The objective of this teaching note is to generate a laboratory exercise, which allows students t... more The objective of this teaching note is to generate a laboratory exercise, which allows students to get a hands-on experience of a cell biology technique. The short duration of the laboratory classes is the biggest challenge with the development of a cell biology lab for an undergraduate curriculum. Therefore, it is necessary to design a laboratory exercise that enables the students to carry out cell biological assays in the desired time. This laboratory exercise focuses on tracking protein expression levels along a spatial (space) and temporal (time) axis in developing Drosophila melanogaster organ primordium. Here we use the protein trap model developed in Drosophila to demonstrate the subcellular localization of proteins. The protein trap transgenic flies have Green Fluorescent Protein (GFP) reporter tags to the full-length endogenous proteins that allow observation of their cellular as well as sub-cellular distribution. Since the life cycle of Drosophila is short, it is easy to r...
Tuberculosis is a major health problem in India, and the emergence of multidrug resistant (MDR) a... more Tuberculosis is a major health problem in India, and the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) has further complicated the situation. Though several studies characterizing drug sensitive and drug resistant strains are available in literature, almost all studies are done on unrelated strains. Therefore, the objective of this study was to compare the proteomic data of four sequential isolates of Mtb from a single patient who developed MDR-TB during the course of anti-tuberculosis therapy (ATT). In this study, using two-dimensional (2D) gel electrophoresis and MALDI-TOF mass spectrometry, we compared and analyzed the cell lysate proteins of Mtb sequential clinical isolates from a patient undergoing anti-TB treatment. The mRNA expression levels of selected identified proteins were determined by quantitative real-time polymerase chain reaction (qRT-PCR). The genotypes of all four isolates remained homologou...
The Drosophila eye-antenna imaginal disc (ead) is a flattened sac of two-layered epithelia, from ... more The Drosophila eye-antenna imaginal disc (ead) is a flattened sac of two-layered epithelia, from which most head structures are derived. Secreted morphogens like Wingless (Wg), Hedgehog (Hh), and Decapentaplegic (Dpp) are important for early patterning of ead, but the underlying mechanisms are still largely unknown. To understand how these morphogens function in the ead of early larval stages, we used wg-LacZ and dpp-Gal4 markers for the examination of wild-type and mutant eads. We found that the ead immediately after hatching was crescent-shaped with the Bolwig's nerve at the ventral edge, suggesting that it consists of dorsal domain. In a subsequent step, transcriptional induction of dpp in the cells along the Bolwig's nerve was followed by rapid growth of the ventral domain. Both Wg and Hh were required for the formation of the ventral domain. Wg was crucial for the growth of the entire ead, but Hh was essential for cell division only in the dorsal domain. In the ventral ...
Sonic hedgehog (Shh) signaling regulates cell proliferation during vertebrate development via ind... more Sonic hedgehog (Shh) signaling regulates cell proliferation during vertebrate development via induction of cell-cycle regulator gene expression or activation of other signalling pathways, prevents cell death by an as yet unclear mechanism and is required for differentiation of retinal cell types. Thus, an unsolved question is how the same signalling molecule can regulate such distinct cell processes as proliferation, cell survival and differentiation. Analysis of the zebrafish shh(-/-) mutant revealed that in this context p53 mediates elevated apoptosis during nervous system and retina development and interferes with retinal proliferation and differentiation. While in shh(-/-) mutants there is activation of p53 target genes and p53-mediated apoptosis, an increase in Hedgehog (Hh) signalling by over-expression of dominant-negative Protein Kinase A strongly decreased p53 target gene expression and apoptosis levels in shh(-/-) mutants. Using a novel p53 reporter transgene, I confirm th...
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1999
Most computational models of protein-ligand interactions consider only the energetics of the fina... more Most computational models of protein-ligand interactions consider only the energetics of the final bound state of the complex and do not examine the dynamics of the ligand as it enters the binding site. We have developed a novel technique for studying the dynamics of protein-ligand interactions based on motion planning algorithms from the field of robotics. Our algorithm uses electrostatic and van der Waals potentials to compute the most energetically favorable path between any given initial and goal ligand configurations. We use probabilistic motion planning to sample the distribution of possible paths to a given goal configuration and compute an energy-based "difficulty weight" for each path. By statistically averaging this weight over several randomly generated starting configurations, we compute the relative difficulty of entering and leaving a given binding configuration. This approach yields details of the energy contours around the binding site and can be used to ch...
