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Total 131414 results found since Jan 2013.

Aldo-keto reductases in retinoid metabolism: Search for substrate specificity and inhibitor selectivity.
Abstract Biological activity of natural retinoids requires the oxidation of retinol to retinoic acid (RA) and its binding to specific nuclear receptors in target tissues. The first step of this pathway, the reversible oxidoreduction of retinol to retinaldehyde, is essential to control RA levels. The enzymes of retinol oxidation are NAD-dependent dehydrogenases of the cytosolic medium-chain (MDR) and the membrane-bound short-chain (SDR) dehydrogenases/reductases. Retinaldehyde reduction can be performed by SDR and aldo-keto reductases (AKR), while its oxidation to RA is carried out by aldehyde dehydrogenases (ALDH)...
Source: Chemico-Biological Interactions - December 3, 2012 Category: Molecular Biology Authors: Porté S, Xavier Ruiz F, Giménez J, Molist I, Alvarez S, Domínguez M, Alvarez R, de Lera AR, Parés X, Farrés J Tags: Chem Biol Interact Source Type: research

Susceptibility gene search for nephropathy and related traits in Mexican-Americans.
Abstract The rising global epidemic of diabetic nephropathy (DN) will likely lead to increase in the prevalence of cardiovascular morbidity and mortality posing a serious burden for public health care. Despite greater understanding of the etiology of diabetes and the development of novel treatment strategies to control blood glucose levels, the prevalence and incidence rate of DN is increasing especially in minority populations including Mexican-Americans. Mexican-Americans with type 2 diabetes (T2DM) are three times more likely to develop microalbuminuria, and four times more likely to develop clinical proteinuri...
Source: Molecular Biology Reports - September 22, 2013 Category: Molecular Biology Authors: Thameem F, Kawalit IA, Adler SG, Abboud HE Tags: Mol Biol Rep Source Type: research

DNA glycosylases search for and remove oxidized DNA bases
This review article presents, an overview of the DNA glycosylases that recognize oxidized DNA bases using the Fpg/Nei family of DNA glycosylases as models for how structure can inform function. For example, even though human NEIL1 and the plant and fungal orthologs lack the zinc finger shown to be required for binding, DNA crystal structures revealed a “zincless finger” with the same properties. Moreover, the “lesion recognition loop” is not involved in lesion recognition, rather, it stabilizes 8‐oxoG in the active site pocket. Unlike the other Fpg/Nei family members, Neil3 lacks two of the three void‐filling r...
Source: Environmental and Molecular Mutagenesis - October 1, 2013 Category: Molecular Biology Authors: Susan S. Wallace Tags: Review Source Type: research

Heparan sulfate 3-O-sulfation: A rare modification in search of a function.
Abstract Many protein ligands bind to heparan sulfate, which results in their presentation, protection, oligomerization or conformational activation. Binding depends on the pattern of sulfation and arrangement of uronic acid epimers along the chains. Sulfation at the C3 position of glucosamine is a relatively rare, yet biologically significant modification, initially described as a key determinant for binding and activation of antithrombin and later for infection by Type I Herpes Simplex virus. In mammals, a family of seven heparan sulfate 3-O-sulfotransferases installs sulfate groups at this position and constitu...
Source: Matrix Biology - December 19, 2013 Category: Molecular Biology Authors: Thacker BE, Xu D, Lawrence R, Esko JD Tags: Matrix Biol Source Type: research

Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data.
Abstract The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of PPI...
Source: Molecular and Cellular Proteomics : MCP - May 7, 2014 Category: Molecular Biology Authors: Boyanova D, Nilla S, Klau GW, Dandekar T, Mueller T, Dittrich M Tags: Mol Cell Proteomics Source Type: research

