K. , Hodge Rebecca D. , Bakken Trygve E. , Miller Jeremy A. , Lein Ed S. , Park Peter J. , Lee Eunjung Alice , Walsh Christopher A. 
Published: April 2020

AbstractElucidating the lineage relationships among different cell types is key to understanding human brain development. Here we developedParallelRNA andDNA analysis afterDeep-sequencing (PRDD-seq), which combines RNA analysis of neuronal cell types with analysis of nested spontaneous DNA somatic mutations as cell lineage markers, identified from joint analysis of single cell and bulk DNA sequencing by single-cell MosaicHunter (scMH). PRDD-seq enables the first-ever simultaneous reconstruction of neuronal cell type, cell lineage, and sequential neuronal formation (“birthdate”) in postmortem human cerebral cortex. Analysis of two human brains showed remarkable quantitative details that relate mutation mosaic frequency to clonal patterns, confirming an early divergence of precursors for excitatory and inhibitory neurons, and an “inside-out” layer formation of excitatory neurons as seen in other species. In addition our analysis allows the first estimate of excitatory neuron-restricted precursors (about 10) that generate the excitatory neurons within a cortical column. Inhibitory neurons showed complex, subtype-specific patterns of neurogenesis, including some patterns of development conserved relative to mouse, but also some aspects of primate cortical interneuron development not seen in mouse. PRDD-seq can be broadly applied to characterize cell identity and lineage from diverse archival samples with single-cell resolution and in potentially any developmental or disease condition.Significance StatementStem cells and progenitors undergo a series of cell divisions to generate the neurons of the brain, and understanding this sequence is critical to studying the mechanisms that control cell division and migration in developing brain. Mutations that occur as cells divide are known as the basis of cancer, but have more recently been shown to occur with normal cell divisions, creating a permanent, forensic map of the clonal patterns that define the brain. Here we develop new technology to analyze both DNA mutations and RNA gene expression patterns in single cells from human postmortem brain, allowing us to define clonal patterns among different types of human brain neurons, gaining the first direct insight into how they form.
Identification of Human Immune Cell Subtypes Most Vulnerable to IL-1β-induced Inflammatory Signaling Using Mass Cytometry
Authors: Kothari Hema , Williams Corey M. , McSkimming Chantel , Vigneshwar Mythili , Zunder Eli R. , McNamara Coleen A. 
Published: April 2020

ABSTRACTIL-1β has emerged as a key mediator of the cytokine storm linked to high morbidity and mortality from COVID-19 and blockade of the IL-1 receptor (IL-1R) with Anakinra has entered clinical trials in COVID-19 subjects. Yet, knowledge of the specific immune cell subsets targeted by IL-1β and IL-1β-induced signaling pathways in humans is limited. Utilizing mass cytometry (CyTOF) of human peripheral blood mononuclear cells, we identified effector memory CD4 T cells and CD4−CD8low/-CD161+T cells as the circulating immune subtypes with the greatest expression of p-NF-κB in response to IL-1β stimulation. Notably, CCR6 distinctly identified T cells most responsive to IL-1β. Other subsets including CD11c myeloid dendritic cells (mDCs), classical monocytes (CM), two subsets of natural killer cells (CD16−CD56brightCD161−and CD16−CD56dimCD161+) and a population of lineage−(Lin-) cells expressing CD161 and CD25 also showed IL-1β-induced expression of p-NF-kB. The IL-1R antagonist, Anakinra significantly inhibited IL-1β-induced p-NF-kB in the CCR6+T cells and CD11c mDCs with a trending inhibition in CD14 monocytes and Lin−CD161+CD25+cells. IL-1β also induced a rapid but much less robust increase in p-p38 expression as compared to p-NF-kB in the majority of these same immune cell subsets. Prolonged IL-1β stimulation greatly increased p-STAT3 and to a much lesser extent p-STAT1 and p-STAT5 in T cell subsets, monocytes, DCs and the Lin−CD161+CD25+cells suggesting IL-1β-induced production of downstream STAT-activating cytokines, consistent with its role in cytokine storm. Interindividual heterogeneity and inhibition of this activation by Anakinra raises the intriguing possibility that assays to measure IL-1β-induced p-NF-kB in CCR6+T cell subtypes could identify those at higher risk of cytokine storm and those most likely to benefit from Anakinra therapy.
Metabolic and functional impairment of CD8+ T cells from the lungs of influenza-infected obese mice
Authors: Green William D. , Al-Shaer Abrar E. , Shi Qing , MacIver Nancie J , Beck Melinda A. , Shaikh Saame Raza 
Published: April 2020

