Biology subjects

Umashankar, S.

Publications and source records attributed to Umashankar, S..

4 recordsLinked to original sources

bioRxiv2020

Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem

Freshwater ecosystems of tropical urban canals systems (TrUCS), are highly dynamic and experience constant pressures from interspersed effects of land-use and rain. The dynamic nature of TrUCS ecosystems presents a unique opportunity to unravel the signature interactions between the macro-organisms (top-down), sedimentary microbial communities (SedMICs), their functioning and the geochemical environment (bottom-up). A systems level understanding of the molecular and mechanistic basis of the highly dynamic behaviour that leads to specific ecosystem outcomes, is currently lacking. Therefore, a research framework to identify the direct link between top-down and bottom-up ecological effects on SedMICs in a highly dynamic urban canal sedimentary system is needed. Here, we present a framework of integrated multi-dimensional data across system-level biotic and abiotic ecological descriptors, such as environmental variables and active SedMICs. We followed the ecosystem shifts after a natural disturbance (rain) in two different anthropogenic disturbance (land-use) regimes. Shifts in profiles of metabolically active community were conserved across different land-use types, indicating resilience to perturbation is an intrinsic property of the TrUCs ecosystem. Three distinct phases, which were dominated sequentially by autotrophy, anoxic-heterotrophy and oxic-heterotrophy, were identified within these shifts. The first two phases were influenced by the bottom-up effects of specific metal-ion combinations of nitrates and sulfates with magnesium, aluminum and iron, and the third phase was triggered by top-down influences of bioturbation. This generalized systems-level approach, which provides an ecosystem-centric understanding of TrUCS and integrates them in sustainable management practices, can also be extended to other freshwater ecosystems.

ecology↗

bioRxiv2020

Neuroinflammation in the normal appearing white matter of multiple sclerosis brain causes abnormalities at the node of Ranvier

Changes to the structure of nodes of Ranvier in the normal-appearing white matter (NAWM) of MS brains are associated with chronic inflammation. We show that the paranodal domains in MS NAWM are longer on average than control, with Kv1.2 channels dislocated into the paranode. These pathological features are reproduced in a model of chronic meningeal inflammation generated by the injection of lentiviral vectors for the lymphotoxin- (LT) and interferon-{gamma} (IFN{gamma}) genes. We show that tumour necrosis factor (TNF), IFN{gamma} and glutamate can provoke paranodal elongation in cerebellar slice cultures, which could be reversed by an NMDA blocker. When these changes were inserted into a computational model to simulate axonal conduction, a rapid decrease in velocity was observed, reaching conduction failure in small diameter axons. We suggest that glial cells activated by proinflammatory cytokines can produce high levels of glutamate, which triggers paranodal pathology, contributing to axonal damage and conduction deficits.

neuroscience↗

bioRxiv2019

Host developmental stage is associated with shifts in the exosphere microbiome of urban-farmed Asian green leafy vegetables

Green leafy vegetables (GLVs) comprise a significant part of urban South-East Asian (SEA) diets and are intensively farmed in SEA cities, including Singapore. Urban farming practices and urban-adapted vegetable cultivars likely select for specific above- and below-ground microbial communities - microbiomes - that assemble in close proximity to the plant tissues - the exosphere. A healthy exosphere microbiome is important for plant growth and safe human consumption. Using 16S rDNA gene amplicon sequencing compositional analyses, we show here that the exosphere microbiome of two commonly-consumed GLVs - Choy Sum (Brassica oleracea Alboglabra Group) and Gai Lan (Brassica chinensis var. parachinensis) - dominated by Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Actinobacteria. Shifts in exosphere microbiome composition were strongly associated with plant developmental stage. Finally, microbial taxa consistently detected in the exosphere comprise a small subset, which are predicted to harbour plant-beneficial traits.\n\nSignificanceAmong plant crops, GLVs form an integral part of the Asian diet, especially so in Southeast Asia. Some of these GLVs have short life-cycles ({bsim}30-45 days), which makes them suitable for urban farms in terms of cost advantage as short cycle crops are preferred in urban farms. From a food-security perspective, GLVs forms an important target food group and efforts are being made to increase its productivity to meet the increasing food demands. Current farming practices often place lot of importance on chemical fertilizers and nutrient inputs to improve the fertility of non-arable urban lands to increase the crop productivity. Furthermore, farms in urban settings are also associated with anthropogenic inputs and eutrophic conditions. These together, contribute to negative environmental externalities questioning the sustainability and eco-sustenance of urban farming. Microbial based management systems can not only resolve these challenging issues, but can also enhance plant growth, nutrient use efficiency and disease tolerance. However, their use as microbial adjuncts to agricultural practices is currently limited in urban environments, which could possibly be due to the restricted knowledge-base on these urban phytobiomes.

systems biology↗

bioRxiv2017

Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism

Enterococci are important human commensals and significant opportunistic pathogens associated with endocarditis, urinary tract infections, wound and surgical site infections, and medical device associated infections. These infections often become chronic upon the formation of biofilm. The biofilm matrix establishes properties that distinguish this state from free-living bacterial cells and increase tolerance to antimicrobial interventions. The metabolic versatility of the Enterococci is reflected in the diversity and complexity of environments and communities in which they thrive. Understanding metabolic factors governing colonization and persistence in different host niches can reveal factors influencing the transition from commensal to opportunistic pathogen. Here, we report a new form of iron-dependent metabolism for Enterococcus faecalis where, in the absence of heme, respiration components can be utilised for extracellular electron transfer (EET). Iron augments E. faecalis biofilm growth and generates alterations in biofilm matrix, cell spatial distribution, and biofilm matrix properties. We identify the genes involved in iron-augmented biofilm growth and show that it occurs by promoting EET to iron within biofilm.\n\nSignificanceBacterial metabolic versatility is often key in dictating the outcome of host-pathogen interactions, yet determinants of metabolic shifts are difficult to resolve. The bacterial biofilm matrix provides the structural and functional support that distinguishes this state from free-living bacterial cells. Here, we show that the biofilm matrix provides access to resources necessary for metabolism and growth which are otherwise inaccessible in the planktonic state. Our data shows that in the absence of heme, components of Enterococcus faecalis respiration (l-lactate dehydrogenase and acetaldehyde dehydrogenase) may function as initiators of EET through the cytoplasmic membrane quinone pool and utilize matrix-associated iron to carry out EET. The presence of iron resources within the biofilm matrix leads to enhanced biofilm growth.

microbiology↗