Conformational variants of the unique family of protease inhibitors annotated as SERPINs are most... more Conformational variants of the unique family of protease inhibitors annotated as SERPINs are most often underrepresented in proteomic analyses. This limits understanding the complex regulation that this family of proteins presents to the networks within the protease web of interactions. Using bead-based separation provided by a family of proteomic enrichment products-notably AlbuVoid™ and AlbuSorb™, we demonstrate their utility to satisfy investigations of serum SERPINs. We also suggest their use to develop functional profiles of the SERPIN proteoforms, and how those can establish relationships to disease phenotypes, gene mutations, and dysregulated mechanisms.
Journal of the Japanese Society of Agricultural Machinery, 2004
Soil properties and yield were recorded in grid-spacing in a West Malaysia paddy field for the ye... more Soil properties and yield were recorded in grid-spacing in a West Malaysia paddy field for the year 2000. Geostatistical analysis showed that soil properties and yield were notably correlated in space, and the range of spatially dependent yield was shorter than the soil properties. Co-kriging was used to estimate spatial pattern of yield with surrogate data (soil properties) was not successful for this field. The spatial yield map illustrated that the middle portion of the plot has lower yield ( 5t/ha).
Summary of studies (Nutrition Bureau for Research and Development, 1992) showing the effect of vi... more Summary of studies (Nutrition Bureau for Research and Development, 1992) showing the effect of vitamin A supplementation on childhood mortality (Values are expressed as relative risk of death in supplemented v. unsupplemented groups) Country Age (months) Effect (relative risk) Sarlahi, Nepal Madurai, India Aceh, Indonesia Jumla, Nepal Java, Indonesia Navrongo, India Hyderabad, India Omdurman, Sudan 6-72 4-59 12-71 1-59 12-70 660 12-59 660 0.7 0.46 0.7 0.74 0.55 0.80 NS NS NS, not significant. mortality at all. In seeking an explanation for why vitamin A should have such striking effects, it is valuable to examine the impact of vitamin A in different populations according to the prevalence of diarrhoea. In the studies in Indonesia and Nepal a high proportion of the deaths were attributable to diarrhoea. In the study in Madurai, South India, which showed no impact of vitamin A supplementation, there was a rather low infant and child mortality rate and, in particular, diarrhoea deaths ...
Evaluating ephemeral gully erosion and economics using AnnAGNPS for Ontario conditions
Erosion of farmland due to climatic and land use changes is very severe on many unprotected farml... more Erosion of farmland due to climatic and land use changes is very severe on many unprotected farmlands around the world. Ephemeral gully erosion significantly to total soil losses alongwith agrochemicals from upland area to stream channels is a serious environmental and productivity problem. The last couple of decades, a few physical and semi-empirical based prediction models have been developed to assess the magnitude of soil erosion phenomena of ephemeral gully so that appropriate conservation measures can be implemented. The available Annualized Agricultural Non-Point Source (AnnAGNPS) model has been used to quantify soil erosion including erosion from ephemeral gullies of three agricultural fields of Kettle Creek watershed area with responses to agricultural management practices. The objective of this study is to identify critical areas where management practices could be implemented and to predict their impact on soil erosion of the watershed. It is noted that there is no study ...
In the current state-of-the-art, a wide variety of devices, from computer clocks to smartphone ac... more In the current state-of-the-art, a wide variety of devices, from computer clocks to smartphone accelerometers and from pressure gauges to atomic force microscope sensors, rely on mechanical resonators, either in microscale or nanoscale. Nanoscale mechanical resonators have even more potential than microscale by offering unprecedented sensitivity through weighing a single proton (10 −24 g) or by measuring aN (10 −18 N) force or μK temperature. The smaller size of nanometric mechanical resonators allows high sensitivity to their environment; ensuring excellent frequency stability, through high resonance frequency with a higher quality factor, Q, takes the best advantage of this sensitivity. At the same time, their smaller dimension makes these more susceptible to environmental fluctuations, such as thermomechanical (TM) noise, and to energy dissipation, which degrades the Q at atmospheric pressure. The First and foremost, I would like to thank my advisor Professor Wayne K. Hiebert. It is his guidance and supports, which enable me to develop the necessary experimental and analytical skills to succeed in this research. His mentorship was not only limited to academic advances but also significantly helpful in developing extracurricular advancements. His serenity in allowing me to discuss and to study random topics is highly appreciated. I want to show my deepest gratitude to Prof. John Beamish and Prof. Richard Marchand, for their helpful advice during my early grad life before joining Hiebert group. I would also like to thank Prof Beamish and John Davis for years of insightful discussions and invaluable feedback on my Ph.D. research. Many thanks to Prof Mark Freeman for his advice to widen knowledge during the weekly Journal Club with his group. This research work has been started with the on-chip devices designed by former grad student of Hiebert's group Dr. Vincent T. K. Sauer. I would like to thank Dr. Sauer for offering his help-no matter what experimental or analytical difficulties I have faced. I am also thankful to my fellow Ph.D. student Dr. Jocelyn Bachmann in troubleshooting experiments at the beginning of my program. I want to thank Mike Xia for his training on GC. Also, I would like to thank my co-worker, Dr. Anandaram Venkatsubranium, for his contributions to extending GC-NOMS project. I want to thank Chittagong University of Engineering and Technology (CUET), Bangladesh for providing me the study-leave for this Ph.D.; I am grateful to all of my colleagues from Department of Physics, CUET for their supports and encouragements. Lastly, I would like to thank all my friends and lab mates who stuck by me for years and made the burden of grad school lighter. Moreover, to my lovely wife Jayanti and our only son Om: your supports and sacrifices have accomplished this research project.
