36 results on '"Dey H"'
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2. Creep Performance and Microstructural Characterization of Electron-Beam Welded 316LN SS-Grade 91 Steel Dissimilar Joint
- Author
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Vanaja, J., Dey, H. C., Prasad Reddy, G. V., Laha, K., and Vasudevan, M.
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- 2023
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3. Design of Microstrip Lowpass Filter in Combination with Defected Ground and Defected Microstrip Structures
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Mondal, P., Dey, H., Parui, S. K., Maharatna, Koushik, editor, Dalapati, Goutam Kumar, editor, Banerjee, P K, editor, Mallick, Amiya Kumar, editor, and Mukherjee, Moumita, editor
- Published
- 2015
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4. Nanomagnet Logic: Routes to Enhanced Dot-Dot Coupling
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Dey, H., primary, Shah, F., additional, Csaba, G., additional, Porod, W., additional, and Bernstein, G. H., additional
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- 2018
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5. Choice of welding consumable and procedure qualification for welding of 304HCu austenitic stainless steel boiler tubes for Indian Advanced Ultra Super Critical power plant
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Srinivasan, G., Dey, H. C., Ganesan, V., Bhaduri, A. K., Albert, S. K., and Laha, K.
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- 2016
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6. Spark Plasma Welding of Austenitic Stainless Steel AISI 304L to Commercially Pure Titanium
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Naveen Kumar, N., Janaki Ram, G. D., Bhattacharya, S. S., Dey, H. C., and Albert, S. K.
- Published
- 2015
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7. Design of Microstrip Lowpass Filter in Combination with Defected Ground and Defected Microstrip Structures
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Mondal, P., primary, Dey, H., additional, and Parui, S. K., additional
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- 2015
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8. Secure multi-gigabit optical link design for high energy physics experiment with acceleration of more secure RC4 variant in reconfigurable platform
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Paul, R., primary, Mitra, J., additional, Dey, H., additional, Sau, S., additional, Baidya, P., additional, Ghosh, R., additional, and Chakrabrti, A., additional
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- 2020
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9. Coherent precession in arrays of dipolar-coupled soft magnetic nanodots.
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Hu, X. K., Dey, H., Liebing, N., Schumacher, H. W., Csaba, G., Orlov, A., Bernstein, G. H., and Porod, W.
- Subjects
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DIPOLE interactions , *SOFT magnetic materials , *COHERENCE (Physics) , *FERROMAGNETIC resonance , *PRECESSION , *MICROMAGNETICS , *MATHEMATICAL models - Abstract
Precession modes of rectangular nanodot arrays with diameters of 90 and 150 nm and varied dipolar interaction are systematically studied by vector network analyzer ferromagnetic resonance, and micromagnetic simulations. The large dots reveal two dominant modes: a low frequency edge mode and a high frequency center mode, while in the smaller dots only the edge mode is observed. With increasing dipolar interaction, the precession-mode frequencies increase. The interaction has a stronger influence on the edge mode than on the center mode, resulting in different precession behaviors in different ranges of magnetic fields: well-separated modes in high fields and a merging of edge and center modes at low fields. At low fields and for strong dipolar interaction, coherent precession of the whole dot array is observed. [ABSTRACT FROM AUTHOR]
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- 2015
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10. Spin wave eigenmodes in single and coupled sub-150nm rectangular permalloy dots.
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Carlotti, G., Tacchi, S., Gubbiotti, G., Madami, M., Dey, H., Csaba, G., and Porod, W.
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SPIN waves ,FERROMAGNETISM ,MAGNETIZATION ,NUCLEAR spin ,MAGNETIC properties - Abstract
We present the results of a Brillouin light scattering investigation of thermally excited spin wave eigenmodes in square arrays of either isolated rectangular dots of permalloy or twins of dipolarly coupled elements, placed side-by-side or head-to-tail. The nanodots, fabricated by e-beam lithography and lift-off, are 20nm thick and have the major size D in the range between 90nm and 150 nm. The experimental spectra show the presence of two main peaks, corresponding to modes localized either at the edges or in the center of the dots. Their frequency dependence on the dot size and on the interaction with adjacent elements has been measured and successfully interpreted on the basis of dynamical micromagnetic simulations. The latter enabled us also to describe the spatial profile of the eigenmodes, putting in evidence the effects induced by the dipolar interaction between coupled dots. In particular, in twinned dots the demagnetizing field is appreciably modified in proximity of the "internal edges" if compared to the "external" ones, leading to a splitting of the edge mode. These results can be relevant for the exploitation of sub-150 nm magnetic dots in new applications, such as magnonic metamaterials, bit-patterned storage media, and nano-magnetic logic devices. [ABSTRACT FROM AUTHOR]
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- 2015
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11. Exchange coupling between laterally adjacent nanomagnets
