sisinthy shivaji | L V Prasad Eye Institute (original) (raw)

Papers by sisinthy shivaji

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2005

A psychrotolerant, Gram-negative, motile bacterium, designated CK 47 T , was isolated from sea wa... more A psychrotolerant, Gram-negative, motile bacterium, designated CK 47 T , was isolated from sea water off the subantarctic Kerguelen islands (506 409 S 686 259 E). The isolate grew optimally at 22 6C and minimum and maximum temperature of growth were 4 and 37 6C, respectively. It required Na + for growth and exhibited optimum growth at pH 8?5 and 4 % NaCl. It utilized hexane, heptane and petroleum ether as sole sources of carbon. Strain CK 47 T had Q9 as the major respiratory quinone and C 16 : 0 (21?7 %), C 17 : 0 (21?3 %), C 18 : 0 (5?7 %), C 18 : 1 v7c (9?0 %) and C 18 : 1 v9c (31?4 %) as predominant fatty acids. The G+C content of the DNA was 58 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that CK 47 T formed a coherent cluster within the genus Marinobacter. It exhibited highest 16S rRNA gene sequence similarity of 96?8 % with Marinobacter lipolyticus. However, the level of DNA-DNA relatedness between strain CK47 T and M. lipolyticus was only 55 %. On the basis of phenotypic characteristics, and phylogenetic and genotypic distinctiveness, strain CK 47 T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter maritimus sp. nov. is proposed, with CK 47 T (=JCM 12521 T =MTCC 6519 T ) as the type strain.

Theriogenology, 2004

The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual s... more The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual semen characteristics, to identify a suitable extender for semen short-term storage, to determine a protocol for cryopreservation of semen and finally to check whether intracloacal insemination would lead to the birth of a chick. Semen characteristics such as semen volume, sperm concentration, sperm motility, and percentage of normal spermatozoa were maximum during the monsoon season. TALP was observed to be the most suitable semen extender and the sperm survived best at 37 8C at a dilution of 1:100 in TALP. Further, cryopreservation studies on pigeon semen indicated that 8% DMSO with or without egg yolk (20%) proved to be a better cryoprotectant compared to glycerol and polyethylene glycol. In addition, the slow freezing protocol was better than the fast-freezing protocol and about 40% of the cryopreserved spermatozoa were motile following thawing. Computer-aided semen analysis indicated that pigeon spermatozoa were extremely active immediately after dilution in TALP and exhibited linear trajectories persisting up to 9 h. But, with time there was a timedependent decrease in the velocity parameters (VAP, VSL, and VCL). Cryopreserved spermatozoa following thawing also exhibited linear trajectories but had reduced velocity as evident from the significant decrease in VAP, VSL, and VCL. Further, artificial inseminations using fresh semen resulted in 45% fertilization and birth of a live chick. #

PLoS ONE, 2012

Background: Majority of the tiger habitat in Indian subcontinent lies within high human density l... more Background: Majority of the tiger habitat in Indian subcontinent lies within high human density landscapes and is highly sensitive to surrounding pressures. These forests are unable to sustain healthy tiger populations within a tiger-hostile matrix, despite considerable conservation efforts. Ranthambore Tiger Reserve (RTR) in Northwest India is one such isolated forest which is rapidly losing its links with other tiger territories in the Central Indian landscape. Non-invasive genetic sampling for individual identification is a potent technique to understand the relationships between threatened tiger populations in degraded habitats. This study is an attempt to establish tiger movement across a fragmented landscape between RTR and its neighboring forests, Kuno-Palpur Wildlife Sanctuary (KPWLS) and Madhav National Park (MNP) based on non-invasively obtained genetic data.

PLoS ONE, 2013

Background: Tiger populations are dwindling rapidly making it increasingly difficult to study the... more Background: Tiger populations are dwindling rapidly making it increasingly difficult to study their dispersal and mating behaviour in the wild, more so tiger being a secretive and solitary carnivore.

PLoS ONE, 2012

Background: Non-invasively collected samples allow a variety of genetic studies on endangered and... more Background: Non-invasively collected samples allow a variety of genetic studies on endangered and elusive species. However due to low amplification success and high genotyping error rates fewer samples can be identified up to the individual level. Number of PCRs needed to obtain reliable genotypes also noticeably increase.

