Microsatellite Development and Application in Pigeonpea (<i>Cajanus cajan </i>(L.) Millsp.)

Pigeonpea is a major legume crop grown in the semi-arid tropics but has been relatively neglected in terms of genomic research. This study aimed at developing molecular markers as a basic requirement towards initiating marker assisted breeding techniques in pigeonpea. Simple Sequence Repeat (SSR) loci of pigeonpea were isolated by screening non-enriched (library A) and enriched (library B) partial genomic libraries with SSR probes. Positive clones were sequenced and primers designed for 152 microsatellite loci, 39 from library A and 113 from library B. Optimisation of reaction conditions was achieved for 51% and 65% of primers designed from library A and B, respectively. For the purpose of exploiting the transferability of SSRs across genera within the legume species, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands. Nineteen out of 20 amplified primers from library A were polymorphic among 15 cultivated and 9 wild species. The diversity analysis revealed contrasted levels of variability within cultivated and wild accessions. A total of 98 alleles were detected at the 19 polymorphic loci with an average of 4.9 alleles per locus while the observed heterozygosity ranged from 0.17 – 0.80 with a mean of 0.42 per locus. Substantially less allelic variation (31 alleles) was observed within the cultivated species than across the wild species (92 alleles). Primers from library B were not tested for amplification in wild species but 35 out of the amplified 73 revealed polymorphism among 24 pigeonpea genotypes. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. Only one of the 39 amplified soybean primers revealed polymorphism among 24 cultivated pigeonpea accessions. No significant relationship was detected between the class of repeats and heterozygosity values. AT and TG class of repeats were the most abundant di-nucleotide repeats in library A and B respectively while TAA and GAA were the most abundant trinucleotide repeats in both libraries. Protein database searches provided putative functions for 21 SSR-containing pigeonpea sequences that would be useful in functional marker development. UPGMA and MDS cluster analysis revealed genetic relationships among recently bred varieties, old varieties and wild accessions. Nine of the markers developed were polymorphic to the parental lines of a F6 Fusarium wilt RIL mapping population that had been developed by ICRISAT breeders. Analysis of allele segregation in the RIL population revealed that all the 9 SSRs segregated in the expected 1:1 ratio and were further tested for any possible linkage with a QTL for resistance to Fusarium wilt. All the polymorphic markers derived from this study are now being used for characterisation and evaluation of pigeonpea germplasm collection at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) headquarters, India. SSRs provide a powerful tool for genomic studies and are recommended for systematic fingerprinting of pigeonpea germplasm

Sensory Attributes of Coffee under Different Shade Regimes and Levels of Management

Despite coffee bean physical and beverage quality attributes being inherent factors, the environment, which includes crop management factors, can play a major role in determining their expression. This study was conducted to evaluate the effect of management and shade levels on beverage quality of coffee. The study was carried out at the Kenya Agricultural and Livestock Research Organization, Coffee Research Institute (KALRO-CRI) farm in Bungoma County, Kenya. The coffee management levels were categorized depending on field operations and application of inputs. The different shade levels were based on the distances from the trunk of shade tree and shading levels were estimated by measuring the Photosynthetic Photon Flux Density (PPFD) in µmol m-2 s-1 using a Line Quantum Sensor. The sensory characteristics fragrance/aroma, flavor, aftertaste, acidity, body, balance and overall were assessed by a panel of seven trained judges. The beverage quality, except for acidity and balance, were largely unaffected by management or shade levels, however trends showed that most of the variables, on average, had higher scores in shade than in full sun. Shade was positively correlated with all sensory variables while management was negatively correlated with all. This suggested that use of shade, under low management, could offset the limited application of external inputs to some extent. Keywords: Coffea arabica, shade, management levels and quality

Integration of HIV Care with Primary Health Care Services: Effect on Patient Satisfaction and Stigma in Rural Kenya.

