scholarly journals Bioinformatics Exploration of Ginseng: A Review

2021 ◽  
Author(s):  
Toluwase Hezekiah Fatoki
Keyword(s):  
De Novo ◽  
Chemical Constituents ◽  
Complex Mixture ◽  
Target Prediction ◽  
Bioactive Constituents ◽  
De Novo Genome Assembly ◽  
Polycomb Protein ◽  
Mitogen Activated Protein ◽  
Growing Conditions ◽  
Coa Reductase

Ginseng contains an extraordinarily complex mixture of chemical constituents that can vary with the species used, the place of origin, and the growing conditions. Various computational analyses which include genomics, transcriptomics, proteomics and bioinformatics have been used to study ginseng plant. A genome-scale metabolic network offers a holistic view of ginsenoside biosynthesis, helps to predict genes associated with the production of pharmacologically vital dammarane-type ginsenosides, and provides insight for improving medicinal values of ginseng by genomics-based breeding. The draft genomic architecture of tetraploid P. ginseng cultivar (cv.) Chunpoong (ChP) by de novo genome assembly, was found to be 2.98 Gbp and consist of 59,352 annotated genes. Presently, bioinformatics exploration of ginseng includes studies on its P-glycoproteins, the impact of cytochrome P-450 on ginseng pharmacokinetics, as well as target prediction and differential gene expression network analyses. This study applauded Betasitosterol and Daucosterin as ginseng bioactive constituents that have several potential pharmacological effects in human, by modulating several proteins which include androgen receptor, HMG-CoA reductase, interlukin-2, and consequently impact the signaling cascade of several kinases such as mitogen-activated protein kinases (MAPKs), as well as many transcription factors such as polycomb protein SUZ12.

scholarly journals Partitioning Pattern of Natural Products Based on Molecular Properties Descriptors Representing Drug-Likeness

Symmetry ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 546
Author(s):  
Miroslava Nedyalkova ◽  
Vasil Simeonov
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
De Novo ◽  
Target Prediction ◽  
Natural Compounds ◽  
Discovery Process ◽  
Drug Discovery Process ◽  
Unique Source ◽  
The Times ◽  
Partitioning Pattern

A cheminformatics procedure for a partitioning model based on 135 natural compounds including Flavonoids, Saponins, Alkaloids, Terpenes and Triterpenes with drug-like features based on a descriptors pool was developed. The knowledge about the applicability of natural products as a unique source for the development of new candidates towards deadly infectious disease is a contemporary challenge for drug discovery. We propose a partitioning scheme for unveiling drug-likeness candidates with properties that are important for a prompt and efficient drug discovery process. In the present study, the vantage point is about the matching of descriptors to build the partitioning model applied to natural compounds with diversity in structures and complexity of action towards the severe diseases, as the actual SARS-CoV-2 virus. In the times of the de novo design techniques, such tools based on a chemometric and symmetrical effect by the implied descriptors represent another noticeable sign for the power and level of the descriptors applicability in drug discovery in establishing activity and target prediction pipeline for unknown drugs properties.

scholarly journals nanotatoR: a tool for enhanced annotation of genomic structural variants

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Surajit Bhattacharya ◽  
Hayk Barseghyan ◽  
Emmanuèle C. Délot ◽  
Eric Vilain
Keyword(s):  
De Novo ◽  
Genome Mapping ◽  
Gene List ◽  
Sufficient Information ◽  
Rna Seq ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Pathogenic Variants ◽  
Increased Sensitivity

Abstract Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity. Results We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.). nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM. Conclusions The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.

scholarly journals Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chunyan Li ◽  
Melisa Olave ◽  
Yali Hou ◽  
Geng Qin ◽  
Ralf F. Schneider ◽  
...  
Keyword(s):  
Coastal Waters ◽  
Genetic Basis ◽  
De Novo ◽  
Ocean Currents ◽  
Rapid Adaptation ◽  
Developmental Gene ◽  
De Novo Genome Assembly ◽  
Biogeographic Patterns ◽  
Hippocampus Erectus ◽  
New Habitats

AbstractSeahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses’ worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring “bony spines” adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.

