Morphological, phytochemical and molecular characterization of five common Jatropha species in the Niger Delta Region of Nigeria

The economic and medicinal important genus Jatropha contains many distinctly different species. To elucidate the genetic relationship of five common occurring Jatropha species namely J. multifida, J. podagrica, J.tanjorernsis, J. curcas, and J. gossypifolia, thirty-nine morphological, six phytochemical features and one arbitrary marker was used to screen and explore their similarity. Morphological data was obtained from the measurement of vegetative and reproductive parts while the presence of five phytochemicals was determined using differentphytochemical tests. The DNA of all five Jatropha species were amplified and sequenced using Ribolose 1, 5- biphosphate carboxylase molecular marker. The DNA sequences were then aligned using the Basic Local Alignment Search Tool for nucleotide 2.8.0 version of the National Center for Biotechnology Information database and phylogenetic trees were constructed using Paleontological Statistical software and Molecular Evolutionary Genetics Analysis version 7.0.26 software. From the results of the classical and phylogenetic cluster analysis, the five Jatropha species was separated into two major clusters. The highly distinctive J. gossypifolia was the only species that clustered separately from the other Jatropha species. Although, J. tanjorensis has been reported to be a hybrid from J. curcas and J. gossypifolia, the species did not segregate and cluster with these species, but segregated with J. multifida, and J.podagrica, indicating that this species is more closely related to J. multifida, and J. podagrica than J. curcas and J.gossypifolia. The result therefore provide information that would be useful in the plant improvement programs for the genus Jatropha.

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Phylogeny and higher classification of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea)*

Zootaxa ◽

10.11646/zootaxa.1668.1.22 ◽

2007 ◽

Vol 1668 (1) ◽

pp. 413-425 ◽

Cited By ~ 66

Author(s):

P. J. GULLAN ◽

L. G. COOK

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Nuclear Dna ◽

Sister Group ◽

Scale Insect ◽

Scale Insects ◽

Morphological Data ◽

Adult Males ◽

Plant Feeding ◽

Phylogenetic Studies

The superfamily Coccoidea contains nearly 8000 species of plant-feeding hemipterans comprising up to 32 families divided traditionally into two informal groups, the archaeococcoids and the neococcoids. The neococcoids form a monophyletic group supported by both morphological and genetic data. In contrast, the monophyly of the archaeococcoids is uncertain and the higher level ranks within it have been controversial, particularly since the late Professor Jan Koteja introduced his multi-family classification for scale insects in 1974. Recent phylogenetic studies using molecular and morphological data support the recognition of up to 15 extant families of archaeococcoids, including 11 families for the former Margarodidae sensu lato, vindicating Koteja’s views. Archaeococcoids are represented better in the fossil record than neococcoids, and have an adequate record through the Tertiary and Cretaceous but almost no putative coccoid fossils are known from earlier. In contrast, the sister group of the scale insects (Aphidoidea) has a more informative Jurassic and Triassic record. Relationships among most scale insect families are unresolved in phylogenetic trees based on nuclear DNA sequences, and most nodes in trees based on morphological data, including those from adult males, are poorly supported. Within the neococcoids, the Eriococcidae is not monophyletic and the monophyly of the Coccidae and Diaspididae may be compromised by the current family-level recognition of a few species-poor autapomorphic groups.

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Record of Copepod Parasite (Pennellidae) in Buccal Cavity and Gill Arch of Cultured Groupers, Epinephelus spp. in Batam, Indonesia

Asian Fisheries Science ◽

10.33997/j.afs.2021.34.4.006 ◽

2021 ◽

Vol 34 (4) ◽

Author(s):