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1997
The structural comparison of proteins has become increasingly important as a means to identify pr... more The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. In this paper we present a new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level. Our technique represents alpha-helices and beta-strands as vectors and uses a set of seven scoring functions to compare pairs of vectors from different proteins. The scores obtained are used in a dynamic programming algorithm that finds the best local alignment of the two sets of vectors. The second step in our algorithm is based on the atomic coordinates of the protein structures and improves the initial vector alignment by iteratively minimizing the RMSD between pairs of nearest atoms from the two proteins. We refine the final alignment by determining a core of well aligned atoms and minimizing the RMSD of this core. In a comparison of our method to Holm and Sander's DALI a...
This paper describes two implementations of a Data Encryption Standard (DES) encryptor/decryptor ... more This paper describes two implementations of a Data Encryption Standard (DES) encryptor/decryptor that operate at data rates up to 12 Gbps. The 12 Gpbs number is faster than any previously published design. In these DES implementations, the key can be changed and the core switched from encryption to decryption mode on a cycle-by-cycle basis with no dead cycles. The designs
Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164), 2001
Page 1. Proceedings of the 2001 IEEE International Conference on Robotics &am... more Page 1. Proceedings of the 2001 IEEE International Conference on Robotics & Automation Seoul, Korea' May 21-26, 2001 Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps Mebmet Serkan ...
Proceedings of the 2002 international workshop on System-level interconnect prediction - SLIP '02, 2002
Abstract We present an FPGA interconnect planning methodology based on the empirical measure know... more Abstract We present an FPGA interconnect planning methodology based on the empirical measure known as Rent's Rule[8]. We show that allocation of wire segment lengths during the FPGA architecture planning phase can be improved by taking into account intercon-nect complexities of the ...
International journal of biochemistry and molecular biology, 2011
Lactoperoxidase (LPO) is a member of the family of mammalian heme peroxidases. It catalyzes the o... more Lactoperoxidase (LPO) is a member of the family of mammalian heme peroxidases. It catalyzes the oxidation of halides and pseudohalides in presence of hydrogen peroxide. LPO has been co-crystallized with inorganic substrates, SCN(-), I(-), Br(-) and Cl(-). The structure determination of the complex of LPO with above four substrates showed that all of them occupied distinct positions in the substrate binding site on the distal heme side. The bound substrate ions were separated from each other by one or more water molecules. The heme iron is coordinated to His-351 N(ϵ2) on the proximal side while it is coordinated to conserved water molecule W-1 on the distal heme side. W-1 is hydrogen bonded to Br(-) ion which is followed by Cl(-) ion with a hydrogen bonded water molecule W-5' between them. Next to Cl(-) ion is a hydrogen bonded water molecule W-7' which in turn is hydrogen bonded to W-8' and N atom of SCN(-). W-80 is hydrogen bonded to W-9' which is hydrogen bonded to...
Developmental fields are subdivided into lineage-restricted cell populations, known as compartmen... more Developmental fields are subdivided into lineage-restricted cell populations, known as compartments. In the eye imaginal disc of Drosophila, dorso-ventral (DV) lineage restriction is the primary event, whereas antero-posterior compartment boundary is the first lineage restriction in other imaginal discs. The Iroquois complex (Iro-C) genes function as dorsal selectors and repress the default, ventral, identity in the eye-head primordium. In Iro-C mutant clones, change of the dorsal identity to default ventral fate leads to generation of ectopic DV boundary, which results in dorsal eye enlargement, and duplication of ventral appendages like antenna and maxillary palp. Similar phenotypes were observed in heads with defective proventriculus (dve) mutant clones. Here, we show that the homeobox gene dve is a downstream effector of Iro-C in the dorsal head capsule (vertex) specification and represses the ventral (antennal) identity. Two homeodomain proteins Distal-less (Dll) and Homothorax...
