LIVIVO - Search results -

Search results

Result 1 - 10 of total 191

Search options

Article ; Online: Quantitative mRNA expression measurement at home.

Pandey, Sonalisa / McCoy, Sara Safa / Stobdan, Tsering / Sahoo, Debashis

2024 Volume 14, Issue 1, Page(s) 1013

Abstract: mRNA measurement is dominated by RT-PCR, which requires expensive laboratory equipment and personnel with advanced degrees. Loop-mediated isothermal amplification (LAMP) is a versatile technique for detecting target DNA and RNA. The sensitivity of LAMP ... ...

Abstract	mRNA measurement is dominated by RT-PCR, which requires expensive laboratory equipment and personnel with advanced degrees. Loop-mediated isothermal amplification (LAMP) is a versatile technique for detecting target DNA and RNA. The sensitivity of LAMP in early reports has been below that of the standard RT-PCR tests. Here, we report the use of a fluorescence-based RT-LAMP protocol to measure CDX2 expression patterns, which match extremely well to the standards of sophisticated RT-PCR techniques (r = 0.99, p < 0.001). The assay works on diverse sample types such as cDNA, mRNA, and direct tissue sample testing in 25 min compared to more than 3 h for RT-PCR. We have developed a new protocol for designing RT-LAMP primers that reduce false positives due to self-amplification and improve quantification. A simple device with a 3D-printed box enables the measurement of mRNA expression at home, outdoors, and point-of-care setting.
MeSH term(s)	RNA, Messenger/genetics ; RNA ; Biological Assay ; DNA Primers ; DNA, Complementary
Chemical Substances	RNA, Messenger ; RNA (63231-63-0) ; DNA Primers ; DNA, Complementary
Language	English
Publishing date	2024-01-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-49651-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: Methionine biosynthetic genes and methionine sulfoxide reductase A are required for Rhizoctonia solani AG1-IA to cause sheath blight disease in rice.

Das, Joyati / Ghosh, Srayan / Tyagi, Kriti / Sahoo, Debashis / Jha, Gopaljee

Microbial biotechnology

2024 Volume 17, Issue 4, Page(s) e14441

Abstract: Rhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host ... ...

Abstract	Rhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host tissues. Understanding R. solani ability to sustain growth under an oxidative-stress-enriched environment is important for developing disease control strategies. Here, we demonstrate that R. solani upregulates methionine biosynthetic genes, including Rs_MET13 during infection in rice, and double-stranded RNA-mediated silencing of these genes impairs the pathogen's ability to cause disease. Exogenous treatment with methionine restores the disease-causing ability of Rs_MET13-silenced R. solani and facilitates its growth on 10 mM H
MeSH term(s)	Methionine Sulfoxide Reductases ; Oryza/microbiology ; Methionine ; Hydrogen Peroxide/pharmacology ; Racemethionine/pharmacology ; Plant Diseases/microbiology ; Rhizoctonia
Chemical Substances	Methionine Sulfoxide Reductases (EC 1.8.4.-) ; Methionine (AE28F7PNPL) ; Hydrogen Peroxide (BBX060AN9V) ; Racemethionine (73JWT2K6T3)
Language	English
Publishing date	2024-04-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2406063-X
ISSN	1751-7915 ; 1751-7915
ISSN (online)	1751-7915
ISSN	1751-7915
DOI	10.1111/1751-7915.14441
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Quantitative mRNA expression measurement at home

Sonalisa Pandey / Sara Safa McCoy / Tsering Stobdan / Debashis Sahoo

Scientific Reports, Vol 14, Iss 1, Pp 1-

2024 Volume 6

Abstract: Abstract mRNA measurement is dominated by RT-PCR, which requires expensive laboratory equipment and personnel with advanced degrees. Loop-mediated isothermal amplification (LAMP) is a versatile technique for detecting target DNA and RNA. The sensitivity ... ...

Abstract	Abstract mRNA measurement is dominated by RT-PCR, which requires expensive laboratory equipment and personnel with advanced degrees. Loop-mediated isothermal amplification (LAMP) is a versatile technique for detecting target DNA and RNA. The sensitivity of LAMP in early reports has been below that of the standard RT-PCR tests. Here, we report the use of a fluorescence-based RT-LAMP protocol to measure CDX2 expression patterns, which match extremely well to the standards of sophisticated RT-PCR techniques (r = 0.99, p < 0.001). The assay works on diverse sample types such as cDNA, mRNA, and direct tissue sample testing in 25 min compared to more than 3 h for RT-PCR. We have developed a new protocol for designing RT-LAMP primers that reduce false positives due to self-amplification and improve quantification. A simple device with a 3D-printed box enables the measurement of mRNA expression at home, outdoors, and point-of-care setting.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: C1QA is an invariant biomarker for tissue macrophages.