Conservation Genetics, 2012

Tiger, being a solitary and territorial animal, often tends to move out of protected areas into t... more Tiger, being a solitary and territorial animal, often tends to move out of protected areas into the surrounding forests. This is especially true in the case of subadult animals leading to escalating conflicts and deaths in the surrounding human-dominated landscapes. Unless adequately protected against various human activities, such corridors and surrounding forests will soon disappear, trapping the animals within protected areas with resultant local extinctions. In this paper we ascertain tiger presence, occupancy and numbers in one such partially protected area, the Sathyamangalam forest, located close to better known tiger reserves in India, through non-invasive faecal DNA analysis. Here we highlight the potential of Sathyamangalam as a tiger habitat. Tiger positive faecal samples were considered as evidence to establish occupancy in two different parts of Sathyamangalam, reserve forest and wildlife sanctuary. We collected 103 faecal samples out of which 69 were tiger positive. Species occupancy (psi), was 0.672 (±0.197) with a detection probability of 0.2 (±0.06) in the wildlife sanctuary area; while psi was 0.72 (±0.2) with detection probability of 0.212 (±0.6) in the reserve forest. Further, number of males and females, as determined in our study, was close to the ideal sex ratio in a healthy forest with good prey abundance. This study also highlights the presence of more females in the reserve forest (n = 10) than the wildlife sanctuary (n = 3) possibly indicating lesser disturbance and more prey availability. We recommend that the reserve forest to the north of Sathyamangalam wildlife sanctuary be declared as a tiger reserve. The wildlife sanctuary could serve as a buffer zone between this reserve and Sathyamangalam town which lies to the south of the forest. Proper protection of Sathyamangalam will go a long way in saving the entire landscape and tigers of the Western Ghats of India.

Mitochondrial DNA Part A, 2016

Current Science, 2007

The rapid and inexplicable decline of the Old World vulture populations across the Indian subcont... more The rapid and inexplicable decline of the Old World vulture populations across the Indian subcontinent is a cause of growing concern among ecologists and conservationists. Survival of these threatened birds may depend on breeding programmes where sex identification plays an important role. Here, a PCR-based method that amplifies a region of the chromo-helicase-DNAbinding gene was modified to identify the sex of individuals of two Gyps species. The results were further reconfirmed by amplification refractory mutation system. This study allowed for the rapid and safe assessment of sex and will facilitate all future efforts in the captive breeding of these birds.

American Journal of Veterinary Research, Jan 2, 2007

Objective-To determine the anesthetic dose and cardiopulmonary effects of xylazine hydrochloride ... more Objective-To determine the anesthetic dose and cardiopulmonary effects of xylazine hydrochloride when used alone or in combination with ketamine hydrochloride and evaluate the efficacy of yohimbine hydrochloride to reverse anesthetic effects in captive Axis deer. Animals-35 adult (10 males and 25 females) Axis deer (Axis axis). Procedures-All deer were anesthetized by IM administration of xylazine (3.5 mg/kg; experiment 1), a combination of ketamine and xylazine (1.25 and 1.5 mg/kg, respectively; experiment 2), or another combination of ketamine and xylazine (2.5 and 0.5 mg/kg, respectively; experiment 3). In addition, female deer were also anesthetized by IM administration of a third combination of ketamine and xylazine (1.5 and 1 mg/kg, respectively; experiment 4). Ten to 40 minutes after induction, anesthesia was reversed by IV administration of yohimbine (5, 8, or 10 mg). Results-In male deer, experiment 3 yielded the most rapid induction of anesthesia. In females, experiment 4 yielded the best induction of anesthesia without adverse effects. All doses of yohimbine reversed anesthesia. Duration of anesthesia before administration of yohimbine had no effect on recovery time. Conclusions and Clinical Relevance-A combination of ketamine and xylazine can be used to induce anesthesia in Axis deer. Furthermore, anesthetic effects can be reversed by administration of yohimbine. (Am J Vet Res 2007;68:20-24).

Theriogenology, Jul 1, 2004

The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual s... more The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual semen characteristics, to identify a suitable extender for semen short-term storage, to determine a protocol for cryopreservation of semen and finally to check whether intracloacal insemination would lead to the birth of a chick. Semen characteristics such as semen volume, sperm concentration, sperm motility, and percentage of normal spermatozoa were maximum during the monsoon season. TALP was observed to be the most suitable semen extender and the sperm survived best at 37 8C at a dilution of 1:100 in TALP. Further, cryopreservation studies on pigeon semen indicated that 8% DMSO with or without egg yolk (20%) proved to be a better cryoprotectant compared to glycerol and polyethylene glycol. In addition, the slow freezing protocol was better than the fast-freezing protocol and about 40% of the cryopreserved spermatozoa were motile following thawing. Computer-aided semen analysis indicated that pigeon spermatozoa were extremely active immediately after dilution in TALP and exhibited linear trajectories persisting up to 9 h. But, with time there was a timedependent decrease in the velocity parameters (VAP, VSL, and VCL). Cryopreserved spermatozoa following thawing also exhibited linear trajectories but had reduced velocity as evident from the significant decrease in VAP, VSL, and VCL. Further, artificial inseminations using fresh semen resulted in 45% fertilization and birth of a live chick. #

