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  1. Article ; Online: Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from

    Bhattacharya, Shreya / Satpati, Priyadarshi

    Journal of chemical information and modeling

    2024  Volume 64, Issue 8, Page(s) 3237–3247

    Abstract: Popular RNA-guided DNA endonuclease Cas9 ... ...

    Abstract Popular RNA-guided DNA endonuclease Cas9 from
    MeSH term(s) Streptococcus pyogenes/enzymology ; CRISPR-Associated Protein 9/metabolism ; CRISPR-Associated Protein 9/chemistry ; CRISPR-Associated Protein 9/genetics ; Mutation ; Molecular Dynamics Simulation ; Nucleotide Motifs ; DNA/metabolism ; DNA/chemistry ; Protein Conformation ; Models, Molecular ; Thermodynamics ; Protein Binding
    Chemical Substances CRISPR-Associated Protein 9 (EC 3.1.-) ; DNA (9007-49-2)
    Language English
    Publishing date 2024-04-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01515
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    Zs.A 1230: Show issues Location:
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  2. Article ; Online: Double pyramidal lobe: a rare encounter in thyroidectomy.

    Pal, Subhadeep / Bhattacharya, Shreya / Banerjee, Devmalya

    ANZ journal of surgery

    2024  Volume 94, Issue 4, Page(s) 761–762

    MeSH term(s) Humans ; Thyroidectomy ; Thyroid Neoplasms/surgery
    Language English
    Publishing date 2024-01-30
    Publishing country Australia
    Document type Case Reports
    ZDB-ID 2050749-5
    ISSN 1445-2197 ; 1445-1433 ; 0004-8682
    ISSN (online) 1445-2197
    ISSN 1445-1433 ; 0004-8682
    DOI 10.1111/ans.18882
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  3. Article ; Online: Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations.

    Bhattacharya, Shreya / Satpati, Priyadarshi

    ACS omega

    2022  Volume 8, Issue 2, Page(s) 1817–1837

    Abstract: The CRISPR/Cas9 system is a popular genome-editing tool with immense therapeutic potential. It is a simple two-component system (Cas9 protein and RNA) that recognizes the DNA sequence on the basis of RNA:DNA complementarity, and the Cas9 protein ... ...

    Abstract The CRISPR/Cas9 system is a popular genome-editing tool with immense therapeutic potential. It is a simple two-component system (Cas9 protein and RNA) that recognizes the DNA sequence on the basis of RNA:DNA complementarity, and the Cas9 protein catalyzes the double-stranded break in the DNA. In the past decade, near-atomic resolution structures at various stages of the CRISPR/Cas9 DNA editing pathway have been reported along with numerous experimental and computational studies. Such studies have boosted knowledge of the genome-editing mechanism. Despite such advancements, the application of CRISPR/Cas9 in therapeutics is still limited, primarily due to off-target effects. Several studies aim at engineering high-fidelity Cas9 to minimize the off-target effects. Molecular Dynamics (MD) simulations have been an excellent complement to the experimental studies for investigating the mechanism of CRISPR/Cas9 editing in terms of structure, thermodynamics, and kinetics. MD-based studies have uncovered several important molecular aspects of Cas9, such as nucleotide binding, catalytic mechanism, and off-target effects. In this Review, the contribution of MD simulation to understand the CRISPR/Cas9 mechanism has been discussed, preceded by an overview of the history, mechanism, and structural aspects of the CRISPR/Cas9 system. These studies are important for the rational design of highly specific Cas9 and will also be extremely promising for achieving more accurate genome editing in the future.
    Language English
    Publishing date 2022-12-30
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c05583
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  4. Article ; Online: One carbon metabolism and its implication in health and immune functions.

    Dang, Shreya / Jain, Arushi / Dhanda, Garima / Bhattacharya, Neetu / Bhattacharya, Amit / Senapati, Sabyasachi

    Cell biochemistry and function

    2024  Volume 42, Issue 1, Page(s) e3926

    Abstract: One carbon (1C) metabolism is critical for cellular viability and physiological homeostasis. Starting from its crucial involvement in purine biosynthesis to posttranslational modification of proteins, 1C metabolism contributes significantly to the ... ...

    Abstract One carbon (1C) metabolism is critical for cellular viability and physiological homeostasis. Starting from its crucial involvement in purine biosynthesis to posttranslational modification of proteins, 1C metabolism contributes significantly to the development and cellular differentiation through methionine and folate cycles that are pivotal for cellular function. Genetic polymorphisms of several genes of these pathways are implicated in disease pathogenesis and drug metabolism. Metabolic products of 1C metabolism have significant roles in epigenetic modifications through DNA and histone protein methylation. Homocysteine is a product that has clinical significance in the diagnosis and prognosis of several critical illnesses, including chronic immune diseases and cancers. Regulation of the function and differentiation of immune cells, including T-cells, B-cells, macrophages, and so forth, are directly influenced by 1C metabolism and thus have direct implications in several immune disease biology. Recent research on therapeutic approaches is targeting nuclear, cytoplasmic, and mitochondrial 1C metabolism to manage and treat metabolic (i.e., type 2 diabetes), neurodegenerative (i.e., Alzheimer's disease), or immune (i.e., rheumatoid arthritis) diseases. 1C metabolism is being explored for therapeutic intervention as a common determinant for a spectrum of immune and metabolic diseases. Identifying the association or correlation between essential metabolic products of this pathway and disease onset or prognosis would further facilitate the clinical monitoring of diseases.
    MeSH term(s) Humans ; Diabetes Mellitus, Type 2 ; Homeostasis ; Alzheimer Disease ; Carbon ; Immunity
    Chemical Substances Carbon (7440-44-0)
    Language English
    Publishing date 2024-01-25
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 283643-9
    ISSN 1099-0844 ; 0263-6484
    ISSN (online) 1099-0844
    ISSN 0263-6484
    DOI 10.1002/cbf.3926
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  5. Article ; Online: Comparative Review Study on the Forest and Biodiversity Management practices between India and Germany

