Molecular Characterization of Anguilla from Cibereum and Sapuregel Rivers Segara Anakan Watersheds Cilacap, Central Java

The taxonomic status of Anguilla species' in river watershed that empties into Segara Anakan Cilacap is uncertain, thereby making it difficult for further studies to be carried out to determine its genetic in that area. Therefore, this study evaluates Anguilla's taxonomic status and population genetic in Cibeureum and Sapuregel River watersheds. Data were obtained from molecular characterization study using cytochrome c oxidase 1, with fourteen Anguilla specimens collected from two sequenced watersheds. Taxonomic status was determined based on homology and divergence values and monophyly of the samples to the reference species. Meanwhile, genetic divergences among samples to the reference species were calculated based on the Juke-Cantor substitution model in DnaSP6. A homology test was performed using a basic local alignment search tool, with monophyly inferred from the cladogram, which was developed using neighbor-joining and maximum likelihood algorithms in MEGAX with 1000 pseudoreplicates and out-group comparison. Furthermore, population genetic was analyzed through polymorphism, haplotype, nucleotide diversity within the population, divergence, and genetic differences. All calculations conducted in Arlequin 3.5 had Anguilla samples comprising of high (99.23% to 99.84%) to low genetic divergences (0.224% to 1.127%). The result shows that cladogram with all Anguilla samples formed a monophyletic clade with A. bicolor, separated from their taxa. Furthermore, Anguilla samples from both watersheds have low genetic polymorphisms with medium to high haplotype and nucleotide diversity. The population's comparison proved that both populations have low genetic divergence, and no genetic difference based on variance analysis (p=0761). Therefore, Anguilla resources in river watersheds that empty into Segara Anakan are a single genetic conservation unit.

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Molecular Barcoding Reveal the Existence of Mole Crabs Emerita emeritus in North Coast of Central Java

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v12i1.20497 ◽

2020 ◽

Vol 12 (1) ◽

pp. 104-110

Author(s):

Dian Bhagawati ◽

Elly Tuti Winarni ◽

Agus Nuryanto

Keyword(s):

Sustainable Use ◽

Taxonomic Status ◽

Single Species ◽

First Record ◽

Genetic Distances ◽

North Coast ◽

Local Alignment ◽

Northern Coast ◽

Molecular Barcoding ◽

Central Java

The existence of mole crabs had been reported from the southern coast of Central Java. However, no mole crab data was available from the northern coast Central Java. This study aimed to figure out the existence of mole crabs in the northern coast of Central Java as revealed from the cytochrome c oxidase 1 (COI) barcoding. Mole crabs samples collected in Sendang Sikucing Beach Kendal. Taxonomic status of the samples was inferred from sequences similarity test using basic local alignment search tool to conspecific sequence deposited in GenBank. Pairwise genetic distances were calculated based on the Kimura 2-parameter model. A phylogenetic tree had reconstructed in molecular evolution genetic analysis (MEGA) software based on neighbor-joining algorithm. Branching reliability was obtained from 1000 bootstraps replication while branching polarity was obtained from the out-group comparison. The mole crab samples from the northern coast of Central Java had unambiguously identified as Emerita emeritus based on high sequences similarities (98.27%-99.70%), low genetic distances (0.002-0.005), and their monophyly with Emerita emeritus (KR047035) in GenBank. Pairwise analysis among each possibility pair of samples had genetic distances ranged between 0.000 and 0.005, indicated that all sample belong to single species. The data provide the first record of the existence of Emerita emeritus in the northern coast of Central Java. Our data on the existence of E. emeritus in the northern coast of Central Java is among essentials information as a scientific basis in creating policy for the management of sustainable use of the mole crabs in the areas.

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Phylogeographic and molecular characterization of Pronghorn spiny lobster (Panulirus penicillatus Olivier, 1791) in the Southern Coast of Java and Lombok, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211227 ◽

2020 ◽

Vol 21 (12) ◽

Author(s):

Irwani ◽

Diah Permata Wijayanti ◽

ANINDIA WIRA SATRIA ◽

AGUS SABDONO

Keyword(s):

Dna Barcoding ◽

Molecular Characterization ◽

Spiny Lobster ◽

Taxonomic Status ◽

Molecular Technique ◽

Southern Coast ◽

Central Java ◽

Nucleotide Divergence ◽

First Time

Abstract. Irwani, Wijayanti DP, Satria AW, Sabdono A. 2020. Phylogeographic and molecular characterization of Pronghorn spiny lobster (Panulirus penicillatus Olivier, 1791) in the Southern Coast of Java and Lombok, Indonesia. Biodiversitas 21: 5691-5697. Panulirus penicillatus is one of the most important lobster species in Central Java. It is one of the most populous species in the southern part of Java and Lombok. However, uncontrolled catching causes a decrease in the population of P. penicillatus. Despite such human threats, information about the taxonomic status of this species is limited. Several previous reports on the taxonomy of this species have always been based on the morphological features that cause ambiguous identification. Therefore, this study aimed to establish the relationships of P. penicillatus in southern parts of the southern part of Java and Lombok by using the molecular technique. Twelve samples were collected from four study areas of the southern coast of the southern part of Java and Lombok and identified using DNA barcoding technique. DNA barcoding technique was used for the first time to identify P. penicillatus in this region. This study demonstrated that all specimens belonged to P. penicillatus. However, one specimen (PPK-06) showed high intraspecies nucleotide divergence that formed a distinct subclade. Therefore, the specimen (PPK-06) could represent a cryptic species within P. penicillatus that needs to be studied further.

