Current Status and Future Perspectives of Bioinformatics in Tanzania

The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and contributing to the development in the rest of the world, it has still not yet fully integrated the tertiary education and research sector in Tanzania. This review aims to introduce a summary of recent achievements, trends and success stories of application of bioinformatics in biotechnology. The applications of bioinformatics in the fields such as molecular biology, biotechnology, medicine and agriculture, the global trend of bioinformatics, accessibility bioinformatics products in Tanzania, bioinformatics training initiatives in Tanzania, the future prospects of bioinformatics use in biotechnology globally and Tanzania in particular are reviewed. The paper is of interest and importance to rouse public awareness of the new opportunities that could be brought about by bioinformatics to address many research problems relevant to Tanzania and sub-Sahara Africa

In vitro antimicrobial activity of extracts of some plant species used in the management of HIV/AIDS in Tanzania

Six plants species (Harungana madagascariensis, Sapium ellipticum, Teclea nobilis, Pseudospondias microcarpa, Rauvolfia vomitoria and Psorospermum febrifugum) which are used in managing HIV/AIDS in Bukoba, Tanzania were screened for their antimicrobial effect on the selected representatives of infectious bacterial and fungal species. Gram-positive bacteria Streptococcus lactis, Gram-negative bacteria Klebsiella pneumoniae and a fungus Candida albicans were tested for their sensitivity to the treatment with selected plants extracts using disc diffusion and broth dilution techniques. Extracts of S. ellipticum, P. febrifegum and P. microcarpa demonstrated growth inhibition of S. lactis with the MIC ranging from 3.2 to 100 mg/ml. The extracts of S. ellipticum, P. febrifegum and T. nobilis demonstrated growth inhibition of K. pneumonia with the MIC ranging from 6.3 to 25 mg/ml. On the other hand, extracts of H. madagascariensis, P. microcarpa and R. vomitoria inhibited growth of C. albicans with the MIC ranging from 12.5 to 50 mg/ml. These results are very promising towards discovery of new antimicrobial drugs especially against neglected S. lactis, K. pneumoniae and invasive Candida infections and could explain the routine use of the plants’ infusions in traditional medicines in Bukoba against HIV/AIDS related illnesses. Key words: Bukoba Tanzania, HIV/AIDS, opportunistic infections, plant extracts, traditional medicin

Methyl-α-D-glucopyranoside from Tulbaghia violacea extract induces apoptosis in vitro in cancer cells

Pro-apoptotic activity of Tulbghia violacea extracts was evaluated in order to understand the mechanisms of action that might be related to its traditional use as anticancer medicine. Apoptosis-guided purification was used to isolate active compound whose chemical structure was solved by using spectros-copic, microanalysis and X-ray crystallography techniques. T. violacea extract kills Chinese hamster ovary cells, MCF7, and HeLa cells through the induction of apoptosis Methyl-a-D-glucopyranoside was identified as one of the main pro-apoptotic compounds present in T. violacea extract. This is the first time ever demonstration that T. violacea contains methyl-a-D-glucopyranoside, which selectively kills cancer cells through apoptosis mechanisms

Cassava Brown Streak Viruses express second 6-kilodalton (6K2) protein with varied polarity and three dimensional (3D) structures: Basis for trait discrepancy between the virus species

Cassava Brown Streak Virus (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV) are the two among six virus species speculated to cause the most catastrophic Brown Streak Disease of Cassava (CBSD) in Africa and Asia. Cassava Brown Streak Virus (CBSV) is hard to breed resistance for compared to Ugandan Cassava Brown Streak Virus (UCBSV) species. This is exemplified by incidences of CBSV species rather than UCBSV species in elite breeding line, KBH 2006/0026 at Bagamoyo, Tanzania. It is not yet understood as to why CBSV species could breakdown CBSD-resistance in the KBH 2006/0026 unlike the UCBSV species. This marks the first in silico study conducted to understand molecular basis for the trait discrepancy between CBSV and UCBSV species from structural biology view point. Following ab initio modelling and analysis of physical-chemical properties of second 6-kilodalton (6K2) protein encoded by CBSV and UCBSV species, using ROBETTA server and Protein Parameters tool, respectively we report that; three dimensional (3D) structures and polarity of the protein differs significantly between the two virus species. (95% and 5%) and (85% and 15%) strains of 20 CBSV and 20 UCBSV species respectively, expressed the protein in homo-trimeric and homo-tetrameric forms, correspondingly. 95% and 85% of studied strain population of the two virus species expressed hydrophilic and hydrophobic 6K2, respectively. Based on findings of the curent study, we hypothesize that; (i) The hydrophilic 6K2 expressed by the CBSV species, favour its faster systemic movement via vascular tissues of cassava host and hence result into higher tissue titres than the UCBSV species encoding hydrophobic form of the protein. t and (ii) The hydrophilic 6K2 expressed byCBSV species have additional interaction advantage with Nuclear Inclusion b protease domain (NIb) and Viral genome-linked protein (VPg), components of Virus Replication Complex (VRC) and hence contributing to faster replication of viral genome than the hydrophobic 6K2 expressed by the UCBSV species. Experimental studies are needed to resolve the 3D structures of the 6K2, VPg and NIb and comprehend complex molecular interactions between them. We suggest that, the 6K2 gene should be targeted for improvement of RNA interference (RNAi)-directed transgenesis of virus-resistant cassava as a more effective way to control the CBSD besides breeding

Comparison of common adverse neonatal outcomes among preterm and term infants at the National Referral Hospital in Tanzania: a case-control study

Background: Neonatal period is a critical period in a child’s heath because it is associated with higher risk of adverse health outcomes. The objective of this study was to assess common adverse health outcomes and compare the risk of such outcomes between preterm and term neonates, in Tanzania. Methods: This was a case-control study involving infants admitted at Muhimbili National Hospital between August and October 2020. About 222 pairs of preterm and term infants were followed until discharge. Logistic regression was used to compare risk of health outcomes. Statistical significance was achieved at p–value < 0.05 and 95% confidence interval. Result: Preterm neonates had increased risk of mortality (OR = 7.2, 95% CI: 3.4-15.1), apnea (OR = 4.7, 95% CI: 3.4 – 15.1), respiratory distress syndrome (OR = 10.9, 95% CI: 6.1 – 19.6), necrotizing enterocolitis (OR = 5.5, 95% CI: 1.2 – 25.3), anemia (OR = 4.3, 95% CI: 2.8 – 6.6), pneumonia (OR = 2.7, 95% CI: 1.6 – 4.6) and sepsis (OR = 2.6, 95% CI: 1.7 – 3.9). No difference in risk of intraventricular hemorrhage, patent ductus arteriosus and jaundice was observed. Conclusion: For promoting neonates' health, prevention and treatment of the higher risk adverse neonatal outcomes should be prioritized

Morphological and Molecular Identification of Pratylenchus goodeyi Associated with Banana in Tanzania

Banana (Musa sp. [L]) is an important staple food and cash crop for about 30 percent of the total population in Tanzania. Root lesion nematodes, particularly Pratylenchus goodeyi, are among the major pests affecting banana production in Tanzania. A combination of morphological and molecular approaches is required for accurate identification of nematodes. In this study, 80 P. goodeyi isolates affecting bananas in Tanzania were identified. Sequence analysis of part of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) regions of ribosomal DNA (rDNA) confirmed the morphological identification of P. goodeyi. DNA sequences were analysed using Geneious version 11.0 software and phylogenetic relationship was constructed using Bayesian inference (BI) method. Morphological identification shows that P. goodeyi in this study resembles P. goodeyi identified from other parts of the world and their sequences clustered closely (98.6 – 99.9 % similarity) with other P. goodeyi sequences in the GenBank. The results obtained from this study will provide an insight on the presence of harmful root lesion nematodes in Tanzanian bananas, contributing to further studies aimed at developing efficient nematode management strategies in Tanzania.Keywords: Genetic variation; Morphology; Musa sp.; Root lesion nematode;

Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates

Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during plant colonization. Active PGPR strain B. atrophaeus UCMB-5137 was studied in this research. RNA sequencing profiles were generated in experiments where root exudate stimulations were used to mimic interactions between bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42, which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49 putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general regulatory network of B. atrophaeus UCMB-5137 genome was designed.This study was funded by the PhD fellowship grant provided by the Southern African Biochemistry and Informatics for Natural Products (SABINA, www.sabina-africa.org/), and the National Research Foundation of South Africa (NRF) grants 73983, 86941 and 93664 for travels and collaboration. Sequencing was funded by the Genomics Research Institute (GRI) at the University of Pretoria.http://www.elsevier.com/locate/gene2017-09-30hb2016BiochemistryMicrobiology and Plant Patholog

Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains

The application of biocontrol biopesticides based on plant growth–promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences’ Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140.The South African National Research Foundation (NRF), the joint NRF/COSTECH (Tanzanian Commission for Science and Technology), joint TIA (Technology Innovation Agency of South Africa)/COSTECHPhD and MSc student fellowship grants from Southern African Biochemistry and Informatics for Natural Products (SABINA, http://www.sabina-africa.org/) and Agroscope through its research program Microbial Biodiversity.http://link.springer.com/journal/2532021-07-10hj2020BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog