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Article ; Online: Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli.

Raghunathan, Nalini / Kapshikar, Rajvardhan M / Leela, Jakku K / Mallikarjun, Jillella / Bouloc, Philippe / Gowrishankar, Jayaraman

Nucleic acids research

2018 Volume 46, Issue 7, Page(s) 3400–3411

Abstract: ... increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived ... R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks ... that R-loop formation from them is curtailed. ...

Abstract	Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
MeSH term(s)	Bacteriophage T4/genetics ; Bridged Bicyclo Compounds, Heterocyclic/pharmacology ; Chromosomes/genetics ; DNA Helicases/genetics ; DNA Replication/genetics ; DNA, Antisense/genetics ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Genes, rRNA/genetics ; Genome, Bacterial/drug effects ; Genome, Bacterial/genetics ; Rho Factor/antagonists & inhibitors ; Rho Factor/genetics ; Ribonuclease H/genetics ; Transcription Termination, Genetic ; Transcription, Genetic ; Viral Proteins/genetics
Chemical Substances	Bridged Bicyclo Compounds, Heterocyclic ; DNA, Antisense ; Rho Factor ; Viral Proteins ; Ribonuclease H (EC 3.1.26.4) ; DNA Helicases (EC 3.6.4.-) ; UvsW protein, Bacteriophage T4 (EC 5.99.-) ; bicozamycin (J03U9E2P82)
Language	English
Publishing date	2018-02-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky118
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Article ; Online: MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes.

Selivanov, Vitaly A / Benito, Adrián / Miranda, Anibal / Aguilar, Esther / Polat, Ibrahim Halil / Centelles, Josep J / Jayaraman, Anusha / Lee, Paul W N / Marin, Silvia / Cascante, Marta

BMC bioinformatics

2017 Volume 18, Issue 1, Page(s) 88

Abstract: ... at https://github.com/seliv55/mid_correct) written in the R programming language, corrects the raw MS ...

Abstract	Background: Tracing stable isotopes, such as Results: Our computer program-MIDcor (free at https://github.com/seliv55/mid_correct) written in the R programming language, corrects the raw MS spectra both for the naturally occurring isotopes and for the overlapping of peaks corresponding to various substances. To this end, the mass spectra of unlabeled metabolites measured in two media are necessary: in a minimal medium containing only derivatized metabolites and chemicals for derivatization, and in a complete cell incubated medium. The MIDcor program calculates the difference (D) between the theoretical and experimentally measured spectra of metabolites containing only the naturally occurring isotopes. The result of comparison of D in the two media determines a way of deciphering the true spectra. (1) If D in the complete medium is greater than that in the minimal medium in at least one peak, then unchanged D is subtracted from the raw spectra of the labeled metabolite. (2) If D does not depend on the medium, then the spectrum probably overlaps with a derivatized fragment of the same metabolite, and D is modified proportionally to the metabolite labeling. The program automatically reaches a decision regarding the way of correction. For some metabolites/fragments in the case (2) D was found to decrease when the tested substance was Conclusion: Using the developed program improves the reliability of stable isotope tracer data analysis.
MeSH term(s)	Carbon Isotopes/chemistry ; Cell Line ; Culture Media/analysis ; Gas Chromatography-Mass Spectrometry ; Humans ; Internet ; Isotope Labeling ; Metabolome ; User-Computer Interface
Chemical Substances	Carbon Isotopes ; Culture Media
Language	English
Publishing date	2017-02-03
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/s12859-017-1513-3
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Article ; Online: Adoption of R etail I nternet B anking

JAYARAMAN MUNUSAMY / ERNEST CYRIL DE RUN / SHANKAR CHELLIAH / SA NMUGAM ANNAMALAH

Journal of Internet Banking and Commerce, Vol 17, Iss 3, Pp 1-

A S tudy of D emographic F actors

2012 Volume 14

Abstract: This study focuses on the adoption of retail internet banking among consumers in the Klang Valley, Malaysia and the impact of demographics factors on such adoption behavior . This study adopts a quantitative approach using surveys conducted at banks. The ...