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Dey, H, primary, Csaba, G, additional, Bernstein, G H, additional, and Porod, W, additional
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- 2016
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12. Shape-Dependent Switching Behavior of Exchange-Coupled Nanomagnet Stacks
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Dey, H., primary, Csaba, G., additional, Shah, F., additional, Bernstein, G. H., additional, and Porod, W., additional
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- 2016
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13. Edge-Mode Resonance-Assisted Switching of Nanomagnet Logic Elements
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Hu, X. K., primary, Dey, H., additional, Liebing, N., additional, Csaba, G., additional, Orlov, A., additional, Bernstein, G. H., additional, Porod, W., additional, Krzysteczko, P., additional, Sievers, S., additional, and Schumacher, H. W., additional
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- 2015
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14. Choice of Welding Consumable and Procedure Qualification for Welding of 304HCu Austenitic Stainless Steel Boiler Tubes for Indian Advanced Ultra Super Critical Power Plant
- Author
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Srinivasan, G., primary, Dey, H. C., additional, Bhaduri, A. K., additional, Albert, S. K., additional, and Jayakumar, T., additional
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- 2015
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15. Spin wave eigenmodes in single and coupled sub-150 nm rectangular permalloy dots
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Carlotti, G., primary, Tacchi, S., additional, Gubbiotti, G., additional, Madami, M., additional, Dey, H., additional, Csaba, G., additional, and Porod, W., additional
- Published
- 2015
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16. Ferromagnetic resonance modes of nanomagnetic logic elements
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Hu, X., primary, Dey, H. S., additional, Liebing, N., additional, Csaba, G., additional, Orlov, A., additional, Bernstein, G. H., additional, Porod, W., additional, Sievers, S., additional, and Schumacher, H. W., additional
- Published
- 2015
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17. Influence of Age on the Electrocardiographic Outline of Large White Yorkshire Piglets.
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Mohapatra, Swagat, Jyotiranjan, T., Dey, H. S., Mahapatra, A. P. K., and Kundu, A. K.
- Abstract
Large White Yorkshire piglets belonging to three different litters aged 2 months (group A), 4 months (group B) and 6 months (group C) were considered for the study. The electrocardiogram was recorded in five male piglets selected from each litter. Highest P-wave amplitude was measured in group A and P-wave recorded positively in all age groups except in one case of group A where it recorded negatively. Highest duration of P-wave was obtained in piglets of group C. The amplitude of QRS complex of all the piglets in group A recorded negatively while in group B and C negative QRS complex featured in only one out of five cases. Incidence of negative amplitude of T wave was observed in one out of five cases in group A and two out of five cases in group B while the amplitude of T wave recorded positively in all the cases in group C. The Q-T interval was measured to be highest in group B. Group C recorded the highest heart rate. [ABSTRACT FROM AUTHOR]
- Published
- 2016
18. Syntaxin 3B: A SNARE Protein Required for Vision.
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Dey H, Perez-Hurtado M, and Heidelberger R
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- Humans, Animals, Vision, Ocular physiology, SNARE Proteins metabolism, SNARE Proteins genetics, Membrane Fusion, Mutation, Qa-SNARE Proteins metabolism, Qa-SNARE Proteins genetics
- Abstract
Syntaxin 3 is a member of a large protein family of syntaxin proteins that mediate fusion between vesicles and their target membranes. Mutations in the ubiquitously expressed syntaxin 3A splice form give rise to a serious gastrointestinal disorder in humans called microvillus inclusion disorder, while mutations that additionally involve syntaxin 3B, a splice form that is expressed primarily in retinal photoreceptors and bipolar cells, additionally give rise to an early onset severe retinal dystrophy. In this review, we discuss recent studies elucidating the roles of syntaxin 3B and the regulation of syntaxin 3B functionality in membrane fusion and neurotransmitter release in the vertebrate retina.
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- 2024
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19. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
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Carlino N, Blanco-Míguez A, Punčochář M, Mengoni C, Pinto F, Tatti A, Manghi P, Armanini F, Avagliano M, Barcenilla C, Breselge S, Cabrera-Rubio R, Calvete-Torre I, Coakley M, Cobo-Díaz JF, De Filippis F, Dey H, Leech J, Klaassens ES, Knobloch S, O'Neil D, Quijada NM, Sabater C, Skírnisdóttir S, Valentino V, Walsh L, Alvarez-Ordóñez A, Asnicar F, Fackelmann G, Heidrich V, Margolles A, Marteinsson VT, Rota Stabelli O, Wagner M, Ercolini D, Cotter PD, Segata N, and Pasolli E
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- Humans, Microbiota genetics, Food Microbiology, Metagenomics methods, Bacteria genetics, Bacteria classification, Metagenome genetics, Gastrointestinal Microbiome genetics
- Abstract
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication., Competing Interests: Declaration of interests D.O. is an employee of QIAGEN GmbH. E.S.K. is an employee of BaseClear B.V., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
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- 2024
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20. Regulation of Syntaxin3B-Mediated Membrane Fusion by T14, Munc18, and Complexin.
