scholarly journals In silico comparative analysis of BRCA2 gene in some selected animal species in Africa

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Olotu TM ◽  
Oladipo EK ◽  
Ajibade OA ◽  
Adeosun I. J ◽  
Adegunloye DV ◽  
...  
Keyword(s):  
In Silico ◽  
Animal Species ◽  
Homo Sapiens ◽  
Cell Structure ◽  
Bird Species ◽  
Brca2 Gene ◽  
African Region ◽  
African Countries ◽  
Multiple Sequence ◽  
Theropithecus Gelada

Background: BRCA2 genes are not only found in humans, but in other animal species. BRCA2 gene plays a vital role in maintaining the stability of a cell's genetic information. BRCA2 is considered as a gatekeeper gene; however, if mutated or abnormally expressed, it causes the destruction of normal cell structure and promotes the growth of cancer cells. Objective: This study aimed to assess the differences and similarities of BRCA2 gene from different animal species in Africa through In silico genomics analysis providing further insight on its comparative genomics features. Materials and Methods: Fifteen nucleotide sequences of BRCA2 gene of different mammals and bird species were retrieved from National Centre for Biotechnology Information (NCBI). Multiple sequence alignment was done with MEGA 7.0 software, while identity and similarities were determined by constructing a pairwise comparison. Conserved domains on the sequences were identified with NCB1-CDD. Results: BRCA2 gene was found to be present not only in humans, but other lower animals and birds across African countries. The phylogenetic tree for Homo sapiens BRCA2 gene in Tunisia belongs to the same ecological niche with the Theropithecus gelada BRCA2 gene in Ethiopia and BRCA2 from the same African region has high bootstrap, implying that they share the same homology. Conserved regions identified in the all the sequences were absent in Miniopterus natalensis and most present in Chrysochloris asiatica, Theropithecus gelada, Apaloderma vittatum, Pterocles gutturalis, Rousettus aegyptiacus, Homo sapiens, Echinops telfairi, and Cavia porcellus. Conclusion: Based on the findings obtained from this study, BRCA2 gene in humans and other lower animals, particularly from same region, share the same homology and similarities.

Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using in silico Method

2012 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Mohd Fakharul Zaman Raja Yahya ◽  
Hasidah Mohd Sidek
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Nuclear Export ◽  
Nuclear Export Signal ◽  
Plasmodium Species ◽  
Mitogen Activated Protein Kinase ◽  
Multiple Sequence ◽  
Wide Range ◽  
Mitogen Activated Protein ◽  
Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range of hosts including humans and rodents. There are two copies of mitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise of presented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series of publicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localized and contain both a nuclear localization signal (NLS) and a Leucine-rich nuclear export signal (NES). The activation motifs of TDY and TSH were found to be fully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection of a multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising of different amino acids present in MAPKJ and MAPK2 respectively, with respect to rodent and human Plasmodia. It is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs. 

Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using In silico Method

2012 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Mohd Fakharul Zaman Raja Yahya ◽  
Hasidah Mohd Sidek
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Nuclear Export ◽  
Nuclear Export Signal ◽  
Plasmodium Species ◽  
Mitogen Activated Protein Kinase ◽  
Multiple Sequence ◽  
Bioinformatic Tools ◽  
Wide Range ◽  
Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range ofhosts including humans and rodents. There are two copies ofmitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise ofpresented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series ofpublicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localizedandcontain both a nuclear localization signal (NLS) anda Leucine-rich nuclear export signal (NES). The activation motifs ofTDYand TSH werefound to befully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection ofa multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising ofdifferent amino acids present in MAPK1 and MAPK2 respectively, with respect to rodent and human Plasmodia. 1t is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs.

Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach

2020 ◽  
Vol 14 (3) ◽  
pp. 235-246
Author(s):  
Sara Abdollahi ◽  
Mohammad H. Morowvat ◽  
Amir Savardashtaki ◽  
Cambyz Irajie ◽  
Sohrab Najafipour ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
In Silico ◽  
Bacterial Species ◽  
Arginine Deiminase ◽  
Antitumor Effects ◽  
Multiple Sequence ◽  
In Silico Studies

Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.

scholarly journals Kenya’s Standard Gauge Railway Project in the Context of Theory and Practice of Regional Planning

2020 ◽  
Vol 10 (2) ◽  
Author(s):  
Leanard Otwori Juma ◽  
Fredrick Adol Gogo ◽  
Ahmed Abduletif Abdulkadr ◽  
Dénes Dávid Lóránt
Keyword(s):  
Regional Planning ◽  
Secondary Data ◽  
Theory And Practice ◽  
Economic Activities ◽  
East African ◽  
African Region ◽  
African Countries ◽  
Transportation Services ◽  
Goods And Services ◽  
The Impact

