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Specialty: Biochemistry

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Total 109410 results found since Jan 2013.

Molecular symmetry-constrained systematic search approach to structure solution of the coiled-coil SRGAP2 F-BARx domain
SRGAP2 (Slit – Robo GTPase-activating protein 2) is a cytoplasmic protein found to be involved in neuronal branching, restriction of neuronal migration and restriction of the length and density of dendritic postsynaptic spines. The extended F-BAR (F-BARx) domain of SRGAP2 generates membrane protrusions when expressed in COS-7 cells, while most F-BARs induce the opposite effect: membrane invaginations. As a first step to understand this discrepancy, the F-BARx domain of SRGAP2 was isolated and crystallized after co-expression with the carboxy domains of the protein. Diffraction data were collected from two significantly n...
Source: Acta Crystallographica Section D - November 28, 2016 Category: Biochemistry Authors: Sporny, M. Guez-Haddad, J. Waterman, D.G. Isupov, M.N. Opatowsky, Y. Tags: exhaustive search SRGAP2 F-BAR coiled coil molecular replacement research papers Source Type: research

Iodine status in Danish pregnant and breastfeeding women including studies of some challenges in urinary iodine status evaluation
Publication date: Available online 1 December 2014 Source:Journal of Trace Elements in Medicine and Biology Author(s): Stine Linding Andersen , Louise Kolding Sørensen , Anne Krejbjerg , Margrethe Møller , Ditte Marie Klitbo , Susanne B Nøhr , Klaus Michael Pedersen , Peter Laurberg Denmark was previously iodine deficient with regional differences. Moderate iodine deficiency appeared in West Denmark and mild iodine deficiency in East Denmark and also Danish pregnant and breastfeeding women suffered from iodine deficiency. The Danish mandatory iodine fortification of salt was introduced in the year 2000 and has increas...
Source: Journal of Trace Elements in Medicine and Biology - December 2, 2014 Category: Biochemistry Source Type: research

Use of human milk in the assessment of toxic metals exposure and essential element status in breastfeeding women and their infants in coastal Croatia
In conclusion, the levels of main toxic metals Cd, Pb and Hg and essential elements Ca, Fe, Cu, Zn and Se in maternal blood and three types of breast milk samples in the studied area of coastal Croatia showed no risk of disrupted essential element levels with regard of toxic metal exposure in both breastfeeding women and their infants.
Source: Journal of Trace Elements in Medicine and Biology - August 2, 2016 Category: Biochemistry Source Type: research

Use of human milk in the assessment of toxic metal exposure and essential element status in breastfeeding women and their infants in coastal Croatia
In conclusion, the levels of main toxic metals Cd, Pb and Hg and essential elements Ca, Fe, Cu, Zn and Se in maternal blood and three types of breast milk samples in the studied area of coastal Croatia showed no risk of disrupted essential element levels with regard of toxic metal exposure in both breastfeeding women and their infants.
Source: Journal of Trace Elements in Medicine and Biology - August 9, 2016 Category: Biochemistry Source Type: research

Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics
This study highlights the use of different database search engines (Comet, X! Tandem, ProteinProspector, and ProteinPilot™) and their respective algorithms to analyse 135 raw tandem mass spectrometry data files from 15 types of pork-based food products. This is the first attempt that has compared different database search engines in the context of halal proteomics to ensure the effectiveness of controlling the FDR. Previous studies were just focused on the advantages of a certain algorithm over another. Moreover, other previous studies also have mainly reported the use of mass spectrometry-based shotgun proteomics for me...
Source: Journal of Proteomics - April 24, 2021 Category: Biochemistry Authors: Siti Hajar Amir Mohd Hafis Yuswan Wan Mohd Aizat Muhammad Kamaruzaman Mansor Mohd Nasir Mohd Desa Yus Aniza Yusof Lai Kok Song Shuhaimi Mustafa Source Type: research

AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results
J Proteomics. 2021 Aug 10:104350. doi: 10.1016/j.jprot.2021.104350. Online ahead of print.ABSTRACTCharacterization of post-translational modifications is among the most challenging tasks in tandem mass spectrometry-based proteomics which has yet to find an efficient solution. The ultra-tolerant (open) database search attempts to meet this challenge. However, interpretation of the mass shifts observed in open search still requires an effective and automated solution. We have previously introduced the AA_stat tool for analysis of amino acid frequencies at different mass shifts and generation of hypotheses on unaccounted in v...
Source: Journal of Proteomics - August 14, 2021 Category: Biochemistry Authors: Lev I Levitsky Julia A Bubis Mikhail V Gorshkov Irina A Tarasova Source Type: research

