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Total 54642 results found since Jan 2013.

On the Mechanism of Homology Search by RecA Protein Filaments.
Abstract Genetic stability is a key factor in maintaining, survival, and reproduction of biological cells. It relies on many processes, but one of the most important is a homologous recombination, in which the repair of breaks in double-stranded DNA molecules is taking place with a help of several specific proteins. In bacteria, this task is accomplished by RecA proteins that are active as nucleoprotein filaments formed on single-stranded segments of DNA. A critical step in the homologous recombination is a search for a corresponding homologous region on DNA, which is called a homology search. Recent single-molecu...
Source: Biophysical Journal - March 13, 2017 Category: Physics Authors: Kochugaeva MP, Shvets AA, Kolomeisky AB Tags: Biophys J Source Type: research

Evaluation of information on the Internet regarding surgical mesh for hernia repair: analysis of websites found through three popular search engines
ConclusionsThese results emphasize the challenges of using an Internet search engine to find comprehensive and appropriate information regarding surgical mesh. This manuscript underscores the importance for physicians to direct patients toward specific websites to mitigate their exposure to websites that are biased and not appropriate for patients searching for an accurate and comprehensive overview of surgical mesh.
Source: Hernia - February 7, 2021 Category: Sports Medicine Source Type: research

Internet search by the patients undergoing  hernia surgery about the disease and surgeon selection
ConclusionsLess than two-thirds of the hernia patients make Internet search about their disease. Higher education level, younger age, patient ’s preference for minimally invasive surgery and living in a city positively affect Internet search rates.
Source: Hernia - January 12, 2022 Category: Sports Medicine Source Type: research

In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search
Nat Struct Mol Biol. 2023 Aug 21. doi: 10.1038/s41594-023-01065-w. Online ahead of print.ABSTRACTHomologous recombination (HR) is a major pathway to repair DNA double-strand breaks (DSB). HR uses an undamaged homologous DNA sequence as a template for copying the missing information, which requires identifying a homologous sequence among megabases of DNA within the crowded nucleus. In eukaryotes, the conserved Rad51-single-stranded DNA nucleoprotein filament (NPF) performs this homology search. Although NPFs have been extensively studied in vitro by molecular and genetic approaches, their in vivo formation and dynamics coul...
Source: Mol Biol Cell - August 21, 2023 Category: Molecular Biology Authors: Siyu Liu Judith Min é-Hattab Marie Villemeur Rapha ël Guerois Henrik Dahl Pinholt Leonid A Mirny Angela Taddei Source Type: research

Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S).
Abstract The advent of complete-genome genotyping across phenotype cohorts has provided a rich source of information for bioinformaticians. However the search for SNPs from this data is generally performed on a study-by-study case without any specific hypothesis of the location for SNPs that are predictive for the phenotype. We have designed a method whereby very large SNP lists (several gigabytes in size), combining several genotyping studies at once, can be sorted and traced back to their ultimate consequence in protein structure. Given a working hypothesis, researchers are able to easily search whole genome gen...
Source: DNA Repair - July 4, 2013 Category: Genetics & Stem Cells Authors: Swett RJ, Elias A, Miller JA, Dyson GE, Andrés Cisneros G Tags: DNA Repair (Amst) Source Type: research

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database
Conclusions: Annokey facilitates the identification of genes related to an area of interest, a task which can be onerous if performed manually on a large number of genes. Annokey provides a way to capitalize on the high quality information provided by the Entrez Gene database allowing both scalability and compatibility with automated analysis pipelines, thus offering the potential to significantly enhance research productivity.
Source: Epidemiologic Perspectives and Innovations - June 26, 2014 Category: Epidemiology Authors: Daniel J ParkTú Nguyen-DumontSori KangKarin VerspoorBernard J Pope Source Type: research