Plos One, 2011

Endometriosis is an estrogen-dependent disease causing pelvic pain and infertility in 10% of repr... more Endometriosis is an estrogen-dependent disease causing pelvic pain and infertility in 10% of reproductive-aged women. Despite a long history of the disease the pathogenesis of endometriosis is poorly understood. It is known that the expression of several proteins is either up or down regulated during endometriosis, but their precise role remains to be determined. DJ-1 is one such protein that is upregulated in eutopic endometrium of women having endometriosis suggesting that DJ-1 may be involved in the pathogenesis of endometriosis. The role of DJ-1 in the pathogenesis of endometriosis was investigated. For this purpose the influence of DJ-1 on endometrial cell survival, attachment, proliferation, migration, and invasion either by overexpressing DJ-1 in normal endometrial cells or by knocking down DJ-1 expression in endometriotic cells using siRNA was investigated. The results indicated that DJ-1 protects endometrial cells from oxidative stress mediated apoptosis. Overexpression of DJ-1 in normal endometrial epithelial cells increases the adhesion on collagen type IV. However, no significant difference was observed incase of stromal cells. It was further demonstrated that DJ-1 regulates cell proliferation, migration, and invasion in normal endometrial and endometriotic epithelial cells whereas in the case of normal endometrial and endometriotic stromal cells, it regulates cell proliferation and invasion but not migration. Furthermore, the present study also indicated that DJ-1 regulates these cellular processes by modulating PI3K/Akt pathway by interacting and negatively regulating PTEN. Abnormally high levels of DJ-1 expression may be involved in endometriosis, possibly by stimulating endometrial cell survival, proliferation, migration, and invasion.

Extremophiles, Mar 4, 2005

In a recent study, we established that psychrophilic Pseudomonas syringae (Lz4W) requires trans-m... more In a recent study, we established that psychrophilic Pseudomonas syringae (Lz4W) requires trans-monounsaturated fatty acid for growth at higher temperatures (Kiran et al. in Extremophiles, 2004). It was also demonstrated that the cti gene was highly conserved and exhibited high sequence identity with cti of other Pseudomonas spp. (Kiran et al. in Extremophiles, 2004). Therefore it would be interesting to understand the expression of the cti gene so as to unravel the molecular basis of adaptation of microorganisms to high temperature. In the present study, the expression of cti was monitored by RT-PCR analysis during different growth stages and under conditions of high temperature and solvent stress in P. syringae. Results indicated that the cti gene is constitutively expressed during different stages of growth and the transcript level is unaltered even under conditions of temperature and solvent stress implying that the observed increase in trans-monounsaturated fatty acids (Kiran et al. in Extremophiles, 2004) is not under transcriptional control. A putative promoter present in the intergenic region of the metH and cti gene has also been characterized. The translation start site ATG, the Shine-Dalgarno sequence AGGA and the transcription start site ''C'' were also identified. These results provide evidence for the first time that the cti gene is constitutively expressed under normal conditions of growth and under conditions of temperature and solvent stress thus implying that the Cti enzyme is post-transcriptionally regulated.

Tumor Biology, 2016

Mitochondrial displacement loop (D-loop) is a hot spot for mitochondrial DNA (mtDNA) alterations ... more Mitochondrial displacement loop (D-loop) is a hot spot for mitochondrial DNA (mtDNA) alterations that effects cellular reactive oxygen species (ROS) generation. Manganese-superoxide dismutase (Mn-SOD) is a major antioxidant enzyme that protects cells from ROS-mediated damage. In the present study, we investigated the relationship between sequence alterations of mitochondrial D-loop and Mn-SOD expression in colorectal cancer (CRC). Genotyping of entire mitochondrial D-loop (1124 bp) was carried out on mtDNA of analogous tumor and normal tissues from 35 CRC patients of south Indian origin by PCR-sequencing analysis. Tumor-specific large-scale mtDNA deletions and Mn-SOD expression was analyzed by PCR and Western blot analysis, respectively. We identified 87 polymorphisms in the D-loop region of tumor and/or control tissues. Polymorphisms were predominantly located in hypervariable region I (67.9 %) than in II (32.1 %) of D-loop. Significantly increased mtDNA microsatellite instability (mtMSI) [310'C' insertion (P = 0.00001) and T16189C (P = 0.0007)] and elevated Mn-SOD expression was observed in tumor tissues compared with controls. Interestingly, mtMSI was significantly high in tumors with Mn-SOD overexpression. Tumor-specific large-scale mtDNA deletions were not observed in CRC tissues. In conclusion, mtMSI and Mn-SOD overexpression are a common event in CRC. The analysis of mtMSI and/or Mn-SOD expression might help to identify patients at high risk for disease outcome, thereby helping to refine therapeutic decisions in CRC.

European Journal of Obstetrics and Gynecology and Reproductive Biology, Jan 9, 2010

subunit of PI3K, resulting in over-activation of Akt signaling . Recently, activating somatic mut... more subunit of PI3K, resulting in over-activation of Akt signaling . Recently, activating somatic mutations of PI3KCA gene were identified in various human cancers particularly in breast, endometroid and clear cell ovarian cancer and also in certain benign diseases . More than 75% of these mutations are clustered in the helical domain encoded by exon 9 and the kinase domain encoded by exon 20. In addition, three hot spot mutations in

European Journal of Obstetrics & Gynecology and Reproductive Biology, 2016

Polycystic ovarian syndrome (PCOS) is a complex and multifactorial disorder believed to be the co... more Polycystic ovarian syndrome (PCOS) is a complex and multifactorial disorder believed to be the consequence of a complex interaction between genetic, immunological, and environmental factors. The main aim of this study was to investigate the association of Connexin37 (Cx37)/Gap junction alpha 4 (GJA4) gene C1019T single nucleotide polymorphism (SNP) with the susceptibility to polycystic ovarian syndrome (PCOS) in South Indian women. This study comprises 98 PCOS patients and 100 healthy women without PCOS of South Indian origin. We genotyped total of seventeen selected Cx37 SNPs including C1019T (rs1764391) by polymerase chain reaction and sequencing analysis. The genotype frequency and allele distributions of cases and controls were analyzed using Fisher's exact test. The genotype and allele frequencies of the C1019T polymorphism significantly differ between cases and controls. The frequencies of C/C genotype (P=0.009) and 'C' allele (P=0.002) of the C1019T polymorphism showed a significant prevalence in cases compared to controls. Our findings suggest that the Cx37 C1019T variation may contribute to the risk of PCOS in the South Indian women.