scholarly journals Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa

2021 ◽  
Author(s):  
Quan-Kuan Shen ◽  
Min-Sheng Peng ◽  
Adeniyi C Adeola ◽  
Ling Kui ◽  
Shengchang Duan ◽  
...  
Keyword(s):  
West Africa ◽  
De Novo ◽  
Guinea Fowl ◽  
Chromatin Interaction ◽  
De Novo Genome Assembly ◽  
Numida Meleagris ◽  
Whole Genomes ◽  
Genomic Analyses ◽  
Related Wild Species ◽  
Wild Progenitors

Abstract Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

Review of treatment and therapeutic targets in brain arteriovenous malformation

2021 ◽  
pp. 0271678X2110267
Author(s):  
Peipei Pan ◽  
Shantel Weinsheimer ◽  
Daniel Cooke ◽  
Ethan Winkler ◽  
Adib Abla ◽  
...  
Keyword(s):  
Animal Models ◽  
De Novo ◽  
Mapk Pathway ◽  
Treatment Options ◽  
Therapeutic Targets ◽  
Current Treatment ◽  
Mitogen Activated Protein Kinase ◽  
De Novo Mutations ◽  
Genetic Syndromes ◽  
Mitogen Activated Protein

Brain arteriovenous malformations (bAVM) are an important cause of intracranial hemorrhage (ICH), especially in younger patients. The pathogenesis of bAVM are largely unknown. Current understanding of bAVM etiology is based on studying genetic syndromes, animal models, and surgically resected specimens from patients. The identification of activating somatic mutations in the Kirsten rat sarcoma viral oncogene homologue (KRAS) gene and other mitogen-activated protein kinase ( MAPK) pathway genes has opened up new avenues for bAVM study, leading to a paradigm shift to search for somatic, de novo mutations in sporadic bAVMs instead of focusing on inherited genetic mutations. Through the development of new models and understanding of pathways involved in maintaining normal vascular structure and functions, promising therapeutic targets have been identified and safety and efficacy studies are underway in animal models and in patients. The goal of this paper is to provide a thorough review or current diagnostic and treatment tools, known genes and key pathways involved in bAVM pathogenesis to summarize current treatment options and potential therapeutic targets uncovered by recent discoveries.

scholarly journals De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

2020 ◽  
Vol 12 (6) ◽  
pp. 905-910 ◽  
Author(s):  
Ruoyu Liu ◽  
Kun Wang ◽  
Jun Liu ◽  
Wenjie Xu ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Metal Ion ◽  
De Novo ◽  
Demographic History ◽  
Gene Families ◽  
Phylogenetic Position ◽  
Cold Seeps ◽  
Nitrogen And Phosphorus ◽  
De Novo Genome Assembly ◽  
A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

scholarly journals Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

GigaScience ◽  
2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Xuewei Li ◽  
Ling Kui ◽  
Jing Zhang ◽  
Yinpeng Xie ◽  
Liping Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Malus X Domestica ◽  
De Novo Genome Assembly

scholarly journals Meraculous: De Novo Genome Assembly with Short Paired-End Reads

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e23501 ◽  
Author(s):  
Jarrod A. Chapman ◽  
Isaac Ho ◽  
Sirisha Sunkara ◽  
Shujun Luo ◽  
Gary P. Schroth ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly

Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing

2021 ◽  
Author(s):  
Minxuan Zhou ◽  
Lingxi Wu ◽  
Muzhou Li ◽  
Niema Moshiri ◽  
Kevin Skadron ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly

scholarly journals Nature of the stimulation of biogenesis of cholesterol in the liver by noradrenaline

1977 ◽  
Vol 162 (3) ◽  
pp. 493-499 ◽  
Author(s):  
R George ◽  
T Ramasarma
Keyword(s):  
Protein Synthesis ◽  
Adrenergic Receptors ◽  
De Novo ◽  
Direct Action ◽  
Time Intervals ◽  
Coa Reductase ◽  
Short Time ◽  
Stimulation Of

1. Administration of noradrenaline increased the incorporation of [1-14C]acetate into hepatic sterols and the activity of liver microsomal 3-hydroxy-3-methylglutaryl-CoA reductase. 2. The stimulation was observed at short time-intervals with a maximum at 4h and was progressive with increasing concentrations of noradrenaline. 3. Protein synthesis de novo was a necessary factor for the effect. 4. The stimulatory effect was not mediated through the adrenergic receptors, but appears to involve a direct action of the hormone within the hepatocyte.

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