ENDANG WIJAYANTI ◽

◽

INDAH ISTIQOMAH ◽

MURWANTOKO MURWANTOKO

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Buccal Cavity ◽

Gill Arch ◽

Group Method ◽

Local Alignment ◽

Cox1 Gene ◽

Copepod Parasite ◽

Adult Copepod ◽

Hybrid Grouper

The crustacean parasites are the most frequently encountered and cause significant economic loss in mariculture. These parasites infect fish fin, skin, gills, and buccal cavity. This study aims to describe copepod parasite in the buccal cavity of cultured groupers, Epinephelus spp., from Batam waters using morphological and molecular biology approaches. The tiger grouper, Epinephelus fuscoguttatus (Forsskal, 1775), and hybrid grouper, Epinephelus sp. showing lethargy and skin darkening were collected from sea cages. The parasite’s morphology was observed using light and scanning electron microscopes. The genomic DNA was isolated from the parasites and used as a template for amplification of cytochrome oxidase subunit-1 (Cox1) gene and followed by sequencing. The fish exhibited red nodules in the mouth cavity, on the lips, and gill arch in varying numbers and size of nodules. The copepodid, chalimus, and adult copepod stages were found from the nodule. Based on the presence of the oral cone, this parasite belonged to Siphonostomatoida order of copepods. Based on the structure of the caudal ramus with four long and four short setae, the first and second pair legs as biramous, and the third pair leg as uniramous, this parasite belonged to Pennellidae family of copepods. Basic local alignment search tool analysis of this Cox1 showed low homology within 80%, indicating that the DNA sequences of the parasite species were not reported in the GenBank. The unweighted pair group method using arithmetic average phylogenetic trees supported that this parasite belonged to the family Pennellidae. This is the first report on the pennellid parasite infection in the buccal cavity and gill arch of cultured groupers in Batam, Indonesia.

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Comparative analysis of genes associated with obesity in humans using bioinformatic data and tools

Balkan Journal of Medical Genetics ◽

10.2478/bjmg-2021-0012 ◽

2021 ◽

Vol 24 (1) ◽

pp. 35-40

Author(s):

ZS Musliji ◽

AK Pollozhani ◽

K Lisichkov ◽

M Deligios ◽

ZT Popovski

Keyword(s):

Phylogenetic Trees ◽

Homo Sapiens ◽

Evolutionary Genetics ◽

Overweight And Obesity ◽

Local Alignment ◽

Peroxisome Proliferator ◽

Research Information ◽

Major Step ◽

Peroxisome Proliferator Activated Receptor ◽

Fatty Acid Binding

Abstract Obesity has become a serious global problem that still needs a solution. One of the factors that leads to obesity is genetic predisposition. The identity and characteristics of the genes involved have not yet been fully confirmed. Analyzing the genetic contribution to obesity is a major step towards the solution. In this in silico study, using online bioinformatics tools, we evaluate the role of four genes that are believed to contribute to obesity. Data were collected and analyzed for the sequences of four so-called obesity genes: FTO (fat mass and obesity-associated protein), PPARG (peroxisome proliferator activated receptor γ), ADRB3 (adrenergic receptor β 3) and FABP2 (fatty acid binding protein 2). In the first part of the research, information about the genes was collected and organized and data in FASTA, format are extracted from the National Center for Biotechnology Information (NCBI). In the second part, all genes were analyzed by comparing three species of organisms, Homo sapiens (human), Mus musculus (mouse) and Gallus (chicken). In the third part of this study, phylogenetic trees were constructed for each of the four genes, using blast local alignment search tool (BLAST) and molecular evolutionary genetics analysis (MEGA X) software. Our analysis reveals that the functions of all these genes are associated with overweight and obesity.

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Genetic Diversity of Cryptosporidium Spp. in Njoro Sub County, Nakuru, Kenya

10.21203/rs.3.rs-621237/v1 ◽

2021 ◽

Author(s):

Walter Miding'a Essendi ◽

Charles Inyagwa Muleke ◽

Miheso Manfred ◽

Elick Onyango Otachi

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Sequence Alignment ◽

Evolutionary Genetics ◽

Domestic Animals ◽

Local Alignment ◽

Cryptosporidium Spp ◽

Potential Source ◽

Search Tool ◽

Great Genetic Diversity

Abstract Cryptosporidium spp. cause Cryptosporidiosis in humans through zoonotic and anthroponotic transmission. Previous studies have illustrated the significance of domestic animals as reservoirs of this parasite. However, there is no information on the Cryptosporidium spp. and genotypes circulating in Njoro Sub County. A total of 2174 samples from humans, cattle, chicken, sheep and goats were assessed for presence of Cryptosporidium spp. Thirty-three positive samples were successfully sequenced. The sequences obtained were compared to Cryptosporidium sequences in the GenBank using NCBI’s (National Center for Biotechnology Information) online BLAST (Basic Local Alignment Search Tool) algorithmic program. Sequence alignment was done using the Clustal W program and phylogenetic analysis was executed in MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The Cryptosporidium spp. present in the watershed showed great genetic diversity with nine (9) Cryptosporidium spp. namely: C. parvum, C. hominis, C. ubiquitum, C. meleagridis, C. andersoni, C. baileyi, C. muris, C. xiaoi and C. viatorum. Cattle were the biggest reservoirs of zoonotic Cryptosporidium spp. hence a potential source of zoonosis in humans while goats had the least species. This is the first study that reported presence of C. viatorum in Kenya.

