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

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.

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

Scientific Reports ◽

10.1038/s41598-021-85815-0 ◽

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.

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Novel mutation in the gonadotropin-releasing hormone receptor (GNRHR) gene in a patient with normosmic isolated hypogonadotropic hypogonadism

Arquivos Brasileiros de Endocrinologia & Metabologia ◽

10.1590/s0004-27302012000800013 ◽

2012 ◽

Vol 56 (8) ◽

pp. 540-544 ◽

Cited By ~ 5

Author(s):

Daiane Beneduzzi ◽

Ericka B. Trarbach ◽

Ana Claudia Latronico ◽

Berenice Bilharinho de Mendonca ◽

Letícia F. G. Silveira

Keyword(s):

In Silico ◽

Novel Mutation ◽

Hypogonadotropic Hypogonadism ◽

In Silico Analysis ◽

Control Group ◽

Coding Region ◽

Novel Variant ◽

Gonadotropin Releasing Hormone Receptor ◽

Inactivating Mutation ◽

Silico Analysis

We report a novel GNRHR mutation in a male with normosmic isolated hypogonadotropic hypogonadism (nIHH). The coding region of the GNRHR gene was amplified and sequenced. Three variants p.[Asn10Lys;Gln11Lys]; [Tyr283His] were identified in the GNRHR coding region in a male with sporadic complete nIHH. The three variants were absent in the controls (130 normal adults). Familial segregation showed that the previously described p.Asn10Lys and p.Gln11Lys are in the same allele, in compound heterozygozity with the novel variant p.Tyr283His. The p.[Asn10Lys;Gln11Lys] are known inactivating mutations. The p.Tyr283His affects a well-conserved residue, and in silico analysis suggested it is a deleterious variant. We describe a novel GNRHR mutation in a male with nIHH. Absence of the mutation in the control group, conservation among species, in silico analysis, and familial segregation suggest that p.Tyr283His, which was identified in compound heterozygozity with the p.[Asn10Lys;Gln11Lys] variants, is an inactivating mutation. Arq Bras Endocrinol Metab. 2012;56(8):540-4

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

Physiological Genomics ◽

10.1152/physiolgenomics.90259.2008 ◽

2008 ◽

Vol 34 (3) ◽

pp. 265-276 ◽

Cited By ~ 25

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.

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In silico analysis of the effect of mutation on epidermal growth factor receptor in non-small-cell lung carcinoma: from mutational analysis to drug designing

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2016.1146165 ◽

2016 ◽

Vol 35 (2) ◽

pp. 427-434 ◽

Cited By ~ 17

Author(s):

Fu-Li Zhao ◽

Guang-Hua Yang ◽

Sen Xiang ◽

Dong-Dong Gao ◽

Chen Zeng

Keyword(s):

Mutational Analysis ◽

Small Cell Lung Carcinoma ◽

Growth Factor Receptor ◽

In Silico Analysis ◽

Small Cell ◽

Small Cell Lung ◽

Cell Lung Carcinoma ◽

Drug Designing ◽

Epidermal Growth ◽

Silico Analysis

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In silico analysis of galactinol synthase genes in common bean (Phaseolus vulgaris L.)

Science and Technology Development Journal ◽

10.32508/stdj.v19i4.684 ◽

2016 ◽

Vol 19 (4) ◽

pp. 45-52

Author(s):

Bang Phi Cao

Keyword(s):

Common Bean ◽

In Silico Analysis ◽

Duplication Event ◽

Expression Level ◽

Phylogenic Tree ◽

Galactinol Synthase ◽

Reproductive Tissues ◽

The Common ◽

First Time ◽

Silico Analysis

Galactinol synthases (GolS, EC 2.4.1.123) belong to the glycosyltransferase 8 family. These enzymes catalyzes galactosylation of myo-inositol to form galactinol, precursor of raffinose which is solube sucrose playing an important role in stress tolerance in plants. We identified and analyzed a total of three GolS encoded genes in the whole genome of common bean. These genes possessed two or three introns. The predicted proteins contained from 322 to 340 amino acids. The common bean GolS proteins contained all conseved motifs that were characterized for other previously known GolSs. These proteins were acidic and weakly hydrophilic. The phylogenic tree constructed from GolS proteins of Arabidopsis, poplar and common bean showed that only one gene duplication event was detected in the commone bean genome. Common bean GolS genes expressed in all vegetative and reproductive tissues. However, the transcript abundances of each gene varied in different tissues. When comparing the expression levels of these three genes as defined RNAseq, we found that the expression level of PvGolS2 was the lowest, PvGolS1 expressed the strogest leaves and stem, while PvGolS3 expressed in roots and nodules. We discovered that Rhizobium incubation affected on the expression of GolS genes for the first time. In the reproductive tissues, PvGolS1 expressed in most studied tissues. Its expression level correlatively increased with the tissue development.

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GABA-Producing Lactococcus lactis Strains Isolated from Camel’s Milk as Starters for the Production of GABA-Enriched Cheese

Foods ◽

10.3390/foods10030633 ◽

2021 ◽

Vol 10 (3) ◽

pp. 633

Author(s):

Begoña Redruello ◽

Yasmine Saidi ◽

Lorena Sampedro ◽

Victor Ladero ◽

Beatriz del Rio ◽

...

Keyword(s):

Lactococcus Lactis ◽

Health Benefits ◽

In Silico Analysis ◽

Bioactive Compound ◽

Starter Cultures ◽

Safety Properties ◽

Camel's Milk ◽

First Time ◽

Multiple Health ◽

Silico Analysis

The multiple health benefits attributed to the bioactive compound γ-aminobutyric acid (GABA) have prompted the food industry to investigate the development of functional GABA-rich foods via the use of GABA-producing microorganisms. This study reports the isolation of six GABA-producing Lactococcus lactis strains from camel’s milk; this is the first time that such microorganisms have been isolated from milk. The sequencing and in silico analysis of their genomes, and the characterisation of their technological and safety properties, confirmed their potential as starters. Experimental cheeses made with all six strains (individually) accumulated GABA at concentrations of up to 457 mg/kg. These GABA-producing L. lactis strains could be used as starter cultures for the manufacture of functional GABA-enriched cheeses that provide health benefits to consumers.

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

Plants ◽

10.3390/plants10010041 ◽

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.

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