scholarly journals Fine-tuning the performance of ddRAD-seq in the peach genome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maximiliano Martín Aballay ◽  
Natalia Cristina Aguirre ◽  
Carla Valeria Filippi ◽  
Gabriel Hugo Valentini ◽  
Gerardo Sánchez
Keyword(s):  
Germplasm Collection ◽  
In Silico Analysis ◽  
Genotyping By Sequencing ◽  
Fine Tuning ◽  
The Novel ◽  
Peach Genome ◽  
Genome Complexity ◽  
Next Generation Sequencing Ngs ◽  
Sample Set ◽  
Silico Analysis

AbstractThe advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.

scholarly journals Cloning and characterization of novel human SLC4A8 gene products encoding Na+-driven Cl−/HCO3− exchanger variants NDCBE-A, -C, and -D

2008 ◽  
Vol 34 (3) ◽  
pp. 265-276 ◽  
Author(s):  
Mark D. Parker ◽  
Patrice Bouyer ◽  
Christopher M. Daly ◽  
Walter F. Boron
Keyword(s):  
In Silico Analysis ◽  
Functional Expression ◽  
Inhibitory Effect ◽  
Functional Difference ◽  
The Novel ◽  
Equivalent Position ◽  
Rapid Amplification ◽  
Novel Exon ◽  
Silico Analysis

The reported sequences of the human and mouse Na+-driven Cl−/HCO3− exchangers (NDCBEs) differ greatly in their extreme cytosolic COOH termini (Ct). In human NDCBE (NDCBE-B), a 17-amino acid (aa) sequence replaces 66 aa at the equivalent position in mouse NDCBE (NDCBE-A). We performed 5′- and 3′-rapid amplification of cDNA ends (RACE) on human brain cDNA, followed by PCR of full-length cDNAs to determine whether the human SLC4A8 gene was capable of producing the mouselike Ct sequence. Our study confirmed the presence in human cDNA of mouse NDCBE-like transcripts (human NDCBE-A) and also disclosed the existence of three further novel NDCBE transcripts that we have called NDCBE-C, NDCBE-D, and NDCBE-D′. The novel NDCBE-C/D/D′ transcripts initiate at a novel “exon 0” positioned ∼35 kb upstream of the first exon of NDCBE-A/B. NDCBE-C/D/D′ protein products are predicted to be truncated by 54 aa in the cytosolic NH2 terminus (Nt) compared with NDCBE-A/B. Our data, combined with a new in silico analysis of partial transcripts reported by others in the region of the human SLC4A8 gene, increase the known extent of the SLC4A8 gene by 49 kb, to 124 kb. A functional comparison of NDCBE-A/B/C/D expressed in Xenopus oocytes demonstrates that the Nt variation does not affect the basal functional expression of NDCBE, but those with the shorter Ct have a 25–50% reduced functional expression compared with those with the longer Ct. By comparison with an artificially truncated NDCBE that contains neither 17-aa nor 66-aa Ct cassette, we determined that the functional difference is unrelated to the 66-aa cassette of NDCBE-A/C, but is instead due to an inhibitory effect of the 17-aa cassette of NDCBE-B/D.

Clinical evaluation and mutational analysis of GALK and GALE genes in patients with galactosemia in Greece: one novel mutation and two rare cases

2017 ◽  
Vol 30 (7) ◽  
Author(s):  
Kleopatra H. Schulpis ◽  
Georgia Thodi ◽  
Konstantinos Iakovou ◽  
Maria Chatzidaki ◽  
Yannis Dotsikas ◽  
...  
Keyword(s):  
Clinical Evaluation ◽  
Mutational Analysis ◽  
Screening Program ◽  
Novel Mutation ◽  
In Silico Analysis ◽  
Speech Development ◽  
The Novel ◽  
Speech Delay ◽  
First Time ◽  
Silico Analysis

AbstractBackground:Deficiencies of galactokinase (GALK) and UDP-epimerase (GALE) are implicated with galactose metabolic disorders. The aim of the study was the identification of mutations inMethods:Five patients with GALK and five with GALE deficiency were picked up via the Neonatal Screening Program. Additionally, two females, 4 years old, were referred with late diagnosed galactosemia, as rare cases. Mutational analysis was conducted via Sanger sequencing, while in silico analysis tools were utilized for the novel mutation. Psychomotor and speech development tests were performed, as well.Results:The mutation p.Pro28Thr was identified in both alleles in GALK-deficient patients of Roma (gypsy) origin, whereas the novel p.Asn39Ser was detected in two non-Roma patients. In GALE-deficient patients benign and/or likely benign mutations were found. Psychomotor and speech delay were determined in the Roma GALK patients. In each of the late diagnosed females, four mutations were identified in all galactosemia-related genes.Conclusions:The mutational spectrums of GALE- and GALK-deficient patients in Greece are presented for the first time along with a clinical evaluation. Mutational analysis in all galactosemia-related genes of symptomatic patients is highly recommended for future cases.

