Article
Biochemistry & Molecular Biology
Griffin Wright, Manoj Sonavane, Natalie R. Gassman
Summary: STAT3 is identified as a novel regulator of XRCC1, with its activation through the IL-6 signaling pathway increasing the expression level of XRCC1 and impacting its role in triple negative breast cancer. The upregulation of XRCC1 is associated with the aggressiveness and chemotherapeutic resistance in cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ashan P. Wettasinghe, Melodee O. Seifi, Marco Bravo, Austen C. Adams, Aman Patel, Monica Lou, Dimithree Kahanda, Hao-Che Peng, Allison L. Stelling, Li Fan, Jason D. Slinker
Summary: DNA helicase activity is crucial for various DNA metabolic processes. This study investigates the binding and activity of helicases StXPB2 and AfXPB, revealing a concentration-dependent activity for AfXPB and a crossover between fast molecular wrench and slower conventional helicase modes. The AfXPB-Bax1 complex inhibits rapid activity, while the StXPB2-Bax1 complex induces rapid kinetics at higher concentrations.
Review
Biochemistry & Molecular Biology
Yuliya Krasikova, Nadejda Rechkunova, Olga Lavrik
Summary: Nucleotide excision repair (NER) is a versatile DNA repair pathway that is linked to neurological degeneration in patients with Xeroderma pigmentosum. Xeroderma pigmentosum patients typically have a high sensitivity to ultraviolet light due to DNA repair defects, leading to multiple skin and eye cancers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Jiahui Zhu, Lexin Liu, Xiaodi Ma, Xinyu Cao, Yu Chen, Xiangping Qu, Ming Ji, Huijun Liu, Chi Liu, Xiaoqun Qin, Yang Xiang
Summary: The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Oxidative stress, especially DNA stimulation, plays a crucial role in pulmonary fibrosis. DNA damage is important in the initiation of IPF and DNA repair systems targeting damage are crucial for lung cell survival. However, existing research has not focused on the role of DNA damage and repair pathways in IPF.
Review
Genetics & Heredity
Apurva Barve, Alisha A. Galande, Saroj S. Ghaskadbi, Surendra Ghaskadbi
Summary: Hydra, discovered in 1744, has become a popular research organism due to its remarkable regeneration capacity, unique tissue dynamics, continuous pattern formation, evolutionary position, and apparent lack of senescence. While there has been extensive research in the field of evolutionary developmental biology of hydra, recent focus has shifted to molecular mechanisms underlying various phenomena. Analysis of DNA repair mechanisms in hydra has revealed high similarity with vertebrate orthologues, hinting at ancient evolutionary origins and highlighting the importance of studying repair components and functions in this early metazoan.
FRONTIERS IN GENETICS
(2021)
Review
Biochemistry & Molecular Biology
Vladimir Shafirovich, Nicholas E. Geacintov
Summary: Base excision repair (BER) and nucleotide excision repair (NER) are two major mechanisms that remove DNA lesions. Experimental evidence shows that oxidatively generated DNA lesions can be repaired by both competitive BER and NER pathways. The interaction between BER and NER pathways in repairing oxidatively generated DNA lesions is crucial for understanding DNA repair mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Maria Ovejero-Sanchez, Rogelio Gonzalez-Sarmiento, Ana Belen Herrero
Summary: This article reviews the alterations in DNA damage response (DDR) pathways in ovarian cancer (OC), and the therapeutic potential of targeting the DDR for the treatment of OC. Failures in DDR have been associated with the development, progression, and chemoresistance of OC. Defects in DNA repair pathways, such as DNA double-strand break repair by homologous recombination and ARID1A mutations, have been found in different OC subtypes. Preclinical and clinical studies have shown promise in targeting the DDR to fight OC.
Article
Biochemistry & Molecular Biology
Michal Hammel, Ishtiaque Rashid, Aleksandr Sverzhinsky, Yasin Pourfarjam, Miaw-Sheue Tsai, Tom Ellenberger, John M. Pascal, In-Kwon Kim, John A. Tainer, Alan E. Tomkinson
Summary: In this study, biophysical methods were used to reveal the shape and conformational flexibility of the XRCC1-DNA ligase III alpha complex (XL), showing that XL is more compact and identifying the components of its molecular interface. The findings suggest a potential new strategy for treating cancer cells deficient in homologous recombination by targeting the XRCC1-DNA ligase III alpha complex.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Oncology
Carmen Ortiz-Sanchez, Jarline Encarnacion-Medina, Jong Y. Park, Natasha Moreno, Gilberto Ruiz-Deya, Jaime Matta
Summary: This study evaluated variations in DNA repair capacity (DRC) in Puerto Rican men with prostate cancer (PCa). The results showed that PCa cases had lower DRC levels compared to controls. Additionally, DRC levels may have the potential to discriminate between aggressive and indolent PCa cases.
