Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm ( Phoenix dactylifera L.) cultivars

Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm ( Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia. Results: Ninety-three novel simple sequence repeat markers were developed and screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs were dinucleotide, 25% tri, 3% tetra and 1% penta nucleotide motives. Twenty-two primers generated a total of 91 alleles with a mean of 4.14 alleles per locus and 100% polymorphism percentage. A 0.595 average polymorphic information content and 0.662 primer discrimination power values were recorded. The expected and observed heterozygosities were 0.676 and 0.763 respectively. Pair-wise similarity values ranged from 0.06 to 0.89 and the overall cultivars averaged 0.41. The UPGMA cluster analysis recovered by principal coordinate analysis illustrated that cultivars tend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) revealed that genetic variation among and within cultivars were 27% and 73%, respectively according to geographical distribution of cultivars. Conclusions: The developed microsatellite markers are additional values to date palm characterization tools that can be used by researchers in population genetics, cultivar identification as well as genetic resource exploration and management. The tested cultivars exhibited a significant amount of genetic diversity and could be suitable for successful breeding program. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

Assessment of laboratory test utilization for HIV/AIDS care in urban ART clinics of Lilongwe, Malawi

Background The 2011 Malawi HIV guidelines promote CD4 monitoring for pre-ART assessment and considering HIVRNA monitoring for ART response assessment, while some clinics used CD4 for both. We assessed clinical ordering practices as compared to guidelines, and determined whether the samples were successfully and promptly processed. Methods We conducted a retrospective review of all patients seen in from August 2010 through July 2011,, in two urban HIV-care clinics that utilized 6-monthly CD4 monitoring regardless of ART status. We calculated the percentage of patients on whom clinicians ordered CD4 or HIVRNA analysis. For all samples sent, we determined rates of successful labprocessing, and mean time to returned results. Results Of 20581 patients seen, 8029 (39%) had at least one blood draw for CD4 count. Among pre-ART patients, 2668/2844 (93.8%) had CD4 counts performed for eligibility. Of all CD4 samples sent, 8082/9207 (89%) samples were successfully processed. Of those, mean time to processing was 1.6 days (s.d 1.5) but mean time to results being available to clinician was 9.3 days (s.d. 3.7). Regarding HIVRNA, 172 patients of 17737 on ART had a blood draw and only 118/213 (55%) samples were successfully processed. Mean processing time was 39.5 days (s.d. 21.7); mean time to results being available to clinician was 43.1 days (s.d. 25.1). During the one-year evaluated, there were multiple lapses in processing HIVRNA samples for up to 2 months. Conclusions Clinicians underutilize CD4 and HIVRNA as monitoring tools in HIV care. Laboratory processing failures and turnaround times are unacceptably high for viral load analysis. Alternative strategies need to be considered in order to meet laboratory monitoring needs.

Assessment of Risk Factors and Prognosis in Asphyxiated Infants

Background: Asphyxia is considered an important cause of morbidity and mortality in neonates. This condition can affect many vital organs including the central nervous system and may eventually lead to death or developmental disorders. Objectives: Considering the high prevalence of asphyxia and its adverse consequences, the present study was conducted to evaluate the risk factors for birth asphyxia and assess their correlation with prognosis in asphyxiated infants. Patients and Methods: This two-year follow-up cohort study was conducted on 260 infants (110 asphyxiated infants and 150 healthy neonates) at Mashhad Ghaem Hospital during 2007 - 2014. Data collection tools consisted of a researcher-designed questionnaire including maternal and neonatal information and clinical/laboratory test results. The subjects were followed-up, using Denver II test for 6, 12, 18, and 24 months (after discharge). For data analysis, t-test was performed, using SPSS version 16.5. P value ≤ 0.05 was considered statistically significant. Results: Of 260 neonates, 199 (76.5%) and 61 (23.5%) cases presented with normal neonatal outcomes and with abnormal neonatal outcomes (developmental delay), respectively. Variables such as the severity of asphyxia (P = 0.000), five-minute Apgar score (P = 0.015), need for ventilation (P = 0.000), and severity of acidosis at birth (P = 0.001) were the major prognostic factors in infants with asphyxia. Additionally, prognosis was significantly poorer in boys and infants with dystocia history (P = 0.000). Conclusions: Prevalence of risk factors for developmental delay including the severity of asphyxia need for mechanical ventilation, and severity of acidosis at birth, dystocia, and Apgar score were lower in surviving infants; therefore, controlling these risk factors may reduce asphyxia-associated complications.