Transcriptomic changes associated with husk scald incidence on pomegranate fruit peel during cold storage

CITATION: Belay, Z. A. et al. 2020. Transcriptomic changes associated with husk scald incidence on pomegranate fruit peel during cold storage. Food Research International, 135. doi:10.1016/j.foodres.2020.109285The original publication is available at https://www.sciencedirect.com/journal/food-research-internationalPomegranate fruit is valued for its social, economic, aesthetic and health benefits. The fruit rapidly loses quality after harvest due to continued metabolic responses and physiological disorders under sub-optimal conditions. The incidence of physiological disorder such as husk scald manifests during storage and commercial shipping, which affects the appearance and limits marketability. Despite the importance of pomegranate husk scald, little information is available about the origin and molecular mechanisms. Therefore, the aim of this study was to investigate the scald incidence of pomegranate fruit at molecular level using RNA-Seq (Ion Proton™ Next Generation Sequencing) by analyzing peel transcriptomic changes. The RNA-seq analysis generated 98,441,278 raw reads. 652 Differentially Expressed Genes (DEGs) with a fold change of > |2|, a p value ≤ 0.05 and a false discovery rate (FDR) of <0.05 were identified between healthy and scald fruit peels. An analysis of the gene ontologies of these DEGs revealed the 432 genes were assigned with molecular functions, 272 as cellular components and 205 as part of biological processes. In this analysis, genes (Pgr023188 and Pgr025081) that encode uncharacterized protein and gene (Pgr007593) that encodes glycosyltransferase showed significantly highest fold changes. Genes (Pgr003448, Pgr006024 and Pgr023696) involved in various iron binding and oxidoreductase activities were significantly suppressed. This is the first transcriptome analysis of pomegranate fruit peel related to husk scald development. Results obtained from this study will add valuable information on husk scald related changes on pomegranate fruit at genomic level and provide insight on other related physiological disorders.https://www.sciencedirect.com/science/article/pii/S0963996920303100?via%3DihubPublishers versio

Distinct host-immune response toward species related intracellular mycobacterial killing : a transcriptomic study

CITATION: Madhvi Abhilasha et al. 2020. Distinct host-immune response toward species related intracellular mycobacterial killing : a transcriptomic study. Virulence, 11(1):170-182, doi:10.1080/21505594.2020.1726561.The original publication is availablle at: https://www.ncbi.nlm.nih.govThe comparison of the host immune response when challenged with pathogenic and nonpatho- genic species of mycobacteria can provide answers to the unresolved question of how pathogens subvert or inhibit an effective response. We infected human monocyte derived macrophages (hMDMs) with different species of mycobacteria, in increasing order of pathogenicity, i.e. M. smegmatis, M. bovis BCG, and M. tuberculosis R179 that had been cultured in the absence of detergents. RNA was isolated post-infection and transcriptomic analysis using amplicons (Ampliseq) revealed 274 differentially expressed genes (DEGs) across three species, out of which we selected 19 DEGs for further validation. We used qRT-PCR to confirm the differential expression of 19 DEGs. We studied biological network through Ingenuity Pathway Analysis® (IPA) which revealed up-regulated pathways of the interferon and interleukin family related to the killing of M. smegmatis. Apart from interferon and interleukin family, we found one up-regulated (EIF2AK2) and two down-regulated (MT1A and TRIB3) genes as unique potential targets found by Ampliseq and qRT-PCR which may be involved in the intracellular mycobacterial killing. The roles of these genes have not previously been described in tuberculosis. Multiplex ELISA of culture supernatants showed increased host immune response toward M. smegmatis as compared to M. bovis BCG and M.tb R179. These results enhance our understanding of host immune response against M.tb infection.Publisher's versio

Genetic differentiation in Horus Chamberlin (Arachnida: Pseudoscorpiones: Olpiidae) as indicated by mitochondrial DNA analysis

Horus is an olpiid pseudoscorpion of which nine species have been described from southern Africa; a tenth, debatable species was described from the Ivory Coast. The two most widely distributed species are H. granulatus and H. obscurus, the former  occurring especially in the west and the other in the east, but their distributions overlap; in two instances they have been  recorded from the same site. All species have a preference for rock outcrops, which are largely disjunct, and their regular prey comprises small ant species. Fieldwork over a period of 15 years indicated a very low dispersal rate; therefore one would expect localized ‘island’ populations rather than widely dispersed species. This means that the current species  delimitations which lump geographically widespread populations may be incorrect. Mitochondrial DNA of specimens from each of 20 different localities across South Africa were analysed to test the hypothesis. Five of these localities did not yield results, but 14 yielded DNA from specimens which proved to belong to Horus and a fifteenth turned out to be a misidentified pseudoscorpion unrelated to Horus. The results were unequivocal: populations from each locality or group of closely-spaced localities were genetically distinct from any other one tested, and the greater the distance between localities, the greater the genetic differences (i.e. significant isolation by distance). This means that the current species delimitations for Horus are incorrect. It will require detailed micro-anatomical study to identify new characteristics on which species delimitations can be based in future.Key words: mitochondrial DNA, pseudoscorpions, Horus, genetic differentiation