    Shreya Bhattacharya

    G-Journal of Environmental Science and Technology, Vol 6, Iss

    2018  Volume 3

    Abstract: The review study aims to identify several chains of socio-political events in the forest and wildlife management sectors in India and Germany, which interfered and affected its natural biodiversity during the 19th century. It also deals with the ... ...

    Abstract The review study aims to identify several chains of socio-political events in the forest and wildlife management sectors in India and Germany, which interfered and affected its natural biodiversity during the 19th century. It also deals with the understanding of formulation of laws as an effort to reduce the impact of exploitation of native forests and biodiversity in the respective countries. The comparative study of forest management of India and Germany dates back to more than hundred years when Sir Dietrich Brandis, a German forester, who is now recognized as the Father of Tropical Forestry was appointed as the forest administrator of India by the British Government. The study explores the critical issues in the forest and biodiversity management sectors that were identified more than a century ago and are still prevalent in many parts of the countries which resulted in severe loss of natural biodiversity. The importance of conservation and restoration along with the formulation of forest and biodiversity laws under several circumstances are also highlighted in the study.
    Keywords Forestry ; Wildlife ; Management ; Biodiversity ; Conservation ; Environmental sciences ; GE1-350
    Subject code 333
    Language English
    Publishing date 2018-12-01T00:00:00Z
    Publisher Environment, Agriculture and Education Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Effects of Perinatally Acquired Cytomegalovirus Infection on Growth Hormone Axis

    Sayan Chatterjee / Shreya Ray Chaudhuri / Subhasish Bhattacharya

    Journal of Clinical and Diagnostic Research, Vol 17, Iss 1, Pp SR01-SR

    2023  Volume 03

    Abstract: Cytomegalovirus (CMV) is one of the most common causes of perinatally acquired infection worldwide. It affects almost every organ system with varied type of clinical manifestation. In this case series, effect of perinatally acquired cytomegalovirus ... ...

    Abstract Cytomegalovirus (CMV) is one of the most common causes of perinatally acquired infection worldwide. It affects almost every organ system with varied type of clinical manifestation. In this case series, effect of perinatally acquired cytomegalovirus infection was studied on relatively unexplored area i.e, on growth hormone axis. Effect of standard antiviral treatment was also studied in these children. Five children were diagnosed to have perinatally acquired cytomegalovirus infection and it was found that all of these children were suffering from growth hormone deficiency (as evidenced by low insulin-like growth factor 1 and insulin-like growth factor binding protein 3 level as well). Some of the children were also found to have other endocrine manifestations like hypothyroidism and hypoglycaemia. They were treated with intravenous Ganciclovir followed by oral Valganciclovir and most of them responded well.
    Keywords endocrine manifestation ; hepatosplenomegaly ; insulin growth factor ; Medicine ; R
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher JCDR Research and Publications Private Limited
    Document type Article ; Online
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  7. Article ; Online: In silico screening and exploration into phenotypic alterations of deleterious oncogenic single nucleotide polymorphisms in HSPB1 gene.

    Bhattacharya, Shreya / Ray, Sujay

    Genomics

    2021  Volume 113, Issue 4, Page(s) 2812–2825

    Abstract: A small heat shock protein, HSP27, encoded by HSPB1 gene strongly favors survival, proliferation and metastasis of cancer cells and its expression is dependent on post-translational modifications like phosphorylation. This study performed an extensive in ...

    Abstract A small heat shock protein, HSP27, encoded by HSPB1 gene strongly favors survival, proliferation and metastasis of cancer cells and its expression is dependent on post-translational modifications like phosphorylation. This study performed an extensive in silico screening of 20 deleterious non-synonymous SNPs in the coding region of HSPB1 gene, among which four were identified to be cancer associated. The SNP variant I181S introduced a new phosphorylation site in position 181, which might elevate the protein's activation potential. Emergence of other post-translational modifications was also observed in SNP variants: L144P and E130K.Significant conformational changes were observed in I181S, L144P and E130K SNP variants with respect to wild-type HSP27. These SNPs appear in one among 10
    MeSH term(s) Carcinogenesis/genetics ; HSP27 Heat-Shock Proteins/genetics ; HSP27 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/genetics ; Humans ; Molecular Chaperones/genetics ; Neoplasms/genetics ; Oncogenes ; Polymorphism, Single Nucleotide
    Chemical Substances HSP27 Heat-Shock Proteins ; HSPB1 protein, human ; Heat-Shock Proteins ; Molecular Chaperones
    Language English
    Publishing date 2021-06-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2021.06.017
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    Zs.A 2367: Show issues Location:
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  8. Article ; Online: E-Protein Protonation Titration-Induced Single-Particle Chemical Force Spectroscopy for Microscopic Understanding and pI Estimation of Infectious DENV.

