Concentrate withdrawal and feed restriction are commonly used to reduce milk production and to facilitate dry-off, but may impair immune function in dairy cows. We investigated the effect of feed rations providing different amounts of nutrients in combination with feed restriction on performance, endocrine, and metabolic responses, as well as on leukocyte function before and after abrupt dry-off. Forty-three cows were studied from d 12 before until d 6 after dry-off (56 d before scheduled calving). Cows were fed experimental concentrates rich in crude protein (nitrogenic, n = 14), glucogenic precursors (glucogenic, n = 14), or lipids (lipogenic, n = 15). On d 3 before dry-off, total feed allowance was restricted to 50% in half of the animals of each dietary group, whereas feed allowance remained unchanged in the other animals. Performance parameters (milk yield, milk composition, and dry matter intake) were recorded, and daily blood and milk samples were taken and analyzed for various metabolic and endocrine parameters. Additionally, activity and mRNA abundance of several genes in leukocytes were measured at selected time points before and after feed restriction and dry-off, respectively. Feed restriction immediately resulted in a negative energy balance and decreased milk production. Concomitantly, concentrations of nonesterified fatty acids increased, whereas insulin, insulin-like growth factor-1, and glucagon decreased. After dry-off, energy balance turned positive and plasma nonesterified fatty acids decreased. Plasma glucose, insulin, and insulin-like growth factor-1 concentrations increased in all groups after dry-off. Glucose, insulin, and glucagon concentrations in plasma were higher in nonrestricted compared with restricted animals after dry-off. The experimental concentrate types marginally affected the investigated metabolic and endocrine factors, with the exception of elevated milk and plasma urea concentrations in cows fed the nitrogenic concentrate. Chemotactic and phagocytic activity of leukocytes were not affected by diets, feed restriction, or dry-off. Likewise, blood leukocyte mRNA abundance encoding for tumor necrosis factor α (TNF), heat shock protein family A (HSP70), and the glucose transporters (GLUT) 1 and 3 remained unchanged throughout the study period. Overall, the short-term negative energy balance induced by feed restriction was temporarily accompanied by metabolic adaptations, but did not alter the studied factors related to the immune system. Metabolic and endocrine adaptations supporting milk synthesis were continued during the first days after dry-off despite cessation of milking. Thus, the abrupt dry-off resulted in a short-term increase of glucose and triglyceride concentrations, with a delayed endocrine response to re-establish nutrient homeostasis in blood. <<<

AbstractThe nature of the representational code underlying conceptual knowledge remains a major unsolved problem in cognitive neuroscience. We assessed the extent to which different representational systems contribute to the instantiation of lexical concepts in high-level, heteromodal cortical areas previously associated with semantic cognition. We found that lexical semantic information can be reliably decoded from a wide range of heteromodal cortical areas in frontal, parietal, and temporal cortex. In most of these areas, we found a striking advantage for experience-based representational structures (i.e., encoding information about sensory-motor, affective, and other features of phenomenal experience), with little evidence for independent taxonomic or distributional organization. These results were found independently for object and event concepts. Our findings indicate that concept representations in heteromodal cortex are based, at least in part, on experiential information. They also reveal that, in most heteromodal areas, event concepts have more heterogeneous representations (i.e., they are more easily decodable) than object concepts, and that other areas beyond the traditional “semantic hubs” contribute to semantic cognition, particularly the posterior cingulate gyrus and the precuneus. <<<

Céline M Laumont, Krystel Vincent, Leslie Hesnard, Éric Audemard, Éric Bonneil, Jean-Philippe Laverdure, Patrick Gendron, Mathieu Courcelles, Marie-Pierre Hardy, Caroline Côté, Chantal Durette, Charles St-Pierre, Mohamed Benhammadi, Joël Lanoix, Suzanne Vobecky, Elie Haddad, Sébastien Lemieux, Pierre Thibault, Claude Perreault <<<

Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but few have been identified thus far. We therefore developed a proteogenomic approach to enable the high-throughput discovery of TSAs coded by potentially all genomic regions. In two murine cancer cell lines and seven human primary tumors, we identified a total of 40 TSAs, about 90% of which derived from allegedly noncoding regions and would have been missed by standard exome-based approaches. Moreover, most of these TSAs derived from nonmutated yet aberrantly expressed transcripts (such as endogenous retroelements) that could be shared by multiple tumor types. Last, we demonstrated that, in mice, the strength of antitumor responses after TSA vaccination was influenced by two parameters that can be estimated in humans and could serve for TSA prioritization in clinical studies: TSA expression and the frequency of TSA-responsive T cells in the preimmune repertoire. In conclusion, the strategy reported herein could considerably facilitate the identification and prioritization of actionable human TSAs. <<<