The objective of this teaching note is to generate a laboratory exercise, which allows students t... more The objective of this teaching note is to generate a laboratory exercise, which allows students to get a hands-on experience of a cell biology technique. The short duration of the laboratory classes is the biggest challenge with the development of a cell biology lab for an undergraduate curriculum. Therefore, it is necessary to design a laboratory exercise that enables the students to carry out cell biological assays in the desired time. This laboratory exercise focuses on tracking protein expression levels along a spatial (space) and temporal (time) axis in developing Drosophila melanogaster organ primordium. Here we use the protein trap model developed in Drosophila to demonstrate the subcellular localization of proteins. The protein trap transgenic flies have Green Fluorescent Protein (GFP) reporter tags to the full-length endogenous proteins that allow observation of their cellular as well as sub-cellular distribution. Since the life cycle of Drosophila is short, it is easy to r...
Tuberculosis is a major health problem in India, and the emergence of multidrug resistant (MDR) a... more Tuberculosis is a major health problem in India, and the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) has further complicated the situation. Though several studies characterizing drug sensitive and drug resistant strains are available in literature, almost all studies are done on unrelated strains. Therefore, the objective of this study was to compare the proteomic data of four sequential isolates of Mtb from a single patient who developed MDR-TB during the course of anti-tuberculosis therapy (ATT). In this study, using two-dimensional (2D) gel electrophoresis and MALDI-TOF mass spectrometry, we compared and analyzed the cell lysate proteins of Mtb sequential clinical isolates from a patient undergoing anti-TB treatment. The mRNA expression levels of selected identified proteins were determined by quantitative real-time polymerase chain reaction (qRT-PCR). The genotypes of all four isolates remained homologou...
The Drosophila eye-antenna imaginal disc (ead) is a flattened sac of two-layered epithelia, from ... more The Drosophila eye-antenna imaginal disc (ead) is a flattened sac of two-layered epithelia, from which most head structures are derived. Secreted morphogens like Wingless (Wg), Hedgehog (Hh), and Decapentaplegic (Dpp) are important for early patterning of ead, but the underlying mechanisms are still largely unknown. To understand how these morphogens function in the ead of early larval stages, we used wg-LacZ and dpp-Gal4 markers for the examination of wild-type and mutant eads. We found that the ead immediately after hatching was crescent-shaped with the Bolwig's nerve at the ventral edge, suggesting that it consists of dorsal domain. In a subsequent step, transcriptional induction of dpp in the cells along the Bolwig's nerve was followed by rapid growth of the ventral domain. Both Wg and Hh were required for the formation of the ventral domain. Wg was crucial for the growth of the entire ead, but Hh was essential for cell division only in the dorsal domain. In the ventral ...
Sonic hedgehog (Shh) signaling regulates cell proliferation during vertebrate development via ind... more Sonic hedgehog (Shh) signaling regulates cell proliferation during vertebrate development via induction of cell-cycle regulator gene expression or activation of other signalling pathways, prevents cell death by an as yet unclear mechanism and is required for differentiation of retinal cell types. Thus, an unsolved question is how the same signalling molecule can regulate such distinct cell processes as proliferation, cell survival and differentiation. Analysis of the zebrafish shh(-/-) mutant revealed that in this context p53 mediates elevated apoptosis during nervous system and retina development and interferes with retinal proliferation and differentiation. While in shh(-/-) mutants there is activation of p53 target genes and p53-mediated apoptosis, an increase in Hedgehog (Hh) signalling by over-expression of dominant-negative Protein Kinase A strongly decreased p53 target gene expression and apoptosis levels in shh(-/-) mutants. Using a novel p53 reporter transgene, I confirm th...
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1999
Most computational models of protein-ligand interactions consider only the energetics of the fina... more Most computational models of protein-ligand interactions consider only the energetics of the final bound state of the complex and do not examine the dynamics of the ligand as it enters the binding site. We have developed a novel technique for studying the dynamics of protein-ligand interactions based on motion planning algorithms from the field of robotics. Our algorithm uses electrostatic and van der Waals potentials to compute the most energetically favorable path between any given initial and goal ligand configurations. We use probabilistic motion planning to sample the distribution of possible paths to a given goal configuration and compute an energy-based "difficulty weight" for each path. By statistically averaging this weight over several randomly generated starting configurations, we compute the relative difficulty of entering and leaving a given binding configuration. This approach yields details of the energy contours around the binding site and can be used to ch...