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Nishad R, Betancourt-Solis M, Dey H, Heidelberger R, and McNew JA
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- Synaptic Transmission genetics, Retina metabolism, SNARE Proteins genetics, SNARE Proteins metabolism, Protein Binding, Membrane Fusion physiology, Synapses metabolism
- Abstract
Retinal neurons that form ribbon-style synapses operate over a wide dynamic range, continuously relaying visual information to their downstream targets. The remarkable signaling abilities of these neurons are supported by specialized presynaptic machinery, one component of which is syntaxin3B. Syntaxin3B is an essential t-SNARE protein of photoreceptors and bipolar cells that is required for neurotransmitter release. It has a light-regulated phosphorylation site in its N-terminal domain at T14 that has been proposed to modulate membrane fusion. However, a direct test of the latter has been lacking. Using a well-controlled in vitro fusion assay, we found that a phosphomimetic T14 syntaxin3B mutation leads to a small but significant enhancement of SNARE-mediated membrane fusion following the formation of the t-SNARE complex. While the addition of Munc18a had only a minimal effect on membrane fusion mediated by SNARE complexes containing wild-type syntaxin3B, a more significant enhancement was observed in the presence of Munc18a when the SNARE complexes contained a syntaxin3B T14 phosphomimetic mutant. Finally, we showed that the retinal-specific complexins (Cpx III and Cpx IV) inhibited membrane fusion mediated by syntaxin3B-containing SNARE complexes in a dose-dependent manner. Collectively, our results establish that membrane fusion mediated by syntaxin3B-containing SNARE complexes is regulated by the T14 residue of syntaxin3B, Munc18a, and Cpxs III and IV.
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- 2023
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21. Integrated gene network analysis sheds light on understanding the progression of Osteosarcoma.
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Dey H, Vasudevan K, Doss C GP, Kumar SU, El Allali A, Alsamman AM, and Zayed H
- Abstract
Introduction: Osteosarcoma is a rare disorder among cancer, but the most frequently occurring among sarcomas in children and adolescents. It has been reported to possess the relapsing capability as well as accompanying collateral adverse effects which hinder the development process of an effective treatment plan. Using networks of omics data to identify cancer biomarkers could revolutionize the field in understanding the cancer. Cancer biomarkers and the molecular mechanisms behind it can both be understood by studying the biological networks underpinning the etiology of the disease., Methods: In our study, we aimed to highlight the hub genes involved in gene-gene interaction network to understand their interaction and how they affect the various biological processes and signaling pathways involved in Osteosarcoma. Gene interaction network provides a comprehensive overview of functional gene analysis by providing insight into how genes cooperatively interact to elicit a response. Because gene interaction networks serve as a nexus to many biological problems, their employment of it to identify the hub genes that can serve as potential biomarkers remain widely unexplored. A dynamic framework provides a clear understanding of biological complexity and a pathway from the gene level to interaction networks., Results: Our study revealed various hub genes viz. TP53, CCND1, CDK4, STAT3, and VEGFA by analyzing various topological parameters of the network, such as highest number of interactions, average shortest path length, high cluster density, etc. Their involvement in key signaling pathways, such as the FOXM1 transcription factor network, FAK-mediated signaling events, and the ATM pathway, makes them significant candidates for studying the disease. The study also highlighted significant enrichment in GO terms (Biological Processes, Molecular Function, and Cellular Processes), such as cell cycle signal transduction, cell communication, kinase binding, transcription factor activity, nucleoplasm, PML body, nuclear body, etc., Conclusion: To develop better therapeutics, a specific approach toward the disease targeting the hub genes involved in various signaling pathways must have opted to unravel the complexity of the disease. Our study has highlighted the candidate hub genes viz. TP53, CCND1 CDK4, STAT3, VEGFA. Their involvement in the major signaling pathways of Osteosarcoma makes them potential candidates to be targeted for drug development. The highly enriched signaling pathways include FOXM1 transcription pathway, ATM signal-ling pathway, FAK mediated signaling events, Arf6 signaling events, mTOR signaling pathway, and Integrin family cell surface interactions. Targeting the hub genes and their associated functional partners which we have reported in our studies may be efficacious in developing novel therapeutic targets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Dey, Vasudevan, Doss C., Kumar, El Allali, Alsamman and Zayed.)
- Published
- 2023
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22. Investigation of tetrasubstituted heterocycles reveals hydantoins as a promising scaffold for development of novel antimicrobials with membranolytic properties.