Abstract	This study focuses on the adoption of retail internet banking among consumers in the Klang Valley, Malaysia and the impact of demographics factors on such adoption behavior . This study adopts a quantitative approach using surveys conducted at banks. The results indicate that while the hypotheses pertaining to gender, race, income, educational l evel and occupation were not supported but age is supported. Therefore, the current research indicates that the age of retail banking consumers affects the adoption of internet banking among Malaysian consumers. The result also suggests that consumers in t he age group below 25 years old are the major contributor to the differences. Based on these findings, we conclude that younger consumers are more likely to adopt internet banking. Therefore, the result suggests implications for retail bankers in Malaysia to adopt appropriate strategies to encourage retail internet banking for other age categories of consumers in Klang Valley. By doing so, it enables the banks in Malaysia to save costs of maintaining physical distribution systems through providing bigger scale of Internet retail banking services
Keywords	etail Internet Banking ; Internet Banking Adopters ; Internet Banking Non - adopters ; Demographic Factors ; Consumers . ; Finance ; HG1-9999 ; Social Sciences ; H
Subject code	303 ; 332
Language	English
Publishing date	2012-12-01T00:00:00Z
Publisher	ARRAY Development
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: R and T states of fluoromethemoglobin probed by ultraviolet resonance Raman spectroscopy.

Jayaraman, V / Rodgers, K R / Mukerji, I / Spiro, T G

Biochemistry

1993 Volume 32, Issue 17, Page(s) 4547–4551

Abstract: Ultraviolet resonance Raman spectra are reported for the fluoride complex of methemoglobin (metHbF), with and without added inositol hexaphosphate (IHP), an allosteric effector known to stabilize the T quaternary structure. Environmental changes in Trp ... ...

Abstract	Ultraviolet resonance Raman spectra are reported for the fluoride complex of methemoglobin (metHbF), with and without added inositol hexaphosphate (IHP), an allosteric effector known to stabilize the T quaternary structure. Environmental changes in Trp and Tyr residues give rise to the difference features, which are similar to those observed in the difference spectrum between deoxyHb and the CO adduct, consistent with T-state formation in metHbF in the presence of IHP. There are, however, important differences. The intensities of the difference signals are attenuated by about one-third, indicating a lower T-state population in the IHP-bound metHbF than in native deoxyHb. And a new signal is seen which arises from the interior tryptophans, probably reflecting a change in their H-bond status associated with the presence of fluoride as the sixth heme ligand in the T state. Implications of these results for the nature of the molecular forces opposing ligation in the T state are discussed.
MeSH term(s)	Hemoglobins/chemistry ; Hemoglobins/metabolism ; Hydrogen Bonding ; Methemoglobin/analogs & derivatives ; Methemoglobin/chemistry ; Methemoglobin/metabolism ; Oxygen/metabolism ; Phytic Acid/pharmacology ; Spectrum Analysis, Raman ; Tryptophan/chemistry ; Ultraviolet Rays
Chemical Substances	Hemoglobins ; methemoglobin fluoride ; Phytic Acid (7IGF0S7R8I) ; Tryptophan (8DUH1N11BX) ; deoxyhemoglobin (9008-02-0) ; Methemoglobin (9008-37-1) ; Oxygen (S88TT14065)
Language	English
Publishing date	1993-05-04
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi00068a009
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Article: The Association of miRNA10a and Glucose Transporters in Oral Squamous Cell Carcinoma With Diabetes: A Pilot Study.

R, Sukanth / R, Priyadharshini / Jayaraman, Selvaraj / Palati, Sinduja

Cureus

2024 Volume 16, Issue 1, Page(s) e51752

Abstract: Introduction: MicroRNAs (miRNAs) are well-established post-translational non-coding RNAs that play crucial roles in mRNA degradation and repression. Glucose transporter 1 (GLUT1) showed correlation along with various miRNA, specifically miRNA10a ... ...

