Plant genomics in Africa: present and prospects

Plants are the world’s most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population’s increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.     

Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan

The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computational tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on specific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the development of bioinformatics in the country.     

MANAGEMENT,CONSERVATION AND RESEARCH OF INTERNATIONALLY SHARED WATERCOURSES IN SOUTIIERN AFRICA—NAMIBIAN EXPERIENCE WITH THE OKAVANGO RIVER AND RIVERS OF THE EASTERN CAPRIVI

Summary

Although the emphasis of the recent National Rivers Research Initiative (now the Research Programme for the Management of Rivers) in South Africa was on river research in that country, the reality is that in southern Africa many watercourses are shared by more than one country. Therefore a central issue in integrated river basin management and development should be the recognition of the principle of international joint planning, conservation, monitoring and research.

Co-operation and a better understanding of shared waters would prevent deleterious impacts, not only in the country where they occur, but also in those downstream. With this in mind, since the early 1980s Namibia has worked on joint cross-border projects in efforts to manage and conserve her shared water bodies. These include joint river gauging exercises, biological control of Saivinia molesta in the eastern Caprivi region and, more recently, the application of a biological monitoring technique, the South African Scoring System version 4, to north-eastern perennial rivers.

The formation of the Joint Permanent Water Commission between Botswana and Namibia enabled the Departments of Water Affairs of both countries to work together on their shared rivers. The establishment of the Permanent Okavango River Basin Water Commission between Angola, Botswana and Namibia in 1994 improved this co-operation even further. Namibia and its' counterparts are thus committed to sharing information, co-ordinating research and monitoring activities and to undertaking detailed studies to improve their knowledge of these shared systems.

Such cross-border co-operation is vital for the survival of shared river systems not only as ecological entities in their own right, but also as sources of water, power and the other resources they provide, both directly and indirectly, to the human and wildlife populations that they support.     

转基因作物在南非的应用及对我国的启示*

2019年是南非转基因作物商业化种植的第22年,3种主要转基因作物:棉花、玉米和大豆共种植了268万公顷,在全球所有转基因作物生产国中排名第八位,在非洲大陆排名第一位。这样一个具有超高转基因作物应用率的国家,有关其转基因商业化进程及现状鲜有系统介绍。综合1996~2019年的国际农业生物技术应用服务组织(International Service for the Acquisition of Agri-biotech Applications,ISAAA)的报告及其他数据资料,对南非转基因作物批准和种植情况、自主研发情况、安全管理制度、进出口情况及公众接受度做了概述,并以此为基础对我国转基因产业提出建议。     

Biotechnology in South Africa

Since adopting the National Biotechnology Strategy in 2001, the South African government has established several regional innovation centres and has put in place initiatives to encourage international partnerships that can spur internal development of life science ventures. This strategy seeks to capitalize on the high quality of research carried out in public research institutions and universities but is hampered, somewhat, by the lack of entrepreneurial culture among South African researchers due to, among other reasons, the expenses involved in registering foreign patents. Although private sector development is still relatively embryonic, start-ups are spinning out of universities and pre-existing companies. These represent a vital source of innovations for commercialization in the future, provided that the challenges facing the emerging South African biotechnology industry can be overcome.     

Ancient origin and recent divergence of a haplochromine cichlid lineage from isolated water bodies in the East African Rift system

Phylogenetic analysis identified haplochromine cichlids from isolated water bodies in the eastern branch of the East African Rift system as an ancient lineage separated from their western sister group in the course of the South Kenyan-North Tanzanian rift system formation. Within this lineage, the close phylogenetic relatedness among taxa indicates a recent common ancestry and historical connections between now separated water bodies. In connection with a total lack of local genetic diversity attributable to population bottlenecks, the data suggest cycles of extinction and colonization in the unstable habitat provided by the small lakes and rivers in this geologically highly active area.     

The conservation imperative and setting plant taxonomic research priorities in South Africa

For more than a decade it has been internationally recognised that efforts should be made to remedy the concern that taxonomy is an endangered discipline in the grips of rapid decline. In acknowledgement of the perceived continuing marginalisation of taxonomy, the Darwin Declaration recognised the need to enhance the taxonomic capacity of members who are party to the CBD, and beyond. South Africa is one of the most biodiversity rich countries globally, and the unique and rich flora of the country brings with it a significant conservation imperative. Although the country, and southern African subregion for that matter, has a strong history of taxonomic endeavour, stretching back for over a century, it also suffers from a lack of human and other resources to adequately address its taxonomic needs. This inevitably calls for a process of priority-setting to ensure the wise use of available funding. As one example, it is shown that 1,009 indigenous South African plant taxa are regarded as Data Deficient for taxonomic reasons, following the completion of a recent comprehensive Red Listing exercise. Although not the only criterion to be considered when prioritising taxonomic research, efforts focused on these groups represent a significant opportunity for taxonomists to align their work with national priorities.     

