Subramanian S

References (22)

Title : Genome sequence and comparative analysis of clavicipitaceous insect-pathogenic fungus Aschersonia badia with Metarhizium spp - Agrawal_2016_BMC.Genomics_17_367
Author(s) : Agrawal Y , Narwani T , Subramanian S
Ref : BMC Genomics , 17 :367 , 2016
Abstract : BACKGROUND: Aschersonia badia [(Ab) Teleomorph: Hypocrella siamensis] is an entomopathogenic fungus that specifically infects scale insects and whiteflies. We present the whole genome sequence of Ab and its comparison with two clavicipitaceous fungi Metarhizium robertsii (MR: generalist entomopathogen) and M. acridum (MAC: acridid-specific entomopathogen) that exhibit variable host preferences. Here, through comparative analysis of pathogen-host interacting genes, carbohydrate active enzymes, secondary metabolite biosynthesis genes, and sexuality genes, we explore the proteins with possible virulence functions in clavicipitaceous fungi. Comprehensive overview of GH18 family chitinases has been provided to decipher the role of chitinases in claviceptaceous fungi that are either host specific or generalists.
RESULTS: We report the 28.8 Mb draft genome of Ab and its comparative genome analysis with MR and MAC. The comparative analyses suggests expansion in pathogen-host interacting gene families and carbohydrate active enzyme families in MR, whilst their contraction in Ab and MAC genomes. The multi-modular NRPS gene (dtxS1) responsible for biosynthesis of the secondary metabolite destruxin in MR is not conserved in Ab, similar to the specialist pathogen MAC. An additional siderophore biosynthetic gene responsible for acquisition of iron was identified in MR. Further, the domain survey of chitinases suggest that the CBM50 (LysM) domains, which participate in chitin-binding functions, were not observed in MAC, but were present in Ab and MR. However, apparent differences in frequency of CBM50 domains associated with chitinases of Ab and MR was identified, where MR chitinases displayed a higher proportion of associated CBM50 domains than Ab chitinases.
CONCLUSIONS: This study suggests differences in distribution of dtxS1 and chitinases in specialists (Ab and MAC) and generalists (MR) fungi. Our analysis also suggests the presence of a siderophore biosynthetic gene in the MR genome which perhaps aids in enhanced virulence potential and host range. The variation in association of CBMs, being higher in generalists (MR) and lower in specialists (Ab and MAC) fungi may further be responsible for the differences in host affiliation.
ESTHER : Agrawal_2016_BMC.Genomics_17_367
PubMedSearch : Agrawal_2016_BMC.Genomics_17_367
PubMedID: 27189621
Gene_locus related to this paper: 9hypo-a0a173g907 , 9hypo-a0a173g924 , 9hypo-a0a173g926 , 9hypo-a0a173g937 , 9hypo-a0a173g946

Title : Cognition enhancing effect of the aqueous extract of Cinnamomum zeylanicum on non-transgenic Alzheimer's disease rat model: Biochemical, histological, and behavioural studies - Madhavadas_2016_Nutr.Neurosci__1
Author(s) : Madhavadas S , Subramanian S
Ref : Nutr Neurosci , :1 , 2016
Abstract : OBJECTIVE: Several dietary supplements are actively being tested for their dual role of alleviating the metabolic perturbations and restricting the consequent cognitive dysfunctions seen in neurodegenerative disorders such as Alzheimer's disease (AD). The aim of the current study was to assess the influence of aqueous extract of cinnamon (CE) on the monosodium glutamate-induced non-transgenic rat model of AD (NTAD) established with insulin resistance, hyperglycaemia, neuronal loss, and cognitive impairment at a very early stage of life.
METHODS: The experimental design included oral administration of CE (50 mg/kg body weight) for 20 weeks to 2-month and 10-month-old NTAD rats. Following the treatments, the animals attained 7 and 15 months of age, respectively. They were then subjected to behavioural testing, biochemical analysis, and stereology experiments.
RESULTS: The results demonstrated that CE treatment improved the insulin sensitivity, increased phosphorylated glycogen synthase kinase-3beta (pGSK3beta), inhibited the cholinesterase activity, and improved the learning ability in NTAD rats. Histological evaluation has shown an increase in neuron count in the DG sub-field of hippocampus upon treatment with CE. DISCUSSION: These beneficial effects of CE are suggestive of considering cinnamon as a dietary supplement in modulating the metabolic changes and cognitive functions.
ESTHER : Madhavadas_2016_Nutr.Neurosci__1
PubMedSearch : Madhavadas_2016_Nutr.Neurosci__1
PubMedID: 27308892