Abstract	Introduction: MicroRNAs (miRNAs) are well-established post-translational non-coding RNAs that play crucial roles in mRNA degradation and repression. Glucose transporter 1 (GLUT1) showed correlation along with various miRNA, specifically miRNA10a expression in lung cancers. The role of miRNA10a along with glucose upregulation leading to cancer proliferation in oral squamous cell carcinoma (OSCC) is unknown. This study aimed to investigate the expression levels of miRNA10a and GLUT1 in OSCC patients with diabetes. Materials and methods: miRNA10a and GLUT1 expression were estimated in OSCC, precancerous, and healthy tissues using quantitative reverse transcriptase polymerase chain reaction (RT-PCR). miRNA10a and GLUT1 expression levels were recorded as fold change. Further, a one-way analysis of variance (ANOVA) test was performed to find whether there is any difference in miRNA10a and GLUT1 expression between OSCC, precancerous, and healthy tissues. Results: The RT-PCR findings revealed an increased expression of miRNA10a and GLUT1 in OSCC compared to precancerous and healthy tissue. There is a positive correlation between miRNA10a and GLUT1 expression levels in both potentially malignant and control tissues, with a marked increase in cancerous tissue. This study demonstrated the significance of upregulated miRNA10a expression, indicating a direct correlation with OSCC proliferation via GLUT1 overexpression. Specifically, miRNA10a exhibited a fold change of 1.2±0.072 in potentially malignant tissue and 1.4±0.05 in cancer tissue, while GLUT1 exhibited a fold change of 1.25±0.092 in potentially malignant tissue and 0.092±0.08 in cancer tissue, respectively. Conclusion: This research highlights the role of miRNA10a in cancer progression by facilitating proliferation through the regulation of GLUT1 in cancerous tissues, particularly in hyperglycemic conditions. This mechanism further contributes to increased glucose transport in cancer patients, which may potentially impede tumor prognosis. These findings underscore the potential significance of targeting miRNA10a and GLUT1 as therapeutic interventions in cancer management.
Language	English
Publishing date	2024-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.51752
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Article: A Common Symptom With an Uncommon Diagnosis: A Case of Primary Esophageal Diffuse Large B-cell Lymphoma.

Narasimha, Shruthi / Zackria, Rasiq / Hughes, Jonathan / Jayaraman, Vijay

Cureus

2024 Volume 16, Issue 1, Page(s) e51885

Abstract: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma. Although it can have gastrointestinal involvement, there are limited recorded cases that show primary esophageal DLBCL. This report discusses the case of an 85-year- ... ...

Abstract	Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin's lymphoma. Although it can have gastrointestinal involvement, there are limited recorded cases that show primary esophageal DLBCL. This report discusses the case of an 85-year-old female who initially presented with weight loss associated with dysphagia and was later diagnosed with an esophageal mass by endoscopy. Pathology showed large, atypical lymphocytes, and the final morphologic, immunohistochemical, and molecular findings were most consistent with a diagnosis of primary esophageal DLBCL.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.51885
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Article ; Online: Mechanistic insights into the conformational changes and alterations in residual communications due to the mutations in the pncA Gene of Mycobacterium tuberculosis: A computational perspective for effective therapeutic solutions.

Jayaraman, Manikandan / Kumar, Rajalakshmi / Panchalingam, Santhiya / Jeyaraman, Jeyakanthan

Computational biology and chemistry

2024 Volume 110, Page(s) 108065

Abstract: Due to its emerging resistance to first-line anti-TB medications, tuberculosis (TB) is one of the most contagious illness in the world. According to reports, the effectiveness of treating TB is severely impacted by drug resistance, notably resistance ... ...

