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Bhat R, Chakraborty M, Glimm T, Stewart TA, Newman SA. Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation. BMC Evol Biol 2016; 16:162. [PMID: 27538950 PMCID: PMC4989294 DOI: 10.1186/s12862-016-0729-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern. RESULTS Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection. CONCLUSION These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods.
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Biswas SN, Chakraborty PP, Chakraborty M. An unusual case of blackwater fever. Indian J Med Microbiol 2016; 34:393-4. [PMID: 27514973 DOI: 10.4103/0255-0857.188373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res 2016; 44:e147. [PMID: 27458204 PMCID: PMC5100563 DOI: 10.1093/nar/gkw654] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/09/2016] [Indexed: 01/19/2023] Open
Abstract
Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a ‘missing manual’ that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.
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Raut AN, Nandanwar SU, Suryawanshi YR, Chakraborty M, Jauhari S, Mukhopadhyay S, Shenoy KT, Bajaj HC. Liquid phase selective hydrogenation of phenol to cyclohexanone over Ru/Al2O3 nanocatalyst under mild conditions. KINETICS AND CATALYSIS 2016. [DOI: 10.1134/s0023158416010110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chakraborty M, Reddy PS, Mustafa G, Rajesh G, Narasu VML, Udayasuriyan V, Rana D. Transgenic rice expressing the cry2AX1 gene confers resistance to multiple lepidopteran pests. Transgenic Res 2016; 25:665-78. [DOI: 10.1007/s11248-016-9954-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/23/2016] [Indexed: 10/22/2022]
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Chakraborty M, Sairam Reddy P, Laxmi Narasu M, Krishna G, Rana D. Agrobacterium-mediated genetic transformation of commercially elite rice restorer line using nptII gene as a plant selection marker. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:51-60. [PMID: 27186018 PMCID: PMC4840146 DOI: 10.1007/s12298-015-0334-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/15/2015] [Accepted: 12/06/2015] [Indexed: 05/29/2023]
Abstract
Transformation of commercially important indica cultivars remains challenging for the scientific community even though Agrobacterium-mediated transformation protocols for a few indica rice lines have been well established. We report successful transformation of a commercially important restorer line JK1044R of indica rice hybrid JKRH 401. While following existing protocol, we optimized several parameters for callusing, regeneration and genetic transformation of JK1044R. Calli generated from the rice scutellum tissue were used for transformation by Agrobacterium harboring pCAMBIA2201. A novel two tire selection scheme comprising of Geneticin (G418) and Paramomycin were deployed for selection of transgenic calli as well as regenerated plantlets that expressed neomycin phosphotransferase-II gene encoded by the vector. One specific combination of G418 (30 mg l(-1)) and Paramomycin (70 mg l(-1)) was very effective for calli selection. Transformed and selected calli were detected by monitoring the expression of the reporter gene uidA (GUS). Regenerated plantlets were confirmed through PCR analysis of nptII and gus genes specific primers as well as dot blot using gus gene specific as probe.
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Chakraborty M, Fry JD. Evidence that Environmental Heterogeneity Maintains a Detoxifying Enzyme Polymorphism in Drosophila melanogaster. Curr Biol 2015; 26:219-223. [PMID: 26748852 DOI: 10.1016/j.cub.2015.11.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/28/2022]
Abstract
Environmental heterogeneity is thought to be an important process maintaining genetic variation in populations [1-4]: if alternative alleles are favored in different environments, a stable polymorphism can be maintained [1, 5, 6]. This situation has been hypothesized to occur in genes encoding multi-substrate enzymes [7], in which changes that increase activity with one substrate typically decrease activity with others [8-10], but examples of polymorphisms maintained by this mechanism are rare. Here, we present evidence that a polymorphism in an enzyme gene in Drosophila melanogaster is maintained by such a trade-off. The mitochondrially localized aldehyde dehydrogenase in D. melanogaster has two important functions: detoxifying acetaldehyde derived from dietary ethanol [11] and detoxifying larger aldehydes produced as byproducts of oxidative phosphorylation [12]. A derived variant of the enzyme, Leu479Phe, is present in moderate frequencies in most temperate populations but is rare in more ethanol-averse tropical populations. Using purified recombinant protein, we show that the Leu-Phe substitution increases turnover rate of acetaldehyde but decreases turnover rate of larger aldehydes. Furthermore, using transgenic fly lines, we show that the substitution increases lifetime fitness on medium supplemented with an ecologically relevant ethanol concentration but decreases fitness on medium lacking ethanol. The strong, opposing selection pressures, coupled with documented highly variable ethanol concentrations in breeding sites of temperate populations, implicate an essential role for environmental heterogeneity in maintaining the polymorphism.