HIV departments within Kenyan health facilities are usually better staffed and equipped than departments offering non-HIV services. Integration of HIV services into primary care may address this issue of skewed resource allocation. Between 2008 and 2010, we piloted a system of integrating HIV services into primary care in rural Kenya. Before integration, we conducted a survey among returning adults ≥18-year old attending the HIV clinic. We then integrated HIV and primary care services. Three and twelve months after integration, we administered the same questionnaires to a sample of returning adults attending the integrated clinic. Changes in patient responses were assessed using truncated linear regression and logistic regression. At 12 months after integration, respondents were more likely to be satisfied with reception services (adjusted odds ratio, aOR 2.71, 95% CI 1.32-5.56), HIV education (aOR 3.28, 95% CI 1.92-6.83), and wait time (aOR 1.97 95% CI 1.03-3.76). Men's comfort with receiving care at an integrated clinic did not change (aOR = 0.46 95% CI 0.06-3.86). Women were more likely to express discomfort after integration (aOR 3.37 95% CI 1.33-8.52). Integration of HIV services into primary care services was associated with significant increases in patient satisfaction in certain domains, with no negative effect on satisfaction

Comparison and Prediction of the above Ground Carbon Storage in Croplands on the Inhabited Slopes on Mount Kilimanjaro (Tanzania) and the Taita Hills (Kenya)

Mount Kilimanjaro and the Taita Hills are adjacent montane areas that experience similar climate and agricultural activity, but which differ in their geologic history, nature of elevation gradients and cultures. We assessed differences in cropland above ground carbon (AGC) between the two sites and against environmental variables. One hectare sampling plots were randomly distributed along elevational gradients stratified by cropland type; AGC was derived from all trees with diameter ≥ 10 cm at breast height in each plot. Predictor variables were physical and edaphic variables and human population. A generalized linear model was used for predicting AGC with AIC used for ranking models. AGC was spatially upscaled in 2 km buffer and visually compared. Kilimanjaro has higher AGC in cropped and agroforestry areas than the Taita Hills, but only significant difference in AGC variation in agroforestry areas (F = 9.36, p = 0.03). AGC in cropped land and agroforestry in Kilimanjaro has significant difference on mean (t = 4.62, p = 0.001) and variation (F = 17.41, p = 0.007). In the Taita Hills, significant difference is observed only on the mean AGC (t = 4.86, p = 0.001). Common tree species that contribute the most to AGC in Kilimanjaro are Albizia gummifera and Persea americana, and in the Taita Hills Grevillea robusta and Mangifera indica . Significant and univariate predictors of AGC in Mount Kilimanjaro are pH (R2 = 0.80, p = 0.00) and EVI (R2 = 0.68, p = 0.00). On Mount Kilimanjaro, the top multivariate model contained SOC, CEC, pH and BLD (R2 = 0.90, p = 0.00), whereas in the Taita Hills, the top multivariate model contained elevation, slope and population (R2 = 0.89, p = 0.00). Despite of the difference in land management history of Mount Kilimanjaro and the Taita Hills, mean of AGC in croplands does not differ significantly. Difference occurs on variation of AGC, type of trees contributing AGC, and environmental variables that explain AGC distribution. The research results provide reference for management of carbon sequestration on inhabited montane areas.Peer reviewe

New microsatellite markers for pigeonpea (cajanus cajan (L.) millsp.)

<p>Abstract</p> <p>Background</p> <p>Pigeonpea is a nutritious tropical legume with several desirable characteristics but has been relatively neglected in terms of research. More efficient improvement can be achieved in this crop through molecular breeding but adequate molecular markers are lacking and no linkage map has been developed so far. Microsatellites remain the markers of choice due to their high polymorphism and their transferability from closely related genera. The overall objective of this study was to develop microsatellite markers from an enriched library of pigeonpea as well as testing the transferability of soybean microsatellites in pigeonpea.</p> <p>Results</p> <p>Primers were designed for 113 pigeonpea genomic SSRs, 73 of which amplified interpretable bands. Thirty-five of the primers revealed polymorphism among 24 pigeonpea breeding lines. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. GT/CA and GAA class of repeats were the most abundant di-nucleotide and tri-nucleotide repeats respectively. Additionally, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands.</p> <p>Conclusion</p> <p>Despite the observed morphological diversity, there is little genetic diversity within cultivated pigeonpea as revealed by the developed microsatellites. Although some of the tested soybean microsatellites may be transferable to pigeonpea, lack of useful polymorphism may hinder their full use. A robust set of markers will still have to be developed for pigeonpea genome if molecular breeding is to be achieved.</p

A youth-centred approach to improving engagement in HIV services: Human-centred design methods and outcomes in a research trial in Kisumu County, Kenya

UNLABELLED: IntroductionInnovative interventions are needed to improve HIV outcomes among adolescents and young adults (AYAs) living with HIV. Engaging AYAs in intervention development could increase effectiveness and youth acceptance, yet research is limited. We applied human-centred design (HCD) to refine adherence-support interventions pretrial and assessed HCD workshop acceptability. METHODS: We applied an iterative, four-phased HCD process in Kenya that included: (1) systematic review of extant knowledge, (2) prioritisation of design challenges, (3) a co-creation workshop and (4) translation tables to pair insights with trial intervention adaptations. The co-creation workshop was co-led by youth facilitators employing participatory activities to inform intervention adaptations. Iterative data analysis included rapid thematic analysis of visualised workshop outputs and notes using affinity mapping and dialogue to identify key themes. We conducted a survey to assess workshop acceptability among participants. RESULTS: Twenty-two participants engaged in the 4-day workshop. Co-creation activities yielded recommendations for improving planned interventions (eg, message frequency and content; strategies to engage hard-to-reach participants), critical principles to employ across interventions (eg, personalisation, AYA empowerment) and identification of unanticipated AYA HIV treatment priorities (eg, drug holidays, transition from adolescent to adult services). We revised intervention content, peer navigator training materials and study inclusion criteria in response to findings. The youth-led HCD workshop was highly acceptable to participants. CONCLUSIONS: Research employing HCD among youth can improve interventions preimplementation through empathy, youth-led inquiry and real-time problem solving. Peer navigation may be most influential in improving retention when engagement with young people is based on mutual trust, respect, privacy and extends beyond HIV-specific support. Identifying opportunities for personalisation and adaptation within intervention delivery is important for AYAs. Patient engagement interventions that target young people should prioritise improved transition between youth and adult services, youth HIV status disclosure, AYA empowerment and healthcare worker responsiveness in interactions and episodic adherence interruptions

Association between Primary Perioperative CEA Ratio, Tumor Site, and Overall Survival in Patients with Colorectal Cancer

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.There are differences in the incidence, clinical presentation, molecular pathogenesis, and outcome of colorectal cancer (CRC) based on tumor location. Emerging research suggests that the perioperative carcinoembryonic antigen (CEA) ratio (post-op/pre-op CEA) is a prognostic factor for CRC patients. We aimed to determine the association between CEA ratio, tumor location, and overall survival (OS) among patients with CRC. We analyzed 427 patients who underwent resection for CRC at the University of Kansas Medical Center. After excluding those without pre- or post-operative CEA data, 207 patients were classified as either high (≥0.5) or low ( 5 ng/mL at the time of recurrence. The Kaplan–Meier method was used to estimate survival rates. The median age was 62 years (inter-quartile range 51–71), 55% were male, 41% were smokers, 71% had left-sided tumors, the median pre-operative CEA was 3.1 ng/mL (inter-quartile range (IQR) 1.5–9.7), and 57% had a CEA ratio ≥0.5. The OS rates were 65.1% and 86.3% in patients with high versus low CEA ratios, respectively (log-rank p-value = 0.045). The OS rates were 64.4% and 77.3% in patients with right-sided vs. left-sided tumors, respectively (log-rank p-value = 0.5). Among patients with CEA levels greater than 5 at the time of recurrence, the OS rates were 42.9% and 43.4% in patients with right-sided vs. left-sided tumors, respectively (log-rank p-value = 0.7). There was a significantly higher survival among patients with low CEA ratios than among those with high CEA ratios. There was no difference in OS between left- versus right-sided tumors. Among patients with CEA elevation > 5 ng/mL at the time of recurrence, there was no difference in OS between left versus right-sided tumors. These findings warrant validation in a larger cohort as our sample size was limited

Genomic resources for pigeonpea

Pigeonpea is increasingly playing a critical role in the lives of many farmers in the semi-arid tropics, where it is grown for both subsistence and commercial use. The recent availability of genomic resources opened a new chapter in pigeonpea breeding and has led to a lot of progress in a relatively short period of time. Molecular markers have been developed and used for germplasm characterization. Both whole genome and transcriptome sequences have further improved our understanding of the genome. This review provides a summary of genomic resources available for pigeonpea breeding and also briefly discusses the way forward for pigeonpea improvement