Fems Yeast Research, Jun 1, 2008

Asporogenus yeast strains W113AT and W113B were isolated from the intestine of a dead Trinket sna... more Asporogenus yeast strains W113AT and W113B were isolated from the intestine of a dead Trinket snake. The two isolates showed 100% sequence similarity in the D1/D2 domain of the large-subunit (LSU) rRNA gene, internal transcribed spacer (ITS) 1-5.8S rRNA gene-ITS2 region and mitochondrial small-subunit rRNA gene and the cytochrome oxidase II gene sequence and also showed similar phenotypic characteristics. The nearest phylogenetic neighbors of W113AT and W113B based on the sequence of the D1/D2 domain of the LSU rRNA gene were Blastobotrys chiropterorum NRRL Y-17017T and Blastobotrys terrestris NRRL Y-17704T with about 98% similarity. The close affiliation of W113AT and W113B with B. chiropterorum NRRL Y-17017T and B. terrestris NRRL Y-17704T was also evident from the high similarity observed in the nucleotide sequences of the mitochondrial small subunit rRNA (96-97.8%) and the cytochrome oxidase II (95.5-95.6%) genes. In the neighbor-joining phylogenetic trees constructed based on the D1/D2 domain or cytochrome oxidase gene, the isolates clustered with the above-mentioned species. However, the isolates showed a number of differences in their phenotypic properties with B. chiropterorum NRRL Y-17017T and B. terrestris NRRL Y-17704T and hence are regarded as representing a novel member of the genus Blastobotrys, for which the name Blastobotrys serpentis sp. nov. is proposed.

Genomics Data, 2015

We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali ... more We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

Frontiers in Microbiology, 2015

Ocean iron fertilization is an approach to increase CO2 sequestration. The Indo-German iron ferti... more Ocean iron fertilization is an approach to increase CO2 sequestration. The Indo-German iron fertilization experiment "LOHAFEX" was carried out in the Southern Ocean surrounding Antarctica in 2009 to monitor changes in bacterial community structure following iron fertilization-induced phytoplankton bloom of the seawater from different depths. 16S rRNA gene libraries were constructed using metagenomic DNA from seawater prior to and after iron fertilization and the clones were sequenced for identification of the major bacterial groups present and for phylogenetic analyses. A total of 4439 clones of 16S rRNA genes from ten 16S rRNA gene libraries were sequenced. More than 97.35% of the sequences represented four bacterial lineages i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes and confirmed their role in scavenging of phytoplankton blooms induced following iron fertilization. The present study demonstrates the response of Firmicutes due to Iron fertilization which was not observed in previous southern ocean Iron fertilization studies. In addition, this study identifies three unique phylogenetic clusters LOHAFEX Cluster 1 (affiliated to Bacteroidetes), 2, and 3 (affiliated to Firmicutes) which were not detected in any of the earlier studies on iron fertilization. The relative abundance of these clusters in response to iron fertilization was different. The increase in abundance of LOHAFEX Cluster 2 and Papillibacter sp. another dominant Firmicutes may imply a role in phytoplankton degradation. Disappearance of LOHAFEX Cluster 3 and other bacterial genera after iron fertilization may imply conditions not conducive for their survival. It is hypothesized that heterotrophic bacterial abundance in the Southern Ocean would depend on their ability to utilize algal exudates, decaying algal biomass and other nutrients thus resulting in a dynamic bacterial succession of distinct genera.

Extremophiles : life under extreme conditions, 2003

Eleven psychrophilic bacteria were isolated from a solid layer of fast ice in the middle of Point... more Eleven psychrophilic bacteria were isolated from a solid layer of fast ice in the middle of Pointe-Geologie Archipelago, Adelie Land, Antarctica. The 11 isolates based on the phenotypic characteristics, chemotaxonomic and phylogenetic analysis have been identified as members of the genus Halomonas. All the isolates at the 16S rDNA sequence level were identical, possessed the 15 conserved nucleotides of the family Halomonadaceae and four nucleotides of the genus Halomonas. Therefore, the 16S rDNA sequence of DD 39 was used for calculating the evolutionary distances and for phylogenetic analysis. It was observed that DD 39 formed a robust cluster with H. variabilis, from which it differed by 0.7%. Further DNA-DNA hybridization studies indicated low DNA-DNA homology (15%) between H. variabilis and DD 39. Between the 11 Antarctic isolates the homology was >85%. In addition it was observed that DD 39 was different from H. variabilis in that it was psychrophilic, could tolerate only up...