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The Influence of Memory-Aware Computation on Distributed BLAST

Current Bioinformatics ◽

10.2174/1574893613666180601080811 ◽

2019 ◽

Vol 14 (2) ◽

pp. 157-163

Author(s):

Majid Hajibaba ◽

Mohsen Sharifi ◽

Saeid Gorgin

Keyword(s):

Search Time ◽

Genomic Research ◽

Local Alignment ◽

Negative Effects ◽

Sequencing Technologies ◽

Percent Improvement ◽

Fast Processing ◽

Search Tool ◽

Memory Awareness ◽

Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

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Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

Scientific Reports ◽

10.1038/s41598-021-81063-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dimitri Boeckaerts ◽

Michiel Stock ◽

Bjorn Criel ◽

Hans Gerstmans ◽

Bernard De Baets ◽

...

Keyword(s):

Machine Learning ◽

Predictive Model ◽

Receptor Binding ◽

Bacterial Infections ◽

Sequence Data ◽

Sequence Similarity ◽

Area Under The Curve ◽

Local Alignment ◽

Search Tool ◽

Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

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Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

Malaria Journal ◽

10.1186/s12936-020-03467-3 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Ommer Mohammed Dafalla ◽

Mohammed Alzahrani ◽

Ahmed Sahli ◽

Mohammed Abdulla Al Helal ◽

Mohammad Mohammad Alhazmi ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Saudi Arabia ◽

Parasite Clearance ◽

Sub Saharan Africa ◽

Local Alignment ◽

Nucleotide Polymorphisms ◽

Gene Encoding ◽

Synonymous Mutations ◽

Search Tool ◽

Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

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New insights on the genetic diversity of the honeybee parasiteNosema ceranaebased onmultilocussequence analysis

Parasitology ◽

10.1017/s0031182013001133 ◽

2013 ◽

Vol 140 (11) ◽

pp. 1346-1356 ◽

Cited By ~ 20

Author(s):

MATHIEU ROUDEL ◽

JULIE AUFAUVRE ◽

BRUNO CORBARA ◽

FREDERIC DELBAC ◽

NICOLAS BLOT

Keyword(s):

Ribosomal Rna ◽

Evolutionary History ◽

Nucleotide Diversity ◽

Selective Pressure ◽

Population Divergence ◽

Environmental Cues ◽

Microsporidian Parasite ◽

High Nucleotide Diversity ◽

Single Host ◽

Parasite Populations

SUMMARYThe microsporidian parasiteNosema ceranaeis a common pathogen of the Western honeybee (Apis mellifera) whose variable virulence could be related to its genetic polymorphism and/or its polyphenism responding to environmental cues. Since the genotyping ofN. ceranaebased on unique marker sequences had been unsuccessful, we tested whether amultilocusapproach, assessing the diversity of ten genetic markers – encoding nine proteins and the small ribosomal RNA subunit – allowed the discrimination betweenN. ceranaevariants isolated from singleA. melliferaindividuals in four distant locations. High nucleotide diversity and allele content were observed for all genes. Most importantly, the diversity was mainly present within parasite populations isolated from single honeybee individuals. In contrast the absence of isolate differentiation precluded anytaxadiscrimination, even through amultilocusapproach, but suggested that similar populations of parasites seem to infect honeybees in distant locations. As statistical evolutionary analyses showed that the allele frequency is under selective pressure, we discuss the origin and consequences ofN. ceranaeheterozygosity in a single host and lack of population divergence in the context of the parasite natural and evolutionary history.

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Population genetic analysis and evidence of inter-specific introgression in Helichrysum armenium and H. rubicundum (Asteraceae)

Genetika ◽

10.2298/gensr1502451t ◽

2015 ◽

Vol 47 (2) ◽

pp. 451-468 ◽

Cited By ~ 2

Author(s):

Malahat Taban ◽

Masoud Sheidai ◽

Zahra Noormohammadi ◽

Narjes Azizi ◽

Somayeh Ghasemzadeh-Baraki ◽

...