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Langer MK, Rahman A, Dey H, Anderssen T, Blencke HM, Haug T, Stensvåg K, Strøm MB, and Bayer A
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- Antimicrobial Cationic Peptides chemistry, Gram-Negative Bacteria, Microbial Sensitivity Tests, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Hydantoins pharmacology, Anti-Infective Agents pharmacology
- Abstract
Mimics of antimicrobial peptides (AMPs) have been proposed as a promising class of antimicrobial agents. We report the analysis of five tetrasubstituted, cationic, amphipathic heterocycles as potential AMP mimics. The analysis showed that the heterocyclic scaffold had a strong influence on the haemolytic activity of the compounds, and the hydantoin scaffold was identified as a promising template for drug lead development. Subsequently, a total of 20 hydantoin derivatives were studied for their antimicrobial potency and haemolytic activity. We found 19 of these derivatives to have very low haemolytic toxicity and identified three lead structures, 2dA, 6cG, and 6dG with very promising broad-spectrum antimicrobial activity. Lead structure 6dG displayed minimum inhibitory concentration (MIC) values as low as 1 μg/mL against Gram-positive bacteria and 4-16 μg/mL against Gram-negative bacteria. Initial mode of action (MoA) studies performed on the amine derivative 6cG, utilizing a luciferase-based biosensor assay, suggested a strong membrane disrupting effect on the outer and inner membrane of Escherichia coli. Our findings show that the physical properties and structural arrangement induced by the heterocyclic scaffolds are important factors in the design of AMP mimics., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Morten B Strøm and Annette Bayer have patent #Barbituric acid derivatives comprising cationic and lipophilic groups. WO2018178198A1. Issued to UiT., (Copyright © 2023 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)
- Published
- 2023
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23. Outer Membrane Integrity-Dependent Fluorescence of the Japanese Eel UnaG Protein in Live Escherichia coli Cells.
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Richard CSM, Dey H, Øyen F, Maqsood M, and Blencke HM
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- Animals, Fluorescence, Green Fluorescent Proteins metabolism, Bilirubin metabolism, Escherichia coli metabolism, Anguilla metabolism
- Abstract
Reporter genes are important tools in many biological disciplines. The discovery of novel reporter genes is relatively rare. However, known reporter genes are constantly applied to novel applications. This study reports the performance of the bilirubin-dependent fluorescent protein UnaG from the Japanese eel Anguilla japonicas in live Escherichia coli cells in response to the disruption of outer membrane (OM) integrity at low bilirubin (BR) concentrations. Using the E. coli wild-type strain MC4100, its isogenic OM-deficient mutant strain NR698, and different OM-active compounds, we show that BR uptake and UnaG fluorescence depend on a leaky OM at concentrations of 10 µM BR and below, while fluorescence is mostly OM integrity-independent at concentrations above 50 µM BR. We suggest that these properties of the UnaG-BR couple might be applied as a biosensor as an alternative to the OM integrity assays currently in use.
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- 2023
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24. Elucidating the mechanism of antimicrobial resistance in Mycobacterium tuberculosis using gene interaction networks.
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G K, Vasudevan K, Dey H, Kausar T, Udhaya Kumar S, Thirumal Kumar D, Zayed H, and George Priya Doss C
- Subjects
- Drug Resistance, Bacterial, Computational Biology, Gene Regulatory Networks, Anti-Bacterial Agents, Mycobacterium tuberculosis
- Abstract
Antimicrobial resistance (AMR) in microorganisms is an urgent global health threat. AMR of Mycobacterium tuberculosis is associated with significant morbidity and mortality. It is of great importance to underpin the resistance pathways involved in the mechanisms of AMR and identify the genes that are directly involved in AMR. The focus of the current study was the bacteria M. tuberculosis, which carries AMR genes that give resistance that lead to multidrug resistance. We, therefore, built a network of 43 genes and examined for potential gene-gene interactions. Then we performed a clustering analysis and identified three closely related clusters that could be involved in multidrug resistance mechanisms. Through the bioinformatics pipeline, we consistently identified six-hub genes (dnaN, polA, ftsZ, alr, ftsQ, and murC) that demonstrated the highest number of interactions within the clustering analysis. This study sheds light on the multidrug resistance of MTB and provides a protocol for discovering genes that might be involved in multidrug resistance, which will improve the treatment of resistant strains of TB., (Copyright © 2022. Published by Elsevier Inc.)
- Published
- 2023
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25. Identification of potential circadian genes and associated pathways in colorectal cancer progression and prognosis using microarray gene expression analysis.
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S SH, G K, Dey H, Sangoji RV, Thirumal Kumar D, Zayed H, Vasudevan K, and George Priya Doss C
- Subjects
- Humans, Databases, Factual, Drug Delivery Systems, Adaptor Proteins, Signal Transducing, Gene Expression Profiling, Colorectal Neoplasms genetics
- Abstract
Colorectal cancer (CRC) is third cancer causing death in the world. CRC is associated with disrupting the circadian rhythm (CR), closely associating the CRC progression and the dysregulation of genes involved in the biological clock. In this study, we aimed to understand the circadian rhythm changes in patients diagnosed with CRC. We used the GEO database with the ID GSE46549 for our analysis, which consists of 32 patients with CRC and one as normal control. Our study has identified five essential genes involved in CRC, HAPLN1, CDH12, IGFBP5, DCHS2, and DOK5, and had different enriched pathways, such as the Wnt-signaling pathway, at different time points of study. As a part of our study, we also identified various related circadian genes, such as CXCL12, C1QTNF2, MRC2, and GLUL, from the Circadian Gene Expression database, that played a role in circadian rhythm and CRC development. As circadian timing can influence the host tissue's ability to tolerate anticancer medications, the genes reported can serve as a potential drug target for treating CRC and become beneficial to translational settings., Competing Interests: Conflict of Interest The authors declare that the study has no conflict of interest., (Copyright © 2023. Published by Elsevier Inc.)