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1997
The structural comparison of proteins has become increasingly important as a means to identify pr... more The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. In this paper we present a new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level. Our technique represents alpha-helices and beta-strands as vectors and uses a set of seven scoring functions to compare pairs of vectors from different proteins. The scores obtained are used in a dynamic programming algorithm that finds the best local alignment of the two sets of vectors. The second step in our algorithm is based on the atomic coordinates of the protein structures and improves the initial vector alignment by iteratively minimizing the RMSD between pairs of nearest atoms from the two proteins. We refine the final alignment by determining a core of well aligned atoms and minimizing the RMSD of this core. In a comparison of our method to Holm and Sander's DALI a...
This paper describes two implementations of a Data Encryption Standard (DES) encryptor/decryptor ... more This paper describes two implementations of a Data Encryption Standard (DES) encryptor/decryptor that operate at data rates up to 12 Gbps. The 12 Gpbs number is faster than any previously published design. In these DES implementations, the key can be changed and the core switched from encryption to decryption mode on a cycle-by-cycle basis with no dead cycles. The designs
Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164), 2001
Page 1. Proceedings of the 2001 IEEE International Conference on Robotics &am... more Page 1. Proceedings of the 2001 IEEE International Conference on Robotics & Automation Seoul, Korea' May 21-26, 2001 Capturing Molecular Energy Landscapes with Probabilistic Conformational Roadmaps Mebmet Serkan ...
Proceedings of the 2002 international workshop on System-level interconnect prediction - SLIP '02, 2002
Abstract We present an FPGA interconnect planning methodology based on the empirical measure know... more Abstract We present an FPGA interconnect planning methodology based on the empirical measure known as Rent's Rule[8]. We show that allocation of wire segment lengths during the FPGA architecture planning phase can be improved by taking into account intercon-nect complexities of the ...
International journal of biochemistry and molecular biology, 2011
Lactoperoxidase (LPO) is a member of the family of mammalian heme peroxidases. It catalyzes the o... more Lactoperoxidase (LPO) is a member of the family of mammalian heme peroxidases. It catalyzes the oxidation of halides and pseudohalides in presence of hydrogen peroxide. LPO has been co-crystallized with inorganic substrates, SCN(-), I(-), Br(-) and Cl(-). The structure determination of the complex of LPO with above four substrates showed that all of them occupied distinct positions in the substrate binding site on the distal heme side. The bound substrate ions were separated from each other by one or more water molecules. The heme iron is coordinated to His-351 N(ϵ2) on the proximal side while it is coordinated to conserved water molecule W-1 on the distal heme side. W-1 is hydrogen bonded to Br(-) ion which is followed by Cl(-) ion with a hydrogen bonded water molecule W-5' between them. Next to Cl(-) ion is a hydrogen bonded water molecule W-7' which in turn is hydrogen bonded to W-8' and N atom of SCN(-). W-80 is hydrogen bonded to W-9' which is hydrogen bonded to...
Developmental fields are subdivided into lineage-restricted cell populations, known as compartmen... more Developmental fields are subdivided into lineage-restricted cell populations, known as compartments. In the eye imaginal disc of Drosophila, dorso-ventral (DV) lineage restriction is the primary event, whereas antero-posterior compartment boundary is the first lineage restriction in other imaginal discs. The Iroquois complex (Iro-C) genes function as dorsal selectors and repress the default, ventral, identity in the eye-head primordium. In Iro-C mutant clones, change of the dorsal identity to default ventral fate leads to generation of ectopic DV boundary, which results in dorsal eye enlargement, and duplication of ventral appendages like antenna and maxillary palp. Similar phenotypes were observed in heads with defective proventriculus (dve) mutant clones. Here, we show that the homeobox gene dve is a downstream effector of Iro-C in the dorsal head capsule (vertex) specification and represses the ventral (antennal) identity. Two homeodomain proteins Distal-less (Dll) and Homothorax...
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