Conference Publications

Permanent URI for this collection

http://hdl.handle.net/10204/11486

Browse

Browsing Conference Publications by browse.metadata.cluster "Next Generation Health"

Now showing 1 - 7 of 7
  • Thumbnail Image
    Item
    CSIR Synthetic Biology and Precision Medicine Centre Bio-foundry Program
    (2022-01) Thimiri Govindaraj, Deepak B
    Global bio-foundry Alliance (GBA) has been established between countries including the UK, US, Japan, Singapore, China, Australia, Denmark, and Canada through 16 research institutions. Global bio-foundry Alliance plays the key role in the synthetic biology drivetowards a new global bioeconomy that is accelerated by advanced technology innovation.Establishment of Biofoundry program in South Africa and in Africa will plan key scientific and the strategic role in promoting synthetic biology and precision medicine program in Africa. This would further enable bioeconomy and industrial development towards SME program. At our CSIR Synthetic Biology and Precision medicine Centre, we are currently establishing biofoundrylab that will implement various synthetic biology and precision medicine projects in South Africa.
  • Thumbnail Image
    Item
    Establishment of synthetic biology innovation and biofoundry lab in South Africa
    (2023-09) Thimiri Govindaraj, Deepak B
    Background: The Global Biofoundry Alliance (GBA) has been established between countries including the UK, US, Japan, Singapore, China, Australia, Denmark, and Canada through 16 research institutions. GBA plays a key role in the synthetic biology drive towards a new global bioeconomy that is accelerated by advanced technology innovation. Establishing a biofoundry program in South Africa and Africa will play a key scientific and strategic role in promoting synthetic biology and precision medicine programs in Africa. This would further enable bioeconomy and industrial development towards the SME program. We are currently establishing a biofoundry lab that will implement various synthetic biology and precision medicine projects in South Africa. Methods: We are currently establishing two research components in the CSIR Synthetic Biology and Precision Medicine Centre Biofoundry program, which includes industrial synthetic biology and functional precision medicine program. We implement the biofoundry biodesign and biological engineering Design-Build-Test-Learn (DBTL) cycle into our industrial synthetic biology and functional precision medicine program. In our industrial synthetic biology program, we are working on a) ValitaCHO: The development of a superior CHO cell line system for hyper-burst protein expression system using directed evolution and synthetic biology approache, and b) Lactochassis: Designer microbes for industrial synthetic biology platform applications. Results: We are currently at the Design phase of the Design-Build-Test-Learn (DBTL) cycle in our industrial synthetic biology and functional precision medicine program. We have so far progressed in generation of the preliminary data on ValitaCHO cell-line chemstress fingerprinting profiling. We are currently designing the directed evolution approach to generate a superior CHO cell line. In the Lactochassis project, we are currently designing the computational biology-based genome mapping for the Lactochassis project. Conclusion: Using the biodesign DBTL cycle, we aim to implement our industrial synthetic biology and cancer precision medicine platform. These platforms will enable the establishment of one of the first Biofoundry labs in Africa.
  • Thumbnail Image
    Item
    Hepatitis B core-based virus-like particles: A platform for vaccine development in plants
    (2021-03) Vahdat, MM; Hemmati, F; Ghorbani, A; Rutkowska, Daria A; Afsharifar, A; Eskandari, MH; Rezaei, N; Niazi, A
    Virus-like particles (VLPs) are a class of structures formed by the self-assembly of viral capsid protein subunits and contain no infective viral genetic material. The Hepatitis B core (HBc) antigen is capable of assembling into VLPs that can elicit strong immune responses and has been licensed as a commercial vaccine against Hepatitis B. The HBc VLPs have also been employed as a platform for the presentation of foreign epitopes to the immune system and have been used to develop vaccines against, for example, influenza A and Foot-and-mouth disease. Plant expression systems are rapid, scalable and safe, and are capable of providing correct post-translational modifications and reducing upstream production costs. The production of HBc-based virus-like particles in plants would thus greatly increase the efficiency of vaccine production. This review investigates the application of plant-based HBc VLP as a platform for vaccine production.
  • Thumbnail Image
    Item
    Plant-derived VLP: A worthy platform to produce vaccine against SARS-CoV-2
    (2021-11) Hemmati, F; Hemmati-Dinarvand, M; Karimzade, M; Rutkowska, Daria A; Eskandari, MH; Khanizadeh, S; Afsharifar, A
    After its emergence in late 2019 SARS-CoV-2 was declared a pandemic by the World Health Organization on 11 March 2020 and has claimed more than 2.8 million lives. There has been a massive global effort to develop vaccines against SARS-CoV-2 and the rapid and low cost production of large quantities of vaccine is urgently needed to ensure adequate supply to both developed and developing countries. Virus-like particles (VLPs) are composed of viral antigens that self-assemble into structures that mimic the structure of native viruses but lack the viral genome. Thus they are not only a safer alternative to attenuated or inactivated vaccines but are also able to induce potent cellular and humoral immune responses and can be manufactured recombinantly in expression systems that do not require viral replication. VLPs have successfully been produced in bacteria, yeast, insect and mammalian cell cultures, each production platform with its own advantages and limitations. Plants offer a number of advantages in one production platform, including proper eukaryotic protein modification and assembly, increased safety, low cost, high scalability as well as rapid production speed, a critical factor needed to control outbreaks of potential pandemics. Plant-based VLP-based viral vaccines currently in clinical trials include, amongst others, Hepatitis B virus, Influenza virus and SARS-CoV-2 vaccines. Here we discuss the importance of plants as a next generation expression system for the fast, scalable and low cost production of VLP-based vaccines.