- Published
- 2023
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26. An integrated gene network analysis to decode the multi-drug resistance mechanism in Klebsiella pneumoniae.
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Dey H, Vasudevan K, Dasegowda KR, Rambabu M, Cn P, and C GPD
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- Humans, Drug Resistance, Multiple, Bacterial genetics, Gene Regulatory Networks, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Microbial Sensitivity Tests, Klebsiella pneumoniae genetics, Klebsiella Infections drug therapy
- Abstract
Antimicrobial resistance (AMR) among microorganisms has become one of the worldwide concerns of this century and continues to challenge us. To properly understand this problem, it is essential to know the genes that cause AMR and their resistance mechanisms. Our present study focused on Klebsiella pneumoniae, which possesses AMR genes conferring resistance against multiple antibiotics. A gene interaction network of 42 functional partners was constructed and analyzed to broaden our understanding. Three closely related clusters (C1-C3) having an association with multi-drug resistance mechanisms were identified by clustering analysis. The enrichment analysis illustrated 30 genes in biological processes, 24 genes in molecular function, and 25 genes in cellular components having a significant role. The analysis of the gene interaction network revealed genes birA2, folP, pabC, folA, gyrB, glmM, gyrA, thyA_2 had maximum no. of interactions with their functional partners viz. 26, 25, 25, 24, 23, 23, 23, 23 respectively and can be considered as hub genes. Analyzing the enriched pathways and Gene Ontologies provides insight into AMR's molecular basis. In addition, the proposed study could aid the researchers in developing new treatment options to combat multi-drug resistant K. pneumoniae., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2022 Elsevier Ltd. All rights reserved.)
- Published
- 2022
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27. Synthesis and Antimicrobial Activity of Short Analogues of the Marine Antimicrobial Peptide Turgencin A: Effects of SAR Optimizations, Cys-Cys Cyclization and Lipopeptide Modifications.
- Author
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Dey H, Simonovic D, Norberg-Schulz Hagen I, Vasskog T, Fredheim EGA, Blencke HM, Anderssen T, Strøm MB, and Haug T
- Subjects
- Humans, Cyclization, Antimicrobial Peptides, Peptides, Cyclic pharmacology, Peptides, Cyclic chemistry, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Escherichia coli, Hemolysis, Lipopeptides pharmacology, Lipopeptides chemistry, Anti-Infective Agents pharmacology, Anti-Infective Agents chemistry
- Abstract
We have synthesised short analogues of the marine antimicrobial peptide Turgencin A from the colonial Arctic ascidian Synoicum turgens. In this study, we focused on a central, cationic 12-residue Cys-Cys loop region within the sequence. Modified (tryptophan- and arginine-enriched) linear peptides were compared with Cys-Cys cyclic derivatives, and both linear and Cys-cyclic peptides were N-terminally acylated with octanoic acid (C
8 ), decanoic acid (C10 ) or dodecanoic acid (C12 ). The highest antimicrobial potency was achieved by introducing dodecanoic acid to a cyclic Turgencin A analogue with low intrinsic hydrophobicity, and by introducing octanoic acid to a cyclic analogue displaying a higher intrinsic hydrophobicity. Among all tested synthetic Turgencin A lipopeptide analogues, the most promising candidates regarding both antimicrobial and haemolytic activity were C12 -cTurg-1 and C8 -cTurg-2 . These optimized cyclic lipopeptides displayed minimum inhibitory concentrations of 4 µg/mL against Staphylococcus aureus , Escherichia coli and the fungus Rhodothorula sp. Mode of action studies on bacteria showed a rapid membrane disruption and bactericidal effect of the cyclic lipopeptides. Haemolytic activity against human erythrocytes was low, indicating favorable selective targeting of bacterial cells.- Published
- 2022
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28. A concise SAR-analysis of antimicrobial cationic amphipathic barbiturates for an improved activity-toxicity profile.
- Author
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Langer MK, Rahman A, Dey H, Anderssen T, Zilioli F, Haug T, Blencke HM, Stensvåg K, Strøm MB, and Bayer A
- Subjects
- Amines, Anti-Bacterial Agents chemistry, Anti-Bacterial Agents pharmacology, Barbiturates pharmacology, Cations chemistry, Cations pharmacology, Hemolysis, Humans, Microbial Sensitivity Tests, Structure-Activity Relationship, Anti-Infective Agents chemistry, Anti-Infective Agents pharmacology, Gram-Negative Bacteria
- Abstract
An amphipathic barbiturate mimic of the marine eusynstyelamides is reported as a promising class of antimicrobial agents. We hereby report a detailed analysis of the structure-activity relationship for cationic amphipathic N,N'-dialkylated-5,5-disubstituted barbiturates. The influence of various cationic groups, hydrocarbon linkers and lipophilic side chains on the compounds' antimicrobial potency and haemolytic activity was studied. A comprehensive library of 58 compounds was prepared using a concise synthetic strategy. We found cationic amine and guanidyl groups to yield the highest broad-spectrum activity and cationic trimethylated quaternary amine groups to exert narrow-spectrum activity against Gram-positive bacteria. n-Propyl hydrocarbon linkers proved to be the best compromise between potency and haemolytic activity. The combination of two different lipophilic side chains allowed for further fine-tuning of the biological properties. Using these insights, we were able to prepare both, the potent narrow-spectrum barbiturate 8a and the broad-spectrum barbiturates 11lG, 13jA and 13jG, all having low or no haemolytic activity. The guanidine derivative 11lG demonstrated a strong membrane disrupting effect in luciferase-based assays. We believe that these results may be valuable in further development of antimicrobial lead structures., (Copyright © 2022 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)
- Published
- 2022
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29. Realization of a Model-Free Pathway for Quantum Dot-Protein Interaction Beyond Classical Protein Corona or Protein Complex.
