Article
Biochemistry & Molecular Biology
Dipanwita Maity, Rajasekhara Reddy Katreddy, Amitava Bandhu
Summary: The study focused on characterizing the Mce1R operon in Mycobacterium tuberculosis, revealing its importance in lipid metabolism/transport, host cell invasion, modulation of host immune response, and pathogenicity. The study identified the DNA-binding activity of Mce1R, showing moderate affinity compared to other regulators within the FCD family. The structural analysis suggested a dynamic N-terminal DNA-binding domain and a stable C-terminal domain, with a cavity containing conserved residues that could serve as a potential target site for novel anti-tuberculosis drug discovery.
MOLECULAR BIOTECHNOLOGY
(2021)
Article
Immunology
Justin H. M. Heltzel, Robert W. Maul, William Yang, Patricia J. Gearhart
Summary: This study demonstrates that the distance between the V region and J gene does not affect the extent of mutation. The majority of mutations occur within a 1 kb region downstream of the J gene, regardless of the specific J gene used. This suggests that mutations are targeted by AID interactions with RNA polymerase II.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Walker Hoolehan, Justin C. Harris, Jennifer N. Byrum, Destiny A. Simpson, Karla K. Rodgers
Summary: V(D)J recombination plays a crucial role in generating a diverse antigen receptor repertoire. Studies have found that the specificity of RAG1/2 for RSS heptamers is primarily determined by DNA structural features dependent on the purine/pyrimidine pattern.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Doris Niewolik, Klaus Schwarz
Summary: The interaction between nuclease ARTEMIS and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) plays a crucial role in the repair of DNA double strand breaks and V(D)J recombination activity. Mutations disrupting this interaction have been found to impair the function of these proteins. Small fragments capable of mediating this interaction have been identified, offering possibilities for the design of specific inhibitors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Engineering, Electrical & Electronic
Jianbo Liu, Xiaohui Li, Xiaola Li, Jing Bai, Yunhua Xu
Summary: A stable LiNbO3 (LN) sol with different Zn2+ contents was prepared and its influence on crystal structure, light transmittance, and J-V curve characteristics was studied. Zn2+ doping did not affect the crystal structure of LN, but increased the grain size of LN films. The highest light transmittance was achieved at a doping amount of 3%. The Pt/LN/LNO structure showed excellent resistance switching (RS) effect, while the In/LN/LNO structure exhibited poor RS effect. The RS effect deteriorated with decreasing temperature, and the refractive index of LN film increased.
MATERIALS SCIENCE IN SEMICONDUCTOR PROCESSING
(2023)
Article
Biology
Magdalena L. Russell, Aisha Souquette, David M. Levine, Stefan A. Schattgen, E. Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G. Thomas, Frederick A. Matsen, Philip Bradley
Summary: The T cell receptor repertoire is influenced by genetic biases and immune exposures. This study identifies specific genetic loci associated with V(D)J recombination probabilities and reveals variations in V(D)J gene usage profiles and the major histocompatibility complex locus that affect the TCR repertoire diversity. Furthermore, variations in genes encoding the Artemis protein and the TdT protein are found to be associated with junctional nucleotide deletion and N-insertion. These findings enhance our understanding of genetically-determined TCR repertoire biases and provide insights into individual variations in immune responses.
Article
Biochemistry & Molecular Biology
Min Gyu Jeong, Kai Zhou, Soyeon Park, HyeongJeon An, Yonghoon Kwon, Yeonho Chang, Do-Hyeon Kim, Sung Ho Ryu
Summary: A new method for analyzing protein interactions in the outer membrane of living cells has been developed, which could provide critical information to understand how cancer cells develop resistance to targeted drug therapies. By investigating weak protein-protein interactions, researchers found that the cancer-linked protein EGFR tends to bind with a range of other proteins, depending on the type of cancer cell studied, potentially contributing to drug resistance.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Kaz Kawamura, Takuma Higuchi, Shigeki Fujiwara
Summary: In budding tunicates, aging is associated with a decrease in mitochondrial respiratory activity due to decreased Tfam gene expression, which can be improved by the transfection of synthetic mRNA of YY1 and Sirt6. This study indicates that YY1 and Sirt6 play important roles in regulating mitochondrial function during aging in budding tunicates.
MOLECULAR AND CELLULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Akanksha Srivastava, Arvind Kumar, Subhankar Biswas, Rajender Kumar, Vaibhav Srivastava, Hema Rajaram, Yogesh Mishra
Summary: This study revealed the role of a global regulator, LexA, in modulating the gamma-radiation stress response of the cyanobacterium Anabaena. Proteome analysis of Anabaena strains subjected to gamma-radiation showed differential accumulation of 41 proteins, corresponding to 29 distinct proteins, with LexA regulating 27 of the corresponding genes. The regulated genes were mainly involved in photosynthesis, carbon assimilation, and oxidative stress alleviation. The study also found that LexA influenced photosynthesis and thylakoid membrane proteome even under normal growth conditions, indicating its role in stress response management.
Article
Plant Sciences
Rosario Sanchez, Irene Gonzalez-Thuillier, Monica Venegas-Caleron, Rafael Garces, Joaquin J. Salas, Enrique Martinez-Force
Summary: This study identified the WRI1 gene in sunflower and characterized its role in regulating plastidial fatty acid synthesis. Sunflower WRI1 acts as a co-regulator for multiple genes involved in oleic acid synthesis.