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Singh SK, Rajawat AS, Rathore BP, Bahuguna IM, Chakraborty M. Detection of Glacier Lakes Buried under Snow by RISAT-1 SAR in the Himalayan Terrain. CURR SCI INDIA 2015. [DOI: 10.18520/cs/v109/i9/1735-1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Singh SK, Rajawat AS, Rathore BP, Bahuguna IM, Chakraborty M. Detection of Glacier Lakes Buried under Snow by RISAT-1 SAR in the Himalayan Terrain. CURR SCI INDIA 2015. [DOI: 10.18520/v109/i9/1735-1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Nandanwar SU, Dabbawala AA, Chakraborty M, Bajaj HC, Mukhopadhyay S, Shenoy KT. Partial hydrogenation of benzene to cyclohexene over Ru/γ-Al2O3 nanocatalyst via w/o microemulsion using boric acid and ethanolamine additives. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-015-2102-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Patel RR, Barad JM, Nandanwar SU, Dabbawala AA, Chakraborty M, Parikh PA, Baja HC. Cellulose supported ruthenium nanoclusters as an efficient and recyclable catalytic system for benzene hydrogenation under mild conditions. KINETICS AND CATALYSIS 2015. [DOI: 10.1134/s002315841502007x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chakraborty M, Fry JD. Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in Drosophila. Mol Biol Evol 2015; 32:1029-38. [PMID: 25564519 DOI: 10.1093/molbev/msu407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A large proportion of duplicates, originating from ubiquitously expressed genes, acquire testis-biased expression. Identifying the underlying cause of this observation requires determining whether the duplicates have altered functions relative to the parental genes. Typically, statistical methods are used to test for positive selection, signature of which in protein sequence of duplicates implies functional divergence. When assumptions are violated, however, such tests can lead to false inference of positive selection. More convincing evidence for naturally selected functional changes would be the occurrence of structural changes with similar functional consequences in independent duplicates of the same gene. We investigated two testis-specific duplicates of the broadly expressed enzyme gene Aldehyde dehydrogenase (Aldh) that arose in different Drosophila lineages. The duplicates show a typical pattern of accelerated amino acid substitutions relative to their broadly expressed paralogs, with statistical evidence for positive selection in both cases. Importantly, in both duplicates, width of the entrance to the substrate binding site, known a priori to influence substrate specificity, and otherwise conserved throughout the genus Drosophila, has been reduced, resulting in narrowing of the entrance. Protein structure modeling suggests that the reduction of the size of the enzyme's substrate entry channel, which is likely to shift substrate specificity toward smaller aldehydes, is accounted for by the positively selected parallel substitutions in one duplicate but not the other. Evolution of the testis-specific duplicates was accompanied by reduction in expression of the ancestral Aldh in males, supporting the hypothesis that the duplicates may have helped resolve intralocus sexual conflict over Aldh function.
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Bala N, Saha S, Chakraborty M, Maiti M, Das S, Basu R, Nandy P. Green synthesis of zinc oxide nanoparticles using Hibiscus subdariffa leaf extract: effect of temperature on synthesis, anti-bacterial activity and anti-diabetic activity. RSC Adv 2015. [DOI: 10.1039/c4ra12784f] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Particle size dependent anti-bacterial and anti-diabetic activities of green synthesized ZnO nanoparticles.
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Majumdar P, Singh SB, Dhara S, Chakraborty M. Influence of boron addition to Ti-13Zr-13Nb alloy on MG63 osteoblast cell viability and protein adsorption. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2014; 46:62-8. [PMID: 25491960 DOI: 10.1016/j.msec.2014.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/02/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022]
Abstract
Cell proliferation, cell morphology and protein adsorption on near β-type Ti-13Zr-13Nb (TZN) alloy and Ti-13Zr-13Nb-0.5B (TZNB) composite have been investigated and compared to evaluate the effect of boron addition which has been added to the Ti alloy to improve their poor tribological properties by forming in situ TiB precipitates. MG63 cell proliferation on substrates with different chemistry but the same topography was compared. The MTT assay test showed that the cell viability on the TZN alloy was higher than the boron containing TZNB composite after 36 h of incubation and the difference was pronounced after 7 days. However, both the materials showed substantially higher cell attachment than the control (polystyrene). For the same period of incubation in fetal bovine serum (FBS), the amount of protein adsorbed on the surface of boron free TZN samples was higher than that in the case of boron containing TZNB composite. The presence of boron in the TZN alloy influenced protein adsorption and cell response and they are lower in TZNB than in TZN as a result of the associated difference in chemical characteristics.