Title : The Neuroprotective Effect of Dark Chocolate in Monosodium Glutamate-Induced Nontransgenic Alzheimer Disease Model Rats: Biochemical, Behavioral, and Histological Studies - Madhavadas_2016_J.Diet.Suppl_13_449
Author(s) : Madhavadas S , Kapgal VK , Kutty BM , Subramanian S
Ref : J Diet Suppl , 13 :449 , 2016
Abstract : The vulnerability to oxidative stress and cognitive decline continue to increase during both normal and pathological aging. Dietary changes and sedentary life style resulting in mid-life obesity and type 2 diabetes, if left uncorrected, further add to the risk of cognitive decline and Alzheimer disease (AD) in the later stages of life. Certain antioxidant agents such as dietary polyphenols, taken in adequate quantities, have been suggested to improve the cognitive processes. In this study, we examined the effect of oral administration of dark chocolate (DC) containing 70% cocoa solids and 4% total polyphenol content for three months at a dose of 500 mg/Kg body weight per day to 17-month-old monosodium glutamate treated obese Sprague-Dawley rats, earlier characterized as a nontransgenic AD (NTAD) rat model after reversal of obesity, diabetes, and consequent cognitive impairments. The results demonstrated that DC reduced the hyperglycemia, inhibited the cholinesterase activity in the hippocampal tissue homogenates, and improved the cognitive performance in spatial memory related Barnes maze task. Histological studies revealed an increase in cell volume in the DC treated rats in the CA3 region of the hippocampus. These findings demonstrated the benefits of DC in enhancing cognitive function and cholinergic activity in the hippocampus of the aged NTAD rats while correcting their metabolic disturbances.
ESTHER : Madhavadas_2016_J.Diet.Suppl_13_449
PubMedSearch : Madhavadas_2016_J.Diet.Suppl_13_449
PubMedID: 26673833

Title : Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus - Sharma_2016_PLoS.One_11_e0148593
Author(s) : Sharma G , Narwani T , Subramanian S
Ref : PLoS ONE , 11 :e0148593 , 2016
Abstract : Myxobacteria, a group of Gram-negative aerobes, belong to the class delta-proteobacteria and order Myxococcales. Unlike anaerobic delta-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales delta-proteobacteria.
ESTHER : Sharma_2016_PLoS.One_11_e0148593
PubMedSearch : Sharma_2016_PLoS.One_11_e0148593
PubMedID: 26900859
Gene_locus related to this paper: 9delt-a0a0h4wwv8 , 9delt-a0a0h4x5w8 , 9delt-a0a0h4xf04

Title : Signaling in the phytomicrobiome: breadth and potential - Smith_2015_Front.Plant.Sci_6_709
Author(s) : Smith DL , Subramanian S , Lamont JR , Bywater-Ekegard M
Ref : Front Plant Sci , 6 :709 , 2015
Abstract : Higher plants have evolved intimate, complex, subtle, and relatively constant relationships with a suite of microbes, the phytomicrobiome. Over the last few decades we have learned that plants and microbes can use molecular signals to communicate. This is well-established for the legume-rhizobia nitrogen-fixing symbiosis, and reasonably elucidated for mycorrhizal associations. Bacteria within the phytomircobiome communicate among themselves through quorum sensing and other mechanisms. Plants also detect materials produced by potential pathogens and activate pathogen-response systems. This intercommunication dictates aspects of plant development, architecture, and productivity. Understanding this signaling via biochemical, genomics, proteomics, and metabolomic studies has added valuable knowledge regarding development of effective, low-cost, eco-friendly crop inputs that reduce fossil fuel intense inputs. This knowledge underpins phytomicrobiome engineering: manipulating the beneficial consortia that manufacture signals/products that improve the ability of the plant-phytomicrobiome community to deal with various soil and climatic conditions, leading to enhanced overall crop plant productivity.
ESTHER : Smith_2015_Front.Plant.Sci_6_709
PubMedSearch : Smith_2015_Front.Plant.Sci_6_709
PubMedID: 26442023