BACKGROUND: Accumulating evidence has shown that disorders in the gut microbiota and derived metabolites affect the development of atherosclerotic cardiovascular disease (ASCVD). However, which and how specific gut microbial metabolites contribute to the progression of atherosclerosis and the clinical relevance of their alterations remain unclear.METHODS: We performed integrated microbiome-metabolome analysis of 30 patients with coronary artery disease (CAD) and 30 age- and sex-matched healthy controls to identify CAD-associated microbial metabolites, which were then assessed in an independent population of patients with ASCVD and controls (n=256). We further investigate the effect of CAD-associated microbial metabolites on atherosclerosis and the mechanisms of the action.RESULTS: Indole-3-propionic acid (IPA), a solely microbially derived tryptophan metabolite, was the most downregulated metabolite in patients with CAD. Circulating IPA was then shown in an independent population to be associated with risk of prevalent ASCVD and correlated with the ASCVD severity. Dietary IPA supplementation alleviates atherosclerotic plaque development in ApoE-/- mice. In murine- and human-derived macrophages, administration of IPA promoted cholesterol efflux from macrophages to ApoA-I through an undescribed miR-142-5p/ABCA1 (ATP-binding cassette transporter A1) signaling pathway. Further in vivo studies demonstrated that IPA facilitates macrophage reverse cholesterol transport, correlating with the regulation of miR-142-5p/ABCA1 pathway, whereas reduced IPA production contributed to the aberrant overexpression of miR-142-5p in macrophages and accelerated the progression of atherosclerosis. Moreover, the miR-142-5p/ABCA1/reverse cholesterol transport axis in macrophages were dysregulated in patients with CAD, and correlated with the changes in circulating IPA levels.CONCLUSIONS: Our study identify a previously unknown link between specific gut microbiota-derived tryptophan metabolite and ASCVD. The microbial metabolite IPA/miR-142-5p/ABCA1 pathway may represent a promising therapeutic target for ASCVD. <<<

Mahan Nekoui , James P. Pirruccello , Paolo Di Achille , Seung Hoan Choi , Samuel N. Friedman , Victor Nauffal , Kenney Ng , Puneet Batra , Jennifer E. Ho , Anthony A. Philippakis , Steven A. Lubitz , Mark E. Lindsay , Patrick T. Ellinor <<<

Background The left ventricular outflow tract (LVOT) and ascending aorta are spatially complex, with distinct pathologies and embryologic origins. Prior work examined the genetics of thoracic aortic diameter in a single plane. Objectives We sought to elucidate the genetic basis for the diameter of the LVOT, aortic root, and ascending aorta. Methods Using deep learning, we analyzed 2.3 million cardiac magnetic resonance images from 43,317 UK Biobank participants. We computed the diameters of the LVOT, the aortic root, and at 6 locations of ascending aorta. For each diameter, we conducted a genome-wide association study and generated a polygenic score. Finally, we investigated associations between these scores and disease incidence. Results A total of 79 loci were significantly associated with at least 1 diameter. Of these, 35 were novel, and most were associated with 1 or 2 diameters. A polygenic score of aortic diameter approximately 13 mm from the sinotubular junction most strongly predicted thoracic aortic aneurysm (n = 427,016; mean HR: 1.42 per SD; 95% CI: 1.34-1.50; P = 6.67 × 10−21). A polygenic score predicting a smaller aortic root was predictive of aortic stenosis (n = 426,502; mean HR: 1.08 per SD; 95% CI: 1.03-1.12; P = 5 × 10−6). Conclusions We detected distinct genetic loci underpinning the diameters of the LVOT, aortic root, and at several segments of ascending aorta. We spatially defined a region of aorta whose genetics may be most relevant to predicting thoracic aortic aneurysm. We further described a genetic signature that may predispose to aortic stenosis. Understanding genetic contributions to proximal aortic diameter may enable identification of individuals at risk for aortic disease and facilitate prioritization of therapeutic targets. <<<

