ABANTIKA GHOSH / IMMUNOLOGIST
RESEARCH PROJECTS
Investigating the role of SAMHD1 in DNA damage-induced cancer cell death
MRC Weatherall Institute of Molecular Medicine, University of Oxford
Events occurring during DNA damage repair via the Homologous Recombination (HR) repair pathway in (A) presence of intact SAMHD1 and (B) absence of SAMHD1.
The protein SAMHD1 plays a critical role in regulating cellular dNTP levels and protecting cells from viral infections. Recent studies have suggested a role of SAMHD1 in DNA damage-induced cell death and cancer. Upon exposure to DNA-damaging agents, cells resort to DNA damage response pathway to repair damage.
Targeting SAMHD1 in cancer cells may sensitize repair-deficient cells to DNA damage-induced cell death from the accumulated lethal DNA lesions of chemotherapy or radiation. This would result in robust detection of the damaged DNA by the cGAS-STING pathway, ultimately leading to cancer cell death. Therefore my MSc dissertation project (2021) at University of Oxford under supervision of Professor Jan Rehwinkel aimed to investigate the role of SAMHD1 in DNA damage-induced cancer cell death in conjunction with the effect of chemotherapeutic drugs.
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Key conclusion from the project:
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The main results from the project did not appear to support the hypothesis that targeting SAMHD1 makes cancer cells more sensitive to DNA damage-induced cell death. The SAMHD1 KO clones did not show significant differences in cell proliferation rates or drug sensitivities to DNA damage-inducing agents. Therefore targeting SAMHD1 solely, might not be an effective strategy to induce lethal DNA damage that would trigger the immune system for cancer cell elimination. Further investigations in other cell lines need to be carried out as results may differ based on specific characteristics of cell lines under observation.
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Skills learnt
• SDS-PAGE • cDNA synthesis • qPCR • PCR • RNA extraction • Protein extraction • in vitro cell culture: cancer cell lines HeLa, HCT-116, MDA-MB-231 • Western blotting • Cell death assays • CRISPR/Cas9 gene editing • Live cell imaging/ analysis • Generation of single-cell clones • BCA assay • Sample preparation for sequencing
Instruments and software: GraphPad Prism, Snapgene, IncuCyte S3, Adobe Illustrator, Confocal, fluorescence and light microscopy, CLARIOstar and spectrophotometer
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Antibiotic Sensitivity Pattern of Staphylococcus aureus isolated from human skin and food samples
Scottish Church College, University of Calcutta
Antibiotic resistance is a critical health concern in the field of medicine and microbiology. One of the most common bacteria, Staphylococcus aureus, a common human skin microflora is a global health concern as it has become resistant to multiple antibiotics, making infections more difficult to treat and increasing the risk of complications and mortality. In this study, we aimed to investigate the antibiotic sensitivity pattern of Staphylococcus aureus isolated from human skin and food samples. In this study, isolated Staphylococcus aureus from different samples like contaminated food samples and human skin were tested for their sensitivity against 12 antibiotics. A comparative sensitivity pattern was also made between S.aureus isolated from food samples and skin directly to determine how human interference might be largely responsible for the spread of drug resistance.
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Key conclusion from the project:
The results showed that Staphylococcus aureus isolates from human skin and food samples exhibited varying degrees of antibiotic resistance however all the strains were methicillin-resistant. The isolates showed high levels of resistance to commonly used beta-lactam antibiotics such as penicillin and ampicillin. The findings highlight the importance of regular monitoring of antibiotic resistance patterns of Staphylococcus aureus isolates. It also emphasizes the need for judicious use of antibiotics to prevent the emergence of antibiotic-resistant strains.
