Effects of step training on the kidneys following spinal cord injury in rats.

Detrusor-sphincter dyssynergia after chronic spinal cord injury (SCI) leads to over-distention, high bladder pressures and vesico-ureteric reflux into the kidney, resulting in repeated infections and pyelonephritis. Given the importance/limited knowledge of SCI effects on the upper urinary tract, this study assessed expression of two proteins in the kidneys of contused (T9) male rats relative to controls that are indicative of tissue stress/damage (TGFβ, CD11b). The impact of two therapeutic rehabilitation strategies, 60 minutes of step training and general exercise, was then assessed on these protein levels relative to non-trained SCI controls, plus the effectiveness of a shorter training duration (30 minutes). Western blots revealed a significant decrease in the expression of TGFβ and a significant increase in CD11b in kidney tissues following SCI. With both types of training and durations, TGFβ but not CD11b expression returned to normal levels, indicating a benefit of exercise for renal health after chronic SCI

Immunoglobulin gene usage and affinity maturation in antiviral antibodies

The ability of antibodies to block infections makes them highly relevant for successful vaccine development. Through the papers described in this thesis, I attempt to characterize the functional and genetic aspects of antiviral antibodies induced by infection and vaccination. In Paper I, we characterized the distribution and maturation of HIV-1 envelope glycoproteins (Env)-specific antibody lineages post-vaccination in different immune compartments of rhesus macaques. Vaccine-induced Env-specific antibody lineages were disseminated across the periphery, lymph node, spleen, and bone marrow (BM) but not in gut tissue. We observed a consistent increase in the somatic hypermutation (SHM) levels of Env-specific antibody sequences after each boost and the SHM levels strongly correlated with the affinity of members from a potent neutralizing antibody lineage. In Paper II, we set out to understand the role of SHM in a broad, potent, public class of antibodies isolated from a healthcare worker who was previously infected with SARS-CoV2. I selected a potent neutralizing antibody and reverted the heavy chain (HC) to the germline sequence. I then sequentially introduced individual or combinations of SHM so that we could test the functional impact of this. We found a substantial gain of antibody potency and breadth when certain SHM mutations were reintroduced, and we identified two key mutations that largely contributed to the breadth of this lineage. Furthermore, we showed that the mature antibody retained neutralizing activity against potential future viral variants by deep mutational scanning (DMS) experiments. A high-resolution structure of this antibody obtained by cryo-electron microscopy (cryo-EM) confirmed important interactions made by the identified SHMs with the SARS-CoV-2 spike (S). In Papers III and IV, we investigated the effect of immunoglobulin heavy chain variable (IGHV) gene polymorphisms on the function of human SARS-CoV-2 antibodies isolated post-infection. We genotyped a cohort of previously infected healthcare workers and evaluated the neutralization activity of germline-reverted and allele-swapped S-specific IGHV1-69*20-using antibodies from two independent donors carrying this allele. Neutralization was retained when reverting the IGHV region to the germline IGHV1- 69∗20 allele but lost when reverting to other IGHV1-69 alleles demonstrating a strong allele-dependence in these antibodies. A high resolution cryo-EM structure of one of the antibodies revealed significant contacts made by two IGHV1-69*20-germline encoded amino acid residues with the S, illustrating the impact of IGHV polymorphisms on antibody functions. We next focused on the IGHV3-30 group of genes, which are frequently used by S-specific antibodies. By IGHV genotype and haplotype analysis we observed that IGHV3-30-3 gene was deleted in many individuals, and the IGHV3-30 alleles were heterogeneously distributed in our cohort. When the IGHV region of an IGHV3-30-3*01 neutralizing antibody was swapped with IGHV3-30 alleles, the neutralization remained unaffected demonstrating functional redundancy within this gene group, at least for this antibody lineage. The results from my doctoral research provide insight into functional and genetic properties of antibodies induced by viral antigens, which have important clinical relevance both for guided-vaccine design and monoclonal antibody therapeutics, and for our general understanding of antibody responses in the population

Sustainable Supply and Supply Chain Mapping - Sri Lankan Tea Supply Chain

Sustainable supply chain management has gained great attention during last few decades. Companies not only need to deliver quality products, but also have to comply with environmental, economical, ethical and social aspects. This has created more challenges for managing the supply chain. Increased customer awareness in sustainability concepts has further increased the challenges. In supply chain management sustainable supply is an important part of any business and it is critical for the success of the whole supply chain. With identifying the importance in these concepts; this paper tries to define the sustainable supply and supply chain mapping using a theoretical framework. It further describes the research methodology that is used to identify the influencing factors on sustainable tea supply in Sri Lanka tea supply chain

Usage of electronic resources by librarians of Sri Lankan universities

The study investigates the usage of the e-resources available through CONSAL (Consortium of Sri Lankan Academic Libraries) and other means for the LIS professionals of the Sri Lankan public universities. A structured questionnaire was used to gather data from 99 librarians working in the Sri Lankan public universities. Findings revealed that 65% frequently use open access material for their research, and the majority (33%) use them for their research, 60% believed that the available e-resources fulfilled their needs. Inability to access the databases from home, absence of some full text articles, lack of relevant material and lack of access to archival material were identified as common barriers to use the e-resources. The study recommends improving access from homes, adding more LIS material and increase training to cover as many LIS professionals to increase the usage. The study is limited to the usage of the e-resources by the Librarians during 2014 and 2015 after the formulation CONSAL

Causal role of histone acetylations in enhancer function

Enhancers control development and cellular function by spatiotemporal regulation of gene expression. Co-occurrence of acetylation of histone H3 at lysine 27 (H3K27ac) and mono methylation of histone H3 at lysine 4 (H3K4me1) has been widely used for identification of active enhancers. However, increasing evidence suggests that using this combination of marks alone for enhancer identification gives an incomplete picture of the active enhancer repertoire. We have shown that the H3 globular domain acetylations, H3K64ac and H3K122ac, and an H4 tail acetylation, H4K16ac, are enriched at active enhancers together with H3K27ac, and also at a large number of enhancers without detectable H3K27ac. We propose that acetylations at these lysine residues of histones H3 and H4 might function by directly affecting chromatin structure, nucleosome–nucleosome interactions, nucleosome stability, and transcription factor accessibility