ReCom: A semi-supervised approach to ultra-tolerant database search for improved identification of modified peptides
We present a proof-of-concept study using Comet-ReCom, an improved version of Comet-PTM. Comet-ReCom increased identification performance of Comet-PTM by 68%. This increased performance of Comet-ReCom to score the MS/MS spectrum comes in parallel with a significantly better assignation of the monoisotopic peak of the precursor peptide in the MS spectrum, even in cases of peptide coelution. Our data demonstrate that open searches using ultra-tolerant mass windows can benefit from using a semi-supervised approach that takes advantage from previous knowledge on the nature of protein modifications. SIGNIFICANCE: The present st...
Source: Journal of Proteomics - July 18, 2023 Category: Biochemistry Authors: Andrea Laguillo-G ómez Enrique Calvo Noa Mart ín-Cófreces Marta Lozano-Prieto Francisco S ánchez-Madrid Jes ús Vázquez Source Type: research

Is exclusive breastfeeding ensuring an optimal micronutrient status and psychomotor development in infants?
PMID: 24845709 [PubMed - as supplied by publisher]
Source: Clinical Biochemistry - May 17, 2014 Category: Biochemistry Authors: Bjørke-Monsen AL Tags: Clin Biochem Source Type: research

Oxytocin, a main breastfeeding hormone, prevents hypertension acquired in utero: A therapeutics preview
Publication date: January 2017 Source:Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1861, Issue 1, Part A Author(s): Froylán Vargas-Martínez, Richard J. Schanler, Steven A. Abrams, Keli M. Hawthorne, Susan Landers, José Guzman-Bárcenas, Onofre Muñoz, Tore Henriksen, Maria Petersson, Kerstin Uvnäs-Moberg, Ismael Jiménez-Estrada Hypertension is a major risk factor for ischemic heart disease and stroke, leading causes of morbidity and death worldwide. Intrauterine growth restriction (IUGR), caused by an excess of glucocorticoid exposure to the fetus, produces an imbalance in oxidative stress altering ...
Source: Biochimica et Biophysica Acta (BBA) General Subjects - October 28, 2016 Category: Biochemistry Source Type: research

The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes
Biochem Soc Trans. 2021 May 18:BST20200709. doi: 10.1042/BST20200709. Online ahead of print.ABSTRACTTranscription factors (TFs) regulate transcription of their target genes by identifying and binding to regulatory regions of the genome among billions of potential non-specific decoy sites, a task that is often presented as a 'needle in the haystack' challenge. The TF search process is now well understood in bacteria, but its characterization in eukaryotes needs to account for the complex organization of the nuclear environment. Here we review how live-cell single molecule tracking is starting to shed light on the TF search ...
Source: Biochemical Society Transactions - May 18, 2021 Category: Biochemistry Authors: Matteo Mazzocca Tom Fillot Alessia Loffreda Daniela Gnani Davide Mazza Source Type: research

Reprint of "pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data".
In this study, we developed a new algorithm called Alioth, to be integrated into the search engine of pFind, for fast and accurate unrestricted database search on high-resolution MS/MS data. An ion index is constructed for both peptide precursors and fragment ions, by which arbitrary digestions and a single site of any modifications and mutations can be searched efficiently. A new re-ranking algorithm is used to distinguish the correct peptide-spectrum matches from random ones. The algorithm is tested on several HCD datasets and the interpretation rate of MS/MS spectra using Alioth is as high as 60%-80%. Peptides from semi...
Source: Journal of Proteomics - July 28, 2015 Category: Biochemistry Authors: Chi H, He K, Yang B, Chen Z, Sun RX, Fan SB, Zhang K, Liu C, Yuan ZF, Wang QH, Liu SQ, Dong MQ, He SM Tags: J Proteomics Source Type: research

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.
Abstract In mass spectrometry-based shotgun proteomics, protein identifications are usually the desired result. However, most of the analytical methods are based on the identification of reliable peptides and not the direct identification of intact proteins. Thus, assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Currently, different protein inference algorithms and tools are available for the proteomics community. Here, we evaluated five software tools for protein inference (PIA, ProteinProphet, Fido, Prote...
Source: Journal of Proteomics - August 3, 2016 Category: Biochemistry Authors: Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y Tags: J Proteomics Source Type: research