Managing Human Tissue Transfer Across National Boundaries – An Approach from an Institution in South Africa

With biobank research on the increase and the history of exploitation in Africa, it has become necessary to manage the transfer of human tissues across national boundaries. There are many accepted templates of Material Transfer Agreements (MTAs) that currently exist internationally. However, these templates do not address the specific concerns of South Africa and even of Africa as a continent. This article will examine three significantly important ethico‐legal concepts that were deliberated and carefully adapted by a South African Institution to suit the transfer of Human Biological Materials (HBMs) and associated data for biobank research, namely: informed consent; benefit sharing arrangements; and ownership together with intellectual property rights in human tissues. The discussion includes an analysis of current practice; the ethico‐legal challenges in the South African/African context; the decisions made with regard to how the related ethico‐legal challenges were addressed in the MTA; and justifications for implementing these decisions. The processes considered could be of benefit to other developing world countries who consider it necessary to manage the transfer of HBMs across national boundaries.     

Donor issues in Indonesia: A developing country in South East Asia

In most developing countries in South East Asia blood services have not been treated properly as an important service to support health program. Indonesia as a large archipelago country in South East Asia has specific obstacles in managing a blood service. To position the country blood service profile especially in term of donor issues, we compared our blood service with that in other South East Asia countries.Indonesia has 17 thousand islands with 220 million inhabitants. Blood services have been mostly run by the Indonesian Red Cross as a government assignment since 1950. Donor recruitment programs have been directed toward 100% of Voluntary Non Remunerated Blood Donor (VNRD), which now have reached 81.3%. Dissemination of information on VNRD, donor recruiter's training and VNRD appreciation programs are strategies to increase and maintain the VNRD.Limited female donors and insufficient blood supply during the fasting month and holidays constitute major challenges. Low hemoglobin level, low body weight and fear are reasons for low number of female donors. Poor management of blood stock during fasting month, long holidays and also poor networking of blood supply are reasons for insufficient blood supply during the year.Considering the great size of Indonesia with different ethnic groups and cultures, worsened by lack of infrastructure, decisive and effective strategies in donor recruitment and retention programs are needed.     

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context.

Availability

MACBenAbim is available from the authors for non-commercial purposes.     

STAKEHOLDER PERSPECTIVES ON ETHICAL CHALLENGES IN HIV VACCINE TRIALS IN SOUTH AFRICA

There is little published literature on the ethical concerns of stakeholders in HIV vaccine trials. This study explored the ethical challenges identified by various stakeholders, through an open-ended, in-depth approach. While the few previous studies have been largely quantitative, respondents in this study had the opportunity to spontaneously identify the issues that they perceived to be of priority concern in the South African context. Stakeholders spontaneously identified the following as ethical priorities: informed consent, social harms, collaborative relationships between research stakeholders, the participation of children and adolescents, access to treatment for participants who become infected with HIV, physical harms, fair participant and community selection, confidentiality, benefits, and payment.
While there is some speculation that research in developing countries poses special ethical challenges, overall no issues were identified that have not been anticipated in international guidance, literature and popular frameworks. However, the South African context affords a distinctive gloss to these expected issues; for example, respondents were concerned that the predominant selection of black participants may perpetuate racist practices of apartheid. Stakeholders should be aware of contextual factors impacting on the implementation of ethical principles. We make a series of recommendations for South African trials, including amendments to the ethical-legal framework and research policies, and, for further research.     

Research on dead human bodies: African perspectives on moral status

A useful concept that can be invoked to resolve complex bioethical issues is that of moral status (or, human dignity). In this article, we apply this concept to dead human bodies in order to support our view that research on such bodies is permissible. Instead of drawing from salient Western theories of human dignity that account for it by appeals to autonomy or rationality, we will base our investigation on emerging conceptions in African theories of moral status as articulated by Thaddeus Metz and Munamato Chemhuru. Our conclusion is that neither of these theories of moral status, one secular, and the other religious, can accommodate the intuition that we have direct duties of respect towards such bodies because, in relation to Metz's conception, they lack the capacity to enter into social relationships while on Chemhuru's conception, dead bodies appear not to have any meaningful purpose within the hierarchy that captures the ontological systems that determine such status. Consequently, we argue that our analysis provides support for the use of unclaimed cadavers in training and research in medical institutions.     

Novel bioinformatic developments for exome sequencing

With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.     

Traditional medicines as a mechanism for driving research innovation in Africa

The outcomes from recent high profile deliberations concerning African health research and economic development all point towards the need for a mechanism to support health innovation on the continent. The mission of the African Network for Drugs and Diagnostics Innovation (ANDI), is to promote and sustain African-led health product innovation to address African public health needs through the assembly of research networks, and building of capacity to support human and economic development. ANDI is widely viewed as the vehicle to implementing some of these recommendations. There is tremendous opportunity for Africa, to leverage the expertise in natural products and traditional medicines in support of this objective to kick-start innovation. This report highlights key recommendations that have emerged through expert forums convened by ANDI on the challenges, opportunities and prospects for investing in this important area of research.     

