Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs

<p>Abstract</p> <p>Background</p> <p>Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of these intersubtype HIV-1 recombinants still require further investigation. All intersubtype HIV-1 recombinants are generated and evolve from initial dual infections, but are difficult to identify in the human population. In vitro studies provide the most practical system to study mechanisms, but the recombination rates are usually very low in dual infections with primary HIV-1 isolates. This study describes the use of HIV-1 isolate-specific siRNAs to enrich intersubtype HIV-1 recombinants and inhibit the parental HIV-1 isolates from a dual infection.</p> <p>Results</p> <p>Following a dual infection with subtype A and D primary HIV-1 isolates and two rounds of siRNA treatment, nearly 100% of replicative virus was resistant to a siRNA specific for an upstream target sequence in the subtype A envelope (<it>env</it>) gene as well as a siRNA specific for a downstream target sequence in the subtype D <it>env </it>gene. Only 20% (10/50) of the replicating virus had nucleotide substitutions in the siRNA-target sequence whereas the remaining 78% (39/50) harbored a recombination breakpoint that removed both siRNA target sequences, and rendered the intersubtype D/A recombinant virus resistant to the dual siRNA treatment. Since siRNAs target the newly transcribed HIV-1 mRNA, the siRNAs only enrich intersubtype env recombinants and do not influence the recombination process during reverse transcription. Using this system, a strong bias is selected for recombination breakpoints in the C2 region, whereas other HIV-1 env regions, most notably the hypervariable regions, were nearly devoid of intersubtype recombination breakpoints. Sequence conservation plays an important role in selecting for recombination breakpoints, but the lack of breakpoints in many conserved env regions suggest that other mechanisms are at play.</p> <p>Conclusion</p> <p>These findings show that siRNAs can be used as an efficient in vitro tool for enriching recombinants, to facilitate further study on mechanisms of intersubytpe HIV-1 recombination, and to generate replication-competent intersubtype recombinant proteins with a breadth in HIV-1 diversity for future vaccine studies.</p

Combine selection for earliness and yield in pedigree developed sorghum (sorghum bicolor l. Moench) progenies in eritrea

Thirteen progenies of sorghum (Sorghum bicolor L. Moench) crosses (Amal and ICSV 91078) that selected using pedigree breeding method, were evaluated along with their parental checks to obtain information on yield potential, earliness, genetic and morphological diversity. The genotypes were evaluated in randomized block design with three replications for three years (2007-2009) at Halhale research center. Significant mean squares were obtained for almost all characters in the individual analysis of variance as well as the combined analysis across seasons, suggesting that, these sorghum genotypes were highly variable for almost all the characters studied, therefore, would respond to selection. Mean values for the combined analysis of the progenies showed that Hal-1-1, Hal-4-9, Hal-13-33, Hal-11-30 and Hal-9-24 were promising cultivars in terms of grain yield and earliness. Combined analyses also showed most characters had relatively higher genotypic and phenotypic variance components and little difference between phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) indicating their variation has a genetic origin that can be exploited for further breeding programs. The genotypes also exhibited varying degrees of heritability estimates. Characters such as plant height, days to 50 % flowering and grain yield responded positively to selection because of high broad sense heritability estimates. High heritability and genetic advance was noted for plant height and days to 50% flowering indicating that these parameters were under additive gene effect and responded well for genetic improvement. However, grain weight showed high heritability with low genetic advance indicating that the trait has non additive gene action and might respond well due to its heterosis

Screening pearl millet against Eritrean isolates of downy mildew

Following the downy mildew survey in 2000, a unique scientific collaboration between Eritrea, ICRISAT and the Centre for Ariz Zone Studies (CAZS) at Bangor, Wales, UK, has produced valuable data on the resistance of 70 pearl millet genotypes to an Eritrean isolate of the pathogen (Sclerospora graminicola). Screening of the genotypes, which included Eritrean landraces and promising new cultivars from ICRISAT populations, was done in a tropical greenhouse at the CAZS. Susceptible control genotypes 7042(S) and HB 3 showed approximately 50% infection (rather less than expected), and the resistant control genotype P 7-3 proved surprisingly susceptible to this isolate of the pathogen. The Bultug Keren landrace was particularly susceptible with an overall mean infection of 79.5%. Three introduced male-sterile lines (ICMA 98333, ICMA 92444 and ICMA 00888) had 0% infection, while three other introductions (ICMA 99111, P 1449-2 and P 310-17B) showed <2% downy mildew incidence

Marker-assisted introgression improves Striga resistance in an Eritrean Farmer-Preferred Sorghum Variety