Despite most African countries having immense natural and human resources potential, the continent has mostly been lagging on matters of economic development. This scenario could primarily be attributed to weak intra-regional and inter-country trade given the poor connectivity, quality, and diversity in transportation services and infrastructure. In this regard, the governments of the greater East African Region representing Tanzania, Rwanda, Burundi, Uganda, South Sudan, Ethiopia and Kenya, therefore, mooted a coordinated vision to develop interlinked regional infrastructure in road and rail transport to allow smooth movement of goods and services.  This paper aimed to critically review the impact of the SGR development on Kenya in the context of regional planning and development. The methodology of the study was a critical review of existing literature and secondary data. Study findings indicated that the development of the (Standard Gauge Railway) SGR is in tandem with the development strategies of other East African Countries. Its development is incorporated in national spatial plans with the rail route targeting regions with viable populations and sustainable economic activities. Criticisms, however, revolve around the ballooning debt to finance infrastructural development and lack of prioritization f mega projects. In conclusion, despite the financial constraints, the SGR is viewed to significantly influence the socio-economic spheres while presenting challenges in the management of landscapes where it traverses in Kenya and the Region.

scholarly journals Analysis of main risk factors contributing to obesity in the region of East Africa: meta-analysis

2020 ◽  
Vol 20 (1) ◽  
pp. 248-256
Author(s):  
Lenka Mařincová ◽  
Simona Šafaříková ◽  
Radka Cahlíková
Keyword(s):  
Risk Factors ◽  
East Africa ◽  
Meta Analysis ◽  
Obesity Prevalence ◽  
East African ◽  
African Region ◽  
African Countries ◽  
Chi Square ◽  
Chi Square Test ◽  
Risk Ratios

Background: Over a few decades obesity has become a major global health problem. Its prevalence worldwide has more than doubled since 1980. The situation is expected to worsen in the future, especially in the developing countries that experience nutrition transition due to economic growth. It contributes to reduction in malnutrition which supports an increase in obesity prevalence. Objectives: The aim of this study was to analyse the predictors of obesity in the region of East Africa. Methods: Meta-analysis of existing studies was used in order to find the different risk factors and their significance in obesity development. Data extracted from 16 published academic research articles described the situation in East African countries. The significance of the effect of each variable was tested by means of an asymptotic chi-square test, or Fisher's exact (factorial) test and the risk ratios were calculated. Results: Based on the chi-square test and the risk ratios of the aggregated data, three risk factors were found to be significant in the development of obesity – gender, type of residence and socio-economic status. In East African countries, women are significantly more likely to be obese. Living in an urban area and socioeconomic status are also positively associated with obesity. Because of insufficient data three other risk factors did not prove to be of any significance – alcohol consumption, smoking and education level. Conclusion: Conclusions of this meta-analysis confirm world trends but we also found results that are not in line with them (e.g. education). This meta-analysis confirms the huge existing research gap concerning obesity predictors in the East African region. Keywords: Obesity; meta-analysis; East Africa. 

scholarly journals IN SILICO ANTIMALARIAL TARGET SELECTION CONSERVED IN FOUR PLASMODIUM SPECIES

2020 ◽  
Author(s):  
Oladoja AWofisayo
Keyword(s):  
Comparative Genomics ◽  
Peer Review ◽  
In Silico ◽  
Drug Targets ◽  
Homo Sapiens ◽  
Mammalian Species ◽  
Target Selection ◽  
Plasmodium Species ◽  
Data Bank ◽  
Sequence Motifs

Objectives: The need for new antimalarials drugs and drug targets is pertinent due to the emergence of drug resistant strains of the parasites. Improper target selection has resulted in therapeutic failure. The genomic/post genomic era has made possible the deciphering of the 3D crystal structures of proteins and DNA which are drug targets and are deposited in the protein data bank. Methods: Novel antimalarial targets obtained from evolutionary conserved short sequence motifs are utilised and are essential in transcription processes in the parasite. The motifs TGCATGCA, GTGCAC and GTGCGTGC were curated from experimental work, validated and analysed via phylogenomics genomics and comparative genomics. PlasmoDB blastn was applied to determine their similarity in Plasmodium vivax, knowlesi, Ovale and yoeli. The complete genome of Plasmodium falciparum vivax, knowlesi, Ovale and yoeli was downloaded from the plasmoDB and their positions determined. Results: The targets are essential, conserved in rodent and mammalian species via phylogenomics with percentage identity and similarity greater than 80%, have no similar genes in the same genome and also found to be selective in the parasites vis-à-vis the Homo sapiens via comparative genomics with 0% identity and similarity in the human genome. Conclusion: The targets reveal at the molecular and biochemical level, the vulnerable regions in the parasite while safe in human hence their choices in subsequent rationale drug discovery and design protocols. Peer Review History: Received: 18 July 2020; Revised: 1 October; Accepted: 12 October, Available online: 15 November 2020 UJPR follows the most transparent and toughest ‘Advanced OPEN peer review’ system. The identity of the authors and, reviewers will be known to each other. This transparent process will help to eradicate any possible malicious/purposeful interference by any person (publishing staff, reviewer, editor, author, etc) during peer review. As a result of this unique system, all reviewers will get their due recognition and respect, once their names are published in the papers. We expect that, by publishing peer review reports with published papers, will be helpful to many authors for drafting their article according to the specifications. Auhors will remove any error of their article and they will improve their article(s) according to the previous reports displayed with published article(s). The main purpose of it is ‘to improve the quality of a candidate manuscript’. Our reviewers check the ‘strength and weakness of a manuscript honestly’. There will increase in the perfection, and transparency. Received file Average Peer review marks at initial stage: 5.5/10 Average Peer review marks at publication stage: 7.0/10 Reviewer(s) detail: Dr. Tamer ELHABIBI, ERU University, Egypt, [email protected] Dr. Soroush Sardari, Biotech Pasteur Institute of Iran, Tehran, Iran, [email protected] Comments of reviewer(s): Similar Articles: IN SILICO LIGAND-BASED 2D PHARMACOPHORE GENERATION FOR H+/K+ ATPASE INHIBITORS