Modeling of ephemeral gully (EG) erosion has lagged that of other soil erosion processes despite ... more Modeling of ephemeral gully (EG) erosion has lagged that of other soil erosion processes despite its major contribution to watershed sediment losses. Several process and semi-empirical based simulation models have been used to assess the occurrence and location of EGs, magnitude of soil losses from EGs, and degradation, aggradation, and transport of sediment through EGs, but no comprehensive EG model exists. This paper reviews these models and presents a thorough discussion of their background, general formulations, key equations, field assessments, assumptions and limitations. Most current EG models evolved from the original formulations used in CREAMS, with incremental improvements by EGEM, WEPP, AnnAGNPS-REGEM, RUSLER-EphGEE models. These models provide process-based estimation of EG processes and field-scale soil-erosion contributions, but all models, except EphGEE, require users to have a priori knowledge of EG locations and all have significant shortcomings. Several topographic index models are discussed that provide simplistic approaches to locate EGs on the landscape using only topographic features. Process-based threshold index models may provide a more robust simulation of EG location and length, though testing has been limited. EG modeling appears to still be in its infancy, with great opportunities for future research, as discussed herein, to improve the understanding and simulation of EG erosion and transport processes.
Over the last decade, infant and young child feeding (IYCF) indicators in India have improved. Ho... more Over the last decade, infant and young child feeding (IYCF) indicators in India have improved. However, poor IYCF practices are still apparent, associated with pervasive high rates of child under-nutrition. Interventions to improve IYCF need augmentation by appropriate policy support to consolidate gains. The aim of this study was to identify opportunities to strengthen and support IYCF policies through a policy content and stakeholder network analysis. IYCF policies and guidelines were systematically mapped and coded using predetermined themes. Six 'net-map' group interviews were conducted for stakeholder analysis with data analyzed using ORA (organizational risk analyzer, copyright Carley, Carnegie Mellon University) software. The study was carried out at a national level and in the states of Maharashtra and unified Andhra Pradesh. Thirty relevant policy documents were identified. Support for IYCF was clearly apparent and was actioned within sectoral policies and strategic...
Abstract LB-065: Comparison of the serum proteome in individuals with cancers versus those without cancer, and its application to wellness
Cancer Research, 2016
For many diseases, pancreatic cancer for example, long term survival is critically dependent upon... more For many diseases, pancreatic cancer for example, long term survival is critically dependent upon early detection. So various strategies for early detectable markers are being investigated. One such strategy is hypothesis driven, first by identifying a singular biomarker, usually derived from genomic analysis of the tumor type, and then determine its derivative protein concentration in blood. This has been challenging as many differentially regulated genes do not generate a differentially regulated protein, or one of sufficient concentration for current means of detection. An alternative biomarker strategy is purely data driven, as panels of proteins may be up and/or down regulated, or altered by post-translational modifications. These can be monitored and quantified to differences in diseased and normal/healthy individuals. In this study we adopt such a data driven strategy using a new product which combines Albumin depletion and on-bead digestion of the enriched serum proteome in ...
Conformational variants of the unique family of protease inhibitors annotated as SERPINs, are mos... more Conformational variants of the unique family of protease inhibitors annotated as SERPINs, are most often underrepresented in proteomic analyses. This limits understanding the complex regulation that this family of proteins presents to the networks within the protease web of interactions. Using bead-based separation provided by the NuGel™ family of proteomic enrichment products-notably AlbuVoid™ & AlbuSorb™, we demonstrate their utility to satisfy investigations of serum SERPINs. We also suggest their use to develop functional profiles of the SERPIN proteoforms, and how those can establish relationships to disease phenotypes, gene mutations, and dysregulated mechanisms.
Functional proteomics relies in part, on the functional or structural features of intact, non-den... more Functional proteomics relies in part, on the functional or structural features of intact, non-denatured proteins. As such, chemical and affinity-based proteomics can be considered a subset of functional proteomics. Regardless of the evolving terminology, the subject of chemical proteomics is to identify, characterize and quantify the binding interactions of small compounds to proteomes. The consideration of those interactions as functional modulators within the cell is paramount to understanding a potential therapeutic compound's mechanism of action. These same tools and methods also can help survey the promiscuous behavior of compounds towards multiple proteins and posit such behavior as deterministic of either toxicity or efficacy. We describe herein, new tools and methods for this purpose, called Compoundcentric Displacement Proteomics (CCDP). Employing a new product-NuGel™ PROfessor™ which can noncovalently bind proteins, a subset of proteins can be displaced upon introduction of soluble small compounds. Coupled to LC-MS, quantitative metrics of these affinity-eluted sub-proteomes help characterize and identify interacting proteins. These new methods gain efficiencies over prior covalentbased substitution methods and can serve applications in drug target deconvolution, on-target/off-target specificity, and personalized medicine.