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC3F2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC3F3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC3F3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement

Topcross hybrids as an entry into commercial seed production of pearl millet in Eastern Africa

Pearl millet topcross hybrids (inbred male-sterile seed parent × open-pollinated variety restorer) based on locally adapted varieties and publicly available seed parents provide an ideal entry point into the commercial hybrid seed business, which can stimulate commercial investment by prospective seed producers. To demonstrate this potential, fifteen topcross hybrids made with the widely adapted variety ICMV 221 were evaluated in Eritrea, Sudan and Kenya for overall field performance, and in India for mechanisms of expression of heterosis and for terminal drought tolerance. Across all evaluation environments, the mean yield heterosis was 8%, with a range of -1% to +19%; six hybrids had a statistically significant, positive across-environment yield heterosis (ranging from +11% to +19%). Significant grain yield heterosis in rainy season environments was a consequence of heterosis in both biomass and harvest index, but not necessarily in any specific yield component. Positive grain yield heterosis under terminal drought stress, a common occurrence in millet-growing environments, was related to positive heterosis for grain size. These results are discussed in terms of their support for topcross hybrids as an entry point for prospective millet seed producers, and a scheme presented for the rapid creation, evaluation and marketing of locally adapted topcross hybrid

Water productivity improvement of cereals and foods legumes in the Atbara Basin of Eritrea

The project ‘Water Productivity Improvement of Cereals and Food Legumes in the Atbara Basin of Eritrea’ is an example of organization and implementation of farmers’ participatory research, conducted utilizing the available indigenous knowledge while empowering farming communities. Farmers have been partners in technology development with extension and research, with full decision-making power in planning, implementation, monitoring, and evaluation. The project produced, in partnership with farmers, new varieties of cereals and food legumes which have proven farmer acceptability; established seed systems which supply farmers with quality seed in a sustainable manner; enhanced farmers’ skills in participatory research and in community based seed production; strengthened the capacity of National Institutions to carry out participatory research and technology transfer, and strengthened linkages between research, seed, and extension departments by working together in cooperation with farmers and farmers’ communities. Working conditions, during the course of the project were not always easy and became challenging towards the end of the project, but to work with farmers and learn from them has been an extremely rewarding experience

Unraveling the effects of management and climate on carbon fluxes of U.S. croplands using the USDA Long-Term Agroecosystem (LTAR) network

Understanding the carbon fluxes and dynamics from a broad range of agricultural systems has the potential to improve our ability to increase carbon sequestration while maintaining crop yields. Short-term, single-location studies have limited applicability, but long-term data from a network of many locations can provide a broader understanding across gradients of climate and management choices. Here we examine eddy covariance measured carbon dioxide (CO2) fluxes from cropland sites across the United States Department of Agriculture’s Long-Term Agroecosystem Research (LTAR) network. The dataset was collected between 2001 and 2020, spanning 13 sites for a total of 182 site-years. Average seasonal patterns of net ecosystem CO2 exchange (NEE), gross primary productivity (GPP), and ecosystem respiration (Reco) were determined, and subsequent regression analysis on these “flux climatologies” was used to identify relationships to mean annual temperature (MAT), mean annual precipitation (MAP), cropping systems, and management practices. At rainfed sites, carbon fluxes were better correlated with MAP (r2 ≤ 0.5) than MAT (r2 ≤ 0.22). Net carbon balance was different among cropping systems (p \u3c 0.001), with the greatest net carbon uptake occurring in sugarcane (Saccharum spp. hybrids) and the least in soybean (Glycine max) fields. Crop type had a greater effect on carbon balance than irrigation management at a Nebraska site. Across cropping systems, grain crops often had higher GPP and were more likely to have net uptake when compared to legume crops. This multi-site analysis highlights the potential of the LTAR network to further carbon flux research using eddy covariance measurements

From Farm to Kitchen : How gender affects production diversity and the dietary intake of farm households in Ethiopia

Open Access via the Wiley Jisc Open Access Agreement. We would like to acknowledge the World Bank LSMS-ISA and Central Statistical Authority (CSA) of Ethiopia for making these data available for the public and Macaulay Development Trust (MDT) for the financial support. Euan Phimister also acknowledges support under the ESRC NEXUS programme in project IEAS/POO2501/1, Improving organic resource use in rural Ethiopia (IPORE). Deborah Roberts acknowledges the support of funding from the Scottish Government's Rural and Environment Science and Analytical Services Division(RESAS). Our thanks are also due to anonymous reviewers for their constructive comments on earlier versions of the paper.Peer reviewedPublisher PD