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Article ; Online: PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity.

Jayakumar, Sundarraj / Patel, Manthan / Boulet, Fanny / Aziz, Hadicha / Brooke, Greg N / Tummala, Hemanth / Pradeepa, Madapura M

Nature communications

2024 Volume 15, Issue 1, Page(s) 361

Abstract: R-loops that accumulate at transcription sites pose a persistent threat to genome integrity. PSIP1 ... sites. Here, we show that PSIP1 interacts with R-loops and other proteins involved in R-loop homeostasis ... including PARP1. Genome-wide mapping of PSIP1, R-loops and γ-H2AX in PSIP1-depleted human and mouse ...

Abstract	R-loops that accumulate at transcription sites pose a persistent threat to genome integrity. PSIP1 is a chromatin protein associated with transcriptional elongation complex, possesses histone chaperone activity, and is implicated in recruiting RNA processing and DNA repair factors to transcription sites. Here, we show that PSIP1 interacts with R-loops and other proteins involved in R-loop homeostasis, including PARP1. Genome-wide mapping of PSIP1, R-loops and γ-H2AX in PSIP1-depleted human and mouse cell lines revealed an accumulation of R-loops and DNA damage at gene promoters in the absence of PSIP1. R-loop accumulation causes local transcriptional arrest and transcription-replication conflict, leading to DNA damage. PSIP1 depletion increases 53BP1 foci and reduces RAD51 foci, suggesting altered DNA repair choice. Furthermore, PSIP1 depletion increases the sensitivity of cancer cells to PARP1 inhibitors and DNA-damaging agents that induce R-loop-induced DNA damage. These findings provide insights into the mechanism through which PSIP1 maintains genome integrity at the site of transcription.
MeSH term(s)	Humans ; Animals ; Mice ; R-Loop Structures/genetics ; Intercellular Signaling Peptides and Proteins ; Cell Line ; DNA Damage ; Transcription Factors/genetics ; Adaptor Proteins, Signal Transducing
Chemical Substances	lens epithelium-derived growth factor ; Intercellular Signaling Peptides and Proteins ; PSIP1 protein, human ; Transcription Factors ; Adaptor Proteins, Signal Transducing
Language	English
Publishing date	2024-01-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44544-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Design and Effect of Resonant Ultrasonic Vibration-Assisted Laser Cladding (R-UVALC) on AlCrFeMnNi High-Entropy Alloy.

Mohsan, Aziz Ul Hassan / Zhang, Mina / Wang, Dafeng / Wang, Yishen / Zhang, Jiahao / Zhou, Yanyuan / Li, Yifei / Zhao, Su

Materials (Basel, Switzerland)

2024 Volume 17, Issue 5

Abstract: The design of the resonant ultrasonic vibration-assisted laser cladding (R-UVALC) setup involved ... in a resonance state. The impact of R-UVALC on AlCrFeMnNi high-entropy alloys was assessed using various ... oxidative in nature. Integrating the R-UVALC setup into a resonance state can significantly enhance ...

Abstract	The design of the resonant ultrasonic vibration-assisted laser cladding (R-UVALC) setup involved employing finite element analysis (FEA) to simulate the ultrasonic transducer, horn, and workpiece in a resonance state. The impact of R-UVALC on AlCrFeMnNi high-entropy alloys was assessed using various ultrasonic vibration amplitudes of 0, 5, 10, and 15 µm, with a constant frequency of 20 kHz. Ultrasonic vibrations reduced pores and cracks and increased the clad breadth, melt pool wetting angle, and laser-clad layer consistency. The columnar elongated grains in proximity to the substrate surface underwent a size reduction and transformed into grains with a more equiaxed shape with the utilization of ultrasonic vibrations at an amplitude of 5 µm. Laser cladding performed without ultrasonic vibrations yields two phases: face-centered cubic (FCC) and body-centered cubic (BCC). However, when the coating is exposed to ultrasonic vibrations with an amplitude of 5 µm, it forms a solitary body-centered cubic (BCC) phase. The microhardness tripled compared to the substrate, and the most significant microhardness value was achieved at 5 µm of ultrasonic vibration. The friction coefficient was assessed at an ambient temperature, revealing that an ultrasonic amplitude yields the lowest friction coefficient, demonstrating the excellent wear resistance properties of the coating. The analysis of the 3D surface profile of the wear indicates that the use of ultrasonic aid with a 5 µm amplitude leads to reduced depth of scars, and the primary wear mechanism observed is abrasive and oxidative wear with fewer grooves and debris. In addition, XPS analysis revealed the presence of metal components in an oxidized condition, suggesting that the wear process is oxidative in nature. Integrating the R-UVALC setup into a resonance state can significantly enhance the efficiency of the laser cladding process in the laser cladding field.
Language	English
Publishing date	2024-02-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma17050969
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Article ; Online: PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity