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Preeyanka N, Akhuli A, Dey H, Chakraborty D, Rahaman A, and Sarkar M
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- Serum Albumin, Bovine chemistry, Silver chemistry, Spectrometry, Fluorescence methods, Protein Corona chemistry, Quantum Dots chemistry
- Abstract
Although in recent times nanoparticles (NPs) are being used in various biological applications, their mechanism of binding interactions still remains hazy. Usually, the binding mechanism is perceived to be mediated through either the protein corona (PC) or protein complex (PCx). Herein, we report that the nanoparticle (NP)-protein interaction can also proceed via a different pathway without forming the commonly observed PC or PCx. In the present study, the NP-protein interaction between less-toxic zinc-silver-indium-sulfide (ZAIS) quantum dots (QDs) and bovine serum albumin (BSA) was investigated by employing spectroscopic and microscopic techniques. Although the analyses of data obtained from fluorescence and thermodynamic studies do indicate the binding between QDs and BSA, they do not provide clear experimental evidence in favor of PC or PCx. Quite interestingly, high-resolution transmission electron microscopy (HRTEM) studies have shown the formation of a new type of species where BSA protein molecules are adsorbed onto some portion of a QD surface rather than the entire surface. To the best of our knowledge, we believe that this is the first direct experimental evidence in favor of a model-free pathway for NP-protein interaction events. Thus, the outcome of the present study, through experimental evidence, clearly suggests that NP-protein interaction can proceed by following a pathway that is different from classical PC and PCx.
- Published
- 2022
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30. Cardiolipin targets a dynamin-related protein to the nuclear membrane.
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Kar UP, Dey H, and Rahaman A
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- Amino Acid Sequence, Dynamins chemistry, Dynamins metabolism, Protein Binding, Protozoan Proteins chemistry, Protozoan Proteins metabolism, Sequence Alignment, Tetrahymena thermophila metabolism, Cardiolipins metabolism, Dynamins genetics, Nuclear Envelope metabolism, Protozoan Proteins genetics, Tetrahymena thermophila genetics
- Abstract
Dynamins are targeted to specific cellular membranes that they remodel via membrane fusion or fission. The molecular basis of conferring specificity to dynamins for their target membrane selection is not known. Here, we report a mechanism of nuclear membrane recruitment of Drp6, a dynamin member in Tetrahymena thermophila . Recruitment of Drp6 depends on a domain that binds to cardiolipin (CL)-rich bilayers. Consistent with this, nuclear localization of Drp6 was inhibited either by depleting cellular CL or by substituting a single amino acid residue that abolished Drp6 interactions with CL. Inhibition of CL synthesis, or perturbation in Drp6 recruitment to nuclear membrane, caused defects in the formation of new macronuclei post-conjugation. Taken together, our results elucidate a molecular basis of target membrane selection by a nuclear dynamin and establish the importance of a defined membrane-binding domain and its target lipid in facilitating nuclear expansion., Competing Interests: UK, HD, AR No competing interests declared, (© 2021, Kar et al.)
- Published
- 2021
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31. Highly efficient energy transfer from a water soluble zinc silver indium sulphide quantum dot to organic J-aggregates.
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Preeyanka N, Dey H, Seth S, Rahaman A, and Sarkar M
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- Energy Transfer, Indium chemistry, Molecular Structure, Particle Size, Semiconductors, Silver chemistry, Solubility, Sulfides chemistry, Surface Properties, Water chemistry, Zinc chemistry, Carbocyanines chemistry, Fluorescent Dyes chemistry, Quantum Dots chemistry
- Abstract
The present work has been carried out with the aim to design and develop an efficient light harvesting inorganic-organic hybrid nanoscale material by employing a less toxic, environment friendly inorganic substance and also to understand the mechanism of inter-particle electronic interaction between the inorganic and organic components of the nanomaterial. Specifically, the inorganic-organic hybrid associate has been made by integrating water soluble semiconductor (zinc-silver-indium-sulfide (ZAIS)) QDs and organic J-aggregates of a cyanine dye (S2165). The fabrication of the present nano-hybrid system has been achieved via electrostatically driven self-assembly of organic dyes over ZAIS QDs. The interaction between QD and J-aggregates has been investigated by using steady state and time resolved fluorescence measurements. Zeta potential measurements have also been performed to understand the role of electrostatic interaction and thermodynamic feasibility of the association process. The investigations have revealed that the energy transfer (ET) process between QD and J-aggregates was mediated through a dipole-dipole mechanism. Interestingly, data analysis based on Förster theory has further revealed that the ET from QD to J-aggregates is very high, indicating efficient electronic coupling between the inorganic QD and the organic J-aggregates. Zeta potential measurements and thermodynamic calculations have demonstrated that the interaction between QD and organic dye is electrostatically driven and the association of organic dyes over QDs is thermodynamically feasible. The outcome of the present study is expected to be helpful in designing efficient nanoscale light harvesting devices. Additionally, fluorescence microscopy and toxicity studies on the QDs have also shown their suitability for biological applications.
