Bulk and Single-Cell RNA Sequencing Elucidate the Etiology of Severe COVID-19.

Coronavirus disease 2019 (COVID-19) is a type of pneumonia caused by the SARS-CoV-2 coronavirus. It can cause acute pulmonary and systemic inflammation, which can lead to death in severely ill patients. This study explores the potential reasons behind severe COVID-19 and its similarities to systemic autoimmune diseases. This study reviewed unbiased high-throughput gene expression datasets, including next-generation and single-cell RNA sequencing. A total of 27 studies and eight meta-analyses were reviewed. The studies indicated that severe COVID-19 is associated with the upregulation of genes involved in pro-inflammatory, interferon, and cytokine/chemokine pathways. Additionally, changes were observed in the proportions of immune cell types in the blood and tissues, along with degenerative alterations in lung epithelial cells. Genomic evidence also supports the association of severe COVID-19 with various inflammatory syndromes, such as neuronal COVID-19, acute respiratory distress syndrome, vascular inflammation, and multisystem inflammatory syndrome. In conclusion, this study suggests that gene expression profiling plays a significant role in elucidating the etiology of severe COVID-19.

Evidence for Multilevel Chemopreventive Activities of Natural Phenols from Functional Genomic Studies of Curcumin, Resveratrol, Genistein, Quercetin, and Luteolin.

Herein, I present an updated and contextualized literature review of functional genomic studies of natural phenols in the context of cancer. I suggest multilevel chemopreventive and anticancer mechanisms of action, which are shared by multiple dietary natural phenols. Specifically, I cite evidence that curcumin and resveratrol have multilevel anti-cancer effects through: (1) inducing either p53-dependent or p53-independent apoptosis in cancer cell lines, (2) acting as potent regulators of expression of oncogenic and anti-oncogenic microRNAs, and (3) inducing complex epigenetic changes that can switch off oncogenes/switch on anti-oncogenes. There is no simple reductionist explanation for anti-cancer effects of curcumin and resveratrol. More generally, multilevel models of chemoprevention are suggested for related natural phenols and flavonoids such as genistein, quercetin, or luteolin.

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.

Mendel proposed an experimentally verifiable paradigm of particle-based heredity that has been influential for over 150 years. The historical arguments have been reflected in the near past as Mendel's concept has been diversified by new types of omics data. As an effect of the accumulation of omics data, a virtual gene concept forms, giving rise to genetical data science. The concept integrates genetical, functional, and molecular features of the Mendelian paradigm. I argue that the virtual gene concept should be deployed pragmatically. Indeed, the concept has already inspired a practical research program related to systems genetics. The program includes questions about functionality of structural and categorical gene variants, about regulation of gene expression, and about roles of epigenetic modifications. The methodology of the program includes bioinformatics, machine learning, and deep learning. Education, funding, careers, standards, benchmarks, and tools to monitor research progress should be provided to support the research program.

Models of the Gene Must Inform Data-Mining Strategies in Genomics.

The gene is a fundamental concept of genetics, which emerged with the Mendelian paradigm of heredity at the beginning of the 20th century. However, the concept has since diversified. Somewhat different narratives and models of the gene developed in several sub-disciplines of genetics, that is in classical genetics, population genetics, molecular genetics, genomics, and, recently, also, in systems genetics. Here, I ask how the diversity of the concept impacts data-integration and data-mining strategies for bioinformatics, genomics, statistical genetics, and data science. I also consider theoretical background of the concept of the gene in the ideas of empiricism and experimentalism, as well as reductionist and anti-reductionist narratives on the concept. Finally, a few strategies of analysis from published examples of data-mining projects are discussed. Moreover, the examples are re-interpreted in the light of the theoretical material. I argue that the choice of an optimal level of abstraction for the gene is vital for a successful genome analysis.

A Contemporary Message from Mendel's Logical Empiricism.

The gene is one of the most fundamental concepts in life sciences, having been developed in the mold of the Mendelian paradigm of heredity, which shaped genetics across 150 years. How could Mendel possibly be so prophetic in the middle of 19th century, using only the small garden of the monastery as his experimental breeding field? I believe that we are indebted to Mendel's mastery of the scientific method, which was far ahead of his time. Although his experimental technology was literally garden-variety, Mendel's excellence in the method of science, algebra, and logical analysis helped him in designing the right experiment and in interpreting the results insightfully. This may be valuable to recall in today's technology-focused culture, where the center of interest tends to be on the generation and description of high-throughput datasets from specialized genomics screens. As Mendel's story suggests, progress in 21st century genetics may also depend on the development of robust concepts and generalizations.