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Skills learnt
• Aseptic techniques • Media preparations • Stock and buffer preparations • Antibiotic susceptibility testing: Kirby–Bauer method • Phage titration • Serial dilution • Isolation, culturing and characterisation of microbes • Micrometry • Staining
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Degradation of triphenylmethane dyes with bacterial consortium
Scottish Church College, University of Calcutta
Triphenylmethane dyes are widely used in various industries, and their effluent discharge can cause significant environmental pollution since these dyes are mostly toxic and carcinogenic to aquatic life, and their accumulation in water bodies can lead to ecological imbalances. The degradation of triphenylmethane dyes with bacterial consortium is a sustainable and effective solution to address this environmental issue as bacteria can break down complex dyes into simpler compounds, which can be easily assimilated by other microorganisms and recycled back into the ecosystem. In this study, we investigated the decolorization of three triphenylmethane dyes: Malachite Green, Crystal Violet and Basic Fuchsin in solution by a bacterial consortium and determine the mechanism of decolorization.
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Key conclusion from the project
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It was found that high efficiency of decolorization dye solutions was observed upon using bacterial consortium in single dye in comparison to a mixed dye solution. The best decolorization was obtained for Malachite Green in single solution. Moreover, UV-visible spectroscopic studies revealed disappearance of the peaks corresponding to absorption maxima of dye mix (585 nm) and arrival of two new peaks at 373 and 519 nm indicating mechanism of decolorization to be likely biodegradation.
Multidrug resistance in dye-decolorizing microbes
Scottish Church College, University of Calcutta
In this study, we analysed two isolated microorganisms from dye-contaminated sites for their sensitivity towards a number of antimicrobial drugs and both of them were found to be resistant to multiple drugs. Although antibiotics are hardly used by the dying industries, the presence of multidrug-resistant organisms is not only surprising but also pose a potential threat of spreading antibiotic resistance both naturally and if used industrially for dye decolourization purpose.
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Key conclusion from the project
It is clearly noted that the two bacterial species, Enterobacter asburiae- XJUHX-4TM and Klebsiella pnumoniae-1TM were potent decolorizer of Triphenylmethane dyes. Additionally, both of them were found to be proficient in terms of reduction of COD and TDS of mixed dye solutions. However, before applying these microbes indiscriminately for the above mentioned purpose, it has to be noted that although they are competent from the economic point of view, in effective treatment of wastewater using microbes due to their inherent quality of producing Although these two species have been isolated from dye contaminated wastewater, where use of antibiotic is practically very much limited, still the high MAR value of the organisms indicate indiscriminate use of antibiotics and their mixing with environmental discharge, that results in transformation of natural ,innocent microbes that could be used for industrial dye removal purpose into posing risks of being superbugs and becoming a cause of global antibiotic resistance.
A study comparing the antibacterial activity of natural and commercial spices, and combined effect of selected spices against E.coli'
SHRM Biotechnologies Pvt. Ltd
Natural spices have been used for centuries in traditional medicine for their antimicrobial properties, and research has often highlighted their potential use as natural preservatives in the food industry. This study focused on comparing the antibacterial activity of natural and commercial spices, valuable insights into the effectiveness of natural remedies compared to synthetic alternatives. The combined effect of selected spices against E.coli to identify synergistic interactions between different compounds to enhance antibacterial properties was also investigated. This independent study can therefore contribute to this field by identifying natural compounds that can be used to combat bacterial infections, potentially reducing the need for antibiotics in the future.
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Key conclusion from the project
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Certain spice extracts exhibit increased antibacterial activity when combined together in a specific ratio, while others show reduced antibacterial effect when mixed. The combination of extracts can result in a synergistic effect, where the combined effect is greater than the sum of their individual effects, leading to an increase in antibacterial activity. Conversely, an antagonistic interaction may occur in some extracts combine.
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RESEARCH INTERESTS
My research interests focuses on the intersection of microbiome, immunity and cancer (cancer-microbiome-immune axis).
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Some potential areas that I would like to explore in this field include studying the influence of host-microbiome interactions on modulating different immune responses in specific cancer types, microbiome and cancer vaccine development, etc.