scholarly journals A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

2017 ◽  
Vol 284 (1855) ◽  
pp. 20170544 ◽  
Author(s):  
Michael Buckley ◽  
Stacey Warwood ◽  
Bart van Dongen ◽  
Andrew C. Kitchener ◽  
Phillip L. Manning
Keyword(s):  
Peptide Sequence ◽  
Bacterial Biofilms ◽  
Sequence Information ◽  
Cross Contamination ◽  
Laboratory Practice ◽  
True Nature ◽  
Struthio Camelus ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Single Peptide

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus . The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.

scholarly journals CirBiTree: Citrullination Site Inference Based on a Fuzzy Neural Network and Flexible Neural Tree

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Chuandong Song ◽  
Haifeng Wang
Keyword(s):  
Neural Network ◽  
Fuzzy Neural Network ◽  
Classification Model ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Post Translational Modification ◽  
Fuzzy Neural ◽  
Human Complex ◽  
Better Than

Emerging evidence demonstrates that post-translational modification plays an important role in several human complex diseases. Nevertheless, considering the inherent high cost and time consumption of classical and typical in vitro experiments, an increasing attention has been paid to the development of efficient and available computational tools to identify the potential modification sites in the level of protein. In this work, we propose a machine learning-based model called CirBiTree for identification the potential citrullination sites. More specifically, we initially utilize the biprofile Bayesian to extract peptide sequence information. Then, a flexible neural tree and fuzzy neural network are employed as the classification model. Finally, the most available length of identified peptides has been selected in this model. To evaluate the performance of the proposed methods, some state-of-the-art methods have been employed for comparison. The experimental results demonstrate that the proposed method is better than other methods. CirBiTree can achieve 83.07% in sn%, 80.50% in sp, 0.8201 in F1, and 0.6359 in MCC, respectively.

scholarly journals Surface Characterization and Physiochemical Evaluation of P(3HB-co-4HB)-Collagen Peptide Scaffolds with Silver Sulfadiazine as Antimicrobial Agent for Potential Infection-Resistance Biomaterial

Polymers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 2454
Author(s):  
Sevakumaran Vigneswari ◽  
Tana Poorani Gurusamy ◽  
Wan M. Khairul ◽  
Abdul Khalil H.P.S. ◽  
Seeram Ramakrishna ◽  
...  
Keyword(s):  
Controlled Release ◽  
Antimicrobial Agent ◽  
Surface Characterization ◽  
Biomedical Application ◽  
Physical And Mechanical Properties ◽  
Silver Sulfadiazine ◽  
Salt Leaching ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Peptide Scaffolds

Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] is a bacterial derived biopolymer widely known for its unique physical and mechanical properties to be used in biomedical application. In this study, antimicrobial agent silver sulfadiazine (SSD) coat/collagen peptide coat-P(3HB-co-4HB) (SCCC) and SSD blend/collagen peptide coat-P(3HB-co-4HB) scaffolds (SBCC) were fabricated using a green salt leaching technique combined with freeze-drying. This was then followed by the incorporation of collagen peptides at various concentrations (2.5–12.5 wt.%) to P(3HB-co-4HB) using collagen-coating. As a result, two types of P(3HB-co-4HB) scaffolds were fabricated, including SCCC and SBCC scaffolds. The increasing concentrations of collagen peptides from 2.5 wt.% to 12.5 wt.% exhibited a decline in their porosity. The wettability and hydrophilicity increased as the concentration of collagen peptides in the scaffolds increased. In terms of the cytotoxic results, MTS assay demonstrated the L929 fibroblast scaffolds adhered well to the fabricated scaffolds. The 10 wt.% collagen peptides coated SCCC and SBCC scaffolds displayed highest cell proliferation rate. The antimicrobial analysis of the fabricated scaffolds exhibited 100% inhibition towards various pathogenic microorganisms. However, the SCCC scaffold exhibited 100% inhibition between 12 and 24 h, but the SBCC scaffolds with SSD impregnated in the scaffold had controlled release of the antimicrobial agent. Thus, this study will elucidate the surface interface-cell interactions of the SSD-P(3HB-co-4HB)-collagen peptide scaffolds and controlled release of SSD, antimicrobial agent.