A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separ... more A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separate complex proteomes from natural sources and analyze protein functions systematically. The technology takes advantage of the powerful resolution of twodimensional gel electrophoresis (2-D Gels). The modification of electrophoretic conditions in combination with a high-resolution protein elution plate supports the recovery of functionally active proteins. As 2DE(2-Dimensional Electrophoresis) resolution can be limited by protein load, we investigated the use of bead based enrichment technologies, called AlbuVoid™ and KinaSorb™ to determine their effect on the proteomic features which can be generated from the PEP platform. Using a variety of substrates and enzyme activity assays, we report on the benefits of combining bead based enrichment to improve the signal report and the features generated for Hexokinase, Protein Kinase, Protease, and Alkaline Phosphatase activities. As a result, the PEP technology allows systematic analysis of large enzyme families and can build a comprehensive picture of protein function from a complex proteome, providing biological insights that could otherwise not be observed if only protein abundances were analyzed.
This paper describes the variations of soil moisture and organic matter using underground image t... more This paper describes the variations of soil moisture and organic matter using underground image textural indices and hyperspectral signatures. The mage textural indices were extracted from video image data by a real-time soil spectrophotometer (RTSS), and hyperspectral signatures were recorded on a portable field spectrophotometer and an AISA airborne sensor for the wheat-growing season at TUAT field. In explaining the variation of soil properties, the neural network (NN) showed consistently outperformed stepwise multiple linear regression (SMLR) and provided minimal prediction errors for spatial soil properties. The result showed that significant improvement had occurred and indicated integrated field spectral signatures with image texture would be an appropriate required in this type of analysis.
In recent times, one of the major challenges in crop cultivation is the proper interpretation of ... more In recent times, one of the major challenges in crop cultivation is the proper interpretation of field maps, which influences the variability of crop yields significantly. The ability to find and comprehend soil factors influencing crop yield variability will enable us to manage the soils efficiently. A study was conducted in a commercial paddy farm at Kahang, Peninsular Malaysia with the objective of quantifying and characterizing the nature of spatial soil nutrients (N, P and K) variation. Soil samples (0-15 cm) were collected at 20 m x 20 m grid pattern from the studied plot (3.85 ha) at the beginning of paddy (MR 211 variety) planting and analyzed for total N, available P and exchangeable K. A GeoExplorer II was used to record the soil sampling points and boundary of the plot to interpret the spatial maps in GIS platform with proper coordinates. Geo-statistical analysis was used to characterize the spatial variation of soil nutrients. The coefficient of variation of soil nutrien...
Diffuse cutaneous mastocytosis with bullous lesions and pulmonary involvement: a rare case
Indian journal of dermatology
Mastocytosis is defined as a heterogeneous group of disorders characterized by an accumulation of... more Mastocytosis is defined as a heterogeneous group of disorders characterized by an accumulation of mast cells in one or more organs, particularly in the skin, bone marrow, liver, spleen and lymph nodes. However here we describe an 11-month-old girl child presented with diffuse cutaneous mastocytosis with bullous lesion, having pulmonary involvement, which is very rare and there is no available case report from India.
The Three-Dimensional X-Ray Crystal Structure of HIV-1 Protease Complexed with a Hydroxyethylene Inhibitor
Advances in Experimental Medicine and Biology, 1991
1. Adv Exp Med Biol. 1991;306:455-60. The three-dimensional x-ray crystal structure of HIV-1 prot... more 1. Adv Exp Med Biol. 1991;306:455-60. The three-dimensional x-ray crystal structure of HIV-1 protease complexed with a hydroxyethylene inhibitor. Graves BJ, Hatada MH, Miller JK, Graves MC, Roy S, Cook CM, Kröhn A, Martin JA, Roberts NA. ...
Gametophytic factors mediate pollen-pistil interactions in maize (Zea mays L.) and play active ro... more Gametophytic factors mediate pollen-pistil interactions in maize (Zea mays L.) and play active roles in limiting gene flow among maize populations and between maize and teosinte. This study was carried out to identify proteins and investigate the mechanism of gametophytic factors using protein analysis. W22 (ga1); which did not carry a gametophytic factor and W22 (Ga1), a near iso-genic line, were used for the proteome investigation. SDS-PAGE was executed to investigate proteins in the pollen and pistil of W22 (ga1) and W22 (Ga1). A total of 44 differentially expressed proteins were identified in the pollen and pistil on SDS-PAGE using LTQ-FTICR MS. Among the 44 proteins, a total of 24 proteins were identified in the pollen of W22 (ga1) and W22 (Ga1) whereas 20 differentially expressed proteins were identified from the pistil of W22 (ga1) and W22 (Ga1). However,
Uploads
Papers by Swapan Roy