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Tamoxifen is the most used hormonal therapy for estrogen receptor positive breast cancer. CYP2D6 is the main enzyme in the metabolic pathway of tamoxifen to endoxifen. Variations in endoxifen plasma concentrations are associated with CYP2D6 polymorphisms. This study aimed to determine the association between the CYP2D6 polymorphisms and endoxifen plasma concentrations in a cohort of Zimbabwean breast cancer patients (n = 40). TaqMan genotyping and copy number assays were done to determine CYP2D6 genotypes. Tamoxifen and metabolites were quantitated using LC-MS/MS. The population had high frequencies of the CYP2D6 reduced function alleles, *17 (15%) and *29 (18%). The median endoxifen concentration was 4.78 ng/ml and 55% of the patients, mostly intermediate metabolizers were below the endoxifen therapeutic threshold 5.97 ng/ml. The CYP2D6 phenotypes and activity scores were significantly associated with endoxifen plasma concentrations (p = 0.0151) and with endoxifen to N-desmethyl tamoxifen ratios (p = 0.0006).

Prostate cancer (PCa) is one of the most common malignancies, and many studies have shown that PCa has a poor prognosis, which varies across different ethnicities. This variability is caused by genetic diversity. High-throughput omics technologies have identified and shed some light on the mechanisms of its progression and finding new biomarkers. Still, a systems biology approach is needed for a holistic molecular perspective. In this study, we applied a multi-omics approach to data analysis using different publicly available omics data sets from diverse populations to better understand the PCa disease etiology. Our study used multiple omic datasets, which included genomic, transcriptomic and metabolomic datasets, to identify drivers for PCa better. Individual omics datasets were analysed separately based on the standard pipeline for each dataset. Furthermore, we applied a novel multi-omics pathways algorithm to integrate all the individual omics datasets. This algorithm applies the p-values of enriched pathways from unique omics data types, which are then combined using the MiniMax statistic of the PathwayMultiomics tool to prioritise pathways dysregulated in the omics datasets. The single omics result indicated an association between up-regulated genes in RNA-Seq data and the metabolomics data. Glucose and pyruvate are the primary metabolites, and the associated pathways are glycolysis, gluconeogenesis, pyruvate kinase deficiency, and the Warburg effect pathway. From the interim result, the identified genes in RNA-Seq single omics analysis are linked with the significant pathways from the metabolomics analysis. The multi-omics pathway analysis will eventually enable the identification of biomarkers shared amongst these different omics datasets to ease prostate cancer prognosis.

The dynamics of COVID-19 disease have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 6139 complete nucleotide genomes from 51 African nations were obtained and analyzed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of SARS-CoV-2 lineages circulating in Africa. We investigated their diversity using several clade and lineage nomenclature systems, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 193 of the 2050 Pango lineages discovered worldwide circulated in Africa after two years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations because they had the most SARS-CoV-2 genomes sampled and sequenced. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa. Genomic surveillance is one of the important techniques in the pandemic preparedness toolbox and to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa, genomic surveillance activities across the continent must be expanded. The effectiveness of molecular surveillance as a method for tracking pandemics strongly depends on continuous and reliable sampling, speedy virus genome sequencing, and prompt reporting and we have to improve in all these aspects in Africa. Additionally, the pandemic breakout revealed that current land-border regulations aimed at limiting virus’s international transmission are ineffective and a lot needs to be done to implement and improve our African land-borders as far as epidemiology is concerned in order to contain such outbreaks in the future.

Aim The efficiency of production depends greatly on knowledge of the plant’s performance (including stress tolerance, nutritional quality and overall yield) and genetics. The review was aimed at gathering information on the conservation of banana germplasm and its potential in breeding programs. Finding out whether banana cultivars being grown in Zimbabwe have been characterized both genetically and morphologically thus creating a catalogue and also assessing production and its impact in Zimbabwean economy. The evaluation of species distribution models that can better extrapolate production to new area within the country. Location Zimbabwe Methods Obtaining information on banana production in Zimbabwe has been done through phone call inquires to research stations and plantations, face to face inquires and literature search on peer-reviewed publications and also greys literature. Results Information obtained through database search was extremely limited. Literature citing banana production in Zimbabwe was not greater than 0.00028%. Interaction with farmers and the department of Agricultural, Technical and Extension Services (AGRITEX) Officers yielded better results showing a clear picture of undocumented relevant banana information. Main Conclusion Characterization of Musa Spp. is a necessity for germplasm conservation, breeding and improved banana production. Currently, there is vast literature on characterized banana accessions across the globe, but limited publicly available information concerning accessions in Zimbabwe. Banana production in Zimbabwe is concentrated in the warm and humid areas and similar climatic conditions are found in areas dotted across Zimbabwe. Using species distribution models, cultivars can be mapped to new environments and this in return expands production area in the country. In so doing, cultivars digital maps are created for ease of banana information access. Cultivar maps and biological information from multi-locational gene banks has great potential for use in banana production improvement programs.

