Vikash Verma - Academia.edu (original) (raw)

Papers by Vikash Verma

Encyclopedia of Biological Chemistry III, 2021

Encyclopedia of Biological Chemistry III, 2021

Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells... more Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. The fact that most eukaryotes reproduce sexually is evidence of its evolutionary success. In many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, offspring that are genetically identical to the parent may appear to be more advantageous. If the parent organism is successfully occupying a habitat, offspring with the same traits would be similarly successful. There is also the obvious benefit to an organism that can produce offspring by asexual budding, fragmentation, or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. There is no need to expend energy finding or attracting a mate. That energy can be spent on producing more offspring. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, in asexual populations every individual is capable of reproduction. In contrast, the males in sexual populations (half the population) are not producing offspring themselves. Because of this, an asexual population can in theory grow twice as fast as a sexual population. This means that in competition, the asexual population would have the advantage. All of these advantages to asexual reproduction, which are also disadvantages to sexual reproduction, should mean that the number of species with asexual reproduction should be more common. However, multicellular organisms that exclusively depend on asexual reproduction are rare. So why is sexual reproduction so common? This is one of the important questions in biology and has been the focus of much research from the latter half of the twentieth century until now.

Molecular Biology of the Cell, 2022

Formation of a bipolar spindle is required for the faithful segregation of chromosomes during cel... more Formation of a bipolar spindle is required for the faithful segregation of chromosomes during cell division. Twenty-five years ago, a transformative insight into how bipolarity is achieved was provided by Rebecca Heald, Eric Karsenti, and colleagues in their landmark publication characterizing a chromatin-mediated spindle assembly pathway in which centrosomes and kinetochores were dispensable. The discovery revealed that bipolar spindle assembly is a self-organizing process where microtubules, which possess an intrinsic polarity, polymerize around chromatin and become sorted by mitotic motors into a bipolar structure. On the 25th anniversary of this seminal paper, we discuss what was known before, what we have learned since, and what may lie ahead in understanding the bipolar spindle.

Encyclopedia of Biological Chemistry III, 2021

Encyclopedia of Biological Chemistry III, 2021

Encyclopedia of Biological Chemistry, 2013

Cells use an extensive toolkit of molecular motors to traffic material, to anchor internal compon... more Cells use an extensive toolkit of molecular motors to traffic material, to anchor internal components in fixed positions, and to control cell shape. There are three large families of motor proteins, myosins, kinesins, and dyneins, which drive these critical motions. Myosins move along actin filaments, transporting cargoes, regulating filament tension and driving muscle contraction. Kinesins and dyneins play similar roles along microtubules, moving largely in opposite directions. Since the emergence of the earliest eukaryotes, evolution has fine-tuned these motors to perform specific tasks within the cell. Their unique mechanical features strongly suggest that even closely related motors within a given family cannot substitute for each other in most cellular roles. However, despite these differences, many of the general features of movement are shared between these three cytoskeletal motors. Here, we examine the common characteristics and limitations of cytoskeletal motors.

In this paper we have described an integrated acquisition platform that includes several techniqu... more In this paper we have described an integrated acquisition platform that includes several techniques previously developed to support users in various ways as they add new knowledge to an intelligent system. As a sum of this integration, the individual techniques can take better advantage of the context in which they are invoked and provide well suggestions to users.

Journal of Nepalgunj Medical College, 2019

Background: Microbial pathogens cause human skin and soft tissue infections (SSTI) and surgical s... more Background: Microbial pathogens cause human skin and soft tissue infections (SSTI) and surgical site infections (SSI) after surgical procedures. These can result in the production of pus, yellowish fluid comprising of dead WBCs and cellular debris. The microorganisms responsible for pus production vary greatly in relation to their spectrum of prevalence in different hospital and also in their antibiotic sensitivity. Further, the antibiotic sensitivity also changes because of the emergence of resistant strains. It is therefore, important that the common bacterial pathogens causing infection in a particular hospital and their sensitivity should be known. This will help in the choice of prophylactic antibiotic and in initiating the empirical antibiotic prescription for the infected cases before the culture sensitivity report is made available which takes about 2-3 days. Objective: To identify the spectrum of aerobic bacteria which are responsible for SSTI and SSI and their antibiotic s...