- Published
- 2020
- Full Text
- View/download PDF
32. NarAB Is an ABC-Type Transporter That Confers Resistance to the Polyether Ionophores Narasin, Salinomycin, and Maduramicin, but Not Monensin.
- Author
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Naemi AO, Dey H, Kiran N, Sandvik ST, Slettemeås JS, Nesse LL, and Simm R
- Abstract
Polyether ionophores are antimicrobial compounds used as feed additives in poultry feed to control diseases caused by coccidia. In addition to the anticoccidial activity of these compounds, polyether ionophores also contain antibacterial properties. Resistance to the polyether ionophore narasin was recently shown to exist on mobile plasmids in Enterococcus faecium and the resistance mechanism was suggested to be associated with a two-gene operon encoding an ABC-type transporter. In this study we demonstrate that the genes encoding the putative narasin resistance mechanism confers reduced susceptibility to the polyether ionophores narasin, salinomycin and maduramicin, but not to monensin and suggest that this resistance mechanism should be referred to as NarAB. Importantly, NarAB does not affect the susceptibility of E. faecium to any of the tested antimicrobial compounds that are used in clinical medicine. However, we show that conjugation in the presence of certain polyether ionophores increases the number of vancomycin resistant E. faecium suggesting that narasin and certain other polyether ionophores can contribute to the persistence of VRE in poultry populations., (Copyright © 2020 Naemi, Dey, Kiran, Sandvik, Slettemeås, Nesse and Simm.)
- Published
- 2020
- Full Text
- View/download PDF
33. Tetrahymena dynamin-related protein 6 self-assembles independent of membrane association.
- Author
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Kar UP, Dey H, and Rahaman A
- Subjects
- Binding Sites, Cloning, Molecular, Dynamins genetics, Dynamins metabolism, Enzyme Assays, Escherichia coli genetics, Escherichia coli metabolism, GTP Phosphohydrolases genetics, GTP Phosphohydrolases metabolism, Gene Expression, Genetic Vectors chemistry, Genetic Vectors metabolism, Guanosine Triphosphate metabolism, Kinetics, Nuclear Envelope chemistry, Nuclear Envelope enzymology, Nuclear Envelope ultrastructure, Osmolar Concentration, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, Protozoan Proteins genetics, Protozoan Proteins metabolism, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Sodium Chloride chemistry, Tetrahymena enzymology, Tetrahymena ultrastructure, Dynamins chemistry, GTP Phosphohydrolases chemistry, Guanosine Triphosphate chemistry, Protozoan Proteins chemistry, Tetrahymena chemistry
- Abstract
Self-assembly on target membranes is one of the important properties of all dynamin family proteins. Drp6, a dynaminrelated protein in Tetrahymena, controls nuclear remodelling and undergoes cycles of assembly/disassembly on the nuclear envelope. To elucidate the mechanism of Drp6 function, we have characterized its biochemical and biophysical properties using size exclusion chromatography, chemical cross-linking and electron microscopy. The results demonstrate that Drp6 readily forms high-molecular-weight self-assembled structures as determined by size exclusion chromatography and chemical cross-linking. Negative stain electron microscopy revealed that Drp6 assembles into rings and spirals at physiological ionic strength. We have also shown that the recombinant Drp6 expressed in bacteria is catalytically active and its GTPase activity is not enhanced by low salt. These results suggest that, in contrast to dynamins but similar to MxA, Drp6 self-assembles in the absence of membrane templates, and its GTPase activity is not affected by ionic strength of the buffer. We discuss the self-assembly structure of Drp6 and explain the basis for lack of membrane-stimulated GTPase activity.
- Published
- 2018
34. Regulation of dynamin family proteins by post-translational modifications.
- Author
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Kar UP, Dey H, and Rahaman A
- Subjects
- Animals, Dynamins genetics, Multigene Family, Phosphorylation, Dynamins metabolism, Protein Processing, Post-Translational physiology
- Abstract
Dynamin superfamily proteins comprising classical dynamins and related proteins are membrane remodelling agents involved in several biological processes such as endocytosis, maintenance of organelle morphology and viral resistance. These large GTPases couple GTP hydrolysis with membrane alterations such as fission, fusion or tubulation by undergoing repeated cycles of self-assembly/disassembly. The functions of these proteins are regulated by various post-translational modifications that affect their GTPase activity, multimerization or membrane association. Recently, several reports have demonstrated variety of such modifications providing a better understanding of the mechanisms by which dynamin proteins influence cellular responses to physiological and environmental cues. In this review, we discuss major post-translational modifications along with their roles in the mechanism of dynamin functions and implications in various cellular processes.