Title : Combination of Spirulina with glycyrrhizin prevents cognitive dysfunction in aged obese rats - Madhavadas_2015_Indian.J.Pharmacol_47_39
Author(s) : Madhavadas S , Subramanian S
Ref : Indian J Pharmacol , 47 :39 , 2015
Abstract : OBJECTIVES: To evaluate the cognition enhancing effect of the combination of Spirulina and glycyrrhizin in monosodium glutamate (MSG)-induced obese aged rats. MATERIALS AND
METHODS: Obesity was induced in rats by administration of MSG (intraperitoneally, 4 mg/g body weight) for 14 consecutive days from day 1 after birth. Subsequently, the animals were allowed to grow for 18 months with food and water ad libitum. Hypercholesterolemia, hyperglycemia, leptin resistance, were monitored in these animals. Cognitive status was assessed by Barne's maze task and hippocampal acetylcholinesterase (AChE) levels. Further, the animals were treated with Spirulina (Sp) (oral route, 1 g/Kg body weight, for 30 days) alone or glycyrrhizin (Gly) alone (intraperitoneal route, 0.1 mg/Kg, on day 15 and day 21), or their combination (SpGly). Counting of the treatment days was done by considering first day of Sp administration as day 1. After the completion of 30 days of Spirulina treatment or 2 doses of Gly administration or the combination (SpGly) treatment, the animals were left for 3 weeks. They were then were assessed for their biochemical and cognitive changes.
RESULTS: The combination of Sp with Gly showed a significant reduction (P < 0.0001) in glucose, cholesterol, leptin levels in the serum with improvement in cognitive functions with concomitant reduction in AChE activity in the hippocampal tissue homogenates (P < 0.0001) of the obese rats. CONCLUSION: SpGly combination has a potential role in reversing cognitive dysfunctions associated with aging and obesity.
ESTHER : Madhavadas_2015_Indian.J.Pharmacol_47_39
PubMedSearch : Madhavadas_2015_Indian.J.Pharmacol_47_39
PubMedID: 25821309

Title : In vitro evaluation of anti-Alzheimer effects of dry ginger (Zingiber officinale Roscoe) extract - Mathew_2014_Indian.J.Exp.Biol_52_606
Author(s) : Mathew M , Subramanian S
Ref : Indian J Exp Biol , 52 :606 , 2014
Abstract : As the disease modifying therapies against Alzheimer's disease (AD) continue to exist as a major challenge of this century, the search for newer drug leads with lesser side effects is on the rise. A large number of plant extracts and phytocompounds are being actively pursued for their anti-Alzheimer effects. In the present study, the antioxidant activity, cholinesterase inhibition, anti-amyloidogenic potential and neuroprotective properties of methanolic extract of dry ginger (GE) have been evaluated. The extract contained 18 +/- 0.6 mg/g gallic acid equivalents of total phenolic content and 4.18 +/- 0.69 mg quercetin equivalents/g of dry material. GE expressed high antioxidant activity with an IC50 value of 70 +/- 0.304 microg/mL in DPPH assay and 845.4 +/- 56.62 microM Fe(II) equivalents/g dry weight in FRAP assay respectively. In Ellman's assay for the cholinesterase inhibitory activity, GE had an IC50 value of 41 +/- 1.2 microg/mL and 52 +/- 2 microg/mL for inhibition of acetyl- and butyrylcholinesterase respectively. Also, GE increased the cell survival against amyloid beta (Abeta) induced toxicity in primary adult rat hippocampal cell culture. Aggregation experiments with the thioflavin T binding studies showed that GE effectively prevented the formation of Abeta oligomers and dissociated the preformed oligomers. These findings suggest that methanolic GE influences multiple therapeutic molecular targets of AD and can be considered as an effective nontoxic neutraceutical supplement for AD.
ESTHER : Mathew_2014_Indian.J.Exp.Biol_52_606
PubMedSearch : Mathew_2014_Indian.J.Exp.Biol_52_606
PubMedID: 24956891