Journal of Mathematical Chemistry, 2020

Nonlinear ultrasound propagation of formamide with 2-methoxyethanol and 2-ethoxyethanol systems a... more Nonlinear ultrasound propagation of formamide with 2-methoxyethanol and 2-ethoxyethanol systems are examined over the entire miscibility range and five different temperatures (303.15 K ≤ T ≤ 323.15 K) using Hartmann, Ballou, Lu, Tong Dong, Beyer and Beyer-Tong Dong methods. The nonlinearity parameter, B/A values are compared using the aforementioned methods in both the binary systems. The isobaric temperature coefficient (u∕ T) P and isothermal pressure coefficient of the ultrasound velocity (u∕ P) T are also calculated. An interconnection between nonlinear ultrasound parameter and the molecular properties e.g. internal pressure, cohesive energy density etc. is also discussed. The excess non-linearity parameter B/ A E plays a key role in determining the extent of intermolecular interactions in binary liquid mixtures. Hence, nonlinear ultrasonic propagation helps in studying the static and dynamic molecular properties of the solvent systems. Keywords Non-linearity parameter • Molecular properties • Formamide • 2-ME • 2-EE List of symbols u Ultrasonic velocity of mixture M Molecular weight x i Mole fraction of ith component x Real volume of the molecules b Van der Waals' constant

Signal Transduction and Targeted Therapy, 2021

Physics and Chemistry of Liquids, 2020

This work reports the volumetric properties of binary mixtures of 2-dimethylaminoethanol (DMAE) a... more This work reports the volumetric properties of binary mixtures of 2-dimethylaminoethanol (DMAE) and 2-diethylaminoethanol (DEAE) with dimethylsulfoxide (DMSO) as a function of composition in the temperature range 298.15-318.15 K at atmospheric pressure. The excess molar volumes, apparent molar volumes, and excess partial molar volumes of both the components were determined in order to reflect several aggregation patterns present in the binary solvent system. The excess molar volumes show positive deviations from ideality. The excess partial molar volumes show complex dependence on composition and temperature. The results were used to investigate intermolecular interaction and structural configuration in these mixtures.

Journal of Cell Biology, 2018

Chromosome congression, the process of positioning chromosomes in the midspindle, promotes the st... more Chromosome congression, the process of positioning chromosomes in the midspindle, promotes the stable transmission of the genome to daughter cells during cell division. Congression is typically facilitated by DNA-associated, microtubule (MT) plus end–directed motors called chromokinesins. The Drosophila melanogaster chromokinesin NOD contributes to congression, but the means by which it does so are unknown in large part because NOD has been classified as a nonmotile, orphan kinesin. It has been postulated that NOD promotes congression, not by conventional plus end–directed motility, but by harnessing polymerization forces by end-tracking on growing MT plus ends via a mechanism that is also uncertain. Here, for the first time, it is demonstrated that NOD possesses MT plus end–directed motility. Furthermore, NOD directly binds EB1 through unconventional EB1-interaction motifs that are similar to a newly characterized MT tip localization sequence. We propose NOD produces congression fo...

Journal of Cell Biology, 2019

Accurate chromosome segregation during cell division requires the spindle assembly checkpoint (SA... more Accurate chromosome segregation during cell division requires the spindle assembly checkpoint (SAC), which detects unattached kinetochores, and an error correction mechanism that destabilizes incorrect kinetochore–microtubule attachments. While the SAC and error correction are both regulated by protein phosphatase 1 (PP1), which silences the SAC and stabilizes kinetochore–microtubule attachments, how these distinct PP1 functions are coordinated remains unclear. Here, we investigate the contribution of PP1, docked on its conserved kinetochore receptor Spc105/Knl1, to SAC silencing and attachment regulation. We find that Spc105-bound PP1 is critical for SAC silencing but dispensable for error correction; in fact, reduced PP1 docking on Spc105 improved chromosome segregation and viability of mutant/stressed states. We additionally show that artificially recruiting PP1 to Spc105/Knl1 before, but not after, chromosome biorientation interfered with error correction. These observations lea...