Horowitz, Amir / Yu, Haocheng / Pandey, Sonalisa / Mishra, Bud / Sahoo, Debashis

bioRxiv : the preprint server for biology

2024

Abstract: Macrophages play a pivotal role in immune responses, particularly in the context of combating microbial threats within tissues. The identification of reliable biomarkers associated with macrophage function is essential for understanding their diverse ... ...

Abstract	Macrophages play a pivotal role in immune responses, particularly in the context of combating microbial threats within tissues. The identification of reliable biomarkers associated with macrophage function is essential for understanding their diverse roles in host defense. This study investigates the potential of C1QA as an invariant biomarker for tissue macrophages, focusing on its correlation with the anti-microbial pathway. C1QA, a component of the complement system, has been previously implicated in various immune functions. Our research delves into the specific association of C1QA with tissue-resident macrophages and its implications in the context of anti-microbial responses. Through comprehensive systems biology and Boolean analysis of gene expression, we aim to establish C1QA as a consistent and reliable marker for identifying tissue macrophages. Furthermore, we explore the functional significance of C1QA in the anti-microbial pathway. This research seeks to provide valuable insights into the molecular mechanisms underlying the anti-microbial functions of tissue macrophages, with C1QA emerging as a potential key player in this intricate regulatory network. Understanding the relationship between C1QA, tissue macrophages, and the anti-microbial pathway could pave the way for the development of targeted therapeutic strategies aimed at enhancing the host's ability to combat infections. Ultimately, our findings contribute to the expanding knowledge of macrophage biology and may have implications for the diagnosis and treatment of infectious diseases.
Language	English
Publishing date	2024-01-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.26.577475
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Boolean implication analysis of single-cell data predicts retinal cell type markers.

Subramanian, Rohan / Sahoo, Debashis

BMC bioinformatics

2022 Volume 23, Issue 1, Page(s) 378

Abstract: Background: The retina is a complex tissue containing multiple cell types that are essential for vision. Understanding the gene expression patterns of various retinal cell types has potential applications in regenerative medicine. Retinal organoids ( ... ...

Abstract	Background: The retina is a complex tissue containing multiple cell types that are essential for vision. Understanding the gene expression patterns of various retinal cell types has potential applications in regenerative medicine. Retinal organoids (optic vesicles) derived from pluripotent stem cells have begun to yield insights into the transcriptomics of developing retinal cell types in humans through single cell RNA-sequencing studies. Previous methods of gene reporting have relied upon techniques in vivo using microarray data, or correlational and dimension reduction methods for analyzing single cell RNA-sequencing data computationally. We aimed to develop a state-of-the-art Boolean method that filtered out noise, could be applied to a wide variety of datasets and lent insight into gene expression over differentiation. Results: Here, we present a bioinformatic approach using Boolean implication to discover genes which are retinal cell type-specific or involved in retinal cell fate. We apply this approach to previously published retina and retinal organoid datasets and improve upon previously published correlational methods. Our method improves the prediction accuracy of marker genes of retinal cell types and discovers several new high confidence cone and rod-specific genes. Conclusions: The results of this study demonstrate the benefits of a Boolean approach that considers asymmetric relationships. We have shown a statistically significant improvement from correlational, symmetric methods in the prediction accuracy of retinal cell-type specific genes. Furthermore, our method contains no cell or tissue-specific tuning and hence could impact other areas of gene expression analyses in cancer and other human diseases.
MeSH term(s)	Cell Differentiation/genetics ; Humans ; Organoids/metabolism ; Pluripotent Stem Cells/metabolism ; RNA/metabolism ; Retina
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-09-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-022-04915-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: An AI-assisted Investigation of Tumor-Associated Macrophages and their Polarization in Colorectal Cancer.

Dadlani, Ekta / Dash, Tirtharaj / Sahoo, Debashis

bioRxiv : the preprint server for biology

2023

Abstract: Tumor-associated Macrophages (or TAMs) are amongst the most common cells that play a significant role in the initiation and progression of colorectal cancer (CRC). Recently, Ghosh et al. proposed distinguishing signatures for identifying macrophage ... ...

