The identification of the methylation patterns of tomato curly stunt virus in resistant and susceptible tomato lines

Tomato curly stunt virus (ToCSV) is a monopartite begomovirus infecting tomatoes in South Africa, with sequence similarity to tomato yellow leaf curl virus (TYLCV). While there are numerous reports on the mechanism of TYLCV resistance in tomato, the underlying mechanisms in the tomato-ToCSV pathosystem is still relatively unknown. The main aim of this study was to investigate and compare the global methylation profile of ToCSV in two near-isogenic tomato lines, one with a tolerant phenotype (T, NIL396) and one with a susceptible phenotype (S, NIL395). Bisulfite conversion and PCR amplification, coupled with a next-generation sequencing approach, were used to elucidate the global pattern of methylation of ToCSV cytosine residues in T and S leave tissue at 35 days post-infection (dpi). The extent of methylation was more pronounced in tolerant plants compared to susceptible plants in all sequence (CG, CHG and CHH) contexts, however, the overall methylation levels were relatively low (<3%). Notably, a significant interaction (p < 0.05) was observed between the viral genomic region and susceptible vs. tolerant status for CG methylated regions where it was observed that the 3'IR CG methylation was significantly (p < 0.05) higher than CG methylation of other genomic regions in tolerant and susceptible plants. Additionally, statistically significant (EdgeR p < 0.05) differentially methylated cytosines were located primarily in the genomic regions V2/V1 and C4/C1 of ToCSV. The relative expression, using RT-qPCR, was also employed in order to quantify the expression of various key methylation-related genes, MET1, CMT2, KYP4/SUVH4, DML2, RDM1, AGO4 and AGO6 in T vs. S plants at 35dpi. The differential expression between T and S was significant for MET1, KYP4/SUVH4 and RDM1 at p<0.05 which further supports more pronounced methylation observed in ToCSV from T plants vs. S plants. While this study provides new insights into the differences in methylation profiles of ToCSV in S vs. T tomato plants, further research is required to link tolerance and susceptibility to ToCSV.

How useful is post-graduate education in biochemistry for entry into the South African labour market?

Biochemistry encompasses a broad range of life science disciplines. Unlike more vocational disciplines such as pharmacy or medicine, the career path associated with biochemistry is less clearly defined. An important question is whether the skills set provided by post-graduate biochemistry education, defined as BSc (Hons.), MSc, or PhD degrees, is aligned with the requirements of a career in academia or industry. This article reports on former post-graduate biochemistry students and their careers and aims to establish whether former post-graduate students perceive a post-graduate qualification in biochemistry as useful for entry into the job market. This article is based on responses of 64 former post-graduate biochemistry students from South African universities who have graduated between 2010 and 2019. Findings show that most post-graduate biochemistry graduates continue a career in academia after graduating. Some pursue a career in the industry, while a very small number of biochemistry post-graduates are currently unemployed. These findings suggest that a post-graduate degree in biochemistry provides the necessary scientific and research skills sought after by the employment sector in South Africa.

Linker Histone H1.2 Directly Activates BAK through the K/RVVKP Motif on the C-Terminal Domain

H1.2 is a key mediator of apoptosis following DNA double-strand breaks. The link between H1.2 and canonical apoptotic pathways is unclear. One study found that H1.2 stimulates cytochrome c (Cyt c) release; in contrast, apoptosis-inducing factor was found to be released in another study. The C-terminal domain (CTD) of H1.2 has been implicated in the latter pathway, but activation of the proapoptotic protein BCL-2 homologous antagonist/killer (BAK) is a common denominator in both pathways. This study aimed to determine whether the CTD of H1.2 is also responsible for mitochondrial Cyt c release and whether a previously identified K/RVVKP motif in the CTD mediates the response. This study investigated if H1.2 mediates apoptosis induction through direct interaction with BAK. We established that the CTD of H1.2 stimulates mitochondrial Cyt c release in vitro in a mitochondrial permeability transition-independent manner and that the substitution of a single valine with threonine in the K/RVVKP motif abolishes Cyt c release. Additionally, we showed that H1.2 directly interacts with BAK with weak affinity and that the CTD of H1.2 mediates this binding. Using two 20-amino acid peptides derived from the CTD of H1.2 and H1.1 (K/RVVKP motif inclusive), we determined the main residues involved in the direct interaction with BAK. We propose that H1.2 operates through the K/RVVKP motif by directly activating BAK through inter- and intramolecular interactions. These findings expand the view of H1.2 as a signal-transducing molecule that can activate apoptosis in a BAK-dependent manner.

Docking data of selected human linker histone variants to the nucleosome

Human linker histones (H1s) are important in chromatin packaging and condensation. The central globular domain of H1 anchors the protein to the nucleosome. The nucleosomal binding modes of different H1 globular domains may affect nucleosomal DNA accessibility in distinct ways. The globular domain structures of human linker histones H1.0 (GH1.0), H1.4 (GH1.4), H1t (GH1t) and H1oo (GH1oo) were homology modelled and energy minimized. A docking algorithm [validated by re-docking GH5 from the GH5-chromatosome crystal structure (PDB: 4QLC) to the nucleosome] was used to dock the modelled domains to the same nucleosome template. In addition, GH1 (PDB: 1GHC) and a protein consisting of the N-terminal and globular domains of H1x (NGH1x) were also docked using this algorithm. Models of these docked structures are presented here in the form of PDB files. The models can be used to gain more insight with regards to the nucleosomal binding modes of H1s and their individual influence on chromatin compaction.