The Journal of Chemical Thermodynamics, 2019

The densitiesq and ultrasonic speeds u for the binary mixture of polyethylene glycol (PEG 200) an... more The densitiesq and ultrasonic speeds u for the binary mixture of polyethylene glycol (PEG 200) and poly ethylene glycol 400 (PEG 400) with N, N dimethylacetamide (DMA) are measured over the entire mole fraction range and at temperatures 303.15, 313.15, and 323.15 K. From the experimental data, and excess molar volume, V E m , excess ultrasonic speed u E , excess isentropic compressibility j E s , Excess intermolecular free length L E f , excess acoustic impedance Z E and excess molar isentropic compressibility K E s;m are evaluated. The partial molar properties and their excess properties are also determined. The solute-solvent interactions are also analyzed using FTIR spectra, recorded at the room temperature.

Biology, 2019

The primary goal of cytokinesis is to produce two daughter cells, each having a full set of chrom... more The primary goal of cytokinesis is to produce two daughter cells, each having a full set of chromosomes. To achieve this, cells assemble a dynamic structure between segregated sister chromatids called the contractile ring, which is made up of filamentous actin, myosin-II, and other regulatory proteins. Constriction of the actomyosin ring generates a cleavage furrow that divides the cytoplasm to produce two daughter cells. Decades of research have identified key regulators and underlying molecular mechanisms; however, many fundamental questions remain unanswered and are still being actively investigated. This review summarizes the key findings, computational modeling, and recent advances in understanding of the molecular mechanisms that control the formation of the cleavage furrow and cytokinesis.

ABSTRACTCell division in animal cells culminates with the formation of a contractile ring that di... more ABSTRACTCell division in animal cells culminates with the formation of a contractile ring that divides the cytosol through formation of a cleavage furrow. Microtubules (MTs) are essential for furrow positioning, but the molecular nature of MT-derived spatial signals is unresolved. In this study essential cytokinesis regulators (the centralspindlin complex, aurora B kinase (ABK), and polo kinase) were visualized in Drosophila melanogaster (Dm) cells and found localize to and track MT plus-ends during cytokinesis. The RhoA GEF Pebble (Dm ECT2) did not robustly tip-track but became enriched at MT plus-tips rapidly following cortical contact resulting in RhoA activation and enrichment of myosin-regulatory light chain. Abrogation of cytokinesis regulator tip-tracking by EB1 depletion or deletion of a novel EB1-interaction motif (hxxPTxh) in the centralspindlin component RacGAP50C resulted in higher incidences of cytokinesis failure. We propose that EB1-dependent, MT plus-tip-based signal...

Encyclopedia of Biological Chemistry III, 2021

Encyclopedia of Biological Chemistry III, 2021

Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells... more Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. The fact that most eukaryotes reproduce sexually is evidence of its evolutionary success. In many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, offspring that are genetically identical to the parent may appear to be more advantageous. If the parent organism is successfully occupying a habitat, offspring with the same traits would be similarly successful. There is also the obvious benefit to an organism that can produce offspring by asexual budding, fragmentation, or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. There is no need to expend energy finding or attracting a mate. That energy can be spent on producing more offspring. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, in asexual populations every individual is capable of reproduction. In contrast, the males in sexual populations (half the population) are not producing offspring themselves. Because of this, an asexual population can in theory grow twice as fast as a sexual population. This means that in competition, the asexual population would have the advantage. All of these advantages to asexual reproduction, which are also disadvantages to sexual reproduction, should mean that the number of species with asexual reproduction should be more common. However, multicellular organisms that exclusively depend on asexual reproduction are rare. So why is sexual reproduction so common? This is one of the important questions in biology and has been the focus of much research from the latter half of the twentieth century until now.

Molecular Biology of the Cell, 2022

Formation of a bipolar spindle is required for the faithful segregation of chromosomes during cel... more Formation of a bipolar spindle is required for the faithful segregation of chromosomes during cell division. Twenty-five years ago, a transformative insight into how bipolarity is achieved was provided by Rebecca Heald, Eric Karsenti, and colleagues in their landmark publication characterizing a chromatin-mediated spindle assembly pathway in which centrosomes and kinetochores were dispensable. The discovery revealed that bipolar spindle assembly is a self-organizing process where microtubules, which possess an intrinsic polarity, polymerize around chromatin and become sorted by mitotic motors into a bipolar structure. On the 25th anniversary of this seminal paper, we discuss what was known before, what we have learned since, and what may lie ahead in understanding the bipolar spindle.