Sundarraj Jayakumar / Manthan Patel / Fanny Boulet / Hadicha Aziz / Greg N. Brooke / Hemanth Tummala / Madapura M. Pradeepa

Nature Communications, Vol 15, Iss 1, Pp 1-

2024 Volume 14

Abstract: Abstract R-loops that accumulate at transcription sites pose a persistent threat to genome ... sites. Here, we show that PSIP1 interacts with R-loops and other proteins involved in R-loop homeostasis ... including PARP1. Genome-wide mapping of PSIP1, R-loops and γ-H2AX in PSIP1-depleted human and mouse ...

Abstract	Abstract R-loops that accumulate at transcription sites pose a persistent threat to genome integrity. PSIP1 is a chromatin protein associated with transcriptional elongation complex, possesses histone chaperone activity, and is implicated in recruiting RNA processing and DNA repair factors to transcription sites. Here, we show that PSIP1 interacts with R-loops and other proteins involved in R-loop homeostasis, including PARP1. Genome-wide mapping of PSIP1, R-loops and γ-H2AX in PSIP1-depleted human and mouse cell lines revealed an accumulation of R-loops and DNA damage at gene promoters in the absence of PSIP1. R-loop accumulation causes local transcriptional arrest and transcription-replication conflict, leading to DNA damage. PSIP1 depletion increases 53BP1 foci and reduces RAD51 foci, suggesting altered DNA repair choice. Furthermore, PSIP1 depletion increases the sensitivity of cancer cells to PARP1 inhibitors and DNA-damaging agents that induce R-loop-induced DNA damage. These findings provide insights into the mechanism through which PSIP1 maintains genome integrity at the site of transcription.
Keywords	Science ; Q
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: New 1,2,3-Triazoles from (R)-Carvone

Ali Oubella / Abdoullah Bimoussa / Abdellah N’ait Oussidi / Mourad Fawzi / Aziz Auhmani / Hamid Morjani / Abdelkhalek Riahi / M’hamed Esseffar / Carol Parish / Moulay Youssef Ait Itto

Molecules, Vol 27, Iss 769, p

Synthesis, DFT Mechanistic Study and In Vitro Cytotoxic Evaluation

2022 Volume 769

Abstract: Aseries of novel 1,4-disubstituted 1,2,3-triazoles were synthesized from an (R)-carvone terminal ...