Title : Effect of treatment for 12 weeks with rilapladib, a lipoprotein-associated phospholipase A2 inhibitor, on arterial inflammation as assessed with 18F-fluorodeoxyglucose-positron emission tomography imaging -
Author(s) : Tawakol A , Singh P , Rudd JH , Soffer J , Cai G , Vucic E , Brannan SP , Tarka EA , Shaddinger BC , Sarov-Blat L , Matthews P , Subramanian S , Farkouh M , Fayad ZA
Ref : J Am Coll Cardiol , 63 :86 , 2014
PubMedID: 23973698

Title : Amyloid beta lowering and cognition enhancing effects of ghrelin receptor analog [D-Lys (3)] GHRP-6 in rat model of obesity - Madhavadas_2014_Indian.J.Biochem.Biophys_51_257
Author(s) : Madhavadas S , Kutty BM , Subramanian S
Ref : Indian J Biochem Biophys , 51 :257 , 2014
Abstract : Obesity arising due to the dietary and life style changes is fast reaching epidemic proportions all over the world. There is increasing evidence that the incidence of Alzheimer disease (AD) is significantly influenced by a cluster of metabolic diseases, including diabetes and obesity. This study was aimed to test the suitability of experimentally-induced obesity in rats as an experimental animal model of AD. We used the procedure of neonatal administration of rats with monosodium L-glutamate (MSG), which generates adult obese animals as our study design and assessed the AD-like changes by measuring amyloid beta (1-42) and acetylcholinesterase (AChE) levels in the hippocampal extracts and cognitive impairments by Barnes maze task. Further, we investigated the influence of anti-obesity substance [D-Lys (3)] GHRP-6 on blood glucose, hippocampal Abeta, AChE levels and restoration of cognitive deficits. Results revealed that administration of MSG to neonatal rats exhibited increased body mass index and serum glucose levels over the controls. Measurement of markers for AD-like molecular changes i.e. amyloid beta (Abeta) and AChE levels showed marked elevation in these two parameters in the hippocampus of MSG-treated rats. Assessment of cognitive abilities by Barnes maze revealed spatial disorientation characteristic of AD. Administration of ghrelin receptor analog [D-Lys (3)] GHRP-6 to obese rats resulted in significant restoration of serum cholesterol, glucose, leptin and ghrelin levels to that of control with concomitant reduction in hippocampal Abeta and AChE levels. In addition, the treated animals exhibited marked improvement in Barne's maze task. These findings suggest that MSG-induced obese rats may serve as non-transgenic animal model for AD research. Further, the results indicate the potential of [D-Lys (3)] GHRP-6 as a promising anti-Alzheimer candidate.
ESTHER : Madhavadas_2014_Indian.J.Biochem.Biophys_51_257
PubMedSearch : Madhavadas_2014_Indian.J.Biochem.Biophys_51_257
PubMedID: 25296496

Title : Grimontia indica AK16(T), sp. nov., isolated from a seawater sample reports the presence of pathogenic genes similar to Vibrio genus - Singh_2014_PLoS.One_9_e85590
Author(s) : Singh A , Vaidya B , Khatri I , Srinivas TN , Subramanian S , Korpole S , Pinnaka AK
Ref : PLoS ONE , 9 :e85590 , 2014
Abstract : Grimontia indica strain AK16(T) sp. nov. is the type strain of G. indica sp. nov. a new species within the genus Grimontia. This strain, whose genome is described here, was isolated from seawater sample collected from southeast coast of Palk Bay, India. G. indica AK16(T) is a Gram-negative, facultative aerobic rod shaped bacterium. There are only two other strains in the genus Grimontia one of which, Grimontia hollisae CIP 101886(T), is a reported human pathogen isolated from human stool sample while the other, 'Grimontia marina IMCC5001(T)', was isolated from a seawater sample. As compared to the pathogenic strain Grimontia hollisae CIP 101886(T), the strain AK16(T) lacks some genes for pathogenesis like the accessory colonization factors AcfA and AcfD, which are required for the colonization of the bacterium in the host body. While it carries some pathogenesis genes like OmpU, which are related to pathogenesis of Vibrio strains. This suggests that the life cycle of AK16(T) may include some pathogenic interactions with marine animal(s), or it may be an opportunistic pathogen. Study of the Grimontia genus is important because of the severe pathogenic traits exhibited by a member of the genus with only three species reported in total. The study will provide some vital information which may be useful in future clinical studies on the genus.
ESTHER : Singh_2014_PLoS.One_9_e85590
PubMedSearch : Singh_2014_PLoS.One_9_e85590
PubMedID: 24465608
Gene_locus related to this paper: 9gamm-r1gxz6 , 9gamm-r1isj4