The identification of novel (CA)n repeats in a microdissection library of chromosome 14q32

On t.p. 'n' in (CA)n is superscript.Thesis (M. Sc.) -- University of Stellenbosch, 1996.One copy microfiche.Full text to be digitised and attached to bibliographic record

Optimisation of automated ribosomal intergenic spacer analysis for the estimation of microbial diversity in fynbos soil

Automated ribosomal intergenic spacer analysis (ARISA) has become a commonly used molecular technique for the study of microbial populations in environmental samples. The reproducibility and accuracy of ARISA, with and without the polymerase chain reaction (PCR) are important aspects that influence the results and effectiveness of these techniques. We used the primer set ITS4/ITS5 for ARISA to assess the fungal community composition of two sites situated in the Sand Fynbos. The primer set proved to deliver reproducible ARISA profiles of the fungal community composition with little variation observed between ARISA-PCRs. Variation that occurred in a sample due to repeated DNA extraction is expected for ecological studies. This reproducibility made ARISA a useful tool for the assessment and comparison of diversity in ecological samples. In this paper, we also offered particular suggestions concerning the binning strategy for the analysis of ARISA profiles

Towards lecture transcription in resource-scarce environments

We present progress towards automated Lecture Transcription (LT) in resource scarce environments. Our development has focused on the transcription of lectures in Afrikaans from two faculties at North-West University. A bootstrapping procedure is followed to filter and select well-aligned segments of speech. These segments are then used to train acoustic models. Initial work towards language modeling for LT in a resource-scarce environment is also presented; manual lecture transcriptions are combined with text mined from other sources such as study guides to train language models. Interpolation results indicate that study guides are a useful resource for language modeling, whereas general text (obtained from a publisher of Afrikaans books) is less useful in this context. Our findings are confirmed by the reduced word error rates (WERs) obtained from our off-line speech-recognition system for Lecture Transcription.http://www.prasa.org/index.php/2012-03-07-10-55-1

Identification of an iron-responsive subtype in two children diagnosed with relapsing-remitting multiple sclerosis using whole exome sequencing

Background: Multiple sclerosis is a disorder related to demyelination of axons. Iron is an essential cofactor in myelin synthesis. Previously, we described two children (males of mixed ancestry) with relapsing-remitting multiple sclerosis (RRMS) where long-term remission was achieved by regular iron supplementation. A genetic defect in iron metabolism was postulated, suggesting that more advanced genetic studies could shed new light on disease pathophysiology related to iron. Methods: Whole exome sequencing (WES) was performed to identify causal pathways. Blood tests were performed over a 10 year period to monitor the long-term effect of a supplementation regimen. Clinical wellbeing was assessed quarterly by a pediatric neurologist and regular feedback was obtained from the schoolteachers. Results: WES revealed gene variants involved in iron absorption and transport, in the transmembrane protease, serine 6 (TMPRSS6) and transferrin (TF) genes; multiple genetic variants in CUBN, which encodes cubilin (a receptor involved in the absorption of vitamin B12 as well as the reabsorption of transferrin-bound iron and vitamin D in the kidneys); SLC25A37 (involved in iron transport into mitochondria) and CD163 (a scavenger receptor involved in hemorrhage resolution). Variants were also found in COQ3, involved with synthesis of Coenzyme Q10 in mitochondria. Neither of the children had the HLA-DRB1*1501 allele associated with increased genetic risk for MS, suggesting that the genetic contribution of iron-related genetic variants may be instrumental in childhood MS. In both children the RRMS has remained stable without activity over the last 10 years since initiation of nutritional supplementation and maintenance of normal iron levels, confirming the role of iron deficiency in disease pathogenesis in these patients. Conclusion: Our findings highlight the potential value of WES to identify heritable risk factors that could affect the reabsorption of transferrin-bound iron in the kidneys causing sustained iron loss, together with inhibition of vitamin B12 absorption and vitamin D reabsorption (CUBN) and iron transport into mitochondria (SLC25A37) as the sole site of heme synthesis. This supports a model for RRMS in children with an apparent iron-deficient biochemical subtype of MS, with oligodendrocyte cell death and impaired myelination possibly caused by deficits of energy- and antioxidant capacity in mitochondria. Keywords: Pediatric onset multiple sclerosis, Genetic variants, Whole exome sequencing, Iron deficiency, Oxidative stress, Mitochondri