ABSTRACTBackgroundObesity increases influenza disease risk in millions of adults worldwide. In this study, we investigated the effect of diet-induced obesity on pulmonary CD8+ T cell metabolism and function as a mechanism of impairment.MethodsMale C57BL/6J mice were fed either control (10% kcal/g) or high-fat (60% kcal/g) diet. Sub-lethal A/PR/8/34 influenza virus infection generated a robust pulmonary immune response. T cell metabolism and function were assessed at day 10 and day 24 post infection.ResultsAt day 10 post infection, CD8+ T cells from obese mice had impaired oxidative and glycolytic metabolism, greater fatty acid uptake, and decreased effector populations and cytokine production. At infection resolution, obese mice had lower numbers of naïve and central memory CD8+ T cell populations in the lungs.ConclusionDiet-induced obesity increases influenza virus pathogenesis through CD8+ T cell mediated metabolic reprogramming resulting in suppressed effector CD8+ T cell function.SummaryDiet-induced obesity impairs the metabolism of pulmonary CD8+ T cells resulting in reduced effector CD8+ T cells and cytokine production following primary influenza infection.
Evolution of cross-tolerance inDrosophila melanogasteras a result of increased resistance to cold stress
Authors: Singh Karan , Samant Manas Arun , Prasad Nagaraj Guru 
Published: April 2020

AbstractCold stress is a critical environmental challenge that affects an organism’s fitness-related traits. InDrosophila, increased resistance to specific environmental stress may lead to increased resistance to other kinds of stress. In the present study, we aimed to understand whether increased cold stress resistance inDrosophila melanogastercan facilitate their ability to tolerate other environmental stresses. For the current study, we used successfully selected replicate populations ofD. melanogasteragainst cold shock and their control population. These selected populations have evolved several reproductive traits, including increased egg viability, mating frequency, male mating ability, ability to sire progenies, and faster recovery for mating latency under cold shock conditions. In the present work, we investigated egg viability and mating frequency with and without heat and cold shock conditions in the selected and their control populations. We also examined resistance to cold shock, heat shock, desiccation, starvation, and survival post-challenge withStaphylococcus succinussubsp.succinusPK-1 in the selected and their control populations.After cold-shock treatment, we found a 1.25 times increase in egg viability and a 1.57 times increase in mating frequency in the selected populations compared to control populations. Moreover, more males (0.87 times) and females (1.66 times) of the selected populations survived under cold shock conditions relative to their controls. After being subjected to heat shock, the selected population’s egg viability and mating frequency increased by 0.30 times and 0.57 times, respectively, compared to control populations. Additionally, more selected males (0.31 times) and females (0.98 times) survived under heat shock conditions compared to the control populations. Desiccation resistance slightly increased in the females of the selected populations relative to their control, but we observed no change in the case of males. Starvation resistance decreased in males and females of the selected populations compared to their controls.Our findings suggest that the increased resistance to cold shock correlates with increased tolerance to heat stress, but this evolved resistance comes at a cost, with decreased tolerance to starvation.
The visual white matter connecting human area prostriata and the thalamus is retinotopically organized
Authors: Kurzawski Jan W. , Mikellidou Kyriaki , Morrone Maria Concetta , Pestilli Franco 
Published: April 2020

