Genetic Transformation of Sweet Potato for Improved Tolerance to Stress: A Review

The sweet potato (Ipomoea batatas Lam) is a major staple food in many parts of the world. Sweet potato leaves and tubers are consumed as food and livestock feed. Biotic and abiotic stresses affect yield leading to a reduction in production. This review analyzes factors limiting sweet potato production and the progress made towards stress tolerance using genetic transformation. Genetic transformation could enhance yield, nutritional value and tolerance to stress. Transgenic sweet potatoes tolerant to biotic and abiotic stress, improved nutritional value and higher yields have been developed. Sweet potato expressing the endotoxin cry8Db, cry7A1 and cry3Ca genes showed lower sweet potato weevil infestation than non-transformed lines. Transgenic cultivar ‘Xushu18’ expressing the oryzacystatin-1 (OC1) gene showed enhanced resistance to sweet potato stem nematodes. Sweet potato line ‘Chikei 682-11’ expressing the coat protein (CP) exhibited resistance to the sweet potato feathery mottle virus (SPFMV). Transgenics expressing the rice cysteine inhibitor gene oryzacystatin-1 (OC1) also exhibited resistance to the SPFMV. Transgenic cultivar ‘Kokei’ expressing the spermidine synthetase gene FSPD1 had higher levels of spermine in the leaves and roots, and displayed enhanced tolerance to drought and salt stress. ‘Shangshu’ variety expressing the IbMas has shown enhanced tolerance to salt stress. Transgenic ‘Lixixiang’ expressing IbMIPSI showed an up-regulation of metabolites involved in stress response to drought, salinity and nematode infestation. Transgenic ‘Yulmi’ sweet potato transformed with copper/zinc superoxide dismutase (CuZnSOD) gene showed an enhanced tolerance to methyl viologen induced oxidative and chilling stress. Similarly, transformation of cultivar ‘Sushu-2’ with betaine aldehyde dehydrogenase (BADH) gene resulted in transgenics tolerant to salt, chilling and oxidative stress. Sweet potato varieties ‘Kokei14’ and ‘Yulmi’ transformed with the bar gene were shown to be tolerant to application of the herbicide Basta. The development of stress tolerant varieties will immensely increase the area under sweet potato production and eventually promote the adoption of sweet potato as a commercial crop. Sweet potato research and breeding for stress tolerance still faces technical and socio-political hurdles. Despite these challenges, genetic transformation remains a viable method with immense potential for the improvement of sweet potato. Key words: Sweet Potato (Ipomoea batatas Lam), Stress, Genetic Transformation, Transgeni

Genetic Improvement of African Maize towards Drought Tolerance: A Review

Africa supports a population of over 1 billion people with over half of them depending on maize for food and feed either directly or indirectly.  Maize in Africa is affected by many stresses, both biotic and abiotic which significantly reduce yields and eventually lead to poor production.  Due to the high demand for maize in the region, different improvement strategies have been employed in an effort to improve production.  These include conventional breeding, molecular breeding, high throughput phenotyping techniques and remote sensing-based techniques.  Conventional breeding techniques such as open pollination have been used to develop drought avoiding maize varieties like the Kito open pollinated variety (OPV) of Tanzania and Guto OPV of Ethiopia.  A combination of conventional breeding and molecular biology techniques has led to improved breeding strategies like the Marker Assisted Back Crossing (MABC) and Marker Assisted Recurrent Selection (MARS).  These techniques have been used to improve drought tolerance in existing inbred maize lines like the CML 247 and CML 176.  Through genetic engineering, different genes including C4-PEPC, NPK1, betA, ZmNF-YB2, cspB, ZmPLC1 and TsVP have been cloned in maize.  Transgenic maize crops expressing these genes have shown increased tolerance to drought stress.  Although there is substantial progress towards developing drought tolerant maize, many African farmers are yet to benefit from this technology.  This is due to lack of an enabling policy framework as well as a limited financial investment in biotechnology research. Keywords: Maize, Drought tolerance, Genetic engineering; Biotechnology; Transgenic crop