Abstract	Tumor-associated Macrophages (or TAMs) are amongst the most common cells that play a significant role in the initiation and progression of colorectal cancer (CRC). Recently, Ghosh et al. proposed distinguishing signatures for identifying macrophage polarization states, namely, immuno-reactive and immuno-tolerant, using the concept of Boolean implications and Boolean networks. Their signature, called the Signature of Macrophage Reactivity and Tolerance (SMaRT), comprises of 338 human genes (equivalently, 298 mouse genes). However, SMaRT was constructed using datasets that were not specialized towards any particular disease. In this paper, (a) we perform a comprehensive analysis of the SMaRT signature on single-cell human and mouse colorectal cancer RNA-seq datasets; (b) we then adopt a technique akin to transfer learning to construct a "refined" SMaRT signature for investigating TAMs and their polarization in the CRC tumor microenvironment. Towards validation of our refined gene signature, we use (a) 5 pseudo-bulk RNA-seq datasets derived from single-cell human datasets; and (b) 5 large-cohort microarray datasets from humans. Furthermore, we investigate the translational potential of our refined gene signature in problems related to MSS/MSI (4 datasets) and CIMP+/CIMP- status (4 datasets). Overall, our refined gene signature and its extensive validation provide a path for its adoption in clinical practice in diagnosing colorectal cancer and associated attributes.
Language	English
Publishing date	2023-08-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.01.551559
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Artificial intelligence-guided discovery of gastric cancer continuum.

Vo, Daniella / Ghosh, Pradipta / Sahoo, Debashis

Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association

2023 Volume 26, Issue 2, Page(s) 286–297

Abstract: Background: Detailed understanding of pre-, early and late neoplastic states in gastric cancer helps develop better models of risk of progression to gastric cancers (GCs) and medical treatment to intercept such progression.: Methods: We built a ... ...

Abstract	Background: Detailed understanding of pre-, early and late neoplastic states in gastric cancer helps develop better models of risk of progression to gastric cancers (GCs) and medical treatment to intercept such progression. Methods: We built a Boolean implication network of gastric cancer and deployed machine learning algorithms to develop predictive models of known pre-neoplastic states, e.g., atrophic gastritis, intestinal metaplasia (IM) and low- to high-grade intestinal neoplasia (L/HGIN), and GC. Our approach exploits the presence of asymmetric Boolean implication relationships that are likely to be invariant across almost all gastric cancer datasets. Invariant asymmetric Boolean implication relationships can decipher fundamental time-series underlying the biological data. Pursuing this method, we developed a healthy mucosa → GC continuum model based on this approach. Results: Our model performed better against publicly available models for distinguishing healthy versus GC samples. Although not trained on IM and L/HGIN datasets, the model could identify the risk of progression to GC via the metaplasia → dysplasia → neoplasia cascade in patient samples. The model could rank all publicly available mouse models for their ability to best recapitulate the gene expression patterns during human GC initiation and progression. Conclusions: A Boolean implication network enabled the identification of hitherto undefined continuum states during GC initiation. The developed model could now serve as a starting point for rationalizing candidate therapeutic targets to intercept GC progression.
MeSH term(s)	Animals ; Mice ; Humans ; Stomach Neoplasms/genetics ; Gastric Mucosa ; Artificial Intelligence ; Gastritis, Atrophic ; Intestinal Neoplasms ; Metaplasia ; Precancerous Conditions ; Helicobacter Infections/drug therapy
Language	English
Publishing date	2023-01-24
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1463526-4
ISSN	1436-3305 ; 1436-3291
ISSN (online)	1436-3305
ISSN	1436-3291
DOI	10.1007/s10120-022-01360-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 5290: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: Anaphylactic Shock After Intramuscular Diclofenac Sodium: A Case Report.

Sahoo, Debashis P / Barman, Bhupen / War, Gwenette A / Gupta, Annu / Tara, Ruth K

Cureus

2024 Volume 16, Issue 2, Page(s) e55279

Abstract: Diclofenac sodium is a commonly used nonsteroidal anti-inflammatory drug. It is widely used for acute and chronic pain management. Side effects, such as fixed drug eruption, asthmatic attack, and vasospastic angina, are commonly seen after the use of ... ...