Search for the Most 'primitive' Membranes and Their Reinforcers: A Review of the Polyprenyl Phosphates Theory.
Abstract Terpenoids have an essential function in present-day cellular membranes, either as membrane reinforcers in Eucarya and Bacteria or as principal membrane constituents in Archaea. We have shown that some terpenoids, such as cholesterol and α, ω-dipolar carotenoids reinforce lipid membranes by measuring the water permeability of unilamellar vesicles. It was possible to arrange the known membrane terpenoids in a 'phylogenetic' sequence, and a retrograde analysis led us to conceive that single-chain polyprenyl phosphates might have been 'primitive' membrane constituents. By using an optical microscopy, we ha...
Source: Origins of Life and Evolution of the Biosphere - October 30, 2014 Category: Molecular Biology Authors: Nakatani Y, Ribeiro N, Streiff S, Gotoh M, Pozzi G, Désaubry L, Milon A Tags: Orig Life Evol Biosph Source Type: research

StemSearch: RNA search tool based on stem identification and indexing
Publication date: 1 October 2014 Source:Methods, Volume 69, Issue 3 Author(s): Nimrod Milo , Sivan Yogev , Michal Ziv-Ukelson The discovery and functional analysis of noncoding RNA (ncRNA) systems in different organisms motivates the development of tools for aiding ncRNA research. Several tools exist that search for occurrences of a given RNA structural profile in genomic sequences. Yet, there is a need for an “RNA BLAST” tool, i.e., a tool that takes a putative functional RNA sequence as input, and efficiently searches for similar sequences in genomic databases, taking into consideration potential secondary structur...
Source: Methods - November 3, 2014 Category: Molecular Biology Source Type: research

Molecular fingerprint similarity search in virtual screening
Publication date: 1 January 2015 Source:Methods, Volume 71 Author(s): Adrià Cereto-Massagué , María José Ojeda , Cristina Valls , Miquel Mulero , Santiago Garcia-Vallvé , Gerard Pujadas Molecular fingerprints have been used for a long time now in drug discovery and virtual screening. Their ease of use (requiring little to no configuration) and the speed at which substructure and similarity searches can be performed with them – paired with a virtual screening performance similar to other more complex methods – is the reason for their popularity. However, there are many types of fingerprints, each representing a d...
Source: Methods - December 25, 2014 Category: Molecular Biology Source Type: research

Next generation sequencing search for uromodulin gene variants related with impaired renal function.
Abstract Uromodulin gene (UMOD) mutations have been linked to rare forms of mendelian dominant medullary cystic kidney disease and familial hyperuricemia. In addition, common single nucleotide polymorphisms in the UMOD promoter have been associated with the risk for impaired renal function and chronic kidney disease. Our main purpose was to identify UMOD variants related with impaired renal function in an elderly population. The UMOD gene was next generation sequenced in a total of 100 healthy individuals with normal or reduced renal function [measured as the rate of estimated glomerular filtration (eGFR)]. The i...
Source: Molecular Biology Reports - June 4, 2015 Category: Molecular Biology Authors: Gómez J, Díaz-Corte C, Tranche S, Alvarez F, Iglesias S, Alonso B, Coto E Tags: Mol Biol Rep Source Type: research

Polymorphism of brain neurotransmitter system genes: Search for pharmacogenetic markers of haloperidol efficiency in Russians and Tatars.
Abstract cccccAntipsychotics are the primary drugs for treating schizophrenia, a severe psychical disease that affects approximately 1% of the population. The mechanism of antipsychotic action has not yet been completely clarified. A number of studies in the field of pharmacogenetics have confirmed the huge influence of several neurotransmitter systems on the efficiency and development of side effects. In the present work, we studied whether there are associations between nine polymorphic variants of five genes of dopaminergic and serotonergic systems (DRD4, HTR2A, TPH1, SLC18A1, and COMT) in schizophrenia patient...
Source: Molekuliarnaia Biologiia - November 1, 2015 Category: Molecular Biology Authors: Gareeva AE, Kinyasheva KO, Galaktionova DY, Sabirov ET, Valinourov RG, Chudinov AV, Zasedatelev AS, Nasedkina TV, Khusnutdinova AE Tags: Mol Biol (Mosk) Source Type: research

