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Article ; Online: Rare genetic disorders in India: Current status, challenges, and CRISPR-based therapy.

Bhattacharyya, Pallabi / Mehndiratta, Kanikah / Maiti, Souvik / Chakraborty, Debojyoti

2024 Volume 49

Abstract: Rare genetic diseases are a group of life-threatening disorders affecting significant populations worldwide and posing substantial challenges to healthcare systems globally. India, with its vast population, is also no exception. The country harbors ... ...

Abstract	Rare genetic diseases are a group of life-threatening disorders affecting significant populations worldwide and posing substantial challenges to healthcare systems globally. India, with its vast population, is also no exception. The country harbors millions of individuals affected by these fatal disorders, which often result from mutations in a single gene. The emergence of CRISPR-Cas9 technology, however, has ushered in a new era of hope in genetic therapies. CRISPR-based treatments hold the potential to precisely edit and correct diseasecausing mutations, offering tailored solutions for rare genetic diseases in India. This review explores the landscape of rare genetic diseases in India along with national policies and major challenges, and examines the implications of CRISPR-based therapies for potential cure. It delves into the potential of this technology in providing personalized and effective treatments. However, alongside these promising prospects, some ethical considerations, regulatory challenges, and concerns about the accessibility of CRISPR therapies are also discussed since addressing these issues is crucial for harnessing the full power of CRISPR in tackling rare genetic diseases in India. By taking a multidisciplinary approach that combines scientific advancements, ethical principles, and regulatory frameworks, these complexities can be reconciled, paving the way for innovative and impactful healthcare solutions for rare diseases in India.
MeSH term(s)	Humans ; Gene Editing ; CRISPR-Cas Systems/genetics ; Rare Diseases/epidemiology ; Rare Diseases/genetics ; Rare Diseases/therapy ; Genetic Therapy ; India
Language	English
Publishing date	2024-02-21
Publishing country	India
Document type	Review ; Journal Article
ZDB-ID	756157-x
ISSN	0973-7138 ; 0250-5991
ISSN (online)	0973-7138
ISSN	0250-5991
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Brain-enriched miR-128: Reduced in exosomes from Parkinson's patient plasma, improves synaptic integrity, and prevents 6-OHDA mediated neuronal apoptosis.

Bhattacharyya, Pallabi / Biswas, Atanu / Biswas, Subhas C

Frontiers in cellular neuroscience

2023 Volume 16, Page(s) 1037903

Abstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with the death of mid-brain dopaminergic neurons. Unfortunately, no effective cure or diagnostic biomarkers for PD are available yet. To address this, the present study ... ...

Abstract	Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with the death of mid-brain dopaminergic neurons. Unfortunately, no effective cure or diagnostic biomarkers for PD are available yet. To address this, the present study focuses on brain-enriched small non-coding regulatory RNAs called microRNAs (miRNAs) that are released into the circulation packaged inside small extracellular vesicles called exosomes. We collected blood samples from PD patients and isolated exosomes from the plasma. qPCR-based detection revealed a particular neuron-enriched miR-128 to be significantly decreased in the patient-derived exosomes. Interestingly, a concomitant decreased expression of miR-128 was observed in the cellular models of PD. Fluorescent live cell imaging and flow-cytometry revealed that over-expression of miR-128 can prevent 6-OHDA-mediated mitochondrial superoxide production and induction of neuronal death respectively. This neuroprotective effect was found to be induced by miR-128-mediated inhibition of FoxO3a activation, a transcription factor involved in apoptosis. miR-128 over-expression also resulted in down-regulation of pro-apoptotic FoxO3a targets- FasL and PUMA, at both transcript and protein levels. Further downstream, miR-128 over-expression inhibited activation of caspases-8, -9 and -3, preventing both the intrinsic and extrinsic pathways of apoptosis. Additionally, over expression of miR-128 prevented down-regulation of synaptic proteins- Synaptophysin and PSD-95 and attenuated neurite shortening, thereby maintaining overall neuronal integrity. Thus, our study depicts the intracellular role of miR-128 in neuronal apoptosis and neurodegeneration and its implications as a biomarker being detectable in the circulating exosomes of PD patient blood. Thus, characterization of such exosomal brain-enriched miRNAs hold promise for effective detection and diagnosis of PD.
Language	English
Publishing date	2023-01-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452963-1
ISSN	1662-5102
ISSN	1662-5102
DOI	10.3389/fncel.2022.1037903
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Poly (ADP-Ribose) Polymerase-1 causes mitochondrial damage and neuron death mediated by Bnip3, J Neurosci. 2014 Nov 26;34(48):15975-87.