Article
Immunology
Anastasia O. Smirnova, Anna M. Miroshnichenkova, Laima D. Belyaeva, Ilya V. Kelmanson, Yuri B. Lebedev, Ilgar Z. Mamedov, Dmitriy M. Chudakov, Alexander Y. Komkov
Summary: Diversity of T-cell receptor (TR) variable domains is generated through recombination of alpha (TRA) and beta (TRB) chains. We analyzed poorly explored partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA and detected a bimodal distribution of D-D junctions indicating two active recombination sites. These rearrangements contribute to TRB V-(D)-J combinatorial diversity and are present in human antigen-experienced memory T cells, showing their role in antigen recognition and immune response.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Infectious Diseases
Yuanyuan Li, Lei Fu, Weiyan Zhang, Xi Chen, Yu Lu
Summary: This study revealed that the Rv1453 protein of Mycobacterium tuberculosis affects its susceptibility to clofazimine by regulating the transcription level of qor, shedding new light on the mechanism of clofazimine resistance.
INFECTION AND DRUG RESISTANCE
(2021)
Review
Cell Biology
Jan-Michael Peters
Summary: Structural maintenance of chromosomes' complexes play a crucial role in folding genomic DNA into loops, especially in V(D)J recombination of antigen receptor genes in B and T cells. Regulating the formation and recombination of chromatin loops ensures the diversity of B-cell receptors and antibodies.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Review
Ecology
Rishi V. Shridharan, Neha Kalakuntla, Narendra Chirmule, Bhavana Tiwari
Summary: Nearly 50% of the human genome is derived from transposable elements, some of which can cause diseases when dysregulated, while others can generate new cellular functions. The adaptive immune system in jawed vertebrates is associated with Class II TEs, and the somatic rearrangement process in T and B cells is also influenced by TEs, laying the foundation for the generation of antibodies and receptors.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Review
Immunology
James R. Hagman, Tessa Arends, Curtis Laborda, Jennifer R. Knapp, Laura Harmacek, Brian P. O'Connor
Summary: CHD4 is essential for the development, proliferation, and survival of B cells, as well as for promoting the recombination of the Ig heavy chain and regulating chromatin accessibility, leading to antibody production and mediating humoral immune responses.
IMMUNOLOGICAL REVIEWS
(2022)
Article
Genetics & Heredity
William Rodgers, Jennifer N. Byrum, Hem Sapkota, Negar S. Rahman, Robert C. Cail, Shuying Zhao, David G. Schatz, Karla K. Rodgers
Article
Biochemistry & Molecular Biology
Jennifer N. Byrum, Shuying Zhao, Negar S. Rahman, Lori M. Gwyn, William Rodgers, Karla K. Rodgers
Article
Chemistry, Multidisciplinary
Shanjana Awasthi, Asokan Anbanandam, Karla K. Rodgers
Article
Biochemistry & Molecular Biology
Xi-Qin Ding, Arjun Thapa, Hongwei Ma, Jianhua Xu, Michael H. Elliott, Karla K. Rodgers, Marci L. Smith, Jin-Shan Wang, Steven J. Pittler, Vladimir J. Kefalov
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Review
Biochemistry & Molecular Biology
Karla K. Rodgers
TRENDS IN BIOCHEMICAL SCIENCES
(2017)
Article
Biochemistry & Molecular Biology
Olga Nikolaeva, Gennadiy Moiseyev, Karla K. Rodgers, Jian-xing Ma
BIOCHEMICAL JOURNAL
(2011)
Article
Biochemistry & Molecular Biology
M. Osman Sheikh, Christopher M. Schafer, John T. Powell, Karla K. Rodgers, Blaine H. M. Mooers, Christopher M. West
Article
Biochemistry & Molecular Biology
Janeen L. Arbuckle, Negar S. Rahman, Shuying Zhao, William Rodgers, Karla K. Rodgers
Article
Biochemistry & Molecular Biology
Dibyendu Chakraborty, Karla K. Rodgers, Shannon M. Conley, Muna I. Naash
Article
Biochemistry & Molecular Biology
Srinivas Chollangi, Timothy Mather, Karla K. Rodgers, John D. Ash
JOURNAL OF BIOLOGICAL CHEMISTRY
(2012)
Article
Cell Biology
Vivek K. Gupta, Ammaji Rajala, Karla K. Rodgers, Raju V. S. Rajala
Article
Multidisciplinary Sciences
William Rodgers, Jennifer N. Byrum, Destiny A. Simpson, Walker Hoolehan, Karla K. Rodgers
Article
Immunology
Jennifer N. Byrum, Walker E. Hoolehan, Destiny A. Simpson, William Rodgers, Karla K. Rodgers
Summary: The study showed that RAG2 plays a role in cellular responses to DNA double strand breaks by undergoing export from the nucleus and enrichment at the centrosome. Overexpression of full length RAG2 increased apoptosis levels in pre-B cells following irradiation, but also improved the rate of recovery after DNA damage.
Article
Biochemistry & Molecular Biology
Walker Hoolehan, Justin C. Harris, Jennifer N. Byrum, Destiny A. Simpson, Karla K. Rodgers
Summary: V(D)J recombination plays a crucial role in generating a diverse antigen receptor repertoire. Studies have found that the specificity of RAG1/2 for RSS heptamers is primarily determined by DNA structural features dependent on the purine/pyrimidine pattern.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Asif Alam Chowdhury, Karla Rodgers, Nachiket M. Godbole, Shanjana Awasthi
Summary: In this study, the stability and structure-activity relationship of the SPA4 peptide were investigated under different conditions. The results showed that the SPA4 peptide remained structurally stable at room temperature and 4°C, with minimal changes in pH, temperature, simulated lung fluids, and chemical components. Additionally, it was found that the SPA4 peptide retained its anti-inflammatory activity in the presence of lactate, which has important implications for its clinical application.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)