Background Local communities in the South Eastern Lowveld of Zimbabwe have adopted the feeding of livestock with Neorautanenia brachypus (Harms) C.A. tuber to mitigate against climate change. Differences within Neorautanenia brachypus (Harms) tuber flesh colour and preferences by cattle have been observed, suggesting possible diversity within the N. brachypus plant community. This study aimed at distinguishing the N. brachypus wild plant species through phenotypic and genetic characterization using morphological descriptors and random amplified polymorphic (RAPD) markers respectively. Leaf samples were selected using judgmental sampling techniques from wards 11–15 in Sengwe (Chiredzi district) for leaf morphology and molecular characterization. RAPD-PCR analysis was done using 18-screened random decamer primers to confirm the diversity in the plant population. The similarity of the biotypes was evaluated using binary coding on the basis of the presence or absence of a morphological indicator as well as distinct DNA amplicon fragments. Primer 7.0.13 was used to estimate morphological and genetic similarities using the unweighted pair group method with arithmetic average (UPGMA). The cluster number was estimated using the Elbow method part of the R package. Results Initially, 14 biotype groups were identified from 96 accessions visually characterized basing of leaf characteristics. All the leaf biotypes displayed arcuate venation with differences observed for leaf shape, tip shape and leaf margins. The 14 biotypes clustered into six groups based on the binary data of the morphological characteristics. RAPD primers generated three hundred and sixty eight distinct amplicons with 77.5% being polymorphic from the 14 biotypes. The number of bands produced per primer ranged from four (OPF-02) to 44 (UBC-746). The PIC value ranged from 0.1327 to 0.1873 for the RAPD primers. Use of molecular markers collapsed the biotypes into five clusters. Both the leaf descriptors and RAPD markers showed the existence of genetic diversity within the wild accessions of N. brachypus. Conclusions A combination of morphological and RAPD markers effectively refined the resolution of the genetic diversity within the N. brachypus wild accessions to nine biotypes. These findings have indicated to the existence of more than one biotype of N. brachypus with potentially different properties. The favorable biotypes can further be promoted through incorporation in pastures as alternative feed or complementary feed to livestock. As such the output of this study will serve as a guide for N. brachypus germplasm management and improvement. Electronic supplementary material The online version of this article (10.1186/s12898-019-0229-9) contains supplementary material, which is available to authorized users.

Polymerase chain reaction (PCR) is a popular molecular tool for detection of bacteria. PCR allows millions of copies of a target segment of DNA to be produced. The DNA is extracted from overnight grown cultures of pure bacterial isolates using either the organo-solvent method or a commercial DNA extraction kit. The quality and purity of the DNA is determined by performing gel electrophoresis on 0.8% agarose gel. The DNA is amplified by performing PCR assay. Bands of approximately 1.5 kb in size are obtained from the amplified products of DNA. The PCR products run on 1.5% agarose gel are visualized with UV light and imaged by gel documentation system. This chapter outlines the protocol for isolation and amplification of DNA from cellulolytic bacteria. Cellulolytic bacteria are considered a potential source of cellulases for pretreatment of crop residues during biogas production. PCR is considered a very powerful, sensitive, specific, fast, and reliable tool in molecular detection and diagnostics.

Polymerase chain reaction (PCR) is a popular molecular tool for detection of bacteria. PCR allows millions of copies of a target segment of DNA to be produced. The DNA is extracted from overnight grown cultures of pure bacterial isolates using either the organo-solvent method or a commercial DNA extraction kit. The quality and purity of the DNA is determined by performing gel electrophoresis on 0.8% agarose gel. The DNA is amplified by performing PCR assay. Bands of approximately 1.5 kb in size are obtained from the amplified products of DNA. The PCR products run on 1.5% agarose gel are visualized with UV light and imaged by gel documentation system. This chapter outlines the protocol for isolation and amplification of DNA from cellulolytic bacteria. Cellulolytic bacteria are considered a potential source of cellulases for pretreatment of crop residues during biogas production. PCR is considered a very powerful, sensitive, specific, fast, and reliable tool in molecular detection and diagnostics.

Additional file 4: Appendix S1. GPS data from leaf collection sites. The file shows the geographical positions from which the Neorautanenia brachypus plants were collected. The coordinates shows the exact sites were plant specimens were collected in the South Eastern Lowveld of Zimbabwe. The selected sites were based on previous work by [4].