Bhattacharyya, Pallabi

Annals of neurosciences

2015 Volume 22, Issue 3, Page(s) 180

Language	English
Publishing date	2015-06-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2576191-2
ISSN	0976-3260 ; 0972-7531
ISSN (online)	0976-3260
ISSN	0972-7531
DOI	10.5214/ans.0972.7531.220309
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Article ; Online: PD_BiBIM: Biclustering-based biomarker identification in ESCC microarray data.

Patowary, Pallabi / Bhattacharyya, Dhruba K

Journal of biosciences

2021 Volume 46

Abstract: To promote diligent analysis of the progression of a disease, it is important to identify interesting biomarkers for the disease. Biclustering has already been established as an effective technique to help identify such biomarkers of high biological ... ...

Abstract	To promote diligent analysis of the progression of a disease, it is important to identify interesting biomarkers for the disease. Biclustering has already been established as an effective technique to help identify such biomarkers of high biological significance. Although in the recent past, a good number of biclustering techniques have been introduced, most of them fail to perform consistently across multiple domains or datasets. To choose a single biclustering technique that can help the accomplishment of such a critical task for multiple diseases with high precision is extremely difficult. Hence, in this study, we considered several biclustering techniques and accepted those techniques and their results which are found significant from enrichment perspective for subsequent analysis. Based on biclustering results, we constructed biological networks and carried out a topological, pathway and causal analysis on the modules extracted from the networks. Our multiobjective study enabled us to identify several biomarkers for esophageal squamous cell carcinoma (ESCC) such as IFNGR1, CLIC1, CDK4, and COPS5, after applying a ranking scheme.
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; COP9 Signalosome Complex/genetics ; COP9 Signalosome Complex/metabolism ; Chloride Channels/genetics ; Chloride Channels/metabolism ; Cluster Analysis ; Computational Biology/methods ; Cyclin-Dependent Kinase 4/genetics ; Cyclin-Dependent Kinase 4/metabolism ; Datasets as Topic ; Esophageal Neoplasms/diagnosis ; Esophageal Neoplasms/genetics ; Esophageal Neoplasms/metabolism ; Esophageal Neoplasms/pathology ; Esophageal Squamous Cell Carcinoma/diagnosis ; Esophageal Squamous Cell Carcinoma/genetics ; Esophageal Squamous Cell Carcinoma/metabolism ; Esophageal Squamous Cell Carcinoma/pathology ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Ontology ; Gene Regulatory Networks ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Molecular Sequence Annotation ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Peptide Hydrolases/genetics ; Peptide Hydrolases/metabolism ; Receptors, Interferon/genetics ; Receptors, Interferon/metabolism ; Interferon gamma Receptor
Chemical Substances	Biomarkers, Tumor ; CLIC1 protein, human ; Chloride Channels ; Intracellular Signaling Peptides and Proteins ; Neoplasm Proteins ; Receptors, Interferon ; CDK4 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22) ; Peptide Hydrolases (EC 3.4.-) ; COPS5 protein, human (EC 3.4.-.-) ; COP9 Signalosome Complex (EC 3.4.19.12)
Language	English
Publishing date	2021-06-20
Publishing country	India
Document type	Journal Article
ZDB-ID	756157-x
ISSN	0973-7138 ; 0250-5991
ISSN (online)	0973-7138
ISSN	0250-5991
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SNMRS: An advanced measure for Co-expression network analysis.

Patowary, Pallabi / Bhattacharyya, Dhruba K / Barah, Pankaj

Computers in biology and medicine

2022 Volume 143, Page(s) 105222

Abstract: The challenge of identifying modules in a gene interaction network is important for a better understanding of the overall network architecture. In this work, we develop a novel similarity measure called Scaling-and-Shifting Normalized Mean Residue ... ...

