Browsing by Author "Bimenya, Gabriel S."

Now showing 1 - 5 of 5
  • Thumbnail Image
    Item
    Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues
    (Analytical biochemistry, 2010) Okello, John B.A.; Zurek, Jaymi; Devault, Alison M.; Kuch, Melanie; Okwi, Andrew L.; Sewankambo, Nelson K.; Bimenya, Gabriel S.; Poinar, Debi; Poinar, Hendrik N.
    Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13 years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen’s WaxFree method and our in-house phenol–chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion’s RecoverAll method recovered the most amplifiable RNA.
  • Thumbnail Image
    Item
    Monitoring the severity of iodine deficiency disorders in Uganda
    (African Health Sciences, 2002) Bimenya, Gabriel S.; Okui, Olico; Kaviri, Dentos; Mbona, Nazarius; Byarugaba, Wilson
    Iodine deficiency disorders (IDD) cover a variety of pathological conditions including goitre, mental retardation and perinatal mortality in millions of individuals globally. IDD was initially identified as a problem in 1970 and was confirmed in 1991. In 1993, the Uganda government introduced a policy of Universal Salt Iodization (USI) requiring all household salt to be iodized. After 5 years this study evaluates the USI programme. Objectives: To determine goitre prevalence rate, establish the proportion of household consuming iodized salt and determine the levels of iodine intake in the sample districts. Methods: A sample of 2880 school children aged 6-12 years from 72 Primary schools in 6 districts of Uganda was studied in October 1999. Goitre was established by palpation, salt iodine was analysed by thiosulphate titration, while urinary iodine was analyzed using ICCIDD recommended method F in which iodine is detected colorimetrically at 410nm. Results: The over all total goitre rate was 60.2% down from 74.3 in 1991 and visible goitre was 30% down from 39.2% in 1991. The propotion of households taking adequately iodized salt was 63.8% and the median urinary iodine was 310μg/L. Whereas 36% of 95 urine samples analysed in 1991 had urinary iodine below 50μg/L, only 5% of the 293 urine samples studied in 1999 had the same urine levels. This represents a considerable improvement in iodine intake which is confirmed by the fact that 63.8% of the study households consume adequately iodized salt. If maintained and evenly spread, this will enable Uganda to control IDD. Conclusion: USI has improved iodine intake in Uganda. However, iodine malnutrition is still a severe public health problem because some communities in this study such as in Kisoro still have low iodine consumption, while others such as Luwero now have iodine excess. The latter is likely to predispose to hyperthyroidism.
  • Thumbnail Image
    Item
    Phytochemicals and uses of Moringa oleifera leaves in Ugandan rural communities
    (Journal of Medicinal Plants Research, 2010) Kasolo, Josephine N.; Bimenya, Gabriel S.; Ojok, Lonzy; Ochieng, Joseph; Ogwal-Okeng, Jasper W.
    Moringa oleifera grown and used in many countries around the world is a multi-purpose tree with medicinal, nutritional and socio-economic values. In Senegal and Benin, M. oleifera leaves are dispensed as powder at health facilities to treat moderate malnutrition in children. It established the medicinal uses of M. oleifera leaves by local communities in Uganda and identified phytochemicals present in M. oleifera leaves extracts. It used quantitative and experimental methods that established the uses, and identified phytochemicals in M. oleifera leaves. Employed serial extractions, using ether, ethanol and water as solvents. The phytochemicals were qualitatively identified using standard chemicals and standard outcomes. Twenty-four medicinal uses of M. oleifera leaves were established. Phytochemicals present included: tannins, steroids and triterpenoids, flavonoids, saponins, anthraquinones, alkaloids and reducing sugars. The local communities in Uganda use M. oleifera leaves to treat common ailments. Presence of phytochemicals in the extracts, indicate possible preventive and curative property of M. oleifera leaves. There is need to standardize M. oleifera leaves use for nutrition and herbal medicine.
  • Thumbnail Image
    Item
    Quantitative Assessment of the Sensitivity of Various Commercial Reverse Transcriptases Based on Armored HIV RNA
    (PLoS ONE, 2010) Okello, John B. A.; Rodriguez, Linda; Poinar, Debi; Bos, Kirsten; Okwi, Andrew L.; Bimenya, Gabriel S.; Sewankambo, Nelson K.; Henry, Kenneth R.; Kuch, Melanie; Poinar, Hendrik N.
    The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues. Methodology/Principal Findings: We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ,1,000 copies, seven of which were sensitive to ,100 copies, while only 5 were sensitive to ,10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays. Conclusions/Significance: We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation.
  • Thumbnail Image
    Item
    The reference range of serum magnesium substance concentration among healthy young adults at Makerere University College of Health Sciences 2012
    (Tanzania Journal of Health Research, 2012) Bimenya, Gabriel S.; Okot, Julius; Othieno, Emmanuel; Kyokunda, Lynnette T.; Ibingira, Charles; Okwi, Andrew L.
    Magnesium is the second most abundant intracellular cation, with only a small proportion of the body’s content being in the extracellular fluid. It is required for the active transport of other cations such as calcium, sodium and potassium across the membrane by active transport system. It is also needed for many intracellular metabolic pathways. This study was carried to establish the reference intervals for serum magnesium substance concentration among healthy medical students in Uganda.