BACKGROUND: Although the American Academy of Sleep Medicine suggests at least 9 h of sleep per day for 6-12-year-olds, children in recent generations often report sleeping less than this amount. Because early adolescence is a crucial period for neurocognitive development, we aimed to investigate how insufficient sleep affects children's mental health, cognition, brain function, and brain structure over 2 years.METHODS: In this propensity score matched, longitudinal, observational cohort study, we obtained data from a population-based sample of 9-10-year-olds from 21 US study sites in the ongoing Adolescent Brain Cognitive Development (ABCD) study. Participants were categorised as having sufficient sleep or insufficient sleep on the basis of a cutoff of 9 h sleep per day. Using propensity score matching, we matched these two groups of participants on 11 key covariates, including sex, socioeconomic status, and puberty status. Participants were excluded from our analysis if they did not pass a baseline resting-state functional MRI quality check or had missing data for the covariates involved in propensity score matching. Outcome measures retrieved from the ABCD study were behavioural problems, mental health, cognition, and structural and resting-state functional brain measures, assessed at baseline and at 2-year follow-up. We examined group differences on these outcomes over those 2 years among all eligible participants. We then did mediation analyses of the neural correlates of behavioural changes induced by insufficient sleep.FINDINGS: Between Sept 1, 2016, and Oct 15, 2018, 11 878 individuals had baseline data collected for the ABCD study, of whom 8323 were eligible and included in this study (4142 participants in the sufficient sleep group and 4181 in the insufficient sleep group). Follow-up data were collected from July 30, 2018, to Jan 15, 2020. We identified 3021 matched sufficient sleep-insufficient sleep pairs at baseline and 749 matched pairs at 2-year follow-up, and observed similar differences between the groups in behaviour and neural measures at both timepoints; the effect sizes of between-group differences in behavioural measures at these two timepoints were significantly correlated with each other (r=0·85, 95% CI 0·73-0·92; p<0·0001). A similar pattern was observed in resting-state functional connectivity (r=0·54, 0·45-0·61; p<0·0001) and in structural measures (eg, in grey matter volume r=0·61, 0·51-0·69; p<0·0001). We found that cortico-basal ganglia functional connections mediate the effects of insufficient sleep on depression, thought problems, and crystallised intelligence, and that structural properties of the anterior temporal lobe mediate the effect of insufficient sleep on crystallised intelligence.INTERPRETATION: These results provide population-level evidence for the long-lasting effect of insufficient sleep on neurocognitive development in early adolescence. These findings highlight the value of early sleep intervention to improve early adolescents' long-term developmental outcomes.FUNDING: National Institutes of Health. <<<

为更好地认识与理解生育政策调整可能带来的人口红利和人力资本红利及其经济影响,本文基于中国生育政策和经济社会发展实践,构建一个异质性居民代际交叠模型,深入考察生育政策（包括最大生育数量限定和超生罚款政策）对经济增长、收入分配和社会养老保障负担的影响及其机理。研究表明,生育政策对不同人力资本居民的生育和子女教育投资决策具有明显的异质性效应,且生育数量限定和超生罚款政策的影响不同。生育数量限定政策放松对经济增长具有"倒U"型影响,对居民收入基尼系数则具有"U"型效应,有利于减轻社会养老保障负担。超生罚款政策放松亦能减轻社会养老保障负担,但会抑制经济增长、加大收入差距。加大公共教育投入总体有助于生育政策放松取得较好效果;降低代际传导性有利于生育数量限定政策放松积极作用的发挥,超生罚款政策放松则具有相反影响。上述发现对于持续优化完善我国生育政策及配套支持措施具有良好启示。 <<<

As an asset pricing model in economics and finance, factor model has been widely used in quantitative investment. Towards building more effective factor models, recent years have witnessed the paradigm shift from linear models to more flexible nonlinear data-driven machine learning models. However, due to low signal-to-noise ratio of the financial data, it is quite challenging to learn effective factor models. In this paper, we propose a novel factor model, FactorVAE, as a probabilistic model with inherent randomness for noise modeling. Essentially, our model integrates the dynamic factor model (DFM) with the variational autoencoder (VAE) in machine learning, and we propose a prior-posterior learning method based on VAE, which can effectively guide the learning of model by approximating an optimal posterior factor model with future information. Particularly, considering that risk modeling is important for the noisy stock data, FactorVAE can estimate the variances from the distribution over the latent space of VAE, in addition to predicting returns. The experiments on the real stock market data demonstrate the effectiveness of FactorVAE, which outperforms various baseline methods. <<<