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2005

A psychrotolerant, Gram-negative, motile bacterium, designated CK 47 T , was isolated from sea wa... more A psychrotolerant, Gram-negative, motile bacterium, designated CK 47 T , was isolated from sea water off the subantarctic Kerguelen islands (506 409 S 686 259 E). The isolate grew optimally at 22 6C and minimum and maximum temperature of growth were 4 and 37 6C, respectively. It required Na + for growth and exhibited optimum growth at pH 8?5 and 4 % NaCl. It utilized hexane, heptane and petroleum ether as sole sources of carbon. Strain CK 47 T had Q9 as the major respiratory quinone and C 16 : 0 (21?7 %), C 17 : 0 (21?3 %), C 18 : 0 (5?7 %), C 18 : 1 v7c (9?0 %) and C 18 : 1 v9c (31?4 %) as predominant fatty acids. The G+C content of the DNA was 58 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that CK 47 T formed a coherent cluster within the genus Marinobacter. It exhibited highest 16S rRNA gene sequence similarity of 96?8 % with Marinobacter lipolyticus. However, the level of DNA-DNA relatedness between strain CK47 T and M. lipolyticus was only 55 %. On the basis of phenotypic characteristics, and phylogenetic and genotypic distinctiveness, strain CK 47 T is considered to represent a novel species of the genus Marinobacter. The name Marinobacter maritimus sp. nov. is proposed, with CK 47 T (=JCM 12521 T =MTCC 6519 T ) as the type strain.

Theriogenology, 2004

The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual s... more The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual semen characteristics, to identify a suitable extender for semen short-term storage, to determine a protocol for cryopreservation of semen and finally to check whether intracloacal insemination would lead to the birth of a chick. Semen characteristics such as semen volume, sperm concentration, sperm motility, and percentage of normal spermatozoa were maximum during the monsoon season. TALP was observed to be the most suitable semen extender and the sperm survived best at 37 8C at a dilution of 1:100 in TALP. Further, cryopreservation studies on pigeon semen indicated that 8% DMSO with or without egg yolk (20%) proved to be a better cryoprotectant compared to glycerol and polyethylene glycol. In addition, the slow freezing protocol was better than the fast-freezing protocol and about 40% of the cryopreserved spermatozoa were motile following thawing. Computer-aided semen analysis indicated that pigeon spermatozoa were extremely active immediately after dilution in TALP and exhibited linear trajectories persisting up to 9 h. But, with time there was a timedependent decrease in the velocity parameters (VAP, VSL, and VCL). Cryopreserved spermatozoa following thawing also exhibited linear trajectories but had reduced velocity as evident from the significant decrease in VAP, VSL, and VCL. Further, artificial inseminations using fresh semen resulted in 45% fertilization and birth of a live chick. #

PLoS ONE, 2012

Background: Majority of the tiger habitat in Indian subcontinent lies within high human density l... more Background: Majority of the tiger habitat in Indian subcontinent lies within high human density landscapes and is highly sensitive to surrounding pressures. These forests are unable to sustain healthy tiger populations within a tiger-hostile matrix, despite considerable conservation efforts. Ranthambore Tiger Reserve (RTR) in Northwest India is one such isolated forest which is rapidly losing its links with other tiger territories in the Central Indian landscape. Non-invasive genetic sampling for individual identification is a potent technique to understand the relationships between threatened tiger populations in degraded habitats. This study is an attempt to establish tiger movement across a fragmented landscape between RTR and its neighboring forests, Kuno-Palpur Wildlife Sanctuary (KPWLS) and Madhav National Park (MNP) based on non-invasively obtained genetic data.

PLoS ONE, 2013

Background: Tiger populations are dwindling rapidly making it increasingly difficult to study the... more Background: Tiger populations are dwindling rapidly making it increasingly difficult to study their dispersal and mating behaviour in the wild, more so tiger being a secretive and solitary carnivore.

PLoS ONE, 2012

Background: Non-invasively collected samples allow a variety of genetic studies on endangered and... more Background: Non-invasively collected samples allow a variety of genetic studies on endangered and elusive species. However due to low amplification success and high genotyping error rates fewer samples can be identified up to the individual level. Number of PCRs needed to obtain reliable genotypes also noticeably increase.

Conservation Genetics, 2012

Tiger, being a solitary and territorial animal, often tends to move out of protected areas into t... more Tiger, being a solitary and territorial animal, often tends to move out of protected areas into the surrounding forests. This is especially true in the case of subadult animals leading to escalating conflicts and deaths in the surrounding human-dominated landscapes. Unless adequately protected against various human activities, such corridors and surrounding forests will soon disappear, trapping the animals within protected areas with resultant local extinctions. In this paper we ascertain tiger presence, occupancy and numbers in one such partially protected area, the Sathyamangalam forest, located close to better known tiger reserves in India, through non-invasive faecal DNA analysis. Here we highlight the potential of Sathyamangalam as a tiger habitat. Tiger positive faecal samples were considered as evidence to establish occupancy in two different parts of Sathyamangalam, reserve forest and wildlife sanctuary. We collected 103 faecal samples out of which 69 were tiger positive. Species occupancy (psi), was 0.672 (±0.197) with a detection probability of 0.2 (±0.06) in the wildlife sanctuary area; while psi was 0.72 (±0.2) with detection probability of 0.212 (±0.6) in the reserve forest. Further, number of males and females, as determined in our study, was close to the ideal sex ratio in a healthy forest with good prey abundance. This study also highlights the presence of more females in the reserve forest (n = 10) than the wildlife sanctuary (n = 3) possibly indicating lesser disturbance and more prey availability. We recommend that the reserve forest to the north of Sathyamangalam wildlife sanctuary be declared as a tiger reserve. The wildlife sanctuary could serve as a buffer zone between this reserve and Sathyamangalam town which lies to the south of the forest. Proper protection of Sathyamangalam will go a long way in saving the entire landscape and tigers of the Western Ghats of India.