LRIG1 gene copy number analysis by ddPCR and correlations to clinical factors in breast cancer.

BACKGROUND: Leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) copy number alterations and unbalanced gene recombination events have been reported to occur in breast cancer. Importantly, LRIG1 loss was recently shown to predict early and late relapse in stage I-II breast cancer. METHODS: We developed droplet digital PCR (ddPCR) assays for the determination of relative LRIG1 copy numbers and used these assays to analyze LRIG1 in twelve healthy individuals, 34 breast tumor samples previously analyzed by fluorescence in situ hybridization (FISH), and 423 breast tumor cytosols. RESULTS: Four of the LRIG1/reference gene assays were found to be precise and robust, showing copy number ratios close to 1 (mean, 0.984; standard deviation, +/- 0.031) among the healthy control population. The correlation between the ddPCR assays and previous FISH results was low, possibly because of the different normalization strategies used. One in 34 breast tumors (2.9%) showed an unbalanced LRIG1 recombination event. LRIG1 copy number ratios were associated with the breast cancer subtype, steroid receptor status, ERBB2 status, tumor grade, and nodal status. Both LRIG1 loss and gain were associated with unfavorable metastasis-free survival; however, they did not remain significant prognostic factors after adjustment for common risk factors in the Cox regression analysis. Furthermore, LRIG1 loss was not significantly associated with survival in stage I and II cases. CONCLUSIONS: Although LRIG1 gene aberrations may be important determinants of breast cancer biology, and prognostic markers, the results of this study do not verify an important role for LRIG1 copy number analyses in predicting the risk of relapse in early-stage breast cancer.

Correction: Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis.

[This corrects the article DOI: 10.1371/journal.pone.0208952.].

Etiology of atherosclerosis informs choice of animal models and tissues for initial functional genomic studies of resveratrol.

Resveratrol, a phytoalexin, is a natural polyphenol synthesized exclusively by plants in response to environmental stresses. However, the molecule has also many exogenous bioactivities in animal cells. These bioactivities may lead to anti-cancer and cardio-protective health benefits. Because cellular responses to the treatment with resveratrol include the changes of expression patterns, functional genomics is an attractive tool to study them. In recent and today's experimental practice, this mostly means microarray profiling of gene expression (using RNAs isolated from bulk tissues). Herein, we review such published studies undertaken in the context of cardiovascular diseases (CVDs). CVDs are a number one public health problem in developed countries, outweighing in magnitude even cancer. In particular, we review the studies of resveratrol in several animal models relevant to CVDs. These models included: normal and pre-mature aging in mice, as well as atherogenic diet in mice / pigs / non-human primates. Additionally, there were few clinical studies published in the context of the comorbidities of atherosclerosis in humans (e.g. obesity, diabetes, hypertension). For the purposes of these studies, three types of samples were most commonly profiled with microarrays: the liver, the skeletal muscle, and peripheral blood mononuclear cells. Resveratrol-induced changes of gene expression typically mimicked those associated with calorie restriction and lifespan extension. They also opposed changes induced by the atherogenic diet. We conclude by discussing few experimental factors that were relatively neglected thus far, but which could be interesting to investigate in the future. These factors include sex and the exact formulation of resveratrol (plant extract, or synthetic chemical).

Correction: Modelling of the breadth of expression from promoter architectures identifies pro-housekeeping transcription factors.

[This corrects the article DOI: 10.1371/journal.pone.0198961.].

Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis.

BACKGROUND: Magic roundabout (ROBO4) is an unusual endothelial-specific paralog of the family of neuronally-expressed axon guidance receptors called roundabouts. Endothelial cells (ECs), whose uninterrupted sheet delimits the lumen of all vertebrate blood vessels and which are absent from invertebrate species, are a vertebrate-specific evolutionary novelty. RESULTS: Herein, the evolutionary mechanism of the duplication, retention and divergence of ROBO4 was investigated for the first time. Phylogenetic analyses carried out suggested that ROBO4 is a fast-evolving paralog of ROBO1 formed at the base of vertebrates. The ancestral expression pattern was neuronal. ROBO4 dramatically shifted its expression and became exceptionally specific to ECs. The data-mining of FANTOM5 and ENCODE reveals that ROBO4's endothelial expression arises from a single transcription start site (TSS), conserved in mouse, controlled by a proximal promoter with a complex architecture suggestive of regulatory neo-functionalization. (An analysis of promoter probabilities suggested the architecture was not due to a chance arrangement of TFBSes). Further evidence for the neo-functionalization of ROBO4 comes from the analysis of its protein interactions, the rates of protein evolution, and of positively selected sites. CONCLUSIONS: The neo-functionalization model explains why ROBO4 protein acquired new context-specific biological functions in the control of angiogenesis. This endothelial-specific roundabout receptor is an illustrative example of the emergence of an essential vertebrate molecular novelty and an endothelial-specific signaling sub-network through 2R-WGD. The emergence of novel cell types, such as ECs, might be a neglected evolutionary force contributing to the high rate of retention of duplicates post-2R-WGD. Crucially, expression neo-functionalization to evolutionarily novel sites of expression conceptually extends the classical model of neo-functionalization.