Eicosapentaenoic acid (EPA), an omega-3 (ω-3) polyunsaturated fatty acid, is an essential nutrient that exhibits antiinflammatory, neuroprotective, and cardiovascular-protective activities. Although EPA is used as a nutrient-based pharmaceutical agent or dietary supplement, its molecular target(s) is debatable. Here, we showed that EPA and its metabolites strongly and reversibly inhibit vesicular nucleotide transporter (VNUT), a key molecule for vesicular storage and release of adenosine triphosphate (ATP) in purinergic chemical transmission. In vitro analysis showed that EPA inhibits human VNUT-mediated ATP uptake at a half-maximal inhibitory concentration (IC) of 67 nM, acting as an allosteric modulator through competition with Cl. EPA impaired vesicular ATP release from neurons without affecting the vesicular release of other neurotransmitters. In vivo, mice showed a delay in the onset of neuropathic pain and resistance to both neuropathic and inflammatory pain. EPA potently attenuated neuropathic and inflammatory pain in wild-type mice but not in mice without affecting the basal nociception. The analgesic effect of EPA was canceled by the intrathecal injection of purinoceptor agonists and was stronger than that of existing drugs used for neuropathic pain treatment, with few side effects. Neuropathic pain impaired insulin sensitivity in previous studies, which was improved by EPA in the wild-type mice but not in the mice. Our results showed that VNUT is a molecular target of EPA that attenuates neuropathic and inflammatory pain and insulin resistance. EPA may represent a unique nutrient-based treatment and prevention strategy for neurological, immunological, and metabolic diseases by targeting purinergic chemical transmission. <<<

Adam Li, Chester Huynh, Zachary Fitzgerald, Iahn Cajigas, Damian Brusko, Jonathan Jagid, Angel O Claudio, Andres M Kanner, Jennifer Hopp, Stephanie Chen, Jennifer Haagensen, Emily Johnson, William Anderson, Nathan Crone, Sara Inati, Kareem A Zaghloul, Juan Bulacio, Jorge Gonzalez-Martinez, Sridevi V Sarma <<<

Over 15 million patients with epilepsy worldwide do not respond to drugs. Successful surgical treatment requires complete removal or disconnection of the seizure onset zone (SOZ), brain region(s) where seizures originate. Unfortunately, surgical success rates vary between 30 and 70% because no clinically validated biological marker of the SOZ exists. We develop and retrospectively validate a new electroencephalogram (EEG) marker-neural fragility-in a retrospective analysis of 91 patients by using neural fragility of the annotated SOZ as a metric to predict surgical outcomes. Fragility predicts 43 out of 47 surgical failures, with an overall prediction accuracy of 76% compared with the accuracy of clinicians at 48% (successful outcomes). In failed outcomes, we identify fragile regions that were untreated. When compared to 20 EEG features proposed as SOZ markers, fragility outperformed in predictive power and interpretability, which suggests neural fragility as an EEG biomarker of the SOZ. <<<

BACKGROUND: For promoting mental health and well-being of individuals, it is important to investigate its association with personal values. However, in Eastern Asian countries, no study has yet investigated the association between personal values in adolescence and mental health and well-being in adulthood. To fill that research gap, we conducted a cross-sectional study based on two online surveys of working populations in Japan and the United States.METHODS: A total of 516 workers from each of the two countries, aged 30-49 years, completed a questionnaire that measured personal values in adolescence, current psychological distress, health-related quality of life, and subjective well-being (satisfaction and happiness). Personal values were measured by items based on Schwartz's theory of basic values and people's commitment to those ten values. Multiple group path analysis was performed to examine the associations between personal values in adolescence and health-related outcomes, grouped by country.RESULTS: Care, graduating from school, and commitment to values were associated with better mental health and well-being in Japanese participants. Belief and challenging were associated with better mental health and well-being in US participants. On the other hand, financial success was associated with poor mental health and well-being in Japanese participants. Avoiding causing trouble and positive evaluation were associated with poor mental health and well-being in the US participants.CONCLUSIONS: Certain personal values and commitment to those values in adolescence may be associated with mental health and well-being in adulthood. To address the limitations of this study, future studies should use a longitudinal design and investigate the interactions among the types of personal values and commitment to the values. <<<

