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

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

Journal of Pediatric Endocrinology and Metabolism ◽

10.1515/jpem-2017-0065 ◽

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.

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In silico analysis of lactate producing metabolic network in Lactococcus lactis

Enzyme and Microbial Technology ◽

10.1016/j.enzmictec.2004.08.032 ◽

2004 ◽

Vol 35 (6-7) ◽

pp. 654-662 ◽

Cited By ~ 4

Author(s):

Jae Wook Nam ◽

Kyoung Hoon Han ◽

En Sup Yoon ◽

Dong Il Shin ◽

Jong Hwa Jin ◽

...

Keyword(s):

Metabolic Network ◽

Lactococcus Lactis ◽

In Silico ◽

In Silico Analysis ◽

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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A Review on the Novel Coronavirus Disease based on In-silico Analysis of Various Drugs and Target Proteins

Journal of Pure and Applied Microbiology ◽

10.22207/jpam.14.spl1.22 ◽

2020 ◽

Vol 14 (suppl 1) ◽

pp. 849-860

Author(s):

Gauravi N. Trivedi ◽

Janhavi T. Karlekar ◽

Hiren A. Dhameliya ◽

Hetalkumar Panchal

Keyword(s):

In Silico ◽

Close Contact ◽

Genome Structure ◽

In Silico Analysis ◽

Bioactive Compound ◽

Host Cells ◽

World Health ◽

Large Set ◽

Genomic Rnas ◽

Silico Analysis

Coronavirus Disease (COVID-19) is a new disease that emerged in Wuhan, China which spreads through close contact of people, often by small droplets produced during coughing or sneezing. Detail mechanism by which it spreads between people are under investigation. The World Health Organization (WHO) declared this disease as a pandemic after the severity of the disease increased. Many scientific reports gathered have suggested many drugs that could be potential candidates for the treatment. Although, clinical effectiveness has not been fully evaluated. In this review, we have aggregated the data from few research articles, official news websites and few review papers regarding its phylogenetic relation, genomic constitution, transmission, replication and in-silico analysis done by researchers for few potent drugs that are currently used to cure COVID-19. SARS-CoV-2 belongs to Betacoronavirus genus with Genome structure consists 14 Open Reading Frames (ORFs) that encode 27 proteins. Coronavirus replicates into the host cells having unique mechanisms like ribosome frame-shifting and synthesis of genomic and sub genomic RNAs. In-silico methods have the advantage that they can make fast predictions for a large set of compounds in a high-throughput mode and also make their prediction based on the structure of a compound even before it has been synthesized. In-silico softwares have been used to find or to improve a novel bioactive compound, which may exhibit a strong affinity to a particular target in the drug development process.

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Insights of the Neofusicoccum parvum–Liquidambar styraciflua Interaction and Identification of New Cysteine-Rich Proteins in Both Species

Journal of Fungi ◽

10.3390/jof7121027 ◽

2021 ◽

Vol 7 (12) ◽

pp. 1027

Author(s):

Rebeca Vázquez-Avendaño ◽

José Benjamín Rodríguez-Haas ◽

Hugo Velázquez-Delgado ◽

Greta Hanako Rosas-Saito ◽

Eric Edmundo Hernández-Domínguez ◽

...

Keyword(s):

In Silico Analysis ◽

Infection Process ◽

Liquidambar Styraciflua ◽

Genomic Databases ◽

Neofusicoccum Parvum ◽

Disease Symptoms ◽

Foliar Tissue ◽

First Time ◽

Silico Analysis

Neofusicoccum parvum belongs to the Botryosphaeriaceae family, which contains endophytes and pathogens of woody plants. In this study, we isolated 11 strains from diseased tissue of Liquidambar styraciflua. Testing with Koch’s postulates—followed by a molecular approach—revealed that N. parvum was the most pathogenic strain. We established an in vitro pathosystem (L. styraciflua foliar tissue–N. parvum) in order to characterize the infection process during the first 16 days. New CysRPs were identified for both organisms using public transcriptomic and genomic databases, while mRNA expression of CysRPs was analyzed by RT-qPCR. The results showed that N. parvum caused disease symptoms after 24 h that intensified over time. Through in silico analysis, 5 CysRPs were identified for each organism, revealing that all of the proteins are potentially secreted and novel, including two of N. parvum proteins containing the CFEM domain. Interestingly, the levels of the CysRPs mRNAs change during the interaction. This study reports N. parvum as a pathogen of L. styraciflua for the first time and highlights the potential involvement of CysRPs in both organisms during this interaction.

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Corrigendum to “In silico analysis of lactate producing metabolic network in Lactococcus lactis” [Enzyme Microb Technol 35 (2004) 654–662]

Enzyme and Microbial Technology ◽

10.1016/j.enzmictec.2005.01.016 ◽

2005 ◽

Vol 37 (3) ◽

pp. 363-364

Author(s):

Jae Wook Nam ◽

Kyoung Hoon Han ◽

En Sup Yoon ◽

Dong Il Shin ◽

Jong Hwa Jin ◽

...

Keyword(s):

Metabolic Network ◽

Lactococcus Lactis ◽

In Silico ◽

In Silico Analysis ◽

Silico Analysis

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Xanthomonas oryzae pv. exoribonuclease R is required for complete virulence in rice, optimal motility, and growth under stress

Phytopathology ◽

10.1094/phyto-07-21-0310-r ◽

2021 ◽

Author(s):

Sharmila Roy ◽

Pragya Mittal ◽

Lavanya Tayi ◽

Sahitya Bondada ◽

Malay K Ray ◽

...

Keyword(s):

Bacterial Blight ◽

Pathogenic Bacteria ◽

Growth Curves ◽

In Silico Analysis ◽

Xanthomonas Oryzae ◽

Rnase R ◽

Amino Acid Sequence Alignment ◽

Suboptimal Temperature ◽

First Time ◽

Silico Analysis

Exoribonuclease R (RNase R) is a 3’ hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is required for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various Xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. In order to study its role in virulence, a gene disruption mutant of Xoo RNase R (rnr –) was generated. The Xoo rnr – mutant is moderately virulence deficient and the complementing strain (rnr –/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient deficient minimal and nutrient optimal media. We observed that rnr – mutant has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C, cold stress) indicate that Xoo rnr – mutant grows slower than Xoo wild type (wt) and complementing strain (rnr –/pHM1::rnr). Taken together, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.

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In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification

Biomolecules ◽

10.3390/biom11071043 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1043

Author(s):

Eric Bernabeu ◽

Jose María Miralles-Robledillo ◽

Micaela Giani ◽

Elena Valdés ◽

Rosa María Martínez-Espinosa ◽

...

Keyword(s):

Catalytic Mechanism ◽

Anthropogenic Activities ◽

In Silico Analysis ◽

Bioinformatic Analysis ◽

Model Organisms ◽

Haloferax Mediterranei ◽

Potential Applications ◽

First Time ◽

Nitrogen Pollutants ◽

Silico Analysis

During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.

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