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https://www.readbyqxmd.com/read/28336253/mitochondrial-matters-mitochondrial-bottlenecks-self-assembling-structures-and-entrapment-in-the-female-germline
#1
Florence L Marlow
Mitochondrial replacement therapy, a procedure to generate embryos with the nuclear genome of a donor mother and the healthy mitochondria of a recipient egg, has recently emerged as a promising strategy to prevent transmission of devastating mitochondrial DNA diseases and infertility. The procedure may produce an embryo that is free of diseased mitochondria. A recent study addresses important fundamental questions about the mechanisms underlying maternal inheritance and translational questions regarding the transgenerational effectiveness of this promising therapeutic strategy...
March 15, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28336065/folding-and-dynamics-based-electrochemical-dna-sensors
#2
Rebecca Y Lai
A number of electrochemical DNA sensors based on the target-induced change in the conformation and/or flexibility of surface-bound oligonucleotides have been developed in recent years. These sensors, which are often termed E-DNA sensors, are comprised of an oligonucleotide probe modified with a redox label (e.g., methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of the target to the DNA probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28335274/metallic-nanostructures-based-on-dna-nanoshapes
#3
REVIEW
Boxuan Shen, Kosti Tapio, Veikko Linko, Mauri A Kostiainen, Jari Jussi Toppari
Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds...
August 10, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335267/dna-based-enzyme-reactors-and-systems
#4
REVIEW
Veikko Linko, Sami Nummelin, Laura Aarnos, Kosti Tapio, J Jussi Toppari, Mauri A Kostiainen
During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways...
July 27, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28330758/regulation-of-type-i-interferon-signaling-in-immunity-and-inflammation-a-comprehensive-review
#5
REVIEW
Kun Chen, Juan Liu, Xuetao Cao
Type I interferons (IFNs) play essential roles in establishing and modulating host defense against microbial infection via induction of IFN-stimulated genes (ISGs) through Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway. However, dysregulation of IFNs production and function could also mediate immune pathogenesis such as inflammatory autoimmune diseases and infectious diseases via aberrantly activating inflammatory responses or improperly suppressing microbial controls...
March 19, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28327556/control-of-structure-specific-endonucleases-to-maintain-genome-stability
#6
REVIEW
Pierre-Marie Dehé, Pierre Henri L Gaillard
Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families - including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes - during processes such as DNA adduct repair, Holliday junction processing and replication stress...
March 22, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28321234/a-review-of-bioinformatics-tools-for-bio-prospecting-from-metagenomic-sequence-data
#7
REVIEW
Despoina D Roumpeka, R John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28320884/replication-restart-in-bacteria
#8
Bénédicte Michel, Steven J Sandler
In bacteria replication forks assembled at a replication origin travel to the terminus, often a few megabases away. They may encounter obstacles that trigger replisome disassembly, rendering replication restart from abandoned forks crucial for cell viability. During the past 25 years the genes that encode replication restart proteins have been identified and genetically characterized. In parallel, the enzymes were purified and analyzed in vitro, where they can catalyze replication initiation in a sequence-independent manner from fork-like DNA structures...
March 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28318351/retinoids-a-journey-from-the-molecular-structures-and-mechanisms-of-action-to-clinical-uses-in-dermatology-and-adverse-effects
#9
Samar Khalil, Tara Bardawil, Carla Stephan, Nadine Darwiche, Ossama Abbas, Abdul Ghani Kibbi, Georges Nemer, Mazen Kurban
Retinoids are a class of compounds derived from vitamin A or have structural and/or functional similarity with vitamin A. They are classified into three generations based on their molecular structures. Inside the body, retinoids bind to several classes of proteins including retinoid-binding proteins and retinoid nuclear receptors. This eventually leads to the activation of specific regulatory regions of DNA - called the retinoic acid response elements - involved in regulating cell growth, differentiation and apoptosis...
March 20, 2017: Journal of Dermatological Treatment
https://www.readbyqxmd.com/read/28318170/-application-of-saliva-in-disease-diagnosis
#10
Cheng Xingqun, Zhou Xuedong, Xu Xin
Saliva is secreted by salivary glands and performs a variety of functions, including mouth cleaning and protection, antibacterial activity, and digestion. With the rapid progress in salivaomics, saliva became recognized as a potential pool of biological markers. Being a non-invasive and safe source, saliva is a potential substitute for blood in diagnosis and prognosis of diseases. This review summarizes the latest advancement in saliva-related studies and presents the potential value of saliva in early diagnosis of oral diseases, such as dental caries, periodontal disease, cancer, diabetes, and other systemic disorders...
December 1, 2016: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28314870/perillyl-alcohol-a-pleiotropic-natural-compound-suitable-for-brain-tumor-therapy-targets-free-radicals
#11
REVIEW
Aline C Gomes, Angélica L Mello, Manuel G Ribeiro, Diogo G Garcia, Clovis O Da Fonseca, Marcela D'Alincourt Salazar, Axel H Schönthal, Thereza Quirico-Santos
Monoterpenes such as limonene and perillyl alcohol (POH) are promising natural compounds with pro-oxidant properties partly due to endoplasmic reticulum (ER) stress-induced cytotoxicity, and antioxidant activity owing to their activity as free radical scavengers, inhibition of coenzyme Q synthesis, activation of antioxidant-responsive elements (inducing detoxification enzymes) and induction of apoptosis. Activation of ER-stress responses generates reactive oxygen species (ROS), which are highly reactive free radicals mainly produced during mitochondrial electron transfer for adenosine triphosphate (ATP) synthesis...