Abstract	Diclofenac sodium is a commonly used nonsteroidal anti-inflammatory drug. It is widely used for acute and chronic pain management. Side effects, such as fixed drug eruption, asthmatic attack, and vasospastic angina, are commonly seen after the use of diclofenac sodium. However, anaphylaxis and anaphylactic shock secondary to injection of diclofenac sodium are rare. Our main aim in reporting this adverse event is to alert healthcare professionals to this potentially life-threatening adverse effect of diclofenac sodium and prompt use of adrenaline for treatment.
Language	English
Publishing date	2024-02-29
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.55279
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Acute Pyelonephritis by Scrub Typhus: A Rare Condition.

Sahoo, Debashis Priyadarshan / Pradhan, Soumya Ranjan / War, Gwenette / Gupta, Annu / Tara, Ruth K

Cureus

2024 Volume 16, Issue 3, Page(s) e55752

Abstract: Scrub typhus is prevalent in tropical countries and can have a varied spectrum of presentations from pneumonia, gastroenteritis, lymphadenitis, meningitis, encephalitis, and acute kidney injury to multi-organ dysfunction syndrome. Urinary tract ... ...

Abstract	Scrub typhus is prevalent in tropical countries and can have a varied spectrum of presentations from pneumonia, gastroenteritis, lymphadenitis, meningitis, encephalitis, and acute kidney injury to multi-organ dysfunction syndrome. Urinary tract infections like cystitis and pyelonephritis are rarely reported. Here we present an atypical presentation of a 53-year-old female with diabetes mellitus who came to the outpatient department with complaints of high-grade fever, burning micturition, and left flank pain for three days and was initially treated outpatient basis with oral antibiotics. However, her deteriorating condition landed her in an emergency in a state of septic shock. She was initially treated with broad-spectrum conventional antibiotics with other supportive medications. Even after confirmation of the diagnosis of left acute pyelonephritis with septic shock, with appropriate antibiotics, her condition was deteriorating. A sterile urine culture raised suspicion of atypical organisms causing the infection. Proper analysis of her history and readily available investigations of IgM against scrub typhus antigen led to a diagnosis of scrub typhus-related left acute pyelonephritis with septic shock. She was treated adequately with an injection of doxycycline, followed by oral tablets of the same, after which she showed drastic improvement in her symptoms, and then she was discharged. Thus, atypical organisms causing urinary tract infections should be kept always in mind, which can be treated easily and if untreated, can lead to life-threatening consequences.
Language	English
Publishing date	2024-03-07
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.55752
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A Boolean approach for novel hypoxia-related gene discovery.

Stobdan, Tsering / Sahoo, Debashis / Haddad, Gabriel G

PloS one

2022 Volume 17, Issue 8, Page(s) e0273524

Abstract: Hypoxia plays a major role in the etiology and pathogenesis of most of the leading causes of morbidity and mortality, whether cardiovascular diseases, cancer, respiratory diseases or stroke. Despite active research on hypoxia-signaling pathways, the ... ...

Abstract	Hypoxia plays a major role in the etiology and pathogenesis of most of the leading causes of morbidity and mortality, whether cardiovascular diseases, cancer, respiratory diseases or stroke. Despite active research on hypoxia-signaling pathways, the understanding of regulatory mechanisms, especially in specific tissues, still remain elusive. With the accessibility of thousands of potentially diverse genomic datasets, computational methods are utilized to generate new hypotheses. Here we utilized Boolean implication relationship, a powerful method to probe symmetrically and asymmetrically related genes, to identify novel hypoxia related genes. We used a well-known hypoxia-responsive gene, VEGFA, with very large human expression datasets (n = 25,955) to identify novel hypoxia-responsive candidate gene/s. Further, we utilized in-vitro analysis using human endothelial cells exposed to 1% O2 environment for 2, 8, 24 and 48 hours to validate top candidate genes. Out of the top candidate genes (n = 19), 84% genes were previously reported as hypoxia related, validating our results. However, we identified FAM114A1 as a novel candidate gene significantly upregulated in the endothelial cells at 8, 24 and 48 hours of 1% O2 environment. Additional evidence, particularly the localization of intronic miRNA and numerous HREs further support and strengthen our finding. Current results on FAM114A1 provide an example demonstrating the utility of powerful computational methods, like Boolean implications, in playing a major role in hypothesis building and discovery.
MeSH term(s)	Cell Hypoxia/genetics ; Endothelial Cells ; Genetic Association Studies ; Humans ; Hypoxia/genetics ; MicroRNAs/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2022-08-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0273524
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito