Identification by molecular techniques of halophilic bacteria producing important enzymes from pristine area in Campeche, Mexico

Isla Arena is located in the coordinate 20° 70´ N - 90° 45´ W, from Campeche, Mexico. In these estuaries, the ocean mixes with fresh water, and ecosystems are concentrated where petenes and pink flamingos proliferate. Crustaceans and mollusks abound in the sea. Despite its enormous marine wealth, there are no studies carried out on which halophilic microorganisms are present in these waters. In this work, the diversity and structure of the microbial community was investigated through a metagenomics approach and corroborated for sequencing of 16S rRNA genes. It was found that the phylum Fimicutes predominates with more than 50%, in almost the same proportion of the class Bacilli and with almost 41% of relative abundance of the order Bacillales. The sequencing results showed that one of the samples presented a high percentage of similarity (99.75%) using the Nucleotide BLAST program with a peculiar microorganism: Bacillus subtilis. This microorganism is one of the best characterized bacteria among the gram-positive ones. Our results demonstrate that B. subtilis can be an efficient source of proteases, lipases and cellulases, from halophilic microbial communities located in poorly explored areas.

Morphological and molecular identification of Cladosporium sphaerospermum isolates collected from tomato plant residues

This study was conducted at the Agriculture College University of Karbala, Iraq to isolate and morphologically and molecularly diagnose thirteen Cladosporium isolates collected from tomato plant residues present in desert regions of Najaf and Karbala provinces, Iraq. We diagnosed the obtained isolates by PCR amplification using the ITS1 and ITS4 universal primer pair followed by sequencing. PCR amplification and analysis of nucleotide sequences using the BLAST program showed that all isolated fungi belong to Cladosporium sphaerospermum. Analysis of the nucleotide sequences of the identified C. sphaerospermum isolates 2, 6, 9, and 10 showed a genetic similarity reached 99%, 98%, 99%, and 99%, respectively, with those previously registered at the National Center for Biotechnology Information (NCBl). By comparing the nucleotide sequences of the identified C. sphaerospermum isolates with the sequences belong to the same fungi and available at NCBI, it was revealed that the identified C. sphaerospermum isolates 2, 6, 9, and 10 have a genetic variation with those previously recorded at the National Center for Biotechnology Information (NCBl); therefore, the identified sequences of C. sphaerospermum isolates have been registered in GenBank database (NCBI) under the accession numbers MN896004, MN896107, MN896963, and MN896971, respectively.

KARAKTERISASI DAN IDENTIFIKASI MOLEKULER BAKTERI PENGHASIL ENZIM PROTEASE DARI TEMPE YANG DIPERJUALBELIKAN DI PASAR LUBUK PAKAM

Protease enzyme is an enzyme that is important in protein breakdown. Animals, plants as well as microorganisms such as bacteria can produce this protease enzyme. In its application protease enzymes can be used in the pharmaceutical industry, detergent industry, skin products as well as food products. Tempe is one of the traditional food products that have been known for a long time, tempeh is made from soybean seeds fermented by mushrooms. Molecular identification can use polymerase chain reaction (PCR) method, PCR is the process of multiplying a certain nucleotide sequence using enzymatic processes in vitro. The presence of protein content in tempeh can be possible the presence of bacteria that can break down proteins in the tempeh, especially tempeh that has been fermented about 48-72 hours. Based on the results of characterization and identification of 5 isolates of tempeh post-fermentation 72 hours, positive results of protease enzymes found in isolate TPLP-1, TPLP-2 and TPLP-5, with the largest zone diameter in isolate TPLP-2 50 mm, then isolate with the highest protease enzyme activity isolate TPLP-2 molecularly identified by identifying the gene 16S rRNA which is subsequently included in the BLAST program and obtained by isolate TPLP-2 identified as Pseudomons stuastzeri.