Abstract	Due to its emerging resistance to first-line anti-TB medications, tuberculosis (TB) is one of the most contagious illness in the world. According to reports, the effectiveness of treating TB is severely impacted by drug resistance, notably resistance caused by mutations in the pncA gene-encoded pyrazinamidase (PZase) to the front-line drug pyrazinamide (PZA). The present study focused on investigating the resistance mechanism caused by the mutations D12N, T47A, and H137R to better understand the structural and molecular events responsible for the resistance acquired by the pncA gene of Mycobacterium tuberculosis (MTB) at the structural level. Bioinformatics analysis predicted that all three mutations were deleterious and located near the active centre of the pncA, affecting its functional activity. Furthermore, molecular dynamics simulation (MDS) results established that mutations significantly reduced the structural stability and caused the rearrangement of FE
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2024.108065
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Article ; Online: Preoperative three-dimensional modelling and virtual reality planning aids nephron sparing surgery in a child with bilateral Wilms tumour.

Banerjee, Avijit / Babu, Ramesh / Jayaraman, Dhaarani / Chilukuri, Srinivas

BMJ case reports

2024 Volume 17, Issue 4

Abstract: Bilateral Wilms tumour (BWT) is a surgically challenging condition. Virtual reality (VR) reconstruction aids surgeons to foresee the anatomy ahead of Nephron Sparing Surgery (NSS). Three-dimensional (3D) visualisation improves the anatomical orientation ... ...

Abstract	Bilateral Wilms tumour (BWT) is a surgically challenging condition. Virtual reality (VR) reconstruction aids surgeons to foresee the anatomy ahead of Nephron Sparing Surgery (NSS). Three-dimensional (3D) visualisation improves the anatomical orientation of surgeons performing NSS. We herewith report a case of BWT where VR planning and 3D printing were used to aid NSS. Conventional imaging is often found to be inadequate while assessing the tumour-organ-vascular anatomy. Advances like VR and 3D printing help surgeons plan better for complex surgeries like bilateral NSS. Next-generation extended reality tools will likely aid robotic-assisted precision NSS and improve patient outcomes.
MeSH term(s)	Child ; Humans ; Kidney Neoplasms/diagnostic imaging ; Kidney Neoplasms/surgery ; Kidney Neoplasms/pathology ; Wilms Tumor/diagnostic imaging ; Wilms Tumor/surgery ; Wilms Tumor/pathology ; Nephrectomy/methods ; Virtual Reality ; Nephrons/surgery ; Nephrons/pathology ; Imaging, Three-Dimensional/methods
Language	English
Publishing date	2024-04-19
Publishing country	England
Document type	Case Reports ; Journal Article
ISSN	1757-790X
ISSN (online)	1757-790X
DOI	10.1136/bcr-2024-260600
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Article: Anticancer Effects of Rosmarinus officinalis Leaf Extract on KB Cell Lines.

Pradeep, V R / Menaka, S / Suresh, Vasugi / Jayaraman, Selvaraj

Cureus

2024 Volume 16, Issue 2, Page(s) e54031

Abstract: Background The value and use of medicinal plants, including the widespread cultivation ... ...

Abstract	Background The value and use of medicinal plants, including the widespread cultivation of
Language	English
Publishing date	2024-02-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.54031
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Article: The Gastrointestinal Stromal Tumor (GIST) of a Pancreatic Cyst.

Zackria, Rasiq / Jayaraman, Vijay

Cureus

2022 Volume 14, Issue 6, Page(s) e26197

Abstract: Gastrointestinal stromal tumors (GISTs) are rare tumors and rarely occur outside of the gastrointestinal (GI) tract. When GISTs originate from outside the GI tract, they are called extra-gastrointestinal stromal tumors (EGISTs). In this article, we ... ...

Abstract	Gastrointestinal stromal tumors (GISTs) are rare tumors and rarely occur outside of the gastrointestinal (GI) tract. When GISTs originate from outside the GI tract, they are called extra-gastrointestinal stromal tumors (EGISTs). In this article, we discuss a case of a 74-year-old woman who presented due to a growing pancreatic lesion on imaging and was subsequently diagnosed with pancreatic EGIST on endoscopic ultrasound with fine-needle aspiration.
Language	English
Publishing date	2022-06-22
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.26197
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