Localization of non-receptor tyrosine kinase (nRTK) variants in solid tumor patients using next-generation sequencing (NGS).

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 1536-1536
Author(s):  
Srishti Sareen ◽  
Matthew Stein ◽  
Lindsay Kaye Morris ◽  
Saradasri Karri ◽  
Kruti Patel ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
In Silico ◽  
Predictive Biomarkers ◽  
In Silico Analysis ◽  
Kinase Domain ◽  
Tyrosine Kinase Domain ◽  
Tumor Patients ◽  
Next Generation Sequencing Ngs ◽  
Silico Analysis ◽  
Generation Sequencing

1536 Background: Non-synonymous SNPs (nsSNPs) in nRTKs may serve as oncologic targets and predictive biomarkers, with significant lesions described in various nRTK regions including the tyrosine kinase domain (TKD). NGS allows the entire coding sequence to be evaluated, facilitating the identification of novel lesions. Methods: We searched all nsSNPs in 14 nRTKs in the tumors of patients (pts) at our institution that received NGS with Caris from 2013-2015 with a diagnosis of advanced breast, colon or lung cancer. Substitutions were classified as either within or extra-TKD; in the case of JAK1-3, pseudokinase domain lesions were also identified. In order to predict the pathogenicity of nsSNPs, in silico analysis with PolyPhen-2 (Harvard) was completed. Results: 356 pts (79 breast, 110 colon and 165 lung (156 NSCLC, 11 small cell)) were identified with a median age of 61 years (range 26-86); 58% female; 62% white, 35% black. 245 variants were found, with 200 nsSNPs and 45 known pathologic mutations (Pmut); Pmut were PIK3CA (21 breast, 13 colon, 5 NSCLC) and AKT1 (6 breast). 169/356 (47%) pts had ≥1 nRTK lesion (0-8). 52/200 (26%) nsSNPs were predicted-damaging (pnsSNPs) with in silico analysis among 49 pts (6 breast, 13 colon and 30 NSCLC). pnsSNPs were found in 14/14 nRTKs with median 3 (1-10). The most frequently mutated nRTKs in breast were SRC (2/2 variants were pnsSNPs) and ABL2 (1/5); in colon ABL1 (5/10), JAK3 (3/27) and CDK12 (2/8); and in NSCLC JAK3 (6/20), BTK (5/8), ABL1 (3/12), JAK2 (3/11), CDK12 (3/9) and JAK1 (3/3). Of 180 nsSNPs with in silico results, 68% were extra-TKD (29/122 variants were pnsSNPs), 23% within the TKD (13/42) and 9% in pseudokinase domains of JAK1-3 (10/16). Notably, 8/10 pseudokinase domain pnsSNPs were in NSCLC pts (3 JAK1, 2 JAK2 and 3 JAK3). Conclusions: > 13% solid tumors held an nRTK nsSNP that was predicted-damaging by in silico analysis, with 69% of these mutations occurring outside of the TKD-proper. Further work is needed to determine how these pnsSNPs affect function and if they are clinically actionable.

scholarly journals Sterols and Triterpenes: Antiviral     Potential Supported by In-Silico Analysis

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Nourhan Hisham Shady ◽  
Khayrya A. Youssif ◽  
Ahmed M. Sayed ◽  
Lassaad Belbahri ◽  
Tomasz Oszako ◽  
...  
Keyword(s):  
Active Sites ◽  
Herbal Medicines ◽  
Specific Treatment ◽  
In Silico Analysis ◽  
The Novel ◽  
Protein Targets ◽  
Drug Candidates ◽  
Novel Coronavirus ◽  
Silico Analysis