NMR assignments of human linker histone H1x N-terminal domain and globular domain in the presence and absence of perchlorate

Human linker histone H1 plays a seminal role in eukaryotic DNA packaging. H1 has a tripartite structure consisting of a central, conserved globular domain, which adopts a winged-helix fold, flanked by two variable N- and C-terminal domains. Here we present the backbone resonance assignments of the N-terminal domain and globular domain of human linker histone H1x in the presence and absence of the secondary structure stabilizer sodium perchlorate. Analysis of chemical shift changes between the two conditions is consistent with induction of transient secondary structural elements in the N-terminal domain of H1x in high ionic strength, which suggests that the N-terminal domain adopts significant alpha-helical conformations in the presence of DNA.

Lipid composition of human meibum

The structure and function of meibomian gland lipids in the tear film are highly complex. Evidence shows that the precorneal tear film consists of discrete layers: the inner mucin layer, the middle aqueous layer and the outer lipid layer. In this review we focus on the outer, biphasic lipid layer of the tear film which consists of a ‘thick’ outer, non-polar layer  and a ‘thin’ inner, polar layer. We discuss the main composition of the polar and non-polar lipids within meibum (wax esters, cholesteryl esters, mono-, di- and tri-acylglycerols, ceramides, phospholipids  et cetera). We address the composition of meibomian lipids in subjects suffering from various ocular diseases in comparison with the composition in healthy individuals. Further analysis is needed to determine whether a correlation exists between the etiology of various ocular diseases and the fluctuation on the lipids as well as to establish whether or not tear lipid analysis can be used as a diagnostic tool.

Immunological and antimicrobial molecules in human tears: a review and preliminary report*

The human tear film is a multi-layered and chemically complex structure, which performs numerous functions relating to the health of the corneal surface.  One of the core functions of the tear film is to protect the eye against invasion by pathogens.  Thus its middle layer, the ‘core aqueous stratum’, harbours a myriad of immunologicaland antimicrobial proteins. In this review we discuss the most abundant of these proteins (immunoglobulins, toll-like receptors, cytokines, lactoferrin, lysozyme, lipocalins, surfactant protein-Aand -D and defensins).  In order to illustrate how the levels of immunological/antimicrobial proteins in tears change in response to eye disease, we review literature in which levels of these proteins have been measured in tears of patients with dry eye disease (DED) and keratoconus (KC).  Finally, we report results of a preliminary study to measure the concentration of secretory immunoglobulin A (sIgA) in the tears of DED and KC patients. The study showed a significant decrease of sIgA levels  in DED compared to control. Further analysis must be done to determine whether or not DED and KC may be associated with differential expression of immune proteins. (S Afr Optom 2012 71(3) 123-132)

Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism

The Vitamin D receptor (VDR) gene encodes a transcription factor which, on activation by vitamin D, modulates diverse biologic processes, including calcium homeostasis and immune function. Genetic variation involving VDR shows striking differences in allele frequency between populations and has been associated with disease susceptibility, including tuberculosis and autoimmunity, although results have often been conflicting. We hypothesized that methylation of VDR may be population specific and that the combination of differential methylation and genetic variation may characterize tuberculosis (TB) predisposition. We use bisulfite conversion and/or pyrosequencing to analyze the methylation status of 17 CpGs of VDR and to genotype 7 SNPs in the 3' CpG Island (CpG island [CGI] 1060), including the commonly studied SNPs ApaI (rs7975232) and TaqI (rs731236). We show that, for lymphoblastoid cell lines from two ethnically diverse populations (Yoruba from HapMap, n = 30 and Caucasians, n = 30) together with TB cases (n = 32) and controls (n = 29) from the Venda population of South Africa, there are methylation variable positions in the 3' end that significantly distinguish ethnicity (9/17 CpGs) and TB status (3/17 CpGs). Moreover, methylation status shows complex association with TaqI genotype highlighting the need to consider both genetic and epigenetic variants in genetic studies of VDR association with disease.

Proteomics approach as a new way to predict tenderness as compared to the classical South African Beef Carcass Classification System

The current South African Beef Carcass Classification System classifies carcasses using physical attributes such as age, fatness code and the conformation of the carcass as the only indicator of tenderness, implying that optimal tender meat is obtained from carcasses from animals with no permanent teeth. Research shows that if we take modern technologies (use of beta-agonists, growth hormones and electrical stimulation amongst others) into account, this is not necessarily true. In this study m. longissimus lumborum samples were collected from Nguni breed animals, snap frozen and stored at −80 ºC for further use in search of protein markers that can be used to predict tenderness in a non-invasive manner. Proteins were extracted in 1 mL TES buffer, isoelectrically focused on strips (pH 5 - 7) and separated by 2D SDS PAGE, stained with coomassie brilliant blue G250) and imaged by a Chemi-doc Mp imager. The results showed differences in protein expression, e.g. some proteins are present at 1 hour post mortem (Day 0) but absent at 3 days post mortem (Day 3). Other proteins showed an increase in expression as ageing progresses. These proteins correlated with myofibril fragments and Warner Bratzler changes which were measured. There are several factors that may be responsible for these changes in differential expression during ageing such as proteolytic action (i.e. calpains and calpastatin system, cathepsins) or maybe apoptosis. The proteins in the profiles of Nguni breed animals which showed differential expression in response to ageing are still to be determined.Keywords: Nguni breed, protein markers for tenderness, two dimensional gel electrophoresis (2D SDS PAGE)