Encyclopedia of Biological Chemistry III, 2021

Encyclopedia of Biological Chemistry III, 2021

Encyclopedia of Biological Chemistry, 2013

Cells use an extensive toolkit of molecular motors to traffic material, to anchor internal compon... more Cells use an extensive toolkit of molecular motors to traffic material, to anchor internal components in fixed positions, and to control cell shape. There are three large families of motor proteins, myosins, kinesins, and dyneins, which drive these critical motions. Myosins move along actin filaments, transporting cargoes, regulating filament tension and driving muscle contraction. Kinesins and dyneins play similar roles along microtubules, moving largely in opposite directions. Since the emergence of the earliest eukaryotes, evolution has fine-tuned these motors to perform specific tasks within the cell. Their unique mechanical features strongly suggest that even closely related motors within a given family cannot substitute for each other in most cellular roles. However, despite these differences, many of the general features of movement are shared between these three cytoskeletal motors. Here, we examine the common characteristics and limitations of cytoskeletal motors.

In this paper we have described an integrated acquisition platform that includes several techniqu... more In this paper we have described an integrated acquisition platform that includes several techniques previously developed to support users in various ways as they add new knowledge to an intelligent system. As a sum of this integration, the individual techniques can take better advantage of the context in which they are invoked and provide well suggestions to users.

Journal of Nepalgunj Medical College, 2019

Background: Microbial pathogens cause human skin and soft tissue infections (SSTI) and surgical s... more Background: Microbial pathogens cause human skin and soft tissue infections (SSTI) and surgical site infections (SSI) after surgical procedures. These can result in the production of pus, yellowish fluid comprising of dead WBCs and cellular debris. The microorganisms responsible for pus production vary greatly in relation to their spectrum of prevalence in different hospital and also in their antibiotic sensitivity. Further, the antibiotic sensitivity also changes because of the emergence of resistant strains. It is therefore, important that the common bacterial pathogens causing infection in a particular hospital and their sensitivity should be known. This will help in the choice of prophylactic antibiotic and in initiating the empirical antibiotic prescription for the infected cases before the culture sensitivity report is made available which takes about 2-3 days. Objective: To identify the spectrum of aerobic bacteria which are responsible for SSTI and SSI and their antibiotic s...

Journal of Mathematical Chemistry, 2020

Nonlinear ultrasound propagation of formamide with 2-methoxyethanol and 2-ethoxyethanol systems a... more Nonlinear ultrasound propagation of formamide with 2-methoxyethanol and 2-ethoxyethanol systems are examined over the entire miscibility range and five different temperatures (303.15 K ≤ T ≤ 323.15 K) using Hartmann, Ballou, Lu, Tong Dong, Beyer and Beyer-Tong Dong methods. The nonlinearity parameter, B/A values are compared using the aforementioned methods in both the binary systems. The isobaric temperature coefficient (u∕ T) P and isothermal pressure coefficient of the ultrasound velocity (u∕ P) T are also calculated. An interconnection between nonlinear ultrasound parameter and the molecular properties e.g. internal pressure, cohesive energy density etc. is also discussed. The excess non-linearity parameter B/ A E plays a key role in determining the extent of intermolecular interactions in binary liquid mixtures. Hence, nonlinear ultrasonic propagation helps in studying the static and dynamic molecular properties of the solvent systems. Keywords Non-linearity parameter • Molecular properties • Formamide • 2-ME • 2-EE List of symbols u Ultrasonic velocity of mixture M Molecular weight x i Mole fraction of ith component x Real volume of the molecules b Van der Waals' constant

Signal Transduction and Targeted Therapy, 2021

Physics and Chemistry of Liquids, 2020

This work reports the volumetric properties of binary mixtures of 2-dimethylaminoethanol (DMAE) a... more This work reports the volumetric properties of binary mixtures of 2-dimethylaminoethanol (DMAE) and 2-diethylaminoethanol (DEAE) with dimethylsulfoxide (DMSO) as a function of composition in the temperature range 298.15-318.15 K at atmospheric pressure. The excess molar volumes, apparent molar volumes, and excess partial molar volumes of both the components were determined in order to reflect several aggregation patterns present in the binary solvent system. The excess molar volumes show positive deviations from ideality. The excess partial molar volumes show complex dependence on composition and temperature. The results were used to investigate intermolecular interaction and structural configuration in these mixtures.

