Wellcome Trust Research Laboratory's List here:
<h3>About Microbiology and Virology Laboratory</h3>
Over the last 25 years, the Microbiology and Virology Laboratory at the Wellcome Trust Research Laboratory has focused on defining the role of viral and parasitic agents in gastroenteritis. We study the molecular epidemiology of the pathogens, clinical features and severity of disease, the immune response to diarrheagenic pathogens and factors influencing the immune response in children.

With researchers from multiple departments at the Christian Medical College, Vellore, we have built a team that has worked with several international partners to establish and further develop rotavirus genotyping methods and specific immunoassays (for antigen and antibody detection). In comprehensive well-designed and conducted studies, we monitor the burden and severity of disease, and the molecular epidemiology of rotavirus, both in the community and the hospital.

Our studies on the protective effect of natural rotavirus infection in an Indian birth cohort found that early infection and frequent reinfection resulted in lower protection than had been reported elsewhere, providing a possible explanation why rotavirus vaccines have lower efficacy in Asia and Africa. Our current studies in collaboration with Stanford, the Center for Disease Control and Prevention and Emory aim to further characterize the immune response to rotavirus vaccines and infection in Indian children. We work with Prof. Nicholas Grassly at Imperial College, London, on studies related to the performance of poliovirus vaccines in India. A separate testing facility has been set up about 8 km away from the hospital campus to conduct these polio related studies.

The laboratory also investigates other enteric pathogens, including noroviruses and several parasites. We have extended our study of infections to the investigation of gut function with clinical and laboratory colleagues across the institution and internationally. In addition to providing support for the evaluation of rotavirus vaccines being made by several manufacturers in India and elsewhere, the laboratory is recognized for its commitment to quality and serves as the WHO SEAR’s Regional Reference Laboratory for Rotavirus and as the Referral Laboratory for the National Rotavirus Surveillance Network coordinated by the Indian Council for Medical Research.
<h3>About Parasitology Laboratory</h3>
The major thrust of our research is on the molecular characterization and epidemiology of enteric parasites. Cryptosporidium spp. is one of the commonest causes of protozoan diarrhea in children in developing countries. Among the ~20 species and 40 zoonotic genotypes documented, most human infections are associated with C. hominis and C. parvum. Isolates from these species are further classified into several distinct subgenotypes based on extensive polymorphisms at the gp40/15 locus. Studies from our laboratory have focused on the molecular epidemiology of cryptosporidiosis in children and in HIV infected adults.

In these studies, several aspects of cryptosporidiosis in children have been addressed including species distribution and subgenotype, spatio-temporal trends with GIS enabled data, IgG response to immunodominant antigens, effect on nutritional status and cognitive function and genetic susceptibility. C. hominis was the predominant species in this community and the predominant subgenotypes were Ie, Ia and Id. In the transmission dynamics study, we used PCR as a screening tool and found a very high burden of disease (60% of children infected) most of which was asymptomatic. Serum antibody response to gp15, an immunodominant antigen measured in children with cryptosporidial diarrhea, showed high seroconversion rates with a peak response at 9 weeks following the infection. We also demonstrated partial subtype specific immunity for the gp40 antigen.
<h3>About Biochemistry Laboratory</h3>
The Wellcome Biochemistry Laboratory has been primarily focused on basic science research examining biochemical mechanisms involved in the pathophysiology of the gastrointestinal mucosa and the liver. Initial research efforts examined fat absorption and malabsorption, and the importance of acid lipase in these processes. Over the last 30 years, the laboratory has explored the role of reactive oxygen species in pathophysiology of the gastrointestinal mucosa and the liver with a recent focus on the role of mitochondria and nitric oxide in modulating these effects.

Our research has identified key mechanistic aspects of free radical induced signaling in a number of conditions such as intestinal ischemia reperfusion and surgical stress, which play an important role in complications such as sepsis and acute respiratory distress syndrome. The role of reactive oxygen species in development of liver cirrhosis-induced alterations in intestinal barrier function and the kidney was also studied.

Though mitochondria have been traditionally studied in the context of cellular metabolism, it is now evident that they also play significant roles in cellular signaling. Investigation of the alterations in mitochondrial function and oxidative stress in the placenta in conditions such as acute fatty liver of pregnancy (AFLP) revealed important roles for these reactive species in induction of liver damage.
<h3>About Histopathology Laboratory</h3>
The Central Electron Microscopy Facility (CEMF) at CMC Vellore offers unique expertise and EM technology for diagnostic and research studies. Diagnostic electron microscopy is carried out by pathologists from the CEMF or the Department of General Pathology, on request. Approximately 300 clinical samples and about 150-300 research samples a year are processed by the laboratory.The majority of clinical samples are renal cases, and there is a dedicated nephroathologist in the unit. The remaining cases are for the evaluation and diagnosis of gastrointestinal , neuro-muscular, liver and dermatological diseases. Digital images are captured and retained in the patients file.

The CEMF is also used for research by scientists from within the institute and outside. Studies range from the normal ultrastructural anatomy of cells and tissues and the pathogenesis of inflammatory and other disorders to the cellular changes that parallel biochemical alterations in the tissue.

Core Capabilities: The CEMF provides Transmission Electron Microscopy (TEM) for biological samples as well as expertise in 3D tomography and negative staining. Cryoelectron microscopy is being developed.

Instrumentation: The EM Lab suite includes two TEM and one a Tecnai 12G2 Biotwin (120KV TEM) and the other a Philips EM201C.

Supporting equipment includes aCryo Vacuum Device for EM studies on Frozen sections, Leica Ultracut UC7 for sectioning ultrathin and cryosections and,a Carbon Coating Unit.

Training: Undergraduate medical students are given an introduction to the use of EM and pathology and Microbiology postgraduate students do a rotation through the lab. Postgraduate students from Nephrology have regular case discussions with a faculty member in the CEMF.

Digital image retention: Images captured for research can be burned to a CD. Images may remain on the hard drive of any given instrument for one month after capture. Lab staff will delete any images remaining in files after one month.
<h3>About Sequencing and Bioinformatics Laboratory</h3>
The sequencing laboratory uses next generation sequencing tools to answer questions of public health importance in India. We use Illumina's Miseq for 16S rRNA sequencing and the QIIME pipeline for microbiome analysis. We have studied the effect of gut microbiota and virome on the performance of oral vaccines, conducted whole genome sequencing of the typhoid bacillus and used Nanopore technology to identify enteroviruses from environmental and human samples. We collaborate with Prof. Nicholas Grassly at Imperial College, on amplicon sequencing of the VP1 region of the enterovirus from multiplexed samples with barcoded primers using the Minion sequencing platform.

With the Department of Gastroenterology, we are now exploring the association of the gut microbiome with inflammatory bowel disease in patients with different clinical stages of Crohn's disease.