Abstract	The challenge of identifying modules in a gene interaction network is important for a better understanding of the overall network architecture. In this work, we develop a novel similarity measure called Scaling-and-Shifting Normalized Mean Residue Similarity (SNMRS), based on the existing NMRS technique [1]. SNMRS yields correlation values in the range of 0 to +1 corresponding to negative and positive dependency. To study the performance of our measure, internal validation of extracted clusters resulting from different methods is carried out. Based on the performance, we choose hierarchical clustering and apply the same using the corresponding dissimilarity (distance) values of SNMRS scores, and utilize a dynamic tree cut method for extracting dense modules. The modules are validated using a literature search, KEGG pathway analysis, and gene-ontology analyses on the genes that make up the modules. Moreover, our measure can handle absolute, shifting, scaling, and shifting-and-scaling correlations and provides better performance than several other measures in terms of cluster-validity indices. Also, SNMRS based module detection method results in interesting biologically relevant patterns from gene microarray and RNA-seq dataset. A set of crucial genes having high relevance with the ESCC are also identified.
Language	English
Publishing date	2022-01-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105222
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Article ; Online: Small Non-coding RNAs

Pallabi Bhattacharyya / Subhas C. Biswas

Frontiers in Microbiology, Vol

Do They Encode Answers for Controlling SARS-CoV-2 in the Future?

2020 Volume 11

Abstract: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus responsible for the current COVID-19 (coronavirus disease 2019) pandemic, which has hit the world since December 2019. It has spread to about 216 countries worldwide, ... ...

Abstract	SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus responsible for the current COVID-19 (coronavirus disease 2019) pandemic, which has hit the world since December 2019. It has spread to about 216 countries worldwide, affecting more than 21.7 million people so far. Although clinical trials of a number of promising antiviral drugs and vaccines against COVID-19 are underway, it is hard to predict how successful these drug- or vaccine-based therapeutics are eventually going to be in combating COVID-19 because most of such therapeutic strategies have failed against human coronaviruses such as SARS-CoV and MERS-CoV (Middle East respiratory syndrome coronavirus) responsible for similar pandemics in the past. In that context, we would like to bring to scientific attention another group of endogenous regulatory molecules, the small non-coding RNAs, especially the microRNAs, which are found to regulate critical cellular pathways in a number of disease conditions, including RNA viral infections. This review will focus on understanding the effect of altered microRNA expression during coronavirus-mediated infections and how it may provide clues for further exploring the pathogenesis of SARS-CoV-2, with a view of developing RNAi-based therapeutics and biomarkers against COVID-19.
Keywords	COVID-19 ; coronaviruses ; RNA viruses ; microRNAs ; non-coding RNAs ; MERS-CoV ; Microbiology ; QR1-502 ; covid19
Subject code	572
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Small Non-coding RNAs: Do They Encode Answers for Controlling SARS-CoV-2 in the Future?

Bhattacharyya, Pallabi / Biswas, Subhas C

Frontiers in microbiology

2020 Volume 11, Page(s) 571553

Abstract	SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus responsible for the current COVID-19 (coronavirus disease 2019) pandemic, which has hit the world since December 2019. It has spread to about 216 countries worldwide, affecting more than 21.7 million people so far. Although clinical trials of a number of promising antiviral drugs and vaccines against COVID-19 are underway, it is hard to predict how successful these drug- or vaccine-based therapeutics are eventually going to be in combating COVID-19 because most of such therapeutic strategies have failed against human coronaviruses such as SARS-CoV and MERS-CoV (Middle East respiratory syndrome coronavirus) responsible for similar pandemics in the past. In that context, we would like to bring to scientific attention another group of endogenous regulatory molecules, the small non-coding RNAs, especially the microRNAs, which are found to regulate critical cellular pathways in a number of disease conditions, including RNA viral infections. This review will focus on understanding the effect of altered microRNA expression during coronavirus-mediated infections and how it may provide clues for further exploring the pathogenesis of SARS-CoV-2, with a view of developing RNAi-based therapeutics and biomarkers against COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-09-18
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.571553
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: PD_BiBIM: Biclustering-based biomarker identification in ESCC microarray data