Abstract	Aseries of novel 1,4-disubstituted 1,2,3-triazoles were synthesized from an (R)-carvone terminal alkyne derivative via a Cu (I)-catalyzed azide–alkyne cycloaddition reaction using CuSO 4 ,5H 2 O as the copper (II) source and sodium ascorbate as a reducing agent which reduces Cu (II) into Cu (I). All the newly synthesized 1,2,3-triazoles 9a – h were fully identified on the basis of their HRMS and NMR spectral data and then evaluated for their cell growth inhibition potential by MTS assay against HT-1080 fibrosarcoma, A-549 lung carcinoma, and two breast adenocarcinoma (MCF-7 and MDA-MB-231) cell lines. Compound 9d showed notable cytotoxic effects against the HT-1080 and MCF-7 cells with IC 50 values of 25.77 and 27.89 µM, respectively, while compound 9c displayed significant activity against MCF-7 cells with an IC 50 value of 25.03 µM. Density functional calculations at the B3LYP/6-31G* level of theory were used to confirm the high reactivity of the terminal alkyne as a dipolarophile. Quantum calculations were also used to investigate the mechanism of both the uncatalyzed and copper (I)-catalyzed azide–alkyne cycloaddition reaction (CuAAC). The catalyzed reaction gives complete regioselectivity via a stepwise mechanism streamlining experimental observations. The calculated free-energy barriers 4.33 kcal/mol and 29.35 kcal/mol for the 1,4- and 1,5-regioisomers, respectively, explain the marked regioselectivity of the CuAAC reaction.
Keywords	(R)-carvone ; 1,2,3-triazole ; DFT calculations ; regioselectivity ; cytotoxic activity ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Response from F R Khan, S M R Kazmi, H K Siddiqui, et al. (J Pak Med Assoc. 2023; 73

Farhan Raza Khan / Syed Murtaza Raza Kazmi / Humayun Kaleem Siddiqui / Ayesha Aziz

Journal of the Pakistan Medical Association, Vol 73, Iss

1275-1279) Prosthetic complications with dental implants: A bibliometric analysis of 20 top cited articles

2023 Volume 11

Abstract: dental implants: a bibliometric analysis of 20 top cited articles. J Pak Med Assoc. PMID: 37427629.”1was published in June 2023. We believe that the reader has mixed up this paper with an earlier paper of ours, titled “A bibliometric analysis of the ... ...

Abstract	dental implants: a bibliometric analysis of 20 top cited articles. J Pak Med Assoc. PMID: 37427629.”1was published in June 2023. We believe that the reader has mixed up this paper with an earlier paper of ours, titled “A bibliometric analysis of the studies on dental implant failure. J Pak Med Assoc. PMID: 35202375.2 Dental implants have two types of failures: surgical (related to implant fixture, its placement techniques and bone biology etc.) and prosthetic (related to implant prosthesis, crown, abutment, other components, or technical issues arising from laboratory made implant prosthesis). The former paper was about identifying the top-cited publications on the surgical failures of implants whereas the latter bibliometrics related to the implant prosthetic complications. Regarding methodology of bibliometrics, the search terms we adopted for the first paper was “dental implant failure” whereas for the second paper, we employed “Prosthetic complication in dental implant” without using any Boolean operator. These key terms were searched in the abstracts using Web of Science, Google Scholar, and other electronic sources published in English language upto June 2021. We employed the option of “cited reference search” for ascertaining the number of citations. To review and synthesise the data, multiple parameters were explored. These included authors, journal, citation count, citation density, keywords and study design, and geographic and institutional affiliation of the first or corresponding authors. The country of literature emergence was determined by the address of the corresponding author. The details of methodology are already shared in the above-mentioned papers. Another important observation made by the reader was that the table 2 and table 3 displayed the same information that has already been shared in table 1. So why was it done? And that too in both the papers. The answer to this question is that although table 1 in both the papers displayed the primary bibliometric data but to stratify the data, ...
Keywords	Medicine ; R
Subject code	001
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Pakistan Medical Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Response from F R Khan, S M R Kazmi, H K Siddiqui, et al. (J Pak Med Assoc. 2023; 73

Farhan Raza Khan / Syed Murtaza Raza Kazmi / Humayun Kaleem Siddiqui / Ayesha Aziz

Journal of the Pakistan Medical Association, Vol 73, Iss

1275-1279) Prosthetic complications with dental implants: A bibliometric analysis of 20 top cited articles