scholarly journals Enteric Fever in Mediterranean North Africa

2009 ◽  
Vol 3 (10) ◽  
pp. 753-761 ◽  
Author(s):  
Khalifa Sifaw Ghenghesh ◽  
Ezzedin Franka ◽  
Khaled Tawil ◽  
Momtaz Wasfy ◽  
Salwa F. Ahmed ◽  
...  
Keyword(s):  
North Africa ◽  
Salmonella Enterica ◽  
Enteric Fever ◽  
Salmonella Typhi ◽  
Multidrug Resistant ◽  
Population Based ◽  
North African ◽  
African Region ◽  
African Countries ◽  
The Mediterranean

Typhoid fever is endemic in the Mediterranean North African countries (Morocco, Algeria, Tunisia, Libya, and Egypt) with an estimated incidence of 10-100 cases per 100,000 persons. Outbreaks caused by Salmonella enterica serovar Typhi are common and mainly due to the consumption of untreated or sewage-contaminated water. Salmonella enterica Paratyphi B is more commonly involved in nosocomial cases of enteric fever in North Africa than expected and leads to high mortality rates among infants with congenital anomalies. Prevalence among travellers returning from this region is low, with an estimate of less than one per 100,000. Although multidrug resistant strains of Salmonella Typhi and Paratyphi are prevalent in this region, the re-emergence of chloramphenicol- and ampicillin-susceptible strains has been observed. In order to better understand the epidemiology of enteric fever in the Mediterranean North African region, population-based studies are needed. These will assist the health authorities in the region in preventing and controlling this important disease.

Potential Drug Target Identification in Porphyromonas gingivalis using In-silico Subtractive Metabolic Pathway Analysis

2021 ◽  
Vol 20 (4) ◽  
pp. 887-896
Author(s):  
Prachi Sao ◽  
Yamini Chand ◽  
Atul Kumar ◽  
Sachidanand Singh
Keyword(s):  
Porphyromonas Gingivalis ◽  
Pathway Analysis ◽  
In Silico ◽  
Drug Targets ◽  
Homo Sapiens ◽  
Medical Science ◽  
Bone Destruction ◽  
Therapeutic Drug ◽  
Potential Drug ◽  
Narrow Spectrum

Introduction: Porphyromonas Gingivalis (P. gingivalis) a primary periodontal disease pathogen. This bacterium affects sub-gingival tissue and leads to loss of teeth and alveolar bone destruction in the acute stage. In recent years, P. gingivalis is often connected with other diseases such as rheumatoid arthritis, diabetes, Alzheimer’s, and heart disease, though the aetiology is still unclear. Objective: The use of commonly available drugs to treat periodontitis results in various side effects, in particular multi-drug resistant strains. As the development of multidrugresistant strains frequently urges the identification of novel drug targets, the aim of this study is to identify specific targets in the narrow spectrum to combat oral pathogens. Methodology: This study used a comparative and subtractive pathway analysis approach to identify potential drug targets specific to P. gingivalis. Results: The in-silico comparison of the P. gingivalis and Homo sapiens (H. sapiens) metabolic pathways resulted in 13 unique pathogen pathways. A homology search of the 67 enzymes in the unique bacterial pathway using the BLASTp program against the Homo sapiens proteome resulted in fifteen possible targets that are non-homologous to the human proteome. Thirteen genes among 15 potent target encoders are key DEG genes indispensable for P. gingivalis’s survival. A comprehensive analysis of the literature identified three potential therapeutic drug targets. Conclusions: The three most relevant drug targets are Arabinose-5-phosphate isomerase, UDP-2,3-diacylglucosamine hydrolase, and Undecaprenyl diphosphatase. Upon corroboration, these targets may give rise to narrow-spectrum antibiotics that can specificallytreat thedental infection. Bangladesh Journal of Medical Science Vol.20(4) 2021 p.887-896

Genes to drug: an in-silico approach to design a drug for Huntington disease (HD) in Homo sapiens

2021 ◽  
Vol 14 (3) ◽  
pp. 190
Author(s):  
Manoj Kumar Sharma ◽  
Manoj Kumar Sharma ◽  
Shivalika Panwar ◽  
Sachin Kumar
Keyword(s):  
Huntington Disease ◽  
In Silico ◽  
Homo Sapiens
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