Article
Biochemistry & Molecular Biology
Anatoly A. Bulygin, Victoria N. Syryamina, Aleksandra A. Kuznetsova, Darya S. Novopashina, Sergei A. Dzuba, Nikita A. Kuznetsov
Summary: This study investigated the molecular events in the process of damage recognition by Apurinic/apyrimidinic endonuclease 1 (APE1) through DEER spectroscopy and kinetic analysis. The results showed that specific mutants of APE1 had higher activity in recognizing and repairing damaged DNA, revealing the factors that affect its substrate specificity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Mansour Akbari, Hilde Loge Nilsen, Nicola Pietro Montaldo
Summary: Mitochondria are essential for cellular energy production and play a crucial role in organismal development and normal function. Understanding the mechanisms of mtDNA maintenance and transcription can provide insights into the pathogenesis of various diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shelby C. Yuhas, Daniel J. Laverty, Huijin Lee, Ananya Majumdar, Marc M. Greenberg
Summary: A potent irreversible inhibitor of DNA polymerase beta has been developed, selectively inactivating the enzyme and preventing its binding with DNA. The inhibitor shows selectivity for the target enzyme and cells, and works synergistically with other drugs to induce cell death.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Cell Biology
Irina Petruseva, Natalia Naumenko, Jochen Kuper, Rashid Anarbaev, Jeannette Kappenberger, Caroline Kisker, Olga Lavrik
Summary: The study investigates the interaction of ctXPD and ctXPD-ctp44 with model DNAs containing bulky lesions, revealing the ability of ctXPD-ctp44 to interact with damaged DNA and suggesting a significant role for the ctp44 subunit in the verification process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ning Tsao, Orlando D. Scharer, Nima Mosammaparast
Summary: DNA damaging agents, such as alkylating agents, have been crucial in cancer therapy for almost a century. The chemistry of alkylating agents and their diverse ways of damaging nucleic acids lead to the activation of various repair pathways to counteract these damages. Moreover, recent studies have highlighted the role of RNA damage in cellular response to these agents, although the understanding of their relationship with established DNA repair pathways is still emerging.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Review
Oncology
Jiale Li, Chang Xu, Qiang Liu
Summary: The transcription factor NRF2 is involved in various DNA repair pathways and plays a crucial role in maintaining genome stability. By understanding the links between NRF2 and DNA damage repair, attention can be drawn to its potential as a target for cancer therapy.
Article
Mathematical & Computational Biology
Ahmad El Askary, Alaa Shafie, Mazen Almehmadi, Hatem H. Allam, Lamiaa K. Elsayyad, Asmaa F. Hassan, Bader B. Althobaiti, Mohamed Mansour Khalifa, Tamer Saber, Aisha H. Alharthi, Amal F. Gharib
Summary: This study investigated the effect of exercise on metabolic status and vitamin D levels in Saudi Arabian patients with type 2 diabetes mellitus. The results showed that the exercise training program significantly improved metabolic control and vitamin D levels.
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE
(2022)
Article
Polymer Science
Iram Ayaz, Muhammad Rizwan, Jeffery Layton Ullman, Hajira Haroon, Abdul Qayyum, Naveed Ahmed, Basem H. Elesawy, Ahmad El Askary, Amal F. Gharib, Khadiga Ahmed Ismail
Summary: Eucalyptus wood was used to prepare biochar, and the study found that different types of biochar showed varying effectiveness in removing fluoride and arsenic at different pH levels. Surface characteristics analyzed by FTIR and isotherm studies revealed the excellent adsorption properties of the biochar, suggesting its potential application for arsenic and fluoride removal from water.
