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https://www.readbyqxmd.com/read/27933525/expression-qtls-mapping-and-analysis-a-bayesian-perspective
#1
Martha Imprialou, Enrico Petretto, Leonardo Bottolo
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27928956/chemical-properties-of-caffeic-and-ferulic-acids-in-biological-system-implications-in-cancer-therapy-a-review
#2
Sarah S Damasceno, Bruna B Dantas, Demetrius Antônio M Araújo, José Galberto M da Costa
Caffeic and ferulic acids have been extensively evaluated for their antioxidant properties in biological system, such activity is responsible for limiting the excessive production of free radical species, that are associated with cell proliferation. However, more recent studies suggest chemopreventive action of these phenolic acids through the regulation of gene expression, chelation and / or reduction of transition metals, covalent adduct formation (which damage DNA) and toxicity. The biological efficacy of these promising chemopreventive agents depends strongly on their chemical structure...
December 8, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27925276/conformational-and-intermolecular-interaction-dynamics-of-photolyase-cryptochrome-proteins-monitored-by-the-time-resolved-diffusion-technique
#3
Masato Kondoh, Masahide Terazima
Cryptochrome (CRY), a blue light sensor protein, possesses a similar domain structure to photolyase (PHR) that, upon absorption of light, repairs DNA damage. In this review, we compare the reaction dynamics of these systems by monitoring the reaction kinetics of conformation change and intermolecular interaction change based on time-dependent diffusion coefficient measurements obtained by using the pulsed laser-induced transient grating technique. Using this method, time-dependent biomolecular interactions, such as transient dissociation reactions in solution, have been successfully detected in real time...
December 7, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27925218/insights-into-light-driven-dna-repair-by-photolyases-challenges-and-opportunities-for-electronic-structure-theory
#4
Shirin Faraji, Andreas Dreuw
UV radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-) ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, i.e. light absorption and resonance energy transfer, photo-induced electron transfer, and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation...
December 7, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27921283/choices-have-consequences-the-nexus-between-dna-repair-pathways-and-genomic-instability-in-cancer
#5
REVIEW
Sonali Bhattacharjee, Saikat Nandi
BACKGROUND: The genome is under constant assault from a multitude of sources that can lead to the formation of DNA double-stand breaks (DSBs). DSBs are cytotoxic lesions, which if left unrepaired could lead to genomic instability, cancer and even cell death. However, erroneous repair of DSBs can lead to chromosomal rearrangements and loss of heterozygosity, which in turn can also cause cancer and cell death. Hence, although the repair of DSBs is crucial for the maintenance of genome integrity the process of repair need to be well regulated and closely monitored...
December 2016: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/27917172/immunization-strategies-against-piscirickettsia-salmonis-infections-review-of-vaccination-approaches-and-modalities-and-their-associated-immune-response-profiles
#6
REVIEW
Øystein Evensen
Salmonid rickettsial septicemia (SRS) is a serious, infectious disease in Chilean salmon farming caused by Piscirickettsia salmonis, causing heavy losses to the salmonid industry. P. salmonis belongs to the Gammaproteobacteria, order Thiotrichales. SRS was first described in Chile in 1989, and infection with P. salmonis has since been described from a high number of fish species and in several geographic regions globally. P. salmonis infection of salmonids causes multifocal, necrotic areas of internal organs such as liver, kidney, and spleen...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27913665/structure-and-function-of-bacterial-h-ns-protein
#7
REVIEW
David C Grainger
The histone-like nucleoid structuring (H-NS) protein is a major component of the folded chromosome in Escherichia coli and related bacteria. Functions attributed to H-NS include management of genome evolution, DNA condensation, and transcription. The wide-ranging influence of H-NS is remarkable given the simplicity of the protein, a small peptide, possessing rudimentary determinants for self-association, hetero-oligomerisation and DNA binding. In this review, I will discuss our understanding of H-NS with a focus on these structural elements...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27908232/iron-sulfur-clusters-in-mitochondrial-metabolism-multifaceted-roles-of-a-simple-cofactor
#8
REVIEW
Johnny Stiban, Minyoung So, Laurie S Kaguni
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908231/the-mitochondrial-genome-the-nucleoid
#9
REVIEW
A A Kolesnikov
Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed.
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27904474/poly-adp-ribose-polymerase-inhibition-reveals-a-potential-mechanism-to-promote-neuroprotection-and-treat-neuropathic-pain
#10
REVIEW
Prashanth Komirishetty, Aparna Areti, Ranadeep Gogoi, Ramakrishna Sistla, Ashutosh Kumar
Neuropathic pain is triggered by the lesions to peripheral nerves which alter their structure and function. Neuroprotective approaches that limit the pathological changes and improve the behavioral outcome have been well explained in different experimental models of neuropathy but translation of such strategies to clinics has been disappointing. Experimental evidences revealed the role of free radicals, especially peroxynitrite after the nerve injury. They provoke oxidative DNA damage and consequent over-activation of the poly(ADP-ribose) polymerase (PARP) upregulates pro-inflammatory pathways, causing bioenergetic crisis and neuronal death...