Study Identification of Some Species of Fish Using the Partial Fragment of Mitochondrial Cytochrome Oxidase Subunit-1Gene (COI) in Danau Panggang, South Borneo

Danau Panggang is a unique habitat for fish species used for food and economic purposes that live in it. This study aims to identify several important and endangered fish species in Danau Panggang using the DNA sequence method and water quality in Danau Panggang. The DNA sequence was then aligned with the RefSeq from the GenBank data library by using the BLAST program of NCBI to find the closest identity associated with several types of fish samples being analyzed. The sequence analysis of the DNA show that some fish species analyzed have specific identifications :Trichopodus pectoralis, Phalacronotus apogon, Belodontichthys dinema, Anabas testudineus, and Leptobarbus hoevenii. Based on the results of the phylogenetic tree, it is also found that the relationship between fish taxons in flooded swamps of Danau Panggang is close to one another.

Data mining of coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

Objective In this study we compare the amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence can lead to different incubation periods and outbreak periods. Our initial question was to compare SARS-CoV-2 to different viruses in the coronavirus family using BLAST program of NCBI and machine learning algorithms. Results The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence. The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can be focused on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.

Subtypes of NanS-p Sialate O-Acetylesterase Encoded by Stx2a Bacteriophages

Shiga toxin (Stx)-producing Escherichia coli strains are foodborne pathogens that can cause severe human diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Stxs are encoded by bacteriophages (Stx phages) which show remarkable variations in genome composition and harbour several genes of unknown function. Recently, a gene encoding a sialate O-acetylesterase (NanS-p) was identified in some relevant Stx2a phages and it was suggested that it could provide advantages for bacterial growth in the gut. The aim of this study was to analyse the presence and sequence of nanS-p genes in available Stx2a phage genomes. A total of 59 DNA sequences of Stx2a phages were extracted from the NCBI GenBank database with the BLAST program using the stx2a sequence from phage 933W as a query sequence, either as complete phage genomes (45) or from bacterial genomes by subsequent analysis with the PHASTER web server (14). Comparative analysis revealed that nanS-p was located downstream of stx2a in all genomes. Twenty different amino acid sequences of NanS-p were identified. Specifically, catalytic esterase domains showed only 11 possible sequences, with differences mainly observed in nine amino acid positions. Sequences corresponding to the N-terminal domain (DUF1737) showed three possible sequences, two of them closely related, while the C-terminal domain was highly variable, with four groups with structural differences. Since sialate O-acetylesterase activity has been determined from particular Stx2a phages, new studies are necessary to evaluate if the NanS-p subtypes identified in the present study also differ in their biological activity.

DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY

The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.

ALeS: Adaptive-length spaced-seed design

Motivation Sequence similarity is the most frequently used procedure in biological research, as proved by the widely used BLAST program. The consecutive seed used by BLAST can be dramatically improved by considering multiple spaced seeds. Finding the best seeds is a hard problem and much effort went into developing heuristic algorithms and software for designing highly sensitive spaced seeds. Results We introduce a new algorithm and software, ALeS, that produces more sensitive seeds than the current state-of-the-art programs, as shown by extensive testing. We also accurately estimate the sensitivity of a seed, enabling its computation for arbitrary seeds. Availability The source code is freely available at github.com/lucian-ilie/ALeS. Supplementary information Supplementary data are available at Bioinformatics online.

Database resources of the National Center for Biotechnology Information

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 34 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface and NCBI datasets. Additional resources that were updated in the past year include PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

Molecular Identification of Endophytic Fungi from Local Rice and Growth Test on Several Types of Culture Media

Local rice is rice that has been cultivated for generations by the community and commonly cultivated without using chemical inputs. Endophytic fungi are fungi that live in the plant tissue and does not cause disease symptoms in the host plants. This study aimed to molecular identifying isolates of MDTA and MDTB endophytic fungi which have been isolated from the local Pulu Mandoti rice plant tissue and growth test on the four types of culture media those were synthetic PDA, natural PDA, MPA, and MEA. The fungi DNA isolation using DNesay Kit. DNA sequencing analysis using the mega BLAST program showed that the MDTB fungus has similarities to Podoscypha bolleana strain 32034 no accession JQ675334 and Podoscypha bolleana strain 32032 no accession JQ675332, whereas the MDTA fungus has similarities to Coprinopsis cinerea A2S3-5 isolate and Coprinopsis cinerea strain CNRMA / F 07-32. The best culture media and sporulation of endophytic fungi is MPA media. This research is the first study to molecular identifying with endophytic fungi from local rice and viability test on the four types of culture media. The results of this study contribute to the diversity of local rice endophytic fungi in Sulawesi.