Mitochondrial DNA Part A, 2016

Current Science, 2007

The rapid and inexplicable decline of the Old World vulture populations across the Indian subcont... more The rapid and inexplicable decline of the Old World vulture populations across the Indian subcontinent is a cause of growing concern among ecologists and conservationists. Survival of these threatened birds may depend on breeding programmes where sex identification plays an important role. Here, a PCR-based method that amplifies a region of the chromo-helicase-DNAbinding gene was modified to identify the sex of individuals of two Gyps species. The results were further reconfirmed by amplification refractory mutation system. This study allowed for the rapid and safe assessment of sex and will facilitate all future efforts in the captive breeding of these birds.

American Journal of Veterinary Research, Jan 2, 2007

Objective-To determine the anesthetic dose and cardiopulmonary effects of xylazine hydrochloride ... more Objective-To determine the anesthetic dose and cardiopulmonary effects of xylazine hydrochloride when used alone or in combination with ketamine hydrochloride and evaluate the efficacy of yohimbine hydrochloride to reverse anesthetic effects in captive Axis deer. Animals-35 adult (10 males and 25 females) Axis deer (Axis axis). Procedures-All deer were anesthetized by IM administration of xylazine (3.5 mg/kg; experiment 1), a combination of ketamine and xylazine (1.25 and 1.5 mg/kg, respectively; experiment 2), or another combination of ketamine and xylazine (2.5 and 0.5 mg/kg, respectively; experiment 3). In addition, female deer were also anesthetized by IM administration of a third combination of ketamine and xylazine (1.5 and 1 mg/kg, respectively; experiment 4). Ten to 40 minutes after induction, anesthesia was reversed by IV administration of yohimbine (5, 8, or 10 mg). Results-In male deer, experiment 3 yielded the most rapid induction of anesthesia. In females, experiment 4 yielded the best induction of anesthesia without adverse effects. All doses of yohimbine reversed anesthesia. Duration of anesthesia before administration of yohimbine had no effect on recovery time. Conclusions and Clinical Relevance-A combination of ketamine and xylazine can be used to induce anesthesia in Axis deer. Furthermore, anesthetic effects can be reversed by administration of yohimbine. (Am J Vet Res 2007;68:20-24).

Theriogenology, Jul 1, 2004

The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual s... more The present study was undertaken in the Blue rock pigeon (Columba livia) to evaluate the annual semen characteristics, to identify a suitable extender for semen short-term storage, to determine a protocol for cryopreservation of semen and finally to check whether intracloacal insemination would lead to the birth of a chick. Semen characteristics such as semen volume, sperm concentration, sperm motility, and percentage of normal spermatozoa were maximum during the monsoon season. TALP was observed to be the most suitable semen extender and the sperm survived best at 37 8C at a dilution of 1:100 in TALP. Further, cryopreservation studies on pigeon semen indicated that 8% DMSO with or without egg yolk (20%) proved to be a better cryoprotectant compared to glycerol and polyethylene glycol. In addition, the slow freezing protocol was better than the fast-freezing protocol and about 40% of the cryopreserved spermatozoa were motile following thawing. Computer-aided semen analysis indicated that pigeon spermatozoa were extremely active immediately after dilution in TALP and exhibited linear trajectories persisting up to 9 h. But, with time there was a timedependent decrease in the velocity parameters (VAP, VSL, and VCL). Cryopreserved spermatozoa following thawing also exhibited linear trajectories but had reduced velocity as evident from the significant decrease in VAP, VSL, and VCL. Further, artificial inseminations using fresh semen resulted in 45% fertilization and birth of a live chick. #