AbstractThe human visual system is capable of processing visual information from fovea to the far peripheral visual field. Recent fMRI studies have shown a full and detailed retinotopic map in area prostriata, located ventro-dorsally and anterior to the calcarine sulcus along the parietooccipital sulcus with strong preference for peripheral and wide-field stimulation. Here, we report the anatomical pattern of white-matter connections between area prostriata and the thalamus encompassing the lateral geniculate nucleus (LGN). We observe a continuous and extended bundle of white matter fibers from which two subcomponents can be extracted: one passing ventrally parallel to the optic radiations (OR) and another passing dorsally circumventing the lateral ventricle. Interestingly, the loop travelling dorsally connects the thalamus with the central visual field representation of prostriata, while the other loop travelling more ventrally connects the LGN with the more peripheral visual field representation. This is consistent with a retinotopic segregation recently demonstrated in the OR, connecting the LGN and V1 in humans. Our results demonstrate for the first time a retinotopic segregation regarding the trajectory of a fiber bundle between the thalamus and an associative visual area.
Sexually dimorphic traits and male-specific differentiation are actively regulated by Doublesex during specific developmental windows inNasonia vitripennis
Authors: Wang Yidong , Rensink Anna , Fricke Ute , Riddle Megan C. , Trent Carol , van de Zande Louis , Verhulst Eveline C. 
Published: April 2020

AbstractSexually dimorphic traits in insects are rapidly evolving due to sexual selection which can ultimately lead to speciation. However, our knowledge of the underlying sex-specific molecular mechanisms is still scarce. Here we show that the highly conserved gene,Doublesex (Dsx),regulates rapidly diverging sexually dimorphic traits in the model parasitoid waspNasonia vitripennis(Hymenoptera: Pteromalidae). We present here the revised fullDsxgene structure with an alternative first exon, and two additional maleNvDsxisoforms, which gives important insights into the evolution of the sex-specific oligomerization domains and C-termini. We show the sex-specificNvDsxexpression throughout development, and demonstrate that transientNvDsxsilencing in different male developmental stages dramatically shifts the morphology of two sexually dimorphic traits from male to female, with the effect being dependent on the timing of silencing. In addition, transient silencing ofNvDsxin early male larvae affects male genitalia tissue growth but not morphology. This indicates that maleNvDsxis actively required to suppress female-specific traits and to promote male-specific traits during specific developmental windows. These results also strongly suggest that inN. vitripennismost sex-specific tissues fully differentiate in the embryonic stage and only need the input ofNvDsxfor growth afterwards. This provides a first insight into the regulatory activity ofDsxin the Hymenoptera and will help to better understand the evolutionary and molecular mechanisms involved in sex-specific development in this parasitoid wasp, which can eventually lead to the development of new synthetic genetics-based tools for biological pest control by parasitoid wasps.Significance StatementIn insects, male and female differentiation is regulated by the highly conserved transcription factor Doublesex (Dsx). The role of Dsx in regulating rapidly evolving sexually dimorphic traits has received less attention, especially in wasps and bees. Here, we mainly focused on Dsx regulation of two sexually dimorphic traits and male genitalia morphology in the parasitoid wasp,Nasonia vitripennis.We demonstrate thatDsxactively regulates male-specific tissue growth and morphology during specific developmental windows. These findings will help to better understand the molecular mechanisms underlying the rapid evolution of sexual differentiation and sexually dimorphic traits in insects, but may also be the starting point for the development of new tools for biological control of pest insects by parasitoid wasps.
Broad and differential animal ACE2 receptor usage by SARS-CoV-2
Authors: Zhao Xuesen , Chen Danying , Szabla Robert , Zheng Mei , Li Guoli , Du Pengcheng , Zheng Shuangli , Li Xinglin , Song Chuan , Li Rui , Guo Ju-Tao , Junop Murray , Zeng Hui , Lin Hanxin 
Published: April 2020