Detection and Profiling of Antibiotic Resistance among Culturable Bacterial Isolates in Vended Food and Soil Samples

The emergence and persistence of antibiotic resistance remain formidable health challenges. This study aimed at detecting and profiling antibiotic resistance of bacterial contaminants in vended food and the environment. Seventy antibiotic-resistant bacterial isolates were isolated from fried fish, African sausages, roasted meat, smokies, samosa, chips (potato fries), vegetable salads, and soil samples collected from Embu Town and Kangaru Market in Embu County, Kenya. The antibiotic susceptibility test, morphological and biochemical characterization, antibiosis assay, polymerase chain reaction-based detection of antibiotic resistance genes, and sequencing of the 16S rRNA gene were done. Analysis of variance on all measured data was done, and Tukey’s honest test was used to compare and separate mean diameters of zones inhibition. Resistance of bacterial isolates to antibiotics was chloramphenicol (90%), cefotaxime (84.29%), nalidixic acid (81.43%), tetracycline (77.14%), amoxicillin (72.86%), gentamycin (48.57%), streptomycin (32.86%), and trimethoprim + sulphamethoxazole (30%). Isolate KMP337, Salmonella spp., exhibited highly significant antibiosis against S. aureus recording a mean inhibition diameter and standard error (SE) of 16.33 ± 0.88 mm, respectively, at P=0.001. The 70 bacterial isolates belonged to Bacillus, Paraclostridium, Lysinibacillus, Virgibacillus, and Serratia genera. The study isolated Bacillus wiedmannii (KC75) which is a risk group 2 as well as Serratia marcescens (KMP95) and Bacillus anthracis (KS606) which are risk group 3 organisms. The presence of antibiotic resistance genes Tet A, BlaTEM, StrB, Dfr A, Amp, and FloR genes was confirmed by a polymerase chain reaction. Samples from Kangaru Market recorded a higher (88.57%) proportion of resistant isolates as compared to isolates from Embu Town (11.43%). The study confirmed the presence of antibiotic-resistant bacteria in vended fast food and the soil in Embu Town and Kangaru Market. This study calls for continuous monitoring of bacterial status and hygienic handling of vended food

Phenotypic Diversity of Doum Palm (Hyphaene compressa), a Semi‐Domesticated Palm in the Arid and Semi‐Arid Regions of Kenya

Hyphaene compressa is an economically important palm in Africa. Despite its significant role in the livelihoods of rural communities, the diversity of doum palm is poorly documented and studied. In addition, it has no model descriptor that can aid such studies. Ninety H. compressa accessions collected from Northern, Eastern, and Coastal regions of Kenya were examined to determine the morphological variability of the vegetative and fruit traits of H. compressa and to identify its morphotypes for improvement. A total of 19 morphological characters including seven quantitative and 12 qualitative traits of fruit and vegetative traits were selected. Linear mixed-effects models, principal component analysis, and linear discriminant analyses were used to assess the variation in the morphological traits of doum palm based on the regions. Hierarchical clustering was performed to identify the morphotypes of H. compressa. There was variability in H. compressa morphological traits, particularly at the Kenyan Coast. All seven quantitative traits were able to effectively discriminate doum palm phenotypically p≤0.001. The 90 accessions clustered into five morphotypes designated as 1, 2, 3, 4, and 5. Morphotype 4 was specific only to the Coastal region. Morphotype 5 had the tallest trees with the biggest fruits and included palms from Eastern and Coastal regions making it the best morphotype for fruit traits. This study will inform the domestication, improvement, and conservation of H. compressa by selecting elite accessions