Invasive <Emphasis Type="Italic">Tamarix</Emphasis> (Tamaricaceae) in South Africa: current research and the potential for biological control

Most species of Tamarix originate in Eurasia and at least five species have become invasive around the world, including South Africa. However, T. usneoides is indigenous to southern Africa, where the potential for biological control of the invasive species is being investigated. Recent research on the invasive species is reviewed here with particular reference to these South African biocontrol efforts. The successful biological control programme against invasive Tamarix in the USA, using several species of “Tamarisk beetle”, is being used as a guide for the South African research. The South African programme is complicated by firstly, the presence of the indigenous T. usneoides which raises the precision of host-specificity required, and secondly, the introduced and indigenous Tamarix have a high intrinsic value for phytoremediation of mine tailings dams in South Africa. The phylogenetic proximity of these Tamarix species to each other has contributed to this challenge, which has nevertheless been successfully addressed by molecular techniques used to separate the species. In addition, classical morphological techniques have been used to separate the Tamarisk beetles, so that now they can generally be matched to Tamarix tree species. Overall, it is concluded that given the broad knowledge now available on the ecology and identity of both the trees and their biocontrol agents, the prospects for successful biological control of Tamarix in South Africa are good.     

Spatial Assessment of Amphibian Chytrid Fungus (Batrachochytrium dendrobatidis) in South Africa Confirms Endemic and Widespread Infection

Chytridiomycosis has been identified as a major cause of global amphibian declines. Despite widespread evidence of Batrachochytrium dendrobatidis infection in South African frogs, sampling for this disease has not focused on threatened species, or whether this pathogen poses a disease risk to these species. This study assessed the occurrence of Bd-infection in South African Red List species. In addition, all known records of infection from South Africa were used to model the ecological niche of Bd to provide a better understanding of spatial patterns and associated disease risk. Presence and prevalence of Bd was determined through quantitative real-time PCR of 360 skin swab samples from 17 threatened species from 38 sites across the country. Average prevalence was 14.8% for threatened species, with pathogen load varying considerably between species. MaxEnt was used to model the predicted distribution of Bd based on 683 positive records for South Africa. The resultant probability threshold map indicated that Bd is largely restricted to the wet eastern and coastal regions of South Africa. A lack of observed adverse impacts on wild threatened populations supports the endemic pathogen hypothesis for southern Africa. However, all threatened species occur within the limits of the predicted distribution for Bd, exposing them to potential Bd-associated risk factors. Predicting pathogen distribution patterns and potential impact is increasingly important for prioritising research and guiding management decisions.     

How Can the Operating Environment for Nutrition Research Be Improved in Sub-Saharan Africa? The Views of African Researchers

Optimal nutrition is critical for human development and economic growth. Sub-Saharan Africa is facing high levels of food insecurity and only few sub-Saharan African countries are on track to eradicate extreme poverty and hunger by 2015. Effective research capacity is crucial for addressing emerging challenges and designing appropriate mitigation strategies in sub-Saharan Africa. A clear understanding of the operating environment for nutrition research in sub-Saharan Africa is a much needed prerequisite. We collected data on the barriers and requirements for conducting nutrition research in sub-Saharan Africa through semi-structured interviews with 144 participants involved in nutrition research in 35 countries in sub-Saharan Africa. A total of 133 interviews were retained for coding. The main barriers identified for effective nutrition research were the lack of funding due to poor recognition by policymakers of the importance of nutrition research and under-utilisation of research findings for developing policy, as well as an absence of research priority setting from within Africa. Current research topics were perceived to be mainly determined by funding bodies from outside Africa. Nutrition researchers argued for more commitment from policymakers at national level. The low capacity for nutrition research was mainly seen as a consequence of insufficient numbers of nutrition researchers, limited skills and a poor research infrastructure. In conclusion, African nutrition researchers argued how research priorities need to be identified by African stakeholders, accompanied by consensus building to enable creating a problem-driven national research agenda. In addition, it was considered necessary to promote interactions among researchers, and between researchers and policymakers. Multidisciplinary research and international and cross-African collaboration were seen as crucial to build capacity in sub-Saharan nutrition research.     

Contrasting the ancestry patterns of three distinct population groups from the northernmost region of South America

Colombia, located in the north of the South American subcontinent is a country of great interest for population genetic studies given its high ethnic and cultural diversity represented by the admixed population, 102 indigenous peoples and African descent populations. In this study, an analysis of the genetic structure and ancestry was performed based on 46 ancestry informative INDEL markers (AIM-INDELs) and considering the genealogical and demographic variables of 451 unrelated individuals belonging to nine Native American, two African American, and four multiple ancestry populations. Measures of genetic diversity, ancestry components, and genetic substructure were analyzed to build a population model typical of the northernmost part of the South American continent. The model suggests three types of populations: Native American, African American, and multiple ancestry. The results support hypotheses posed by other authors about issues like the peopling of South America and the existence of two types of Native American ancestry. This last finding could be crucial for future research on the peopling of Colombia and South America in that a single origin of all indigenous communities should not be assumed. It then would be necessary to consider other events that could explain their genetic variability and complexity throughout the continent.     

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.