Biology subjects

Rao, M. S.

Publications and source records attributed to Rao, M. S..

5 recordsLinked to original sources

bioRxiv2025

Protocol for Extracting Circulating Cell-Free DNA from Murine Saliva: Insights into Oral and Systemic Disease Research

Circulating cell-free DNA (cfDNA) consists of small fragments of extracellular DNA from mammalian and bacterial cells found in bodily fluids such as blood and saliva, and it has been strongly recognized as a critical biomarker for various disease diagnoses, prognoses, and therapeutic monitoring. In this study, we present a reproducible protocol for efficiently isolating cfDNA from murine saliva using an innovative swabbing method in conjunction with the QIAamp MinElute ccfDNA Mini Kit. The quantification of isolated cfDNA is detected by a Qubit Fluorometer. Moreover, qualification assessment is conducted through BioAnalyzer analysis. This protocol facilitates research on saliva-derived cfDNA in the context of oral and systemic diseases in murine models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/645839v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@19ce903org.highwire.dtl.DTLVardef@85fa20org.highwire.dtl.DTLVardef@1e869eaorg.highwire.dtl.DTLVardef@181c340_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Reduction of right-hemispheric auditory cortex activity in response to speech in more experienced paediatric cochlear implant users

In case of severe hearing loss early in life or congenital deafness, cochlear implants (CIs) represent the method of choice to restore hearing and enable language acquisition. While speech intelligibility has been shown to improve during the first year after implantation to then reach a plateau, the underlying neuroplastic changes are poorly understood. Here, we longitudinally compared the cortical processing of speech stimuli in a case-control design with two groups of pre-lingually deafened CI users (4.4 vs. 25.8 months of CI experience) and an age-matched control group with normal hearing (NH; mean group ages [~]9 years). In two experiments, participants were presented with running speech and vowel sequences while fNIRS and EEG data were obtained simultaneously. Despite trends in this direction, cortical activity did not increase significantly with more CI experience and did not approach the higher levels observed in the NH controls. However, in the speech experiment, the less experienced CI group showed an abnormal shift of activity to the right hemisphere not observed in the other two groups. These results hence imply that adaptation to CI-based hearing is not characterised by a gradual increase of activity in left-hemispheric language network, but a reduction of abnormal activity elsewhere.

neuroscience↗

bioRxiv2021

Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study, 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127, expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result, individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

molecular biology↗

bioRxiv2021

Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

plant biology↗

bioRxiv2018

INDEX-db: The Indian Exome Reference database (Phase-I)

Deep sequencing based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. The bigger challenge now is to ascertain pathological significance to the array of identified variants to specific disease conditions. Differential selection pressure may impact frequency of genetic variations, and thus the detection of association with disease conditions, across populations. To understand the genotype to phenotype correlations, it thus becomes important to first understand the genetic variation spectrum of a population by creating a reference map. In this study, we report the development of phase I of a new database of coding variations, from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanism at the clinical, genetic and cellular level.\n\nDatabase URL: http://indexdb.ncbs.res.in

genomics↗