ABSTRACTThe COVID-19 pandemic has caused an unprecedented global public health and economy crisis. The origin and emergence of its causal agent, SARS-CoV-2, in the human population remains mysterious, although bat and pangolin were proposed to be the natural reservoirs. Strikingly, comparing to the SARS-CoV-2-like CoVs identified in bats and pangolins, SARS-CoV-2 harbors a polybasic furin cleavage site in its spike (S) glycoprotein. SARS-CoV-2 uses human ACE2 as its receptor to infect cells. Receptor recognition by the S protein is the major determinant of host range, tissue tropism, and pathogenesis of coronaviruses. In an effort to search for the potential intermediate or amplifying animal hosts of SARS-CoV-2, we examined receptor activity of ACE2 from 14 mammal species and found that ACE2 from multiple species can support the infectious entry of lentiviral particles pseudotyped with the wild-type or furin cleavage site deficient S protein of SARS-CoV-2. ACE2 of human/rhesus monkey and rat/mouse exhibited the highest and lowest receptor activity, respectively. Among the remaining species, ACE2 from rabbit and pangolin strongly bound to the S1 subunit of SARS-CoV-2 S protein and efficiently supported the pseudotyped virus infection. These findings have important implications for understanding potential natural reservoirs, zoonotic transmission, human-to-animal transmission, and use of animal models.ImportanceSARS-CoV-2 uses human ACE2 as primary receptor for host cell entry. Viral entry mediated by the interaction of ACE2 with spike protein largely determines host range and is the major constraint to interspecies transmission. We examined the receptor activity of 14 ACE2 orthologues and found that wild type and mutant SARS-CoV-2 lacking the furin cleavage site in S protein could utilize ACE2 from a broad range of animal species to enter host cells. These results have important implications in the natural hosts, interspecies transmission, animal models and molecular basis of receptor binding for SARS-CoV-2.
Production of a tributyltin-binding protein 2 knockout mutant strain of Japanese medaka,Oryzias latipes
Authors: Kato-Unoki Yoko , Takai Yuki , Nagano Yosuke , Matsunaga Satoshi , Enoki Shintaro , Takamura Takumi , Kim Sangwan , Kinoshita Masato , Kitano Takeshi , Shimasaki Yohei , Oshima Yuji 
Published: April 2020

ABSTRACTTributyltin-binding proteins (TBT-bps), members of the lipocalin family, bind TBT in fish blood and are presumed to contribute to detoxification of TBT. Recent studies have shown that many fish species have TBT-bp genes, and that these genes are induced by stresses such as exposure to chemicals or fish pathogenic bacteria. However, the function of TBT-bps, and the mechanisms of their induction and detoxification activity are still unclear. Here, towards elucidating the functions of TBT-bp2, we produced a TBT-bp2 knockout (TBT-bp2-/-) strain of Japanese medaka,Oryzias latipes, by using the CRISPR/Cas9 system. Gene expression of the mutated TBT-bp2 was reduced, and the cDNA sequencing and predicted protein structure suggested possible loss of function. However, the fish could be grown under normal conditions. Exposure of the TBT-bp2-/-strain of medaka to various stresses in future experiments is expected to contribute to our understanding of this novel detoxification system in aquatic organisms.
Gene interfered-ferroptosis therapy of cancer
Authors: Gao Jinliang , Luo Tao , Lin Na , Wang Jinke 
Published: April 2020

AbstractAlthough some effective therapies have been available for cancer, it still poses a great threat to human health and life due to its drug resistance and low response in patients. Here, we developed a novel therapy named as gene interfered-ferroptosis therapy (GIFT) by combining iron nanoparticles and cancer-specific gene interference. Using a promoter consisted of a NF-κB decoy and a minimal promoter (DMP), we knocked down the expression of two iron metabolism-related genes (FPN and Lcn2) selectively in cancer cells. At the same time, we treated cells with Fe3O4nanoparticles. As a result, a significant ferroptosis was induced in a wide variety of cancer cells representing various hematological and solid tumors. However, the same treatment had no effect on normal cells. By using AAV and PEI-coated Fe3O4nanoparticles as gene vectors, we found that the tumor growth in mice could be also significantly inhibited by the intravenously injected GIFT reagents. By detecting ROS, iron content and gene expression, we confirmed that the mechanism underlying the therapy is gene inference-enhanced ferroptosis.
A heuristic model of the effects of phenotypic robustness in adaptive evolution
Authors: Rigato Emanuele , Fusco Giuseppe 
Published: April 2020