Molecular neuroscience at its "high": bibliometric analysis of the most cited papers on endocannabinoid system, cannabis and cannabinoids.

BACKGROUND: Cannabis, cannabinoids and endocannabinoids are heavily investigated topics with many articles published every year. We aimed to identify the 100 most cited manuscripts among the vast literature and analyze their contents. METHODS: Web of Science (WoS) Core Collection was searched to identify the 100 most cited relevant manuscripts, which were analyzed with reference to (1) authorship, (2) institution, (3) country, (4) document type, (5) journal, (6) publication year, (7) WoS category, and (8) citation count. Semantic content and citation data of the manuscripts were analyzed with VOSviewer. RESULTS: The most cited manuscripts were published between 1986 and 2016, with the majority being published in the 2000s (n = 51). The number of citations for the top 100 articles ranged from 469 to 3651, with a median citation count of 635.5. The most prolific authors were Vincenzo Di Marzo (n = 11) and Daniele Piomelli (n = 11). The major contributing countries were USA (n = 49), Italy (n = 22), UK (n = 19), and France (n = 11). The most prolific institutions were University of California (n = 14), National Research Council of Italy (n = 12) and National Institutes of Health USA (n = 12). The manuscripts consisted of original articles (n = 75), reviews (n = 24) and a note (n = 1). The most dominant journal was Nature (n = 15). The major WoS categories associated were Multidisciplinary sciences (n = 31), Neurosciences (n = 20), Pharmacology / Pharmacy (n = 16), and General / Internal Medicine (n = 11). CONCLUSIONS: The top-ranked manuscripts among the 100 were concerning analgesia, weight loss, long-term potentiation, depolarization-induced suppression of inhibition, opiates and other topics. Cannabinoid type 1 (CB1) receptor was studied by more of the top 100 papers in comparison to cannabinoid type 2 (CB2) receptor. The most frequently mentioned chemicals in these publications were 2-arachidonoylglycerol, tetrahydrocannabinol, and anandamide. Together, these manuscripts comprise the most highly cited publications in the topic, literally the molecular neuroscience at its "high".

Ethnopharmacological Applications Targeting Alcohol Abuse: Overview and Outlook.

Excessive alcohol consumption is the cause of several diseases and thus is of a major concern for society. Worldwide alcohol consumption has increased by many folds over the past decades. This urgently calls for intervention and relapse counteract measures. Modern pharmacological solutions induce complete alcohol self-restraint and prevent relapse, but they have many side effects. Natural products are most promising as they cause fewer adverse effects. Here we discuss in detail the medicinal plants used in various traditional/folklore medicine systems for targeting alcohol abuse. We also comprehensively describe preclinical and clinical studies done on some of these plants along with the possible mechanisms of action.

Modelling of the breadth of expression from promoter architectures identifies pro-housekeeping transcription factors.

Understanding how regulatory elements control mammalian gene expression is a challenge of post-genomic era. We previously reported that size of proximal promoter architecture predicted the breadth of expression (fraction of tissues in which a gene is expressed). Herein, the contributions of individual transcription factors (TFs) were quantified. Several technologies of statistical modelling were utilized and compared: tree models, generalized linear models (GLMs, without and with regularization), Bayesian GLMs and random forest. Both linear and non-linear modelling strategies were explored. Encouragingly, different models led to similar statistical conclusions and biological interpretations. The majority of ENCODE TFs correlated positively with housekeeping expression, a minority correlated negatively. Thus, housekeeping expression can be understood as a cumulative effect of many types of TF binding sites. This is accompanied by the exclusion of fewer types of binding sites for TFs which are repressors, or support cell lineage commitment or temporarily inducible or spatially-restricted expression.

Nutrients Composition in Fit Snacks Made from Ostrich, Beef and Chicken Dried Meat.