Plos One, 2011

Endometriosis is an estrogen-dependent disease causing pelvic pain and infertility in 10% of repr... more Endometriosis is an estrogen-dependent disease causing pelvic pain and infertility in 10% of reproductive-aged women. Despite a long history of the disease the pathogenesis of endometriosis is poorly understood. It is known that the expression of several proteins is either up or down regulated during endometriosis, but their precise role remains to be determined. DJ-1 is one such protein that is upregulated in eutopic endometrium of women having endometriosis suggesting that DJ-1 may be involved in the pathogenesis of endometriosis. The role of DJ-1 in the pathogenesis of endometriosis was investigated. For this purpose the influence of DJ-1 on endometrial cell survival, attachment, proliferation, migration, and invasion either by overexpressing DJ-1 in normal endometrial cells or by knocking down DJ-1 expression in endometriotic cells using siRNA was investigated. The results indicated that DJ-1 protects endometrial cells from oxidative stress mediated apoptosis. Overexpression of DJ-1 in normal endometrial epithelial cells increases the adhesion on collagen type IV. However, no significant difference was observed incase of stromal cells. It was further demonstrated that DJ-1 regulates cell proliferation, migration, and invasion in normal endometrial and endometriotic epithelial cells whereas in the case of normal endometrial and endometriotic stromal cells, it regulates cell proliferation and invasion but not migration. Furthermore, the present study also indicated that DJ-1 regulates these cellular processes by modulating PI3K/Akt pathway by interacting and negatively regulating PTEN. Abnormally high levels of DJ-1 expression may be involved in endometriosis, possibly by stimulating endometrial cell survival, proliferation, migration, and invasion.

Extremophiles, Mar 4, 2005

In a recent study, we established that psychrophilic Pseudomonas syringae (Lz4W) requires trans-m... more In a recent study, we established that psychrophilic Pseudomonas syringae (Lz4W) requires trans-monounsaturated fatty acid for growth at higher temperatures (Kiran et al. in Extremophiles, 2004). It was also demonstrated that the cti gene was highly conserved and exhibited high sequence identity with cti of other Pseudomonas spp. (Kiran et al. in Extremophiles, 2004). Therefore it would be interesting to understand the expression of the cti gene so as to unravel the molecular basis of adaptation of microorganisms to high temperature. In the present study, the expression of cti was monitored by RT-PCR analysis during different growth stages and under conditions of high temperature and solvent stress in P. syringae. Results indicated that the cti gene is constitutively expressed during different stages of growth and the transcript level is unaltered even under conditions of temperature and solvent stress implying that the observed increase in trans-monounsaturated fatty acids (Kiran et al. in Extremophiles, 2004) is not under transcriptional control. A putative promoter present in the intergenic region of the metH and cti gene has also been characterized. The translation start site ATG, the Shine-Dalgarno sequence AGGA and the transcription start site ''C'' were also identified. These results provide evidence for the first time that the cti gene is constitutively expressed under normal conditions of growth and under conditions of temperature and solvent stress thus implying that the Cti enzyme is post-transcriptionally regulated.

Tumor Biology, 2016

Mitochondrial displacement loop (D-loop) is a hot spot for mitochondrial DNA (mtDNA) alterations ... more Mitochondrial displacement loop (D-loop) is a hot spot for mitochondrial DNA (mtDNA) alterations that effects cellular reactive oxygen species (ROS) generation. Manganese-superoxide dismutase (Mn-SOD) is a major antioxidant enzyme that protects cells from ROS-mediated damage. In the present study, we investigated the relationship between sequence alterations of mitochondrial D-loop and Mn-SOD expression in colorectal cancer (CRC). Genotyping of entire mitochondrial D-loop (1124 bp) was carried out on mtDNA of analogous tumor and normal tissues from 35 CRC patients of south Indian origin by PCR-sequencing analysis. Tumor-specific large-scale mtDNA deletions and Mn-SOD expression was analyzed by PCR and Western blot analysis, respectively. We identified 87 polymorphisms in the D-loop region of tumor and/or control tissues. Polymorphisms were predominantly located in hypervariable region I (67.9 %) than in II (32.1 %) of D-loop. Significantly increased mtDNA microsatellite instability (mtMSI) [310'C' insertion (P = 0.00001) and T16189C (P = 0.0007)] and elevated Mn-SOD expression was observed in tumor tissues compared with controls. Interestingly, mtMSI was significantly high in tumors with Mn-SOD overexpression. Tumor-specific large-scale mtDNA deletions were not observed in CRC tissues. In conclusion, mtMSI and Mn-SOD overexpression are a common event in CRC. The analysis of mtMSI and/or Mn-SOD expression might help to identify patients at high risk for disease outcome, thereby helping to refine therapeutic decisions in CRC.

European Journal of Obstetrics and Gynecology and Reproductive Biology, Jan 9, 2010

subunit of PI3K, resulting in over-activation of Akt signaling . Recently, activating somatic mut... more subunit of PI3K, resulting in over-activation of Akt signaling . Recently, activating somatic mutations of PI3KCA gene were identified in various human cancers particularly in breast, endometroid and clear cell ovarian cancer and also in certain benign diseases . More than 75% of these mutations are clustered in the helical domain encoded by exon 9 and the kinase domain encoded by exon 20. In addition, three hot spot mutations in

European Journal of Obstetrics & Gynecology and Reproductive Biology, 2016

Polycystic ovarian syndrome (PCOS) is a complex and multifactorial disorder believed to be the co... more Polycystic ovarian syndrome (PCOS) is a complex and multifactorial disorder believed to be the consequence of a complex interaction between genetic, immunological, and environmental factors. The main aim of this study was to investigate the association of Connexin37 (Cx37)/Gap junction alpha 4 (GJA4) gene C1019T single nucleotide polymorphism (SNP) with the susceptibility to polycystic ovarian syndrome (PCOS) in South Indian women. This study comprises 98 PCOS patients and 100 healthy women without PCOS of South Indian origin. We genotyped total of seventeen selected Cx37 SNPs including C1019T (rs1764391) by polymerase chain reaction and sequencing analysis. The genotype frequency and allele distributions of cases and controls were analyzed using Fisher's exact test. The genotype and allele frequencies of the C1019T polymorphism significantly differ between cases and controls. The frequencies of C/C genotype (P=0.009) and 'C' allele (P=0.002) of the C1019T polymorphism showed a significant prevalence in cases compared to controls. Our findings suggest that the Cx37 C1019T variation may contribute to the risk of PCOS in the South Indian women.