Evaluation of prokaryotic diversity of five hot springs in Eritrea

Abstract Background Total community rDNA was used to determine the diversity of bacteria and archaea from water, wet sediment and microbial mats samples of hot springs in the Eastern lowlands of Eritrea. The temperatures of the springs range from 49.5 °C to 100 °C while pH levels varied from 6.97 to 7.54. Akwar and Maiwooi have high carbonate levels. The springs near the seashore, Garbanabra and Gelti, are more saline with higher levels of sodium and chlorides. Elegedi, situated in the Alid volcanic area, has the highest temperature, iron and sulfate concentrations. Results The five hot springs shared 901 of 4371 OTUs recovered while the three sample types (water, wet sediment and microbial mats) also shared 1429 OTUs. The Chao1 OTU estimate in water sample was significantly higher than the wet sediment and microbial mat samples. As indicated by NMDS, the community samples at genus level showed location specific clustering. Certain genera correlated with temperature, sodium, carbonate, iron, sulfate and ammonium levels in water. The abundant phyla included Proteobacteria (6.2–82.3%), Firmicutes (1.6–63.5%), Deinococcus-Thermus (0.0–19.2%), Planctomycetes (0.0–11.8%), Aquificae (0.0–9.9%), Chlorobi (0.0–22.3%) and Bacteroidetes (2.7–8.4%). Conclusion There were significant differences in microbial community structure within the five locations and sample types at OTU level. The occurence of Aquificae, Deinococcus-Thermus, some Cyanobacteria and Crenarchaeota were highly dependent on temperature. The Halobacterium, unclassified Thaumarchaeota, Actinobacteria and Cyanobacteria showed significant correlation with salinity occurring abundantly in Garbanabra and Gelti. Firmicutes and unclassified Rhodocylaceae were higher in the microbial mat samples, while Archaea were prominent in the wet sediment samples

Cervical Dysplasia, Infection, and Phylogeny of Human Papillomavirus in HIV-Infected and HIV-Uninfected Women at a Reproductive Health Clinic in Nairobi, Kenya

High risk human Papillomavirus (HPV) infections ultimately cause cervical cancer. Human Immunodeficiency Virus (HIV) infected women often present with multiple high-risk HPV infections and are thus at a higher risk of developing cervical cancer. However, information on the circulating high-risk HPV genotypes in Kenya in both HIV-infected and HIV-uninfected women is still scanty. This study is aimed at determining the phylogeny and the HPV genotypes in women with respect to their HIV status and at correlating this with cytology results. This study was carried out among women attending the Reproductive Health Clinic at Kenyatta National Hospital, a referral hospital in Nairobi, Kenya. A cross-sectional study recruited a total of 217 women aged 18 to 50 years. Paired blood and cervical samples were obtained from consenting participants. Blood was used for serological HIV screening while cervical smears were used for cytology followed by HPV DNA extraction, HPV DNA PCR amplification, and phylogenetic analysis. Out of 217 participants, 29 (13.4%) were HIV seropositive, while 68 (31.3%) were positive for HPV DNA. Eight (3.7%) of the participants had abnormal cervical cytology. High-risk HPV 16 was the most prevalent followed by HPV 81, 73, 35, and 52. One participant had cervical cancer, was HIV infected, and had multiple high-risk infections with HPV 26, 35, and 58. HPV 16, 6, and 81 had two variants each. HPV 16 in this study clustered with HPV from Iran and Africa. This study shows the circulation of other HPV 35, 52, 73, 81, 31, 51, 45, 58, and 26 in the Kenyan population that play important roles in cancer etiology but are not included in the HPV vaccine. Data from this study could inform vaccination strategies. Additionally, this data will be useful in future epidemiological studies of HPV in Nairobi as the introduction or development of new variants can be detected

Data from: Hepatitis B virus sero-profiles and genotypes in HIV-1 infected and uninfected injection and non-injection drug users from coastal Kenya

Background: Information about HBV sero-markers, infection stages and genotypes in HIV-1 infected and uninfected injection and non-injection drug users (IDUs) in Kenya remains elusive. Methods: A cross-sectional study examining HBV sero-marker, infection stages and genotypes was conducted among HIV-1 infected and uninfected, respectively, IDUs (n = 157 and n = 214) and non-IDUs (n = 139 and n = 48), and HIV-1 uninfected non-drug using controls (n = 194) from coastal, Kenya. HBV sero-marker and infection stages were based on HBV 5-panel rapid test plasma sero-reactivity. DNA was extracted from acute and chronic plasma samples and genotypes established by nested-PCR and direct sequencing. Results: HBsAg positivity was higher in HIV-1 infected IDUs (9.6 %) relative to HIV-1 uninfected IDUs (2.3 %), HIV-1 infected non-IDUs (3.6 %), HIV-1 uninfected non-IDUs (0.0 %) and non-drug users (2.6 %; P = 0.002). Contrastingly, HBsAb positivity was higher in HIV-1 uninfected IDUs (14.6 %) and non-IDUs (16.8) in comparison to HIV-1 infected IDUs (8.3 %), and non-IDUs (8.6 %), and non-drug users (8.2 %; P = 0.023). HBcAb positivity was higher in HIV-1 infected IDUs (10.2 %) compared to HIV-1 uninfected IDUs (3.3 %), HIV-1 infected non-IDUs (6.5 %), HIV-1 uninfected non-IDUs (2.1 %) and non-drug users (4.6 %; P = 0.038). Acute (5.7 %, 1.4 %, 0.0 %, 0.0 % and 1.5 %) and chronic (5.1 %, 0.9 %, 3.6 %, 0.0 % and 1.5 %) stages were higher in HIV-1 infected IDUs, compared to HIV-1 uninfected IDUs, HIV-1 infected and uninfected non-IDUs and non-drug users, respectively. However, vaccine type response stage was higher in HIV-1 uninfected IDUs (15.4 %) relative to HIV-1 infected IDUs (6.4 %), and HIV-1 infected (6.5 %), and uninfected (10.4 %) non-IDUs, and non-drug users (5.7 %; P = 0.003). Higher resolved infection rates were also recorded in HIV-1 uninfected IDUs (11.2 %) compared to HIV-1 infected IDUs (8.3 %), and HIV-1 infected (7.2 %), uninfected (6.3 %) non-IDUs, and non-drug users (6.7 %; P = 0.479), respectively. Only A1 genotype showing minimal diversity was detected among the study participants. Conclusion: HBV sero-markers and infection staging are valuable in diagnosis and genotyping of HBV infections. Among IDUs, higher HBsAg and HBcAb positivity in HIV-1 infected and higher HBsAb positivity in HIV-1 negative IDUs suggests frequent exposure. Additionally, HBV genotype A is the dominant circulating genotype in both high and low risk populations of Kenya

Hepatitis B virus sero-profiles and genotypes in HIV-1 infected and uninfected injection and Non-injection drug users from coastal Kenya