Title : In vitro screening for anti-cholinesterase and antioxidant activity of methanolic extracts of ayurvedic medicinal plants used for cognitive disorders - Mathew_2014_PLoS.One_9_e86804
Author(s) : Mathew M , Subramanian S
Ref : PLoS ONE , 9 :e86804 , 2014
Abstract : Inhibition of Acetylcholinesterase (AChE) is still considered as the main therapeutic strategy against Alzheimer's disease (AD). Many plant derived phytochemicals have shown AChE inhibitory activity in addition to the currently approved drugs for AD. In the present study, methanolic extracts of 20 plants used in Indian Ayurvedic system of medicine for improving cognitive function were screened for acetylcholinesterase inhibitory activity by Ellman's microplate colorimetric method. Out of 20 extracts, Emblica officinalis, Nardostachys jatamansi, Nelumbo nucifera, Punica granatum and Raulfia Serpentina showed IC50 values <100 microg/ml for acetylcholinesterase inhibitory activity. Antioxidant activities of these plants were assessed by DPPH scavenging assay. Among the extracts used, antioxidant activity was highest for Terminalia chebula and Emblica officinalis with IC50 values <10 microg/ml. Considering the complex multifactorial etiology of AD, these plant extracts will be safer and better candidates for the future disease modifying therapies against this devastating disease.
ESTHER : Mathew_2014_PLoS.One_9_e86804
PubMedSearch : Mathew_2014_PLoS.One_9_e86804
PubMedID: 24466247

Title : Draft Genome Sequence of an Alphaproteobacterium, Caenispirillum salinarum AK4(T), Isolated from a Solar Saltern - Khatri_2013_Genome.Announc_1_e00199
Author(s) : Khatri I , Singh A , Korpole S , Pinnaka AK , Subramanian S
Ref : Genome Announc , 1 :e00199 , 2013
Abstract : We report the 4.9-Mb genome sequence of Caenispirillum salinarum AK4(T) isolated from a sediment sample collected from a solar saltern at Kakinada, Andhra Pradesh, India.
ESTHER : Khatri_2013_Genome.Announc_1_e00199
PubMedSearch : Khatri_2013_Genome.Announc_1_e00199
PubMedID: 23409257
Gene_locus related to this paper: 9prot-k9hby5 , 9prot-k9h6r8 , 9prot-k9gvg0 , 9prot-k9hxc6 , 9prot-k9hgf9 , 9prot-k9h698

Title : Evidence of a new metabolic capacity in an emerging diarrheal pathogen: lessons from the draft genomes of Vibrio fluvialis strains PG41 and I21563 - Khatri_2013_Gut.Pathog_5_20
Author(s) : Khatri I , Mahajan S , Dureja C , Subramanian S , Raychaudhuri S
Ref : Gut Pathog , 5 :20 , 2013
Abstract : BACKGROUND: Vibrio fluvialis is an emerging diarrheal pathogen for which no genome is currently available. In this work, draft genomes of two closely related clinical strains PG41 and I21563 have been explored.
RESULTS: V. fluvialis strains PG41 and I21563 were sequenced on the Illumina HiSeq 1000 platform to obtain draft genomes of 5.3 Mbp and 4.4 Mbp respectively. Our genome data reveal the presence of genes involved in ethanolamine utilization, which is further experimentally confirmed by growth analysis.
CONCLUSIONS: Combined in silico and growth analysis establish a new metabolic capacity of V. fluvialis to harvest energy from ethanolamine.
ESTHER : Khatri_2013_Gut.Pathog_5_20
PubMedSearch : Khatri_2013_Gut.Pathog_5_20
PubMedID: 23895343
Gene_locus related to this paper: vibfl-s7jn27 , vibfl-s7jp13 , vibfl-s7hvp8 , vibfl-s7jsn3 , vibfl-s7jrv9