- Published
- 2017
- Full Text
- View/download PDF
35. Spin-orbit torque-assisted switching in magnetic insulator thin films with perpendicular magnetic anisotropy.
- Author
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Li P, Liu T, Chang H, Kalitsov A, Zhang W, Csaba G, Li W, Richardson D, DeMann A, Rimal G, Dey H, Jiang JS, Porod W, Field SB, Tang J, Marconi MC, Hoffmann A, Mryasov O, and Wu M
- Abstract
As an in-plane charge current flows in a heavy metal film with spin-orbit coupling, it produces a torque on and thereby switches the magnetization in a neighbouring ferromagnetic metal film. Such spin-orbit torque (SOT)-induced switching has been studied extensively in recent years and has shown higher efficiency than switching using conventional spin-transfer torque. Here we report the SOT-assisted switching in heavy metal/magnetic insulator systems. The experiments used a Pt/BaFe12O19 bilayer where the BaFe12O19 layer exhibits perpendicular magnetic anisotropy. As a charge current is passed through the Pt film, it produces a SOT that can control the up and down states of the remnant magnetization in the BaFe12O19 film when the film is magnetized by an in-plane magnetic field. It can reduce or increase the switching field of the BaFe12O19 film by as much as about 500 Oe when the film is switched with an out-of-plane field.
- Published
- 2016
- Full Text
- View/download PDF
36. Longitudinal immune profiles in type 1 leprosy reactions in Bangladesh, Brazil, Ethiopia and Nepal.
- Author
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Khadge S, Banu S, Bobosha K, van der Ploeg-van Schip JJ, Goulart IM, Thapa P, Kunwar CB, van Meijgaarden KE, van den Eeden SJ, Wilson L, Kabir S, Dey H, Goulart LR, Lobato J, Carvalho W, Bekele Y, Franken KL, Aseffa A, Spencer JS, Oskam L, Otttenhoff TH, Hagge DA, and Geluk A
- Subjects
- Bangladesh, Brazil, Cytokines blood, Ethiopia, Female, Host-Pathogen Interactions, Humans, Immunity, Humoral immunology, Interleukin-10 blood, Interleukin-17 blood, Leprosy diagnosis, Leukocytes, Mononuclear immunology, Leukocytes, Mononuclear microbiology, Male, Middle Aged, Mycobacterium leprae immunology, Nepal, Prospective Studies, Biomarkers analysis, Cytokines immunology, Leprosy immunology, Mycobacterium leprae pathogenicity
- Abstract
Background: Acute inflammatory reactions are a frequently occurring, tissue destructing phenomenon in infectious- as well as autoimmune diseases, providing clinical challenges for early diagnosis. In leprosy, an infectious disease initiated by Mycobacterium leprae (M. leprae), these reactions represent the major cause of permanent neuropathy. However, laboratory tests for early diagnosis of reactional episodes which would significantly contribute to prevention of tissue damage are not yet available. Although classical diagnostics involve a variety of tests, current research utilizes limited approaches for biomarker identification. In this study, we therefore studied leprosy as a model to identify biomarkers specific for inflammatory reactional episodes., Methods: To identify host biomarker profiles associated with early onset of type 1 leprosy reactions, prospective cohorts including leprosy patients with and without reactions were recruited in Bangladesh, Brazil, Ethiopia and Nepal. The presence of multiple cyto-/chemokines induced by M. leprae antigen stimulation of peripheral blood mononuclear cells as well as the levels of antibodies directed against M. leprae-specific antigens in sera, were measured longitudinally in patients., Results: At all sites, longitudinal analyses showed that IFN-γ-, IP-10-, IL-17- and VEGF-production by M. leprae (antigen)-stimulated PBMC peaked at diagnosis of type 1 reactions, compared to when reactions were absent. In contrast, IL-10 production decreased during type 1 reaction while increasing after treatment. Thus, ratios of these pro-inflammatory cytokines versus IL-10 provide useful tools for early diagnosing type 1 reactions and evaluating treatment. Of further importance for rapid diagnosis, circulating IP-10 in sera were significantly increased during type 1 reactions. On the other hand, humoral immunity, characterized by M. leprae-specific antibody detection, did not identify onset of type 1 reactions, but allowed treatment monitoring instead., Conclusions: This study identifies immune-profiles as promising host biomarkers for detecting intra-individual changes during acute inflammation in leprosy, also providing an approach for other chronic (infectious) diseases to help early diagnose these episodes and contribute to timely treatment and prevention of tissue damage.
- Published
- 2015
- Full Text
- View/download PDF
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