Keyword(s):

Population Genetic ◽

Structural Changes ◽

Genetic Difference ◽

Genetic Admixture ◽

Specific Gene ◽

Population Genetic Study ◽

Population Genetic Analysis ◽

Closely Related Species ◽

Geographical Populations ◽

Genetic Stratification

Helichrysum armenium and H. rubicundum are two medicinally important plants of Iran that are distributed in various regions of the country. They are extensively used by locals as medicinal plants and a great negative selection pressure is applied on them. Therefore, due to importance of these plant species, we performed a population genetic study in both species. For this study, we used 66 randomly collected plants from 24 geographical populations of Helichrysum armenium and H. rubicundu. These species had areas of overlap and contact and we found some intermediate plants that were included in our study too. UPGMA and MDS analyses revealed morphological separation of these closely related species and placed intermediate plants in an intermediate position. ISSR analysis revealed inter-population genetic diversity and K-Means clustering and STRUCTURE analyses revealed populations. Genetic stratification in both species. Genetic difference of the studied populations was not correlated to geographical distance. Triangle plot of Bayesian analysis and NeighborNet plot showed inter-specific gene flow. The studied populations showed plants with 2n = 2x = 14 and 2n = 4x = 28 chromosomes and differed significantly in their meiotic behavior. Therefore, a combination of genetic stratification, and genetic admixture as well as polyploidy and chromosomes structural changes, have played rule in Helichrysum diversification.

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Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

E3S Web of Conferences ◽

10.1051/e3sconf/202132201038 ◽

2021 ◽

Vol 322 ◽

pp. 01038

Author(s):

Tuah N. M. Wulandari

Keyword(s):

Phylogenetic Tree ◽

Coi Gene ◽

Local Alignment ◽

Mtdna Sequences ◽

Mitochondrial Coi ◽

Search Tool ◽

Very High ◽

I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

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A Case Report on Genetic Analysis of Exon2 of Thyroid Transcription Factor 2 Gene in Congenital Hypothyroidism Patient

European Journal of Medical and Health Sciences ◽

10.24018/ejmed.2021.3.2.744 ◽

2021 ◽

Vol 3 (2) ◽

pp. 19-21

Author(s):

Marjia Khatun ◽

Laila Anjuman Banu

Keyword(s):

Transcription Factor ◽

Pediatric Patient ◽

Congenital Hypothyroidism ◽

Sanger Sequencing ◽

Demographic Data ◽

Local Alignment ◽

Cycle Sequencing ◽

Thyroid Transcription Factor ◽

Search Tool ◽

Information Database

A-3-year- old Bangladeshi pediatric patient named Tasin was presented with a diagnosed case of congenital hypothyroidism (CH). This type of hypothyroidism may occur due to the alteration in the nucleotide sequences of the Thyroid transcription factor 2 gene. Few studies are present on the genetic basis of this disease. CH is common in Bangladesh, may be due to geographical variation or other causes. Therefore, this study was conducted to identify whether there was any genetic alteration in the exon2 of Thyroid transcription factor 2 gene. With due procedure and permission from the guardian of the pediatric patient, socio-demographic data was collected. Isolation of DNA, quantitation and qualitation of DNA was ensured, polymerase chain reaction (PCR) was performed, the amplicons that was obtained from PCR; validated visually by gel electrophoresis methods; cycle sequencing was performed by Sanger sequencing. The chromatogram data that was obtained from Sanger sequencing was analyzed and compared with the National Center for Biotechnology Information database by Basic Local Alignment Search Tool search. Sanger sequencing revealed substitution (c.1051G>T) in the Sequence Tagged Site of the exon2 of Thyroid transcription factor 2 gene and this is new variants and not reported in National Center for Biotechnology Information database.

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CaPSY1 gene plays likely the key role in carotenoid metabolism of pepper (Capsicum annuum) at ripening

Functional Plant Biology ◽

10.1071/fp19287 ◽

2021 ◽

Vol 48 (2) ◽

pp. 141

Author(s):

Xiaochun Wei ◽

Chunyang Meng ◽

Yuxiang Yuan ◽

Ujjal Kumar Nath ◽

Yanyan Zhao ◽

...

Keyword(s):

Developmental Stages ◽

Carotenoid Biosynthesis ◽

Local Alignment ◽

Fruit Colour ◽

Virus Induced Gene Silencing ◽

Carotenoid Metabolism ◽

Pepper Fruit ◽

Search Tool ◽

Pepper Genome ◽

Aba Content

Phytoene synthase (PSY) is the first committed enzyme in carotenoid biosynthesis, which plays important role in ripen fruit colour. However, the roles of CaPSY genes are not explained detail in ripen pepper fruit colour. In this study, three CaPSY genes (CaPSY1, CaPSY2 and CaPSY3) were identified through basic local alignment search tool (BLAST) in pepper genome. Among them, CaPSY1 was predicted as putative candidate based on relative expression values using five developmental stages of fruit in Zunla-1 cultivar and also in ripen fruits of five contrasting pepper lines. The CaPSY1 was characterised functionally through virus-induced gene silencing (VIGS) in ripen fruits and overexpression in Arabidopsis thaliana (L.) Heynh. Silencing of CaPSY1 gene altered colour with increased lutein and decreased zeaxanthin content in pepper fruits. The transgenic Arabidopsis line CaPSY1 gene showed higher expression of PSY1 gene compared with WT and dwarf phenotype due to reduction of GA3 (gibberellic acid) and higher abscisic acid (ABA) content. Our results confirmed that CaPSY1 gene involved in carotenoid metabolism in ripen pepper fruit and provide clue to develop bright red coloured pepper lines through breeding.

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