Biology subjects

Rani, A.

Publications and source records attributed to Rani, A..

3 recordsLinked to original sources

bioRxiv2025

Aldehyde dehydrogenase protein: a placental glycogen trophoblast marker suitable to monitor placental pathologies in mouse models

This study focuses on developing new approaches to identify and quantify glycogen trophoblast cells in the placenta. Due to limitations with currently available methods, alternative markers for these cells are being explored. Here we report on one promising candidate, Aldh1a3, a gene that was recently shown to be expressed in the mouse placenta only in glycogen trophoblast cells and their progenitors. Our study validates ALDH1A3 protein as glycogen trophoblast marker in the mouse placenta with high specificity when compared to CDKN1C (p57KIP2). This marker will be useful for the isolation of the glycogen trophoblast subpopulation and facilitate examining its function in placental programming and understanding its role in pathological pregnancy models. Furthermore, trophoblast giant cells with high expression of ALDH1A3 were detected in the decidua of human term placentas. These were interspersed with extravillous interstitial trophoblast cells or were located distal of the interstitial trophoblast layer of the decidua basalis.

developmental biology↗

bioRxiv2019

Darwinian selection analysis of the two-component system PmrAB indicates there could be lingering delay in emergence of colistin resistance in Acinetobacter baumannii

Investigations on the selection pressure acting on point mutations in PmrAB two-component system may provide insights into the future of colistin therapy in Acinetobacter baumannii, since mutations in pmrAB are implicated in colistin resistance. We performed adaptive selection analysis of pmrAB and compared with the available data on colistin resistant strains. We analysed PmrAB sequences in 3113 draft genomes of A. baumannii obtained from RefSeq database. Adaptive selection analysis was performed by two widely used programs namely, HyPhy and PAML. In addition, to examine the reliability of the approach, the same analysis was performed on gyrA of Escherichia coli and Salmonella enterica, since adaptive mutations on gyrA confer quinolone resistance. Mutations that had caused colistin resistance were found to be neither adaptive nor polymorphic, rather they occur at sites that are either under neutral or purifying selection. Strong negative evolutionary selection pressure is also observed at sites throughout both PmrA and PmrB. Sites with high levels of polymorphisms in PmrAB were found to be under neutral selection. Notably, there was no sign of positive selection. Some of them are rather deleterious. These conditions might be maintaining the incidence of colistin resistance in A. baumannii under check. Therefore, in the context of colistin resistance, natural selection plays only a minor role and we assert that in future, A. baumannii may not be able to sustain and successfully disseminate colistin resistance. Therefore, at present the concerns raised about continuing the usage of colistin for the treatment against A. baumannii infections appears to be unnecessary.

microbiology↗

bioRxiv2018

Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics

It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of the study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced and determine if the data are comparable on different platforms. In this study, we perform ultra-deep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We validated the sequencing and analysis methods using different Illumina platform, and with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are more highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome, and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.

microbiology↗