Journal of Cell Biology, 2018

Chromosome congression, the process of positioning chromosomes in the midspindle, promotes the st... more Chromosome congression, the process of positioning chromosomes in the midspindle, promotes the stable transmission of the genome to daughter cells during cell division. Congression is typically facilitated by DNA-associated, microtubule (MT) plus end–directed motors called chromokinesins. The Drosophila melanogaster chromokinesin NOD contributes to congression, but the means by which it does so are unknown in large part because NOD has been classified as a nonmotile, orphan kinesin. It has been postulated that NOD promotes congression, not by conventional plus end–directed motility, but by harnessing polymerization forces by end-tracking on growing MT plus ends via a mechanism that is also uncertain. Here, for the first time, it is demonstrated that NOD possesses MT plus end–directed motility. Furthermore, NOD directly binds EB1 through unconventional EB1-interaction motifs that are similar to a newly characterized MT tip localization sequence. We propose NOD produces congression fo...

Journal of Cell Biology, 2019

Accurate chromosome segregation during cell division requires the spindle assembly checkpoint (SA... more Accurate chromosome segregation during cell division requires the spindle assembly checkpoint (SAC), which detects unattached kinetochores, and an error correction mechanism that destabilizes incorrect kinetochore–microtubule attachments. While the SAC and error correction are both regulated by protein phosphatase 1 (PP1), which silences the SAC and stabilizes kinetochore–microtubule attachments, how these distinct PP1 functions are coordinated remains unclear. Here, we investigate the contribution of PP1, docked on its conserved kinetochore receptor Spc105/Knl1, to SAC silencing and attachment regulation. We find that Spc105-bound PP1 is critical for SAC silencing but dispensable for error correction; in fact, reduced PP1 docking on Spc105 improved chromosome segregation and viability of mutant/stressed states. We additionally show that artificially recruiting PP1 to Spc105/Knl1 before, but not after, chromosome biorientation interfered with error correction. These observations lea...

The Journal of Chemical Thermodynamics, 2019

The densitiesq and ultrasonic speeds u for the binary mixture of polyethylene glycol (PEG 200) an... more The densitiesq and ultrasonic speeds u for the binary mixture of polyethylene glycol (PEG 200) and poly ethylene glycol 400 (PEG 400) with N, N dimethylacetamide (DMA) are measured over the entire mole fraction range and at temperatures 303.15, 313.15, and 323.15 K. From the experimental data, and excess molar volume, V E m , excess ultrasonic speed u E , excess isentropic compressibility j E s , Excess intermolecular free length L E f , excess acoustic impedance Z E and excess molar isentropic compressibility K E s;m are evaluated. The partial molar properties and their excess properties are also determined. The solute-solvent interactions are also analyzed using FTIR spectra, recorded at the room temperature.

Biology, 2019

The primary goal of cytokinesis is to produce two daughter cells, each having a full set of chrom... more The primary goal of cytokinesis is to produce two daughter cells, each having a full set of chromosomes. To achieve this, cells assemble a dynamic structure between segregated sister chromatids called the contractile ring, which is made up of filamentous actin, myosin-II, and other regulatory proteins. Constriction of the actomyosin ring generates a cleavage furrow that divides the cytoplasm to produce two daughter cells. Decades of research have identified key regulators and underlying molecular mechanisms; however, many fundamental questions remain unanswered and are still being actively investigated. This review summarizes the key findings, computational modeling, and recent advances in understanding of the molecular mechanisms that control the formation of the cleavage furrow and cytokinesis.

ABSTRACTCell division in animal cells culminates with the formation of a contractile ring that di... more ABSTRACTCell division in animal cells culminates with the formation of a contractile ring that divides the cytosol through formation of a cleavage furrow. Microtubules (MTs) are essential for furrow positioning, but the molecular nature of MT-derived spatial signals is unresolved. In this study essential cytokinesis regulators (the centralspindlin complex, aurora B kinase (ABK), and polo kinase) were visualized in Drosophila melanogaster (Dm) cells and found localize to and track MT plus-ends during cytokinesis. The RhoA GEF Pebble (Dm ECT2) did not robustly tip-track but became enriched at MT plus-tips rapidly following cortical contact resulting in RhoA activation and enrichment of myosin-regulatory light chain. Abrogation of cytokinesis regulator tip-tracking by EB1 depletion or deletion of a novel EB1-interaction motif (hxxPTxh) in the centralspindlin component RacGAP50C resulted in higher incidences of cytokinesis failure. We propose that EB1-dependent, MT plus-tip-based signal...