Aspergillus fumigatus is an environmental saprobe and opportunistic human fungal pathogen. Despite an estimated annual occurrence of more than 300,000 cases of invasive disease worldwide, a comprehensive survey of the genomic diversity present in A. fumigatus-including the relationship between clinical and environmental isolates and how this genetic diversity contributes to virulence and antifungal drug resistance-has been lacking. In this study we define the pan-genome of A. fumigatus using a collection of 300 globally sampled genomes (83 clinical and 217 environmental isolates). We found that 7,563 of the 10,907 unique orthogroups (69%) are core and present in all isolates and the remaining 3,344 show presence/absence of variation, representing 16-22% of the genome of each isolate. Using this large genomic dataset of environmental and clinical samples, we found an enrichment for clinical isolates in a genetic cluster whose genomes also contain more accessory genes, including genes coding for transmembrane transporters and proteins with iron-binding activity, and genes involved in both carbohydrate and amino-acid metabolism. Finally, we leverage the power of genome-wide association studies to identify genomic variation associated with clinical isolates and triazole resistance as well as characterize genetic variation in known virulence factors. This characterization of the genomic diversity of A. fumigatus allows us to move away from a single reference genome that does not necessarily represent the species as a whole and better understand its pathogenic versatility, ultimately leading to better management of these infections. <<<

MOTIVATION: Deciphering the language of non-coding DNA is one of the fundamental problems in genome research. Gene regulatory code is highly complex due to the existence of polysemy and distant semantic relationship, which previous informatics methods often fail to capture especially in data-scarce scenarios.RESULTS: To address this challenge, we developed a novel pre-trained bidirectional encoder representation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts. We compared DNABERT to the most widely used programs for genome-wide regulatory elements prediction and demonstrate its ease of use, accuracy and efficiency. We show that the single pre-trained transformers model can simultaneously achieve state-of-the-art performance on prediction of promoters, splice sites and transcription factor binding sites, after easy fine-tuning using small task-specific labeled data. Further, DNABERT enables direct visualization of nucleotide-level importance and semantic relationship within input sequences for better interpretability and accurate identification of conserved sequence motifs and functional genetic variant candidates. Finally, we demonstrate that pre-trained DNABERT with human genome can even be readily applied to other organisms with exceptional performance. We anticipate that the pre-trained DNABERT model can be fined tuned to many other sequence analyses tasks.AVAILABILITY AND IMPLEMENTATION: The source code, pretrained and finetuned model for DNABERT are available at GitHub (https://github.com/jerryji1993/DNABERT).SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. <<<

Bin Tean Teh, Kevin Lim, Chern Han Yong, Cedric Chuan Young Ng, Sushma Ramesh Rao, Vikneswari Rajasegaran, Weng Khong Lim, Choon Kiat Ong, Ki Chan, Vincent Kin Yuen Cheng, Poh Sheng Soh, Sanjay Swarup, Steven G Rozen, Niranjan Nagarajan, Patrick Tan <<<

Durian (Durio zibethinus) is a Southeast Asian tropical plant known for its hefty, spine-covered fruit and sulfury and onion-like odor. Here we present a draft genome assembly of D. zibethinus, representing the third plant genus in the Malvales order and first in the Helicteroideae subfamily to be sequenced. Single-molecule sequencing and chromosome contact maps enabled assembly of the highly heterozygous durian genome at chromosome-scale resolution. Transcriptomic analysis showed upregulation of sulfur-, ethylene-, and lipid-related pathways in durian fruits. We observed paleopolyploidization events shared by durian and cotton and durian-specific gene expansions in MGL (methionine γ-lyase), associated with production of volatile sulfur compounds (VSCs). MGL and the ethylene-related gene ACS (aminocyclopropane-1-carboxylic acid synthase) were upregulated in fruits concomitantly with their downstream metabolites (VSCs and ethylene), suggesting a potential association between ethylene biosynthesis and methionine regeneration via the Yang cycle. The durian genome provides a resource for tropical fruit biology and agronomy. <<<