The acute respiratory syndrome caused by the novel coronavirus (SARS-CoV-2) caused severe panic all over the world. The coronavirus (COVID-19) outbreak has already brought massive human suffering and major economic disruption and unfortunately, there is no specific treatment for COVID-19 so far. Herbal medicines and purified natural products can provide a rich resource for novel antiviral drugs. Therefore, in this review, we focused on the sterols and triterpenes as potential candidates derived from natural sources with well-reported in vitro efficacy against numerous types of viruses. Moreover, we compiled from these reviewed compounds a library of 162 sterols and triterpenes that was subjected to a computer-aided virtual screening against the active sites of the recently reported SARS-CoV-2 protein targets. Interestingly, the results suggested some compounds as potential drug candidates for the development of anti-SARS-CoV-2 therapeutics.

scholarly journals In-silico analysis of heat shock protein 47 for identifying the novel therapeutic agents in the management of oral submucous fibrosis

2014 ◽  
Vol 25 (5) ◽  
pp. 580 ◽  
Author(s):  
JayasankarP Pillai ◽  
GirishJ Parmar ◽  
Rakesh Rawal ◽  
GirishR Chauhan ◽  
RajarajeswariJ Pillai ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
In Silico ◽  
Oral Submucous Fibrosis ◽  
In Silico Analysis ◽  
Therapeutic Agents ◽  
The Novel ◽  
Submucous Fibrosis ◽  
Silico Analysis ◽  
Novel Therapeutic

scholarly journals Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

2020 ◽  
Author(s):  
Elena Susana Barbieri ◽  
Tamara Rubilar ◽  
Ayelén Gázquez ◽  
Marisa Avaro ◽  
Erina Noé Seiler ◽  
...  
Keyword(s):  
Sea Urchin ◽  
In Silico ◽  
In Silico Analysis ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
Therapeutic Drug ◽  
The Novel ◽  
Novel Coronavirus ◽  
Silico Analysis

Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.<br>

scholarly journals Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

2020 ◽  
Author(s):  
Elena Susana Barbieri ◽  
Tamara Rubilar ◽  
Ayelén Gázquez ◽  
Marisa Avaro ◽  
Erina Noé Seiler ◽  
...  
Keyword(s):  
Sea Urchin ◽  
In Silico ◽  
In Silico Analysis ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
Therapeutic Drug ◽  
The Novel ◽  
Novel Coronavirus ◽  
Silico Analysis

Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.<br>

scholarly journals A novel mutation in the RRM2 domain of TDP-43 in a Brazilian sporadic ALS patient.

2021 ◽  
Author(s):  
Amanda Cambraia ◽  
Mario Campos Junior ◽  
Fernanda Gubert ◽  
Juliana Ferreira Vasques ◽  
Marli Pernes da Silva Loureiro ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Rio De Janeiro ◽  
Novel Mutation ◽  
In Silico Analysis ◽  
Sporadic Als ◽  
Sporadic Cases ◽  
Next Generation Sequencing Ngs ◽  
Als Patients ◽  
Silico Analysis ◽  
Lateral Sclerosis

Introduction: Amyotrophic Lateral Sclerosis (ALS) is an adult-onset progressive and fatal neurodegenerative disease that selectively affects upper and lower motor neurons. Death occurs within 3 to 5 years of onset, usually from respiratory complications. Most cases of ALS are sporadic (SALS), but familial forms of the disease (FALS) represent approximately 10% of the cases. More than 30 genes have been associated with ALS and mutations in these genes account for more than a half of all familial cases and about 10% of sporadic cases. One of the most prevalent genes is TARDBP, responsible for approximately 4-6% of FALS and nearly 1-2% of SALS cases. The aim of this study was to perform the screening of known ALS genes, to increase the knowledge of the mutations that circulate in the population from Rio de Janeiro. Methods: The screening of mutations was performed through the Illumina Next Generation Sequencing (NGS) platform with the use of a sequencing panel that contained the TARDBP, SOD1, FUS, VAPB, SMN1 and SMN2 genes. Results: A novel missense mutation (p.Phe194Leu) in exon 5 of the TARDBP gene was found in a sporadic male patient who died at the age of 58 (2018). The mutation, a TTT/CTT substitution, was not detected in any mutation databases and in the literature. In silico analysis of this variant with different algorithms were performed and the results pointed to a probably damaging impact and that the mutation is disease causing. Conclusion: Through the study of the ALS genes by the NGS, we were able to identify a novel TARDBP mutation in a non-familial ALS patient. In addition, this study also increases the number of known TARDBP mutations in ALS patients and our knowledge of the mutations that affect the patients from of population from Rio de Janeiro.

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