2023 Volume 11

Abstract	dental implants: a bibliometric analysis of 20 top cited articles. J Pak Med Assoc. PMID: 37427629.”1was published in June 2023. We believe that the reader has mixed up this paper with an earlier paper of ours, titled “A bibliometric analysis of the studies on dental implant failure. J Pak Med Assoc. PMID: 35202375.2 Dental implants have two types of failures: surgical (related to implant fixture, its placement techniques and bone biology etc.) and prosthetic (related to implant prosthesis, crown, abutment, other components, or technical issues arising from laboratory made implant prosthesis). The former paper was about identifying the top-cited publications on the surgical failures of implants whereas the latter bibliometrics related to the implant prosthetic complications. Regarding methodology of bibliometrics, the search terms we adopted for the first paper was “dental implant failure” whereas for the second paper, we employed “Prosthetic complication in dental implant” without using any Boolean operator. These key terms were searched in the abstracts using Web of Science, Google Scholar, and other electronic sources published in English language upto June 2021. We employed the option of “cited reference search” for ascertaining the number of citations. To review and synthesise the data, multiple parameters were explored. These included authors, journal, citation count, citation density, keywords and study design, and geographic and institutional affiliation of the first or corresponding authors. The country of literature emergence was determined by the address of the corresponding author. The details of methodology are already shared in the above-mentioned papers. Another important observation made by the reader was that the table 2 and table 3 displayed the same information that has already been shared in table 1. So why was it done? And that too in both the papers. The answer to this question is that although table 1 in both the papers displayed the primary bibliometric data but to stratify the data, ...
Keywords	Medicine ; R
Subject code	001
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Pakistan Medical Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Response from F R Khan, S M R Kazmi, H K Siddiqui, et al. (J Pak Med Assoc. 2023; 73

Farhan Raza Khan / Syed Murtaza Raza Kazmi / Humayun Kaleem Siddiqui / Ayesha Aziz

Journal of the Pakistan Medical Association, Vol 73, Iss

1275-1279) Prosthetic complications with dental implants: A bibliometric analysis of 20 top cited articles

2023 Volume 11

Abstract	dental implants: a bibliometric analysis of 20 top cited articles. J Pak Med Assoc. PMID: 37427629.”1was published in June 2023. We believe that the reader has mixed up this paper with an earlier paper of ours, titled “A bibliometric analysis of the studies on dental implant failure. J Pak Med Assoc. PMID: 35202375.2 Dental implants have two types of failures: surgical (related to implant fixture, its placement techniques and bone biology etc.) and prosthetic (related to implant prosthesis, crown, abutment, other components, or technical issues arising from laboratory made implant prosthesis). The former paper was about identifying the top-cited publications on the surgical failures of implants whereas the latter bibliometrics related to the implant prosthetic complications. Regarding methodology of bibliometrics, the search terms we adopted for the first paper was “dental implant failure” whereas for the second paper, we employed “Prosthetic complication in dental implant” without using any Boolean operator. These key terms were searched in the abstracts using Web of Science, Google Scholar, and other electronic sources published in English language upto June 2021. We employed the option of “cited reference search” for ascertaining the number of citations. To review and synthesise the data, multiple parameters were explored. These included authors, journal, citation count, citation density, keywords and study design, and geographic and institutional affiliation of the first or corresponding authors. The country of literature emergence was determined by the address of the corresponding author. The details of methodology are already shared in the above-mentioned papers. Another important observation made by the reader was that the table 2 and table 3 displayed the same information that has already been shared in table 1. So why was it done? And that too in both the papers. The answer to this question is that although table 1 in both the papers displayed the primary bibliometric data but to stratify the data, ...
Keywords	Medicine ; R
Subject code	001
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Pakistan Medical Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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

Article: Response from F R Khan, S M R Kazmi, H K Siddiqui, et al. (J Pak Med Assoc. 2023; 73: 1275 -1279) " Prosthetic Complications With Dental Implants: A Bibliometric Analysis Of 20 Top Cited Articles".

Khan, Farhan Raza / Raza Kazmi, Syed Murtaza / Siddiqui, Humayun Kaleem / Aziz, Ayesha

JPMA. The Journal of the Pakistan Medical Association

2023 Volume 73, Issue 11, Page(s) 2308

MeSH term(s)	Humans ; Dental Implants ; Bibliometrics
Chemical Substances	Dental Implants
Language	English
Publishing date	2023-11-27
Publishing country	Pakistan
Document type	Journal Article
ZDB-ID	603873-6
ISSN	0030-9982
ISSN	0030-9982
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Article ; Online: Separation and purification of quinolyridine alkaloids from seeds of Thermopsis lanceolata R. Br. by conventional and pH-zone-refining counter-current chromatography.