Article
Biology
Sadaf Naz, Sadia Alam, Waseem Ahmed, Shah Masaud Khan, Abdul Qayyum, Maimoona Sabir, Alia Naz, Asia Iqbal, Yamin Bibi, Sobia Nisa, Amany Salah Khalifa, Amal F. Gharib, Ahmad El Askary
Summary: The study evaluated the chemical composition and antibacterial activity of Adhatoda vasica, Amaranthus hybridus, and Aloe barbadensis, suggesting that these plants have a strong profile of antioxidants and various enzymes, making them a promising alternative for treating bacterial infections._gc.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biology
Attia Shah, Sadia Alam, Muhammad Kabir, Sajjad Fazal, Adnan Khurshid, Asia Iqbal, Muhammad Mumtaz Khan, Waqar Khan, Abdul Qayyum, Mubashar Hussain, Ahmad El Askary, Amal F. Gharib, Basem H. Elesawy, Yamin Bibi
Summary: The acquisition and dispersal of multi-drug resistance (MDR) genes by pathogenic bacteria have become a global issue. Wild migratory birds contribute to the spread of MDR pathogens and genes through their consumption of contaminated food and water. This study isolated Escherichia fergusonii from blood, saliva, and intestines of migratory birds, and assessed their resistance to different antibiotics. The findings highlight the prevalence of MDR strains in these birds and the need for surveillance of zoonotic pathogens.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biology
Sammyia Jannat, Mahmood Ul Hassan, Muhammad Kausar Nawaz Shah, Asad Hussain Shah, Anila Fariq, Suman Mehmood, Abdul Qayyum, Amal F. Gharib, Ahmad El Askary
Summary: The peanut crop in rainfed areas of Pakistan is facing challenges due to global warming, especially the temperature fluctuations and changes in rain patterns. This study aims to develop early maturing hybrids to adapt to the changing climate and reduce yield losses. Through line into tester mating design, F-1 hybrids were produced and evaluated based on early maturity and yield-related attributes. Promising parental lines and hybrid combinations with early maturity genes and high yields were identified for the development of short duration varieties.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Mathematical & Computational Biology
Amal F. Gharib, Wael H. Elsawy, Amani A. Alrehaili, Hanan S. Amin, Hayaa M. Alhuthali, Maha M. Bakhuraysah, Ahmad El Askary
Summary: In esophageal cancer, SOX2 acts as an oncogene while miR-126 acts as a tumor suppressor gene. Overexpression of SOX2 and downregulation of miR-126 are associated with poor prognosis.
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE
(2022)
Article
Multidisciplinary Sciences
Sabina Asghar, Aziz Ur Rehman, Nadeem Ahmad, Sadia Ajmal, Aneela Ahsan, Saima Gulnaz, Makky Javed, Javed Ahmad, Javed Iqbal, Sumera Bibi, Sajid Fiaz, Basem H. Elesawy, Ahmad El Askary, Khadiga Ahmed Ismail, Amal F. Gharib, Ahsan Mohyo-ud-Din, Muhammad Ijaz Tabassum, Abdul Qayyum
Summary: A total of 341 entries consisting of 250 genotypes/lines and 91 gene differentials were tested for leaf rust in Punjab. Genotype HYT 60-5 and genes Lr-19, Lr-26 and Lr27+31 showed no disease symptoms and can be used in future breeding material development. Furthermore, 43 entries displayed excellent disease progression pattern for durable rust resistance breeding.
Article
Immunology
Hayaa M. Alhuthali, Mazen Almehmadi, Eman F. Ataya, Hind A. Alzahrani, Amani A. Alrehaili, Maha M. Bakhuraysah, Fouzeyyah Ali Alsaeedi, Ahad Amer Alsaiari, Mohamed M. Khalifa, Amal F. Gharib
Summary: A study was conducted to evaluate the characteristics of diabetic and pre-diabetic COVID-19 patients and their correlation with neutrophils, which are critical cells in COVID-19 development. The results showed that neutrophil count was directly correlated with the severity of the disease and inflammatory factors, and inversely associated with vitamin D levels in diabetic and pre-diabetic patients.
EUROPEAN JOURNAL OF INFLAMMATION
(2023)
Article
Medicine, Research & Experimental
Amani A. Alrehaili, Amal F. Gharib, Saleh Ali Alghamdi, Ayman Alhazmi, Saad S. Al-shehri, Howaida M. Hagag, Fouzeyyah Ali Alsaeedi, Hayaa M. Alhuthali, Nermin Raafat, Rasha L. Etewa, Wael H. Elsawy
Summary: This study evaluated the role of 5-hydroxymethylcytosine (5-hmC) and TET enzymes in non-small cell lung cancer (NSCLC) patients. The results showed that the levels of 5-hmC and TET1, TET2, and TET3 mRNA were significantly reduced in NSCLC tissues, and this reduction was correlated with adverse clinical features. Therefore, 5-hmC levels and TET gene downregulation could serve as valuable prognostic biomarkers for NSCLC.