The aim of the study was to compare three types of meat snacks made from ostrich, beef, and chicken meat in relation to their nutrients content including fat, fatty acids, heme iron, and peptides, like anserine and carnosine, from which human health may potentially benefit. Dry meat samples were produced, from one type of muscle, obtained from ostrich (m.ambiens), beef (m. semimembranosus), and broiler chicken meat (m. pectoralis major). The composition of dried ostrich, beef, and chicken meat, with and without spices was compared. We show that meat snacks made from ostrich, beef, and chicken meat were characterized by high concentration of nutrients including proteins, minerals (heme iron especially in ostrich, than in beef), biologically active peptides (carnosine-in beef, anserine-in ostrich then in chicken meat). The, beneficial to human health, n-3 fatty acids levels differed significantly between species. Moreover, ostrich jerky contained four times less fat as compared to beef and half of that in chicken. In conclusion we can say that dried ostrich, beef, and chicken meat could be a good source of nutritional components.

Vascular smooth muscle cell proliferation as a therapeutic target. Part 2: Natural products inhibiting proliferation.

Many natural products have been so far tested regarding their potency to inhibit vascular smooth muscle cell proliferation, a process involved in atherosclerosis, pulmonary hypertension and restenosis. Compounds studied in vitro and in vivo as VSMC proliferation inhibitors include, for example indirubin-3'-monoxime, resveratrol, hyperoside, plumericin, pelargonidin, zerumbone and apamin. Moreover, taxol and rapamycin, the most prominent compounds applied in drug-eluting stents to counteract restenosis, are natural products. Numerous studies show that natural products have proven to yield effective inhibitors of vascular smooth muscle cell proliferation and ongoing research effort might result in the discovery of further clinically relevant compounds.

Vascular smooth muscle cell proliferation as a therapeutic target. Part 1: molecular targets and pathways.

Cardiovascular diseases are a major cause of human death worldwide. Excessive proliferation of vascular smooth muscle cells contributes to the etiology of such diseases, including atherosclerosis, restenosis, and pulmonary hypertension. The control of vascular cell proliferation is complex and encompasses interactions of many regulatory molecules and signaling pathways. Herein, we recapitulated the importance of signaling cascades relevant for the regulation of vascular cell proliferation. Detailed understanding of the mechanism underlying this process is essential for the identification of new lead compounds (e.g., natural products) for vascular therapies.

Ethnopharmacological Approaches for Dementia Therapy and Significance of Natural Products and Herbal Drugs.

Dementia is a clinical syndrome wherein gradual decline of mental and cognitive capabilities of an afflicted person takes place. Dementia is associated with various risk factors and conditions such as insufficient cerebral blood supply, toxin exposure, mitochondrial dysfunction, oxidative damage, and often coexisting with some neurodegenerative disorders such as Alzheimer's disease (AD), Huntington's disease (HD), and Parkinson's disease (PD). Although there are well-established (semi-)synthetic drugs currently used for the management of AD and AD-associated dementia, most of them have several adverse effects. Thus, traditional medicine provides various plant-derived lead molecules that may be useful for further medical research. Herein we review the worldwide use of ethnomedicinal plants in dementia treatment. We have explored a number of recognized databases by using keywords and phrases such as "dementia", "Alzheimer's," "traditional medicine," "ethnopharmacology," "ethnobotany," "herbs," "medicinal plants" or other relevant terms, and summarized 90 medicinal plants that are traditionally used to treat dementia. Moreover, we highlight five medicinal plants or plant genera of prime importance and discuss the physiological effects, as well as the mechanism of action of their major bioactive compounds. Furthermore, the link between mitochondrial dysfunction and dementia is also discussed. We conclude that several drugs of plant origin may serve as promising therapeutics for the treatment of dementia, however, pivotal evidence for their therapeutic efficacy in advanced clinical studies is still lacking.

The functional genomic studies of resveratrol in respect to its anti-cancer effects.

Resveratrol has anti-cancer effects in vitro, and hypothetical chemopreventive effects in vivo. Effects are pleiotropic, mediated by changes in expression of many genes and epigenetic reprogramming. Thus, they are well suited for functional genomic studies. We carried out systematic review of such studies (reflecting also on technological progress). Differentially expressed genes commonly linked to resveratrol treatment were linked to cell cycle, proliferation, and apoptosis. However, it is unclear if these are primary and specific targets of resveratrol. We conclude by discussing areas where additional functional genomic studies are desirable, including experiments that better model in vivo effects of dietary intake.

Corrigendum: Ethnopharmacological Approaches for Therapy of Jaundice: Part II. Highly Used Plant Species from Acanthaceae, Euphorbiaceae, Asteraceae, Combretaceae, and Fabaceae Families.

[This corrects the article on p. 519 in vol. 8, PMID: 28848436.].