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Bhat R, Chakraborty M, Mian IS, Newman SA. Structural divergence in vertebrate phylogeny of a duplicated prototype galectin. Genome Biol Evol 2014; 6:2721-30. [PMID: 25260584 PMCID: PMC4224342 DOI: 10.1093/gbe/evu215] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Prototype galectins, endogenously expressed animal lectins with a single carbohydrate recognition domain, are well-known regulators of tissue properties such as growth and adhesion. The earliest discovered and best studied of the prototype galectins is Galectin-1 (Gal-1). In the Gallus gallus (chicken) genome, Gal-1 is represented by two homologs: Gal-1A and Gal-1B, with distinct biochemical properties, tissue expression, and developmental functions. We investigated the origin of the Gal-1A/Gal-1B divergence to gain insight into when their developmental functions originated and how they could have contributed to vertebrate phenotypic evolution. Sequence alignment and phylogenetic tree construction showed that the Gal-1A/Gal-1B divergence can be traced back to the origin of the sauropsid lineage (consisting of extinct and extant reptiles and birds) although lineage-specific duplications also occurred in the amphibian and actinopterygian genomes. Gene synteny analysis showed that sauropsid gal-1b (the gene for Gal-1B) and its frog and actinopterygian gal-1 homologs share a similar chromosomal location, whereas sauropsid gal-1a has translocated to a new position. Surprisingly, we found that chicken Gal-1A, encoded by the translocated gal-1a, was more similar in its tertiary folding pattern than Gal-1B, encoded by the untranslocated gal-1b, to experimentally determined and predicted folds of nonsauropsid Gal-1s. This inference is consistent with our finding of a lower proportion of conserved residues in sauropsid Gal-1Bs, and evidence for positive selection of sauropsid gal-1b, but not gal-1a genes. We propose that the duplication and structural divergence of Gal-1B away from Gal-1A led to specialization in both expression and function in the sauropsid lineage.
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Sellappan B, Chakraborty M, Cherian S. Congenital hypothyroidism presenting as pseudo-obstruction in preterm infants. BMJ Case Rep 2014; 2014:bcr2013201082. [PMID: 24832703 PMCID: PMC4025204 DOI: 10.1136/bcr-2013-201082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2014] [Indexed: 11/03/2022] Open
Abstract
Congenital hypothyroidism (CH) presenting as acute pseudo-obstruction is uncommon. We report two premature infants presenting with acute bowel obstruction subsequently diagnosed to have CH. Both responded well to medical management with thyroid supplementation.
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Kumar A, Koch A, Borthakur R, Chakraborty M, De A, Phukan A, Bez G, Lal R. Synthesis and spectroscopic characterization of monometallic molybdenum (VI) complexes derived from bis(2-hydroxy-1-naphthaldehyde)succinoyldihydrazone. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Vadakkekara R, Chakraborty M, Parikh PA. Synthesis, characterization, and application of monodisperse gelatin-stabilized silver nanospheres in reduction of aromatic nitro compounds. COLLOID JOURNAL 2014. [DOI: 10.1134/s1061933x14010153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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De D, Chakraborty M, Majumdar S, Giri S. Bandgap engineering through nanocrystalline magnetic alloy grafting on reduced graphene oxide. Phys Chem Chem Phys 2014; 16:19661-7. [DOI: 10.1039/c4cp02259a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Grafting of nanocrystalline Co80Ni20on reduced graphene oxide causes a significantly large moment (1.2μB), ∼10 times localization of conductivity and significant magnetoconductance of hybrid-materials, which is promising toward spintronic applications.
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Suryawanshi YR, Chakraborty M, Jauhari S, Mukhopadhyay S, Shenoy KT, Shridharkrishna R. Microwave irradiation solvothermal technique: an optimized protocol for size-control synthesis of Ru nanoparticles. CRYSTAL RESEARCH AND TECHNOLOGY 2013. [DOI: 10.1002/crat.201200412] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Nandanwar SU, Chakraborty M, Mukhopadhyay S, Shenoy KT. Benzene hydrogenation over highly active monodisperse Ru/γ-Al2O3 nanocatalyst synthesized by (w/o) reverse microemulsion. REACTION KINETICS MECHANISMS AND CATALYSIS 2012. [DOI: 10.1007/s11144-012-0526-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Raji V, Chakraborty M, Parikh PA. Synthesis of Starch-Stabilized Silver Nanoparticles and Their Antimicrobial Activity. PARTICULATE SCIENCE AND TECHNOLOGY 2012. [DOI: 10.1080/02726351.2011.626510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Majumdar P, Singh S, Dhara S, Chakraborty M. Influence of in situ TiB reinforcements and role of heat treatment on mechanical properties and biocompatibility of Ti-alloys. J Mech Behav Biomed Mater 2012; 10:1-12. [DOI: 10.1016/j.jmbbm.2012.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 02/13/2012] [Accepted: 02/19/2012] [Indexed: 10/28/2022]
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Yu T, Jain A, Chakraborty M, Wilson N, Hill A. Factors Influencing the Likelihood of Female Medical Students Pursuing Surgery: A Critical Review. J Surg Res 2012. [DOI: 10.1016/j.jss.2011.11.908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Mukherjee S, Chakraborty M, Panda A, Bhattacharya S, Moulik S. Physicochemistry of bis-alkyltrimethylammonium dichromate, tungstate and molybdate amphiphiles: Synthesis, characterization, behaviors at the air–water interface and self-aggregation in aqueous medium. Colloids Surf A Physicochem Eng Asp 2011. [DOI: 10.1016/j.colsurfa.2011.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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