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Identifikasi molekuler rotifer Brachionus sp. asal perairan Tumpaan, Minahasa Selatan

JURNAL PESISIR DAN LAUT TROPIS ◽

10.35800/jplt.5.1.2017.15006 ◽

2017 ◽

Vol 5 (1) ◽

pp. 56

Author(s):

Jefri Sahari ◽

Joice Rimper ◽

Stenly Wullur

Keyword(s):

Brachionus Plicatilis ◽

Evolutionary Genetics ◽

Read Length ◽

Local Alignment ◽

Chain Reaction ◽

Query Cover ◽

Rotifer Brachionus Plicatilis ◽

Search Tool ◽

Polymerase Chain ◽

Dna Template

Rotifer yang digunakan dalam penelitian ini berasal dari Tumpaan, Minahasa Selatan dan telah dikultur massal selama beberapa generasi. DNA genom rotifer diekstraksi mengikuti prosedur qiagen DNeasy Blood & Tissue kit; amplifikasi gen COI (Cytochrome oxidase sub unit 1) dilakukan dengan bantuan mesin PCR (Polymerase chain reaction) menggunakan primer universal (LCO1490 (forward) dan HCO2198 (reverse));dan dilanjutkan dengan pengurutan nukleotida produk PCR. Pengolahan data hasil sekuens dilakukan dengan menggunakan program ABsequens dan MEGA (Molecular Evolutionary Genetics Analysis) Identifikasi spesies dilakukan dengan menggunakan teknik BLAST (Basic Local Alignment Search Tool) di situs Genbank. Hasil amplifikasi gen COI menggunakan DNA template ekstrak DNA genom rotifer terobservasi adanya pita DNA pada posisi sekitar 700 bp.Kualitas hasil pengurutan nukeotida menggunakan produk PCR menunjukan nilai CRL (contignous read length) dan QV20+(quality value lebih besar dari 20) yang tinggi (>600 nukleotida).Hasil BLAST menunjukkan bahwa rotifer dalam penelitian ini merujuk pada rotifer Brachionus plicatilis complex spesies.Maximum dan total score, prosentase query cover dan prosentase identity masing-masing pada nilai1003-1116, 87-96% dan 96-97%.

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Algoritma Needleman-Wunsch dalam Menentukan Tingkat Kemiripan Urutan DNA Rusa Timor (Cervus timorensis) dan Rusa Merah (Cervus elaphus)

EIGEN MATHEMATICS JOURNAL ◽

10.29303/emj.v3i2.65 ◽

2020 ◽

Vol 3 (2) ◽

pp. 125

Author(s):

Hibban Kholiq ◽

Mamika Ujianita Romdhini ◽

Marliadi Susanto

Keyword(s):

Dna Sequence ◽

Sequence Alignment ◽

Cervus Elaphus ◽

Dna Sequences ◽

Sequence Data ◽

Local Alignment ◽

Base Pairs ◽

European Continent ◽

Dna Sequence Data ◽

Search Tool

Sequence alignment is a basic method in sequence analysis. This method is used to determine the similaritiy level of DNA sequences. The Needleman-Wunsch algorithm is an algorithm that can be used to solve the problem of sequence alignment. This research shows that the relation T (i, j) used in the Needleman-Wunsch algorithm is a function where T: (ℕ0 ℕ0) → ℤ. The function T (i, j) is a recursive function. Moreover, DNA sequence data used are DNA sequences from the Timor Deer, which are the identities of the provinces of West Nusa Tenggara and Red Deer, which are typical deer from the European continent as a comparison. The DNA sequence data was obtained from BLAST (Basic Local Alignment Search Tool). Based on the alignment, the most optimal alignment is obtained by forming 666 base pairs sequences with 322 matches, 230 missmatches and 114 gaps, meaning that the two DNA sequences have a 48% similarity (322/666).

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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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