Title : Draft Genome Sequence of the Opportunistic Human Pathogen Morganella morganii SC01 - Khatri_2013_Genome.Announc_1_E00051
Author(s) : Khatri I , Dureja C , Raychaudhuri S , Subramanian S
Ref : Genome Announc , 1 : , 2013
Abstract : We report the 4.1-Mb draft genome sequence of Morganella morganii SC01, a gammaproteobacterium, isolated from an Indian human fecal sample.
ESTHER : Khatri_2013_Genome.Announc_1_E00051
PubMedSearch : Khatri_2013_Genome.Announc_1_E00051
PubMedID: 23405333
Gene_locus related to this paper: 9entr-x6pmn0 , mormo-w1aha7

Title : Draft Genome Sequence of Plant Growth-Promoting Rhizobacterium Pantoea sp. Strain AS-PWVM4 - Khatri_2013_Genome.Announc_1_e00947
Author(s) : Khatri I , Kaur S , Devi U , Kumar N , Sharma D , Subramanian S , Saini AK
Ref : Genome Announc , 1 : , 2013
Abstract : Nonpathogenic Pantoea spp. have been shown to confer biofertilizer and biocontrol activities, indicating their potential for increasing crop yield. Herein, we provide the high-quality genome sequence of Pantoea sp. strain AS-PWVM4, a Gram-negative motile plant growth-promoting rhizobacterium isolated from a pomegranate plant. The 4.9-Mb genome contains genes related to plant growth promotion and the synthesis of siderophores.
ESTHER : Khatri_2013_Genome.Announc_1_e00947
PubMedSearch : Khatri_2013_Genome.Announc_1_e00947
PubMedID: 24309733
Gene_locus related to this paper: 9entr-u2ml62 , 9entr-u2ml82 , pansa-e6w851

Title : Draft Genome Sequence of a Plant Growth-Promoting Rhizobacterium, Serratia fonticola Strain AU-P3(3) - Devi_2013_Genome.Announc_1_e00946
Author(s) : Devi U , Khatri I , Kumar N , Kumar L , Sharma D , Subramanian S , Saini AK
Ref : Genome Announc , 1 :e00946 , 2013
Abstract : Plant growth-promoting rhizobacteria (PGPR), found in the rhizospheric region of plants, not only suppress plant disease, but also directly improve plant health by improving the availability of nutrients and by providing phytostimulants. Herein, we report the high-quality genome sequence of Serratia fonticola strain AU-P3(3), a PGPR of the pea plant, which confers phosphate solubilization, indole-3-acetic acid production, ammonia production, hydrogen cyanide (HCN) production, and siderophore production and also confers activity against Rhizoctonia species. The 5.02-Mb genome sequence contains genes related to plant growth promotion and biocontrol activities.
ESTHER : Devi_2013_Genome.Announc_1_e00946
PubMedSearch : Devi_2013_Genome.Announc_1_e00946
PubMedID: 24233592
Gene_locus related to this paper: serfo-u2m865 , serpl-s4yi15

Title : Draft Genome Sequence of Plant-Growth-Promoting Rhizobacterium Serratia fonticola Strain AU-AP2C, Isolated from the Pea Rhizosphere - Devi_2013_Genome.Announc_1_e01022
Author(s) : Devi U , Khatri I , Kumar N , Sharma D , Subramanian S , Saini AK
Ref : Genome Announc , 1 : , 2013
Abstract : Plant health can be augmented by plant-growth-promoting rhizobacteria (PGPR) that confer biofertilizer, phytostimulation, and biocontrol activities. Herein, we provide the high-quality draft genome sequence of Serratia fonticola strain AU-AP2C, a Gram-negative motile PGPR of the pea plant, conferring phosphate solubilization, ammonia production, and antifungal activity against Fusarium sp. The 4.9-Mb genome contains genes related to plant growth promotion and synthesis of siderophores.
ESTHER : Devi_2013_Genome.Announc_1_e01022
PubMedSearch : Devi_2013_Genome.Announc_1_e01022
PubMedID: 24309742
Gene_locus related to this paper: serfo-u2m4p0 , serfo-u2m865 , serpl-s4yi15