Anti-methicillin-resistant Staphylococcus aureus (MRSA) activity of Rubiaceae, Fabaceae and Poaceae plants: A search for new sources of useful alternative antibacterials against MRSA infections.
In this study, we evaluated the effects of the extracts of the leaves of species from the Rubiaceae (Galium aparine L. and Asperula arvensis L.), Fabaceae (Lathyrus aphaca L. and Vicia narbonensis L.) and Poaceae (Digitaria sanguinalis (L.) Scop. and Hordeum murinum L.) plant families on a wide and extensive panel of isolated methicillin-resistant Staphylococcus aureus strains (MRSA). The effects of the methanolic leaf extracts of Rubiaceae, Fabaceae and Poaceae plants on MRSA were evaluated by the disc diffusion assay and the broth dilution method. Among a total of 177 S. aureus isolates, 92 (51.97%) were found to be meth...
Source: Cellular and Molecular Biology - September 3, 2016 Category: Molecular Biology Tags: Cell Mol Biol (Noisy-le-grand) Source Type: research

Erratum to: A representation of a compressed de Bruijn graph for  pan-genome analysis that enables search.
Erratum to: A representation of a compressed de Bruijn graph for pan-genome analysis that enables search. Algorithms Mol Biol. 2016;11:28 Authors: Beller T, Ohlebusch E Abstract [This corrects the article DOI: 10.1186/s13015-016-0083-7.]. PMID: 27933096 [PubMed - in process]
Source: Algorithms for Molecular Biology : AMB - December 11, 2016 Category: Molecular Biology Authors: Beller T, Ohlebusch E Tags: Algorithms Mol Biol Source Type: research

Pyrimidine Metabolism in Schistosomes: A comparison with Other Parasites and the Search for Potential Chemotherapeutic Targets
Publication date: Available online 21 July 2017 Source:Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology Author(s): Mahmoud H. el Kouni Schistosomes are responsible for the parasitic disease schistosomiasis, an acute and chronic parasitic ailment that affects more than 240 million people in 70 countries worldwide. It is the second most devastating parasitic disease after malaria. At least 200,000 deaths per year are associated with the disease. In the absence of the availability of vaccines, chemotherapy is the main stay for combating schistosomiasis. The antischistosomal arsenal is curren...
Source: Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology - July 21, 2017 Category: Molecular Biology Source Type: research

Search for Functionally Significant Motifs and Amino Acid Residues of Actin.
Abstract The scientific interest to the structural and functional properties of actin is determined by its abundance in cells. Being an important component of the cytoskeleton, actin is involved in many protein-protein interactions. Using crystal structures and molecular models, we have mapped the amino acid residues that are involved in these interactions and form the ATP-binding site of the actin monomer. Moreover, using mass spectrometry and high-performance liquid chromatography methods, we have discovered the regions of the amino acid sequence of actin that form the core of the actin fibril. According to the ...
Source: Molekuliarnaia Biologiia - January 1, 2018 Category: Molecular Biology Authors: Tikhomirova TS, Ievlev RS, Suvorina MY, Bobyleva LG, Vikhlyantsev IM, Surin AK, Galzitskaya OV Tags: Mol Biol (Mosk) Source Type: research

SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space
We present SVDquest∗, a new method for constructing species trees using site patterns that is guaranteed to produce species trees that satisfy at least as many quartet trees as SVDquartets+PAUP∗. We show that SVDquest∗ is competitive with ASTRAL and ASTRID (two leading summary methods) in terms of topological accuracy, and tends to be more accurate than ASTRAL and ASTRID under conditions with relatively high gene tree estimation error. SVDquest∗ is available in open source form at https://github.com/pranjalv123/SVDquest. Graphical abstract
Source: Molecular Phylogenetics and Evolution - March 10, 2018 Category: Molecular Biology Source Type: research