  • Thumbnail Image
    Item
    Synthetic biology meets precision medicine: Drug repurposing for blood cancer precision medicine
    (2021-11) Thimiri Govindaraj, Deepak B
    Optimizing Drug discovery and Translation is one of the key tracks in Global Challenges Annual meeting 2019 and is the critical factor in achieving UN Sustainable Development Goals 3 Good Health and Well Being. WHO reports Cancer is the second leading cause of death globally. The aim of the proposal is to establish robust drug screening platform which can identify drugs and drug combinations that are effective in precision medicine for relapsed individual South African Leukemia patients.
  • No Thumbnail Available
    Item
    Uncovering influential factors of civil unrest in South Africa: A machine learning and OSINT approach
    (2023-12) Ndlovu, Lungisani; De Kock, Antonie J; Mkuzangwe, Nenekazi NP; Thwala, Ntombizodwa; Mokoena, Chantel JM; Matimatjatji, Rethabile J
    Continuous monitoring of the risk of civil unrest events and predicting their occurrence is of paramount importance. This task involves identifying and understanding the primary factors that contribute to such events, especially in regions with unique dynamics, such as South Africa. Although many global and South African-specific studies have conducted research on predicting the frequency or probability of these events, there is a notable gap in identifying the influential factors behind them. This study unveiled several contributing factors, including demanding behaviour, power outages, service delivery, wage disputes, acts of violence, gender-based conflicts, and unemployment rates. These factors, individually or collectively, contribute to the complexity of civil unrest in the region. The 2021 South African unrest, also known as the July 2021 riots, the Zuma unrest, or Zuma riots, serves as an example. This event was triggered by the imprisonment of former president Jacob Zuma for contempt of court, inciting his followers to demand his release, a situation aligning with the 'demanding behaviour' influential factor identified in our study. We used advanced data analysis and machine learning techniques to explore these factors. Specifically, the Logit model was used to determine the coefficients that optimally fit the data, establishing significant relationships between these factors and incidents of civil unrest. Our research not only offers insights on influential factors, but also presents a predictive framework. We evaluated logistic regression, support vector clustering, decision tree classifier, and random forest classifier models to predict civil unrest. The results showed that the decision tree and the random forest classifiers perform better, achieving an accuracy of 98%, compared to logistic regression and support vector clustering, which have an accuracy of 97%.
  • Thumbnail Image
    Item
    Urine-HILIC: Automated sample preparation for bottom-up urinary proteome profiling in clinical proteomics
    (2023-09) Govender, Ireshyn S; Mokoena, Rethabile; Stoychev, Stoyan; Naicker, Previn
    Urine provides a diverse source of information related to a patient’s health status and is ideal for clinical proteomics due to its ease of collection. To date, most methods for the preparation of urine samples lack the throughput required to analyze large clinical cohorts. To this end, we developed a novel workflow, urine-HILIC (uHLC), based on an on-bead protein capture, clean-up, and digestion without the need for bottleneck processing steps such as protein precipitation or centrifugation. The workflow was applied to an acute kidney injury (AKI) pilot study. Urine from clinical samples and a pooled sample was subjected to automated sample preparation in a KingFisher™ Flex magnetic handling station using the novel approach based on MagReSyn® HILIC microspheres. For benchmarking, the pooled sample was also prepared using a published protocol based on an on-membrane (OM) protein capture and digestion workflow. Peptides were analyzed by LCMS in data-independent acquisition (DIA) mode using a Dionex Ultimate 3000 UPLC coupled to a Sciex 5600 mass spectrometer. The data were searched in Spectronaut™ 17. Both workflows showed similar peptide and protein identifications in the pooled sample. The uHLC workflow was easier to set up and complete, having less hands-on time than the OM method, with fewer manual processing steps. Lower peptide and protein coefficient of variation was observed in the uHLC technical replicates. Following statistical analysis, candidate protein markers were filtered, at =8.35-fold change in abundance, =2 unique peptides and =1% false discovery rate, and revealed 121 significant, differentially abundant proteins, some of which have known associations with kidney injury. The pilot data derived using this novel workflow provide information on the urinary proteome of patients with AKI. Further exploration in a larger cohort using this novel high-throughput method is warranted.