Title : Draft genome sequence of Rhodovulum sp. strain PH10, a phototrophic alphaproteobacterium isolated from a soil sample of mangrove of Namkhana, India - Khatri_2012_J.Bacteriol_194_6363
Author(s) : Khatri I , Nupur , Korpole S , Subramanian S , Pinnaka AK
Ref : Journal of Bacteriology , 194 :6363 , 2012
Abstract : We report the 4.8-Mb draft genome of Rhodovulum sp. strain PH10, a phototrophic bacterium belonging to class Alphaproteobacteria, isolated from a soil sample collected from the mangrove forest of Namkhana in India. This genome is the first from the genus Rhodovulum and will lead to a better understanding of the genes/pathways involved in activities like phototrophic growth and nitrogen fixation in this group of bacteria.
ESTHER : Khatri_2012_J.Bacteriol_194_6363
PubMedSearch : Khatri_2012_J.Bacteriol_194_6363
PubMedID: 23105089
Gene_locus related to this paper: 9rhob-j6j4b1 , 9rhob-j6j056 , 9rhob-j6ug77 , 9rhob-j9dsh3 , 9rhob-j6lde4

Title : Genome sequence of the halotolerant bacterium Imtechella halotolerans K1T - Kumar_2012_J.Bacteriol_194_3731
Author(s) : Kumar S , Vikram S , Subramanian S , Raghava GP , Pinnaka AK
Ref : Journal of Bacteriology , 194 :3731 , 2012
Abstract : We report the 3.087-Mb genome sequence of Imtechella halotolerans K1(T), isolated from an estuarine water sample collected from Kochi, Kerala, India. Strain K1 was recently reported as a novel genus of the family Flavobacteriaceae.
ESTHER : Kumar_2012_J.Bacteriol_194_3731
PubMedSearch : Kumar_2012_J.Bacteriol_194_3731
PubMedID: 22740661
Gene_locus related to this paper: 9flao-i0wf68 , 9flao-i0we86

Title : Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300 - Vikram_2012_J.Bacteriol_194_3543
Author(s) : Vikram S , Kumar S , Subramanian S , Raghava GP
Ref : Journal of Bacteriology , 194 :3543 , 2012
Abstract : We report the 8.231-Mb genome sequence of Rhodococcus imtechensis RKJ300, isolated from pesticide-contaminated soil in Punjab, India. The genome sequence of the strain RKJ300 will be helpful in exploring the molecular pathways involved in the degradation of nitrophenols.
ESTHER : Vikram_2012_J.Bacteriol_194_3543
PubMedSearch : Vikram_2012_J.Bacteriol_194_3543
PubMedID: 22689233
Gene_locus related to this paper: rhoop-pcaL , rhosr-q0sgc8 , rhosr-q0sh74 , rhoob-c1b934 , rhosr-q0sab7 , 9noca-i0wah3 , rhoob-c1asm3 , 9noca-i0wkn6 , 9noca-i0wm39 , rhoop-k8x8c5

Title : The DNA sequence, annotation and analysis of human chromosome 3 - Muzny_2006_Nature_440_1194
Author(s) : Muzny DM , Scherer SE , Kaul R , Wang J , Yu J , Sudbrak R , Buhay CJ , Chen R , Cree A , Ding Y , Dugan-Rocha S , Gill R , Gunaratne P , Harris RA , Hawes AC , Hernandez J , Hodgson AV , Hume J , Jackson A , Khan ZM , Kovar-Smith C , Lewis LR , Lozado RJ , Metzker ML , Milosavljevic A , Miner GR , Morgan MB , Nazareth LV , Scott G , Sodergren E , Song XZ , Steffen D , Wei S , Wheeler DA , Wright MW , Worley KC , Yuan Y , Zhang Z , Adams CQ , Ansari-Lari MA , Ayele M , Brown MJ , Chen G , Chen Z , Clendenning J , Clerc-Blankenburg KP , Davis C , Delgado O , Dinh HH , Dong W , Draper H , Ernst S , Fu G , Gonzalez-Garay ML , Garcia DK , Gillett W , Gu J , Hao B , Haugen E , Havlak P , He X , Hennig S , Hu S , Huang W , Jackson LR , Jacob LS , Kelly SH , Kube M , Levy R , Li Z , Liu B , Liu J , Liu W , Lu J , Maheshwari M , Nguyen BV , Okwuonu GO , Palmeiri A , Pasternak S , Perez LM , Phelps KA , Plopper FJ , Qiang B , Raymond C , Rodriguez R , Saenphimmachak C , Santibanez J , Shen H , Shen Y , Subramanian S , Tabor PE , Verduzco D , Waldron L , Wang Q , Williams GA , Wong GK , Yao Z , Zhang J , Zhang X , Zhao G , Zhou J , Zhou Y , Nelson D , Lehrach H , Reinhardt R , Naylor SL , Yang H , Olson M , Weinstock G , Gibbs RA
Ref : Nature , 440 :1194 , 2006
Abstract : After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
ESTHER : Muzny_2006_Nature_440_1194
PubMedSearch : Muzny_2006_Nature_440_1194
PubMedID: 16641997
Gene_locus related to this paper: human-AADAC , human-AADACL2 , human-ABHD5 , human-ABHD6 , human-ABHD10 , human-ABHD14A , human-APEH , human-BCHE , human-CIB , human-LIPH , human-MGLL , human-NLGN1 , human-PLA1A