Sleep stage classification is essential for sleep assessment and disease diagnosis. Although previous attempts to classify sleep stages have achieved high classification performance, several challenges remain open: 1) How to effectively utilize time-varying spatial and temporal features from multi-channel brain signals remains challenging. Prior works have not been able to fully utilize the spatial topological information among brain regions. 2) Due to the many differences found in individual biological signals, how to overcome the differences of subjects and improve the generalization of deep neural networks is important. 3) Most deep learning methods ignore the interpretability of the model to the brain. To address the above challenges, we propose a multi-view spatial-temporal graph convolutional networks (MSTGCN) with domain generalization for sleep stage classification. Specifically, we construct two brain view graphs for MSTGCN based on the functional connectivity and physical distance proximity of the brain regions. The MSTGCN consists of graph convolutions for extracting spatial features and temporal convolutions for capturing the transition rules among sleep stages. In addition, attention mechanism is employed for capturing the most relevant spatial-temporal information for sleep stage classification. Finally, domain generalization and MSTGCN are integrated into a unified framework to extract subject-invariant sleep features. Experiments on two public datasets demonstrate that the proposed model outperforms the state-of-the-art baselines. <<<

Computation-intensive design problems are becoming increasingly common in manufacturing industries. The computation burden is often caused by expensive analysis and simulation processes in order to reach a comparable level of accuracy as physical testing data. To address such a challenge, approximation or metamodeling techniques are often used. Metamodeling techniques have been developed from many different disciplines including statistics, mathematics, computer science, and various engineering disciplines. These metamodels are initially developed as “surrogates” of the expensive simulation process in order to improve the overall computation efficiency. They are then found to be a valuable tool to support a wide scope of activities in modern engineering design, especially design optimization. This work reviews the state-of-the-art metamodel-based techniques from a practitioner’s perspective according to the role of metamodeling in supporting design optimization, including model approximation, design space exploration, problem formulation, and solving various types of optimization problems. Challenges and future development of metamodeling in support of engineering design is also analyzed and discussed. <<<

Plant volatiles are used not only by herbivorous insects to find their host plants, but also by the natural enemies of the herbivores to find their prey. There is also increasing evidence that plant volatiles, in addition to species-specific pheromones, help these insects to find mating partners. Plant structures such as flowers, fruit, and leaves are frequently rendezvous sites for mate-seeking insects. Here we propose that the combined use of plant volatiles and pheromones can efficiently guide insects to these sites, where they will have access to both mates and food. This notion is supported by the fact that plant volatiles can stimulate the release of sex pheromones and can render various insects more receptive to potential mates. <<<

Jiyoon Lee, Cyrus C Rabbani, Hongyu Gao, Matthew R Steinhart, Benjamin M Woodruff, Zachary E Pflum, Alexander Kim, Stefan Heller, Yunlong Liu, Taha Z Shipchandler, Karl R Koehler <<<

The skin is a multilayered organ, equipped with appendages (that is, follicles and glands), that is critical for regulating body temperature and the retention of bodily fluids, guarding against external stresses and mediating the sensation of touch and pain. Reconstructing appendage-bearing skin in cultures and in bioengineered grafts is a biomedical challenge that has yet to be met. Here we report an organoid culture system that generates complex skin from human pluripotent stem cells. We use stepwise modulation of the transforming growth factor β (TGFβ) and fibroblast growth factor (FGF) signalling pathways to co-induce cranial epithelial cells and neural crest cells within a spherical cell aggregate. During an incubation period of 4-5 months, we observe the emergence of a cyst-like skin organoid composed of stratified epidermis, fat-rich dermis and pigmented hair follicles that are equipped with sebaceous glands. A network of sensory neurons and Schwann cells form nerve-like bundles that target Merkel cells in organoid hair follicles, mimicking the neural circuitry associated with human touch. Single-cell RNA sequencing and direct comparison to fetal specimens suggest that the skin organoids are equivalent to the facial skin of human fetuses in the second trimester of development. Moreover, we show that skin organoids form planar hair-bearing skin when grafted onto nude mice. Together, our results demonstrate that nearly complete skin can self-assemble in vitro and be used to reconstitute skin in vivo. We anticipate that our skin organoids will provide a foundation for future studies of human skin development, disease modelling and reconstructive surgery. <<<

Joseph M Replogle, Reuben A Saunders, Angela N Pogson, Jeffrey A Hussmann, Alexander Lenail, Alina Guna, Lauren Mascibroda, Eric J Wagner, Karen Adelman, Gila Lithwick-Yanai, Nika Iremadze, Florian Oberstrass, Doron Lipson, Jessica L Bonnar, Marco Jost, Thomas M Norman, Jonathan S Weissman <<<

A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells. We use transcriptional phenotypes to predict the function of poorly characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena-from RNA processing to differentiation. We leverage this ability to systematically identify genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene and cellular function. <<<