March 17, 2017: Archivum Immunologiae et Therapiae Experimentalis
https://www.readbyqxmd.com/read/28303166/single-molecule-studies-of-high-mobility-group-b-architectural-dna-bending-proteins
#12
REVIEW
Divakaran Murugesapillai, Micah J McCauley, L James Maher, Mark C Williams
Protein-DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function...
February 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28299649/covalent-modifications-of-runx-proteins-structure-affects-function
#13
Ezra Blumenthal, Sarah Greenblatt, Guang Huang, Koji Ando, Ye Xu, Stephen D Nimer
The RUNX family of transcription factors plays important roles in tissue-specific gene expression. Many of their functions depend on specific post-translational modifications (PTMs), and in this review, we describe how PTMs govern RUNX DNA binding, transcriptional activity, protein stability, cellular localization, and protein-protein interactions. We also report how these processes can be disrupted in disease settings. Finally, we describe how alterations of RUNX1, or the enzymes that catalyze its post-translational modifications, contribute to hematopoietic malignancies...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28299614/lamin-a-c-cardiomyopathies-current-understanding-and-novel-treatment-strategies
#14
REVIEW
Xi Wang, Allyson Zabell, Wonshill Koh, W H Wilson Tang
Dilated cardiomyopathy (DCM) is the third leading cause of heart failure in the USA. A major gene associated with DCM with cardiac conduction system disease is lamin A/C (LMNA) gene. Lamins are type V filaments that serve a variety of roles, including nuclear structure support, DNA repair, cell signaling pathway mediation, and chromatin organization. In 1999, LMNA was found responsible for Emery-Dreifuss muscular dystrophy (EDMD) and, since then, has been found in association with a wide spectrum of diseases termed laminopathies, including LMNA cardiomyopathy...
March 2017: Current Treatment Options in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28297628/genetic-basis-of-acute-lymphoblastic-leukemia
#15
Ilaria Iacobucci, Charles G Mullighan
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, and despite cure rates exceeding 90% in children, it remains an important cause of morbidity and mortality in children and adults. The past decade has been marked by extraordinary advances into the genetic basis of leukemogenesis and treatment responsiveness in ALL. Both B-cell and T-cell ALL comprise multiple subtypes harboring distinct constellations of somatic structural DNA rearrangements and sequence mutations that commonly perturb lymphoid development, cytokine receptors, kinase and Ras signaling, tumor suppression, and chromatin modification...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28295846/the-enigmatic-oncogene-and-tumor-suppressor-like-properties-of-rad54b-insights-into-genome-instability-and-cancer
#16
REVIEW
Erin N McAndrew, Kirk J McManus
One of the major challenges to the cell is to ensure genome stability, which can be compromised through endogenous errors or exogenous DNA damaging agents, such as ionizing radiation or common chemotherapeutic agents. To maintain genome stability the cell has a multifaceted line of defense, including cell cycle checkpoints and DNA damage repair pathways. RAD54B is involved in many of these pathways and thus exhibits a role in maintaining and repairing genome stability following DNA damage. RAD54B is involved in cell cycle regulation after DNA damage and participates in homologous recombinational repair, which ensures the precise repair of the most deleterious DNA lesions, double-stranded breaks...
March 13, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28294975/reverse-transcription-in-the-saccharomyces-cerevisiae-long-terminal-repeat-retrotransposon-ty3
#17
REVIEW
Jason W Rausch, Jennifer T Miller, Stuart F J Le Grice
Converting the single-stranded retroviral RNA into integration-competent double-stranded DNA is achieved through a multi-step process mediated by the virus-coded reverse transcriptase (RT). With the exception that it is restricted to an intracellular life cycle, replication of the Saccharomyces cerevisiae long terminal repeat (LTR)-retrotransposon Ty3 genome is guided by equivalent events that, while generally similar, show many unique and subtle differences relative to the retroviral counterparts. Until only recently, our knowledge of RT structure and function was guided by a vast body of literature on the human immunodeficiency virus (HIV) enzyme...
March 15, 2017: Viruses
https://www.readbyqxmd.com/read/28289517/retroviral-integrase-protein-and-intasome-nucleoprotein-complex-structures
#18
REVIEW
Julia Grawenhoff, Alan N Engelman
Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase (IN) protein. IN catalyzes two distinct chemical reactions: 3'-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3'-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus (PFV)...
February 26, 2017: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28288698/crispr-system-for-genome-engineering-the-application-for-autophagy-study
#19
Jianzhou Cui, Shirley Jia Li Chew, Yin Shi, Zhiyuan Gong, Han-Ming Shen
CRISPR/Cas9 is the latest tool introduced in the field of genome engineering and is so far the best genome-editing tool as compared to its precedents such as, meganucleases, zinc finger nucleases (ZFNs) and transcription activator-like effectors (TALENs). The simple design and assembly of the CRISPR/Cas9 system makes genome editing easy to perform as it uses small guide RNAs that correspond to their DNA targets for high efficiency editing. This has helped open the doors for multiplexible genome targeting in many species that were intractable using old genetic perturbation techniques...
March 14, 2017: BMB Reports
https://www.readbyqxmd.com/read/28286741/sampling-strategies-for-three-dimensional-spatial-community-structures-in-ibd-microbiota-research
#20
REVIEW
Shaocun Zhang, Xiaocang Cao, He Huang
Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD...
2017: Frontiers in Cellular and Infection Microbiology
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