Ning, Fansheng / Zhu, Heng / Yan, Huijiao / Liu, Jiguo / Aziz, Shahid / Hussain, Hidayat / Song, Xiangyun / Xie, Lei / Meng, Zhaoqing / Cao, Guiyun / Wang, Daijie

Journal of separation science

2023 Volume 46, Issue 16, Page(s) e2300053

Abstract: In this work, the preparative separation of quinolyridine alkaloids from seeds of T. lanceolata by conventional and pH-zone-refining counter-current chromatography. Traditional counter-current chromatography separation was performed by a flow-rate ... ...

Abstract	In this work, the preparative separation of quinolyridine alkaloids from seeds of T. lanceolata by conventional and pH-zone-refining counter-current chromatography. Traditional counter-current chromatography separation was performed by a flow-rate changing strategy with a solvent system of ethyl acetate-n-butanol-water (1:9:10, v/v) and 200 mg sample loading. Meanwhile, the pH-zone-refining mode was adopted for separating 2.0 g crude alkaloid extracts with the chloroform-methanol-water (4:3:3, v/v) solvent system using the stationary and mobile phases of 40 mM hydrochloric acid and 10 mM triethylamine. Finally, six compounds, including N-formylcytisine (two conformers) (1), N-acetycytisine (two conformers) (2), (-)-cytisine (3), 13-β-hydroxylthermopsine (4), N-methylcytisine (5), and thermopsine (6) were successfully obtained in the two counter-current chromatography modes with the purities over 96.5%. Moreover, we adopted nuclear magnetic resonance and mass spectrometry for structural characterization. Based on the obtained findings, the pH-zone-refining mode was the efficient method to separate quinolyridine alkaloids relative to the traditional mode.
MeSH term(s)	Plant Extracts/chemistry ; Countercurrent Distribution/methods ; Hydrogen-Ion Concentration ; Chromatography, High Pressure Liquid/methods ; Alkaloids/analysis ; Solvents/chemistry ; Water ; Seeds/chemistry
Chemical Substances	Plant Extracts ; Alkaloids ; Solvents ; Water (059QF0KO0R)
Language	English
Publishing date	2023-06-27
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2047990-6
ISSN	1615-9314 ; 1615-9306
ISSN (online)	1615-9314
ISSN	1615-9306
DOI	10.1002/jssc.202300053
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: New 1,2,3-Triazoles from (R)-Carvone: Synthesis, DFT Mechanistic Study and In Vitro Cytotoxic Evaluation.

Oubella, Ali / Bimoussa, Abdoullah / N'ait Oussidi, Abdellah / Fawzi, Mourad / Auhmani, Aziz / Morjani, Hamid / Riahi, Abdelkhalek / Esseffar, M'hamed / Parish, Carol / Ait Itto, Moulay Youssef

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 3

Abstract: Aseries of novel 1,4-disubstituted 1,2,3-triazoles were synthesized from an (R)-carvone terminal ...

Abstract	Aseries of novel 1,4-disubstituted 1,2,3-triazoles were synthesized from an (R)-carvone terminal alkyne derivative via a Cu (I)-catalyzed azide-alkyne cycloaddition reaction using CuSO
MeSH term(s)	Carbon-13 Magnetic Resonance Spectroscopy ; Cell Line, Tumor ; Cycloaddition Reaction ; Cyclohexane Monoterpenes/chemistry ; Cyclohexane Monoterpenes/pharmacology ; Density Functional Theory ; Drug Screening Assays, Antitumor ; Humans ; In Vitro Techniques ; Proton Magnetic Resonance Spectroscopy ; Triazoles/chemical synthesis ; Triazoles/chemistry ; Triazoles/pharmacology
Chemical Substances	Cyclohexane Monoterpenes ; Triazoles ; carvone (75GK9XIA8I)
Language	English
Publishing date	2022-01-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27030769
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