Fems Yeast Research, Jun 1, 2008

Asporogenus yeast strains W113AT and W113B were isolated from the intestine of a dead Trinket sna... more Asporogenus yeast strains W113AT and W113B were isolated from the intestine of a dead Trinket snake. The two isolates showed 100% sequence similarity in the D1/D2 domain of the large-subunit (LSU) rRNA gene, internal transcribed spacer (ITS) 1-5.8S rRNA gene-ITS2 region and mitochondrial small-subunit rRNA gene and the cytochrome oxidase II gene sequence and also showed similar phenotypic characteristics. The nearest phylogenetic neighbors of W113AT and W113B based on the sequence of the D1/D2 domain of the LSU rRNA gene were Blastobotrys chiropterorum NRRL Y-17017T and Blastobotrys terrestris NRRL Y-17704T with about 98% similarity. The close affiliation of W113AT and W113B with B. chiropterorum NRRL Y-17017T and B. terrestris NRRL Y-17704T was also evident from the high similarity observed in the nucleotide sequences of the mitochondrial small subunit rRNA (96-97.8%) and the cytochrome oxidase II (95.5-95.6%) genes. In the neighbor-joining phylogenetic trees constructed based on the D1/D2 domain or cytochrome oxidase gene, the isolates clustered with the above-mentioned species. However, the isolates showed a number of differences in their phenotypic properties with B. chiropterorum NRRL Y-17017T and B. terrestris NRRL Y-17704T and hence are regarded as representing a novel member of the genus Blastobotrys, for which the name Blastobotrys serpentis sp. nov. is proposed.

Genomics Data, 2015

We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali ... more We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

Frontiers in Microbiology, 2015

Ocean iron fertilization is an approach to increase CO2 sequestration. The Indo-German iron ferti... more Ocean iron fertilization is an approach to increase CO2 sequestration. The Indo-German iron fertilization experiment "LOHAFEX" was carried out in the Southern Ocean surrounding Antarctica in 2009 to monitor changes in bacterial community structure following iron fertilization-induced phytoplankton bloom of the seawater from different depths. 16S rRNA gene libraries were constructed using metagenomic DNA from seawater prior to and after iron fertilization and the clones were sequenced for identification of the major bacterial groups present and for phylogenetic analyses. A total of 4439 clones of 16S rRNA genes from ten 16S rRNA gene libraries were sequenced. More than 97.35% of the sequences represented four bacterial lineages i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes and confirmed their role in scavenging of phytoplankton blooms induced following iron fertilization. The present study demonstrates the response of Firmicutes due to Iron fertilization which was not observed in previous southern ocean Iron fertilization studies. In addition, this study identifies three unique phylogenetic clusters LOHAFEX Cluster 1 (affiliated to Bacteroidetes), 2, and 3 (affiliated to Firmicutes) which were not detected in any of the earlier studies on iron fertilization. The relative abundance of these clusters in response to iron fertilization was different. The increase in abundance of LOHAFEX Cluster 2 and Papillibacter sp. another dominant Firmicutes may imply a role in phytoplankton degradation. Disappearance of LOHAFEX Cluster 3 and other bacterial genera after iron fertilization may imply conditions not conducive for their survival. It is hypothesized that heterotrophic bacterial abundance in the Southern Ocean would depend on their ability to utilize algal exudates, decaying algal biomass and other nutrients thus resulting in a dynamic bacterial succession of distinct genera.

Extremophiles : life under extreme conditions, 2003

Eleven psychrophilic bacteria were isolated from a solid layer of fast ice in the middle of Point... more Eleven psychrophilic bacteria were isolated from a solid layer of fast ice in the middle of Pointe-Geologie Archipelago, Adelie Land, Antarctica. The 11 isolates based on the phenotypic characteristics, chemotaxonomic and phylogenetic analysis have been identified as members of the genus Halomonas. All the isolates at the 16S rDNA sequence level were identical, possessed the 15 conserved nucleotides of the family Halomonadaceae and four nucleotides of the genus Halomonas. Therefore, the 16S rDNA sequence of DD 39 was used for calculating the evolutionary distances and for phylogenetic analysis. It was observed that DD 39 formed a robust cluster with H. variabilis, from which it differed by 0.7%. Further DNA-DNA hybridization studies indicated low DNA-DNA homology (15%) between H. variabilis and DD 39. Between the 11 Antarctic isolates the homology was >85%. In addition it was observed that DD 39 was different from H. variabilis in that it was psychrophilic, could tolerate only up...