October 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/27903819/towards-designing-new-nano-scale-protein-architectures
#11
REVIEW
Jana Aupič, Fabio Lapenta, Žiga Strmšek, Roman Jerala
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903453/repair-of-8-oxo-7-8-dihydroguanine-in-prokaryotic-and-eukaryotic-cells-properties-and-biological-roles-of-the-fpg-and-ogg1-dna-n-glycosylases
#12
Serge Boiteux, Franck Coste, Bertrand Castaing
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases...
November 26, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27897116/the-molecular-mechanisms-and-the-role-of-hnrnp-k-protein-post-translational-modification-in-dna-damage-repair
#13
Jing Lu, Feng-Hou Gao
DNA damage repair is a kind of cellular self-protection mechanism that some relevant proteins are activated when DNA damage response happens in order to maintain the intracellular function stability and structure integrity. Post-translational modifications (PTMs) of proteins can rapidly confers to them more complicated structure and sophisticated function by covalently combining with different small molecules with target proteins, which in turn plays an important regulatory role in DNA damage repair. It was reported that heterogeneous nuclear ribonucleoprotein K (hnRNP K) could be involved in DNA damage repair process under the regulation of its many post-translational modifications, including methylation, ubiquitination, sumoylation and phosphorylation...
November 29, 2016: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#14
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27894771/radiation-induced-dna-protein-cross-links-mechanisms-and-biological-significance
#15
Toshiaki Nakano, Xu Xu, Amir M H Salem, Mahmoud I Shoulkamy, Hiroshi Ide
Ionizing radiation produces various DNA lesions such as base damage, DNA single-strand breaks (SSBs), DNA double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, the biological significance of DPCs remains elusive. In this article, we focus on radiation-induced DPCs and review the current understanding of their induction, properties, repair, and biological consequences. When cells are irradiated, the formation of base damage, SSBs, and DSBs are promoted in the presence of oxygen. Conversely, that of DPCs is promoted in the absence of oxygen, suggesting their importance in hypoxic cells, such as those present in tumors...
November 25, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27891621/animal-cryptochromes-divergent-roles-in-light-perception-circadian-timekeeping-and-beyond
#16
Alicia K Michael, Jennifer L Fribourgh, Russell N Van Gelder, Carrie L Partch
Cryptochromes are evolutionarily related to the light-dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: Drosophila-like CRYs that act as non-visual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate-like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors...
November 28, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27891613/a-review-of-spectroscopic-and-biophysical-chemical-studies-of-the-complex-of-cpd-photolyase-and-cryptochrome-dash-with-substrate-dna
#17
Johannes P M Schelvis, Yvonne M Gindt
CPD photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair cyclobutane pyrimidine dimers (CPD) on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, though some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue-light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH...
November 28, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27888239/the-increasing-diversity-of-functions-attributed-to-the-safb-family-of-rna-dna-binding-proteins
#18
REVIEW
Michael Norman, Caroline Rivers, Youn-Bok Lee, Jalilah Idris, James Uney
RNA-binding proteins play a central role in cellular metabolism by orchestrating the complex interactions of coding, structural and regulatory RNA species. The SAFB (scaffold attachment factor B) proteins (SAFB1, SAFB2 and SAFB-like transcriptional modulator, SLTM), which are highly conserved evolutionarily, were first identified on the basis of their ability to bind scaffold attachment region DNA elements, but attention has subsequently shifted to their RNA-binding and protein-protein interactions. Initial studies identified the involvement of these proteins in the cellular stress response and other aspects of gene regulation...
December 1, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27888145/critical-role-of-hnrnp-a1-in-activating-kras-transcription-in-pancreatic-cancer-cells-a-molecular-mechanism-involving-g4-dna
#19
REVIEW
Susanna Cogoi, Valentina Rapozzi, Sabina Cauci, Luigi E Xodo
KRAS is one of the most mutated genes in human cancer. Its crucial role in the tumourigenesis of pancreatic ductal adenocarcinoma (PDAC) has been widely demonstrated. As this deadly cancer does not sufficiently respond to conventional chemotherapies, it is important to increase our knowledge of pancreatic cancer biology, in particular how oncogenic KRAS is regulated. The promoter of KRAS contains a GA-element composed of runs of guanines that fold into a G4 structure. This unusual DNA conformation is recognized by several nuclear proteins, including MAZ and hnRNP A1...
November 22, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27885504/plant-dicer-like-proteins-double-stranded-rna-cleaving-enzymes-for-small-rna-biogenesis
#20
Akihito Fukudome, Toshiyuki Fukuhara
Dicer, a double-stranded RNA (dsRNA)-specific endoribonuclease, plays an essential role in triggering both transcriptional and post-transcriptional gene silencing in eukaryotes by cleaving dsRNAs or single-stranded RNAs bearing stem-loop structures such as microRNA precursor transcripts into 21- to 24-nt small RNAs. Unlike animals, plants have evolved to utilize at least four Dicer-like (DCL) proteins. Extensive genetic studies have revealed that each DCL protein participates in a specific gene silencing pathway, with some redundancy...
November 24, 2016: Journal of Plant Research
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