Title : The DNA sequence and biological annotation of human chromosome 1 - Gregory_2006_Nature_441_315
Author(s) : Gregory SG , Barlow KF , McLay KE , Kaul R , Swarbreck D , Dunham A , Scott CE , Howe KL , Woodfine K , Spencer CC , Jones MC , Gillson C , Searle S , Zhou Y , Kokocinski F , McDonald L , Evans R , Phillips K , Atkinson A , Cooper R , Jones C , Hall RE , Andrews TD , Lloyd C , Ainscough R , Almeida JP , Ambrose KD , Anderson F , Andrew RW , Ashwell RI , Aubin K , Babbage AK , Bagguley CL , Bailey J , Beasley H , Bethel G , Bird CP , Bray-Allen S , Brown JY , Brown AJ , Buckley D , Burton J , Bye J , Carder C , Chapman JC , Clark SY , Clarke G , Clee C , Cobley V , Collier RE , Corby N , Coville GJ , Davies J , Deadman R , Dunn M , Earthrowl M , Ellington AG , Errington H , Frankish A , Frankland J , French L , Garner P , Garnett J , Gay L , Ghori MR , Gibson R , Gilby LM , Gillett W , Glithero RJ , Grafham DV , Griffiths C , Griffiths-Jones S , Grocock R , Hammond S , Harrison ES , Hart E , Haugen E , Heath PD , Holmes S , Holt K , Howden PJ , Hunt AR , Hunt SE , Hunter G , Isherwood J , James R , Johnson C , Johnson D , Joy A , Kay M , Kershaw JK , Kibukawa M , Kimberley AM , King A , Knights AJ , Lad H , Laird G , Lawlor S , Leongamornlert DA , Lloyd DM , Loveland J , Lovell J , Lush MJ , Lyne R , Martin S , Mashreghi-Mohammadi M , Matthews L , Matthews NS , Mclaren S , Milne S , Mistry S , Moore MJ , Nickerson T , O'Dell CN , Oliver K , Palmeiri A , Palmer SA , Parker A , Patel D , Pearce AV , Peck AI , Pelan S , Phelps K , Phillimore BJ , Plumb R , Rajan J , Raymond C , Rouse G , Saenphimmachak C , Sehra HK , Sheridan E , Shownkeen R , Sims S , Skuce CD , Smith M , Steward C , Subramanian S , Sycamore N , Tracey A , Tromans A , Van Helmond Z , Wall M , Wallis JM , White S , Whitehead SL , Wilkinson JE , Willey DL , Williams H , Wilming L , Wray PW , Wu Z , Coulson A , Vaudin M , Sulston JE , Durbin R , Hubbard T , Wooster R , Dunham I , Carter NP , McVean G , Ross MT , Harrow J , Olson MV , Beck S , Rogers J , Bentley DR , Banerjee R , Bryant SP , Burford DC , Burrill WD , Clegg SM , Dhami P , Dovey O , Faulkner LM , Gribble SM , Langford CF , Pandian RD , Porter KM , Prigmore E
Ref : Nature , 441 :315 , 2006
Abstract : The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.
ESTHER : Gregory_2006_Nature_441_315
PubMedSearch : Gregory_2006_Nature_441_315
PubMedID: 16710414
Gene_locus related to this paper: human-LYPLAL1 , human-PPT1 , human-TMCO4 , human-TMEM53