Patowary, Pallabi / Bhattacharyya, Dhruba K

Journal of biosciences. 2021 Sept., v. 46, no. 3

2021

Abstract	To promote diligent analysis of the progression of a disease, it is important to identify interesting biomarkers for the disease. Biclustering has already been established as an effective technique to help identify such biomarkers of high biological significance. Although in the recent past, a good number of biclustering techniques have been introduced, most of them fail to perform consistently across multiple domains or datasets. To choose a single biclustering technique that can help the accomplishment of such a critical task for multiple diseases with high precision is extremely difficult. Hence, in this study, we considered several biclustering techniques and accepted those techniques and their results which are found significant from enrichment perspective for subsequent analysis. Based on biclustering results, we constructed biological networks and carried out a topological, pathway and causal analysis on the modules extracted from the networks. Our multi-objective study enabled us to identify several biomarkers for esophageal squamous cell carcinoma (ESCC) such as IFNGR1, CLIC1, CDK4, and COPS5, after applying a ranking scheme.
Keywords	biomarkers ; data collection ; microarray technology ; squamous cell carcinoma ; topology
Language	English
Dates of publication	2021-09
Size	p. 56.
Publishing place	Springer India
Document type	Article
ZDB-ID	756157-x
ISSN	0973-7138 ; 0250-5991
ISSN (online)	0973-7138
ISSN	0250-5991
DOI	10.1007/s12038-021-00171-5
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Small Non-coding RNAs

Bhattacharyya, Pallabi / Biswas, Subhas C.

Frontiers in Microbiology

Do They Encode Answers for Controlling SARS-CoV-2 in the Future?

2020 Volume 11

Keywords	Microbiology (medical) ; Microbiology ; covid19
Publisher	Frontiers Media SA
Publishing country	ch
Document type	Article ; Online
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.571553
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: How Sexual and Gender-Based Violence Affects the Settlement Experiences Among Yazidi Refugee Women in Canada

Pallabi Bhattacharyya / Labe Songose / Lori Wilkinson

Frontiers in Human Dynamics, Vol

2021 Volume 3

Abstract: Gender and sexual violence is historically used as a weapon of war. Yazidi women resettled in Canada directly from northern Iraq after the 2014 Daesh-led attacks in the Sinjar region. This direct resettlement experience makes the Yazidi refugees a very ... ...

Abstract	Gender and sexual violence is historically used as a weapon of war. Yazidi women resettled in Canada directly from northern Iraq after the 2014 Daesh-led attacks in the Sinjar region. This direct resettlement experience makes the Yazidi refugees a very distinct group from a resettlement perspective. The severe human rights violations and sexual and gender-based violence they have experienced has affected both their physical and mental health. However, research on pre-arrival trauma and its impact on resettlement has been limited to individual post-arrival psychological interventions without considering how pre-arrival trauma experiences may affect their overall settlement experience. Our paper focuses on the settlement challenges and needs of 21 Yazidi women resettled in the four Canadian cities with the largest Yazidi communities. Because the resettlement of the Yazidi often happened within weeks after their release from captivity, the structural deficiencies within the Canadian settlement network revealed challenges for resettlement organizations in terms of how they assist those with acute trauma. We argue that although the Canadian resettlement program is generous in many ways, it falls short of adequately addressing trauma at the acute stage, especially sexual and gender-based violence as experienced by the Yazidi women and children. Our analysis reveals that single-female-headed families, particularly those with young children, have a difficult time navigating the resettlement system in Canada. We have identified the resettlement experiences of Yazidi women and recommend resettlement to happen in three stages, to account for the acute level of trauma this particular group faces. The first stage lasts between six weeks and three months as many women require more dedicated support from settlement providers for housing, language, and health. The second stage is a period of adjustment which occurs within the next eighteen months, depending on the available support these refugee women have to navigate the different settlement services. The third stage begins sometime after the second year when many women can start navigating the social support, education and health systems independently. Thinking of how SGBV may influence the resettlement process in these three stages is a good way for us to consider the additional assistance that may be needed and how they may better access resettlement services.
Keywords	sexual and gender-based violence ; yazidi women ; resettlement experiences ; PTSD ; access post-arrival services ; Social Sciences ; H
Subject code	360
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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