    Ghosal, Manorama / Rakshit, Tatini / Bhattacharya, Shreya / Bhattacharyya, Sankar / Satpati, Priyadarshi / Senapati, Dulal

    The journal of physical chemistry. B

    2024  Volume 128, Issue 13, Page(s) 3133–3144

    Abstract: The ionization state of amino acids on the outer surface of a virus regulates its physicochemical properties toward the sorbent surface. Serologically different strains of the dengue virus (DENV) show different extents of infectivity depending upon their ...

    Abstract The ionization state of amino acids on the outer surface of a virus regulates its physicochemical properties toward the sorbent surface. Serologically different strains of the dengue virus (DENV) show different extents of infectivity depending upon their interactions with a receptor on the host cell. To understand the structural dependence of E-protein protonation over its sequence dependence, we have followed E-protein titration kinetics both experimentally and theoretically for two differentially infected dengue serotypes, namely, DENV-2 and DENV-4. We have performed E-protein protonation titration-induced single-particle chemical force spectroscopy using an atomic force microscope (AFM) to measure the surface chemistry of DENV in physiological aqueous solutions not only to understand the charge distribution dynamics on the virus surface but also to estimate the isoelectric point (pI) accurately for infectious dengue viruses. Cryo-EM structure-based theoretical pI calculations of the DENV-2 surface protein were shown to be consistent with the evaluated pI value from force spectroscopy measurements. We also highlighted here the role of the microenvironment around the titrable residues (in the 3D-folded structure of the protein) in altering the p
    MeSH term(s) Humans ; Dengue/metabolism ; Dengue Virus
    Language English
    Publishing date 2024-03-21
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.4c00057
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  9. Article ; Online: A Brief Overview on HIV Infection, Diagnosis and Treatment.

    Saha, Mrinmoy / Bhattacharya, Shreya

    Current topics in medicinal chemistry

    2020  Volume 19, Issue 30, Page(s) 2739–2741

    MeSH term(s) Anti-HIV Agents/administration & dosage ; Anti-HIV Agents/classification ; Anti-HIV Agents/therapeutic use ; Drug Therapy, Combination ; HIV Infections/diagnosis ; HIV Infections/drug therapy ; HIV Infections/virology ; Humans ; Quality of Life
    Chemical Substances Anti-HIV Agents
    Language English
    Publishing date 2020-01-07
    Publishing country United Arab Emirates
    Document type Journal Article ; Review
    ZDB-ID 2064823-6
    ISSN 1873-4294 ; 1568-0266
    ISSN (online) 1873-4294
    ISSN 1568-0266
    DOI 10.2174/156802661930200103091335
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    Zs.A 5572: Show issues Location:
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  10. Article ; Online: Towards Simultaneous Noninvasive Arterial and Venous Oxygenation Monitoring with Wearable E-Tattoo.

    Tan, Philip / Wang, Eric / Tamma, Shreya / Bhattacharya, Sarnab / Lu, Nanshu

    Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

    2023  Volume 2023, Page(s) 1–4

    Abstract: While noninvasive arterial blood oxygenation is easily estimated using peripheral pulse oximeters, noninvasive venous blood oxygenation monitoring is still a critical unmet need. Critical conditions that lead to inefficient extraction of oxygen from the ... ...

    Abstract While noninvasive arterial blood oxygenation is easily estimated using peripheral pulse oximeters, noninvasive venous blood oxygenation monitoring is still a critical unmet need. Critical conditions that lead to inefficient extraction of oxygen from the blood, such as sepsis or shock, can only be detected by analyzing the oxygen content of the venous blood. In this work, we introduce a soft wearable e-tattoo sensor that simultaneously measures the arterial and venous pulses from the wrist. First, we prove that the origin of the signal is venous pulsatility. We hypothesize that a significant obstacle for simultaneous SaO2 and SvO2 extraction is the close proximity of the artery and vein, thus leading to crosstalk. We characterize this crosstalk with simulation, in vitro, and in vivo experiments. Finally, we offer a potential solution for minimizing the crosstalk through spatial filtering.Clinical Relevance- This lays foundational work for a novel method of noninvasively and simultaneously measuring arterial and venous blood oxygenation to improve clinical diagnoses of sepsis, shock, and metabolic abnormalities.
    MeSH term(s) Humans ; Tattooing ; Oxygen ; Sepsis ; Arteries ; Wearable Electronic Devices
    Chemical Substances Oxygen (S88TT14065)
    Language English
    Publishing date 2023-12-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2694-0604
    ISSN (online) 2694-0604
    DOI 10.1109/EMBC40787.2023.10340010
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