Large-Scale Recurrent Neural Network Based Modelling of Gene Regulatory Network Using Cuckoo Search-Flower Pollination Algorithm.
Authors: Mandal S, Khan A, Saha G, Pal RK Abstract The accurate prediction of genetic networks using computational tools is one of the greatest challenges in the postgenomic era. Recurrent Neural Network is one of the most popular but simple approaches to model the network dynamics from time-series microarray data. To date, it has been successfully applied to computationally derive small-scale artificial and real-world genetic networks with high accuracy. However, they underperformed for large-scale genetic networks. Here, a new methodology has been proposed where a hybrid Cuckoo Search-Flower Pollination Algorithm...
Source: Advances in Bioinformatics - March 20, 2016 Category: Bioinformatics Tags: Adv Bioinformatics Source Type: research

MINIREVIEW: The Homology Search Molecular Biophysics
Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechan...
Source: Journal of Biological Chemistry - May 26, 2016 Category: Chemistry Authors: Greene, E. C. Tags: Minireviews Source Type: research

Failure of Nasa's Kepler telescope puts search for another Earth in peril
Telescope orbiting the Sun has lost part of its stabilising system, making it too inaccurate to hunt for another EarthNasa's hunt for other planets that could harbour life faces a setback: its Kepler space telescope is broken and, since it is in orbit around the Sun, may prove impossible to fix.The failure of stabilising systems on the spacecraft could mean an end to the $600m mission's search, although Kepler has already outlived official expectations and the space agency is not yet ready to call it quits. The telescope has discovered scores of planets but only two so far that show strong signs of being habitable."I would...
Source: Guardian Unlimited Science - May 16, 2013 Category: Science Tags: United States Nasa Satellites World news guardian.co.uk Space Science Source Type: news

Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging
The ability of DNA glycosylases to rapidly and efficiently detect lesions among a vast excess of nondamaged DNA bases is vitally important in base excision repair (BER). Here, we use single molecule imaging by atomic force microscopy (AFM) supported by a 2-aminopurine fluorescence base flipping assay to study damage search by human thymine DNA glycosylase (hTDG), which initiates BER of mutagenic and cytotoxic G:T and G:U mispairs in DNA. Our data reveal an equilibrium between two conformational states of hTDG–DNA complexes, assigned as search complex (SC) and interrogation complex (IC), both at target lesions and und...
Source: Nucleic Acids Research - March 12, 2015 Category: Research Authors: Buechner, C. N., Maiti, A., Drohat, A. C., Tessmer, I. Tags: Genome integrity, repair and replication Source Type: research

In Search of Genes that Were Lost in Longer-Lived Mammals
In conclusion, the developed method and its software allowed us to identify a short list of presumably lost genes associated with a long lifespan in Euarchontoglires. The predicted lost genes largely demonstrate specific expressions in reproductive organs, which agrees with Williams' hypothesis concerning the reallocation of the physiological resources of the body between self-maintenance and reproduction (transition from r-strategy to К-strategy in the species evolution). The loss of some predicted vomeronasal and olfactory receptor genes in human and naked mole-rat conforms to their specific anatomical features. We sugg...
Source: Fight Aging! - November 26, 2019 Category: Research Authors: Reason Tags: Daily News Source Type: blogs

Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.
Abstract To perform their functions, transcription factors and DNA-repair/modifying enzymes randomly search DNA in order to locate their specific targets on DNA. Discrete-state stochastic kinetic models have been developed to explain how the efficiency of the search process is influenced by the molecular properties of proteins and DNA as well as by other factors such as molecular crowding. These theoretical models not only offer explanations on the relation of microscopic processes to macroscopic behavior of proteins, but also facilitate the analysis and interpretation of experimental data. In this review article,...
Source: Biophysical Chemistry - December 10, 2020 Category: Chemistry Authors: Iwahara J, Kolomeisky AB Tags: Biophys Chem Source Type: research

GSE179641 Cohesin regulates homology search during recombinational DNA repair Hi-C
This study identifies multiple direct and indirect ways by which cohesin regulates homology search during HR repair. 
Source: GEO: Gene Expression Omnibus - July 21, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Saccharomyces cerevisiae W303 Source Type: research