AbstractBackground: Information about HBV sero-markers, infection stages and genotypes in HIV-1 infected and uninfectedinjection and non-injection drug users (IDUs) in Kenya remains elusive.Methods: A cross-sectional study examining HBV sero-marker, infection stages and genotypes was conductedamong HIV-1 infected and uninfected, respectively, IDUs (n = 157 and n = 214) and non-IDUs (n = 139 and n = 48),and HIV-1 uninfected non-drug using controls (n = 194) from coastal, Kenya. HBV sero-marker and infection stageswere based on HBV 5-panel rapid test plasma sero-reactivity. DNA was extracted from acute and chronic plasmasamples and genotypes established by nested-PCR and direct sequencing.Results: HBsAg positivity was higher in HIV-1 infected IDUs (9.6 %) relative to HIV-1 uninfected IDUs (2.3 %), HIV-1infected non-IDUs (3.6 %), HIV-1 uninfected non-IDUs (0.0 %) and non-drug users (2.6 %; P = 0.002). Contrastingly,HBsAb positivity was higher in HIV-1 uninfected IDUs (14.6 %) and non-IDUs (16.8) in comparison to HIV-1 infectedIDUs (8.3 %), and non-IDUs (8.6 %), and non-drug users (8.2 %; P = 0.023). HBcAb positivity was higher in HIV-1infected IDUs (10.2 %) compared to HIV-1 uninfected IDUs (3.3 %), HIV-1 infected non-IDUs (6.5 %), HIV-1 uninfectednon-IDUs (2.1 %) and non-drug users (4.6 %; P = 0.038). Acute (5.7 %, 1.4 %, 0.0 %, 0.0 % and 1.5 %) and chronic(5.1 %, 0.9 %, 3.6 %, 0.0 % and 1.5 %) stages were higher in HIV-1 infected IDUs, compared to HIV-1 uninfectedIDUs, HIV-1 infected and uninfected non-IDUs and non-drug users, respectively. However, vaccine type responsestage was higher in HIV-1 uninfected IDUs (15.4 %) relative to HIV-1 infected IDUs (6.4 %), and HIV-1 infected(6.5 %), and uninfected (10.4 %) non-IDUs, and non-drug users (5.7 %; P = 0.003). Higher resolved infection rateswere also recorded in HIV-1 uninfected IDUs (11.2 %) compared to HIV-1 infected IDUs (8.3 %), and HIV-1 infected(7.2 %), uninfected (6.3 %) non-IDUs, and non-drug users (6.7 %; P = 0.479), respectively. Only A1 genotype showingminimal diversity was detected among the study participants.Conclusion: HBV sero-markers and infection staging are valuable in diagnosis and genotyping of HBV infections.Among IDUs, higher HBsAg and HBcAb positivity in HIV-1 infected and higher HBsAb positivity in HIV-1 negativeIDUs suggests frequent exposure. Additionally, HBV genotype A is the dominant circulating genotype in both highand low risk populations of Kenya

Potential human pathogenic bacteria in five hot springs in Eritrea revealed by next generation sequencing

<div><p>Human pathogens can survive and grow in hot springs. For water quality assessment, <i>Escherichia coli</i> or <i>Enterococci</i> are the main thermotolerant enteric bacteria commonly used to estimate the load of pathogenic bacteria in water. However, most of the environmental bacteria are unculturable thus culture methods may cause bias in detection of most pathogens. Illumina sequencing can provide a more comprehensive and accurate insight into environmental bacterial pathogens, which can be used to develop better risk assessment methods and promote public health awareness. In this study, high-throughput Illumina sequencing was used to identify bacterial pathogens from five hot springs; Maiwooi, Akwar, Garbanabra, Elegedi and Gelti, in Eritrea. Water samples were collected from the five hot springs. Total community DNA was extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4—V7) of the extracted DNA was amplified and library construction done according to Illumina sequencing protocol. The sequence reads (length >200 bp) from Illumina sequencing libraries ranged from 22,091 sequences in the wet sediment sample from Garbanabra to 155,789 sequences in the mat sample from Elegedi. Taxonomy was assigned to each OTU using BLASTn against a curated database derived from GreenGenes, RDPII, SILVA SSU Reference 119 and NCBI. The proportion of potential pathogens from the water samples was highest in Maiwooi (17.8%), followed by Gelti (16.7%), Akwar (13.6%) and Garbanabra (10.9%). Although the numbers of DNA sequence reads from Illumina sequencing were very high for the Elegedi (104,328), corresponding proportion of potential pathogens very low (3.6%). Most of the potential pathogenic bacterial sequences identified were from <i>Proteobacteria</i> and <i>Firmicutes</i>. <i>Legionella</i> and <i>Clostridium</i> were the most common detected genera with different species. Most of the potential pathogens were detected from the water samples. However, sequences belonging to <i>Clostridium</i> were observed more abundantly from the mat samples. This study employed high-throughput sequencing technologies to determine the presence of pathogenic bacteria in the five hot springs in Eritrea.</p></div