AbstractA recent theoretical, deterministic model of the effects of phenotypic robustness on adaptive evolutionary dynamics showed that a certain level of phenotypic robustness (critical robustness) is a necessary condition for adaptation to occur and to be maintained in the course of evolution in most real organismal systems. We built an individual-based heuristic model to verify the soundness of these theoretical results through computer simulation, testing expectations under a range of scenarios for the relevant parameters of the evolutionary dynamics. These include the mutation probability, the presence of stochastic effects, the introduction of environmental influences and the possibility for some features of the population (like selection coefficients and phenotypic robustness) to change themselves during adaptation. Overall, we found a good match between observed and expected results, even for evolutionary parameter values that violate some of the assumptions of the deterministic model, and that robustness can itself evolve. However, from more than one simulation it appears that very high robustness values, higher than the critical value, can limit or slow-down adaptation. This possible trade-off was not predicted by the deterministic model.
Circuits in the absence of cortical layers: increased callosal connectivity in reeler mice revealed by brain-wide input mapping of VIP neurons in barrel cortex
Authors: Hafner Georg , Guy Julien , Witte Mirko , Truschow Pavel , Rüppel Alina , Sirmpilatze Nikoloz , Dadarwal Rakshit , Boretius Susann , Staiger Jochen F. 
Published: April 2020

ABSTRACTThe neocortex is composed of layers. Whether layers constitute an essential framework for the formation of functional circuits is not well understood. We investigated if neurons require the layer organization to be embedded into brain-wide circuits using the reeler mouse. This mutant is characterized by a migration deficit of cortical neurons so that no layers are formed. Still, neurons retain their properties and reeler mice show little cognitive impairment. We focused on VIP neurons because they are known to receive strong long-range inputs and have a typical laminar bias towards upper layers. In reeler these neurons are more distributed across the cortex. We mapped the brain-wide inputs of VIP neurons in barrel cortex of wildtype and reeler mice with rabies virus tracing. Innervation by subcortical inputs was not altered in reeler, in contrast to the cortical circuitry. Numbers of long-range ipsilateral cortical inputs were reduced in reeler, while contralateral inputs were strongly increased. Reeler mice had more callosal projection neurons. Hence, the corpus callosum was larger in reeler as shown by structural imaging. We argue that in the absence of cortical layers, circuits with subcortical structures are maintained but cortical neurons establish a different network capable to preserve cognitive functions.
Combining In Vivo Corneal Confocal Microscopy with Deep Learning-based Analysis Reveals Sensory Nerve Fiber Loss in Acute SIV Infection
Authors: McCarron Megan E. , Weinberg Rachel L. , Izzi Jessica M. , Queen Suzanne E. , Misra Stuti L. , Russakoff Daniel B. , Oakley Jonathan D. , Mankowski Joseph L. 
Published: April 2020

AbstractPurposeTo characterize corneal subbasal nerve plexus morphologic features usingin vivocorneal confocal microscopy (IVCM) in normal and SIV-infected macaques and to implement automated assessments using novel deep learning-based methods customized for macaque studies.MethodsIn vivo corneal confocal microscopy images were collected from both male and female age-matched specific-pathogen free rhesus and pigtailed macaques housed at the Johns Hopkins University breeding colony using the Heidelberg HRTIII with Rostock Corneal Module. We also obtained repeat IVCM images of 12 SIV-infected animals including pre-infection and 10 day post-SIV infection time-points. All IVCM images were analyzed using a novel deep convolutional neural network architecture developed specifically for macaque studies.ResultsDeep learning-based segmentation of subbasal nerves in IVCM images from macaques demonstrated that corneal nerve fiber length (CNFL) and fractal dimension measurements did not differ between species, but pigtailed macaques had significantly higher baseline corneal nerve fiber tortuosity than rhesus macaques (P = 0.005). Neither sex nor age of macaques was associated with differences in any of the assessed corneal subbasal nerve parameters. In the SIV/macaque model of HIV, acute SIV infection induced significant decreases in both corneal nerve fiber length and fractal dimension (P= 0.01 and P= 0.008 respectively).ConclusionsThe combination of IVCM and objective, robust, and rapid deep-learning analysis serves as a powerful noninvasive research and clinical tool to track sensory nerve damage, enabling early detection of neuropathy. Adapting the deep-learning analyses to human corneal nerve assessments will refine our ability to predict and monitor damage to small sensory nerve fibers in a number of clinical settings including HIV, multiple sclerosis, Parkinson’s disease, diabetes, and chemotherapeutic neurotoxicity.