Article
Chemistry, Medicinal
Amany Belal, Amani Elsayed, Amal F. Gharib, Maram Abdullah Ali Alqarni, Aiten M. Soliman, Ahmed B. M. Mehany, Mohamed A. Elanany
Summary: This research identified a potential novel inhibitor 29 through virtual screening, which showed favorable interaction with SARS-CoV-2 protease and higher limiting action on the enzyme. This provides evidence for the potential of evodiamine compounds in antiviral research.
NATURAL PRODUCT COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Samia S. Sadaf, Ali Hazazi, Samia S. Alkhalil, Ahad Amer Alsaiari, Amal F. Gharib, Hayaa M. Alhuthali, Shanika Rana, Abdulaziz A. Aloliqi, Alaa Abdulaziz Eisa, Mohammad Raghibul Hasan, Kapil Dev
Summary: Breast cancer is a deadly disease with global significance, and understanding its various factors, genetic mutations, and pathways is crucial for improving treatment. The forkhead-box gene family has a significant impact on the growth and progression of breast cancer. This article explores different forkhead genes, their role in cancer development, drug resistance, interaction with microRNAs, potential as therapeutic targets, and their association with stem cells.
Article
Medical Laboratory Technology
Amal F. Gharib, Ahmad El Askary, Mazen Almehmadi, Hatem H. Allam, Lamiaa K. Elsayyad, Bader B. Althobaiti, Ebtehal AbdulAziz Almoudhi, Sara H. Alwethenany, Rana A. Al Zahrani, Alaa Shafie
Summary: This study aimed to evaluate the relationship between vitamin D deficiency, dyslipidemia, and obesity with the incidence of coronary artery disease in type 2 diabetes mellitus patients in Saudi Arabia. The results showed significantly decreased levels of serum vitamin D and high density lipoprotein cholesterol (HDL-C) in diabetic patients, particularly those with coronary artery disease and obesity. Diabetic patients also had significantly higher levels of fasting blood glucose, total cholesterol, triglycerides, low density lipoprotein cholesterol (LDL-C), and body mass index (BMI) compared to the control group. There were significant negative correlations between serum vitamin D and blood glucose, cholesterol, triglycerides, LDL-C levels, and BMI, while positive correlations were observed with HDL-C in all diabetic patient groups.
CLINICAL LABORATORY
(2022)
Article
Medical Laboratory Technology
Mazen Almehmadi, Magdi M. Salih, Alaa Shafie, Abdulaziz Alsharif, Naif Alsiwiehr, Ahmad El-Askary, Khalid Alzahrani, Ayman Al-Hazmi, Abdulelah Aljuaid, Osama Abdulazziz, Abdulraheem A. Almalki, Mamdouh Allahyani, Emad Eed, Ahmad M. Alharbi, Mustafa Halawi, Hatem H. Allam, Hisham Abutawil, Ebtisam Alosimi, Amal F. Gharib
Summary: This study evaluated the seroprevalence of IgM and IgG antibodies against SARS-CoV-2 in breast cancer patients after receiving two doses of Pfizer-BioNTech COVID-19 vaccine. The results showed significant differences in the positivity rates of IgM and IgG antibodies after one month and three months. These findings highlight the importance of screening for antibody response in breast cancer patients after vaccination.
CLINICAL LABORATORY
(2022)
Article
Biology
Amal F. Gharib, Howaida M. Hagag, Amani A. Alrehaili, Maha M. Bakhuraysah, Afaf Alharthi, Fouzeyyah Ali Alsaeedi, Hayaa M. Alhuthali, Wael H. Elsawy
Summary: MIR-181b plays a crucial role in non-small cell lung cancer (NSCLC), and its downregulation is associated with invasiveness and metastases. Therefore, MIR-181b may serve as a molecular marker for assessing the aggressiveness and prognosis of NSCLC.
BIOSCIENCE RESEARCH
(2022)
Article
Medicine, Research & Experimental
Amal F. Gharib, Taisir Saber, Ahmad EL Askary, Afaf Alharthi, Nouf Ali Alsalmi, Saja Talal Alhashmi, Rana Fawaz Al-Asiri, Alaa Shafie
Summary: This study found that increased serum HIF-1 alpha levels are associated with dyslipidemia in Saudi patients with T2DM, particularly those with coronary artery disease.