Purification, Characterization, and Heterologous Expression in Fusarium venenatum of a Novel Serine Carboxypeptidase from Aspergillus oryzae

1999 ◽  
Vol 65 (8) ◽  
pp. 3298-3303 ◽  
Author(s):  
Alexander M. Blinkovsky ◽  
Tony Byun ◽  
Kimberly M. Brown ◽  
Elizabeth J. Golightly
Keyword(s):  
Molecular Weight ◽  
Aspergillus Oryzae ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Peptide Sequence ◽  
Sequence Information ◽  
Serine Carboxypeptidase ◽  
Recombinant Enzymes ◽  
Molecular Weights ◽  
Fusarium Venenatum

ABSTRACT A novel serine carboxypeptidase (EC 3.4.16.1 ) was found in anAspergillus oryzae fermentation broth and was purified to homogeneity. This enzyme has a molecular weight of ca. 67,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its specific activity is 21 U/mg for carbobenzoxy (Z)-Ala-Glu at pH 4.5 and 25°C. It has a ratio of bimolecular constants for Z-Ala-Lys and Z-Ala-Phe of 3.75. Optimal enzyme activity occurs at pH 4 to 4.5 and 58 to 60°C for Z-Ala-Ile. The N terminus of this carboxypeptidase is blocked. Internal fragments, obtained by cyanogen bromide digestion, were sequenced. PCR primers were then made based on the peptide sequence information, and the full-length gene sequence was obtained. An expression vector that contained the recombinant carboxypeptidase gene was used to transform aFusarium venenatum host strain. The transformed strain ofF. venenatum expressed an active recombinant carboxypeptidase. In F. venenatum, the recombinant carboxypeptidase produced two bands which had molecular weights greater than the molecular weight of the native carboxypeptidase from A. oryzae. Although the molecular weights of the native and recombinant enzymes differ, these enzymes have very similar kinetic parameters.

scholarly journals Effect of Oral Ingestion of Low-Molecular Collagen Peptides Derived from Skate (Raja Kenojei) Skin on Body Fat in Overweight Adults: A Randomized, Double-Blind, Placebo-Controlled Trial

Marine Drugs ◽  
2019 ◽  
Vol 17 (3) ◽  
pp. 157 ◽  
Author(s):  
Young Tak ◽  
Yun Kim ◽  
Jeong Lee ◽  
Yu-Hyun Yi ◽  
Young Cho ◽  
...  
Keyword(s):  
Body Fat ◽  
Animal Studies ◽  
Controlled Trial ◽  
Intervention Group ◽  
Control Group ◽  
Double Blind ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Skin Collagen ◽  
Overweight Adults

Recent animal studies found the potential of a collagen peptide derived from skate skin to have anti-obesity effects through the suppression of fat accumulation and regulation of lipid metabolism. However, no studies have yet been performed in humans. Here, this very first human randomized, placebo-controlled, and double-blinded study was designed to investigate the efficacy and tolerability of skate skin collagen peptides (SCP) for the reduction of body fat in overweight adults. Ninety healthy volunteers (17 men) aged 41.2 ± 10.4 years with a mean body mass index of 25.6 ± 1.9 kg/m2 were assigned to the intervention group (IG), which received 2000 mg of SCP per day or to the control group (CG) given the placebo for 12 weeks and 81 (90%) participants completed the study. Changes in body fat were evaluated using dual energy X-ray absorptiometry as a primary efficacy endpoint. After 12 weeks of the trial, the percentage of body fat and body fat mass (kg) in IG were found to be significantly better than those of subjects in CG (−1.2% vs. 2.7%, p = 0.024 and −1.2 kg vs. 0.3 kg, p = 0.025). Application of SCP was well tolerated and no notable adverse effect was reported from both groups. These results suggest the beneficial potential of SCP in the reduction of body fat in overweight adults.

scholarly journals LC provides peptide sequence information

2007 ◽  
Vol 79 (1) ◽  
pp. 23-23
Author(s):  
Elizabeth Zubritsky
Keyword(s):  
Peptide Sequence ◽  
Sequence Information

scholarly journals Prolonged Collagen Peptide Supplementation and Resistance Exercise Training Affects Body Composition in Recreationally Active Men

Nutrients ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 1154 ◽  
Author(s):  
Marius Kirmse ◽  
Vanessa Oertzen-Hagemann ◽  
Markus de Marées ◽  
Wilhelm Bloch ◽  
Petra Platen
Keyword(s):  
Body Composition ◽  
Exercise Training ◽  
Resistance Exercise ◽  
Fat Free Mass ◽  
Food Record ◽  
Resistance Exercise Training ◽  
Cross Sectional ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Double Blinded

We aimed to determine the effects of long-term collagen peptide (CP) supplementation and resistance exercise training (RET) on body composition, strength, and muscle fiber cross-sectional area (fCSA) in recreationally active men. Fifty-seven young men were randomly and double-blinded divided into a group receiving either collagen peptides (COL, 15 g/day) or a placebo (PLA). Strength testing, bioimpedance analysis, and muscle biopsies were used prior to and after an RET intervention. Food record protocols were performed during the RET intervention. The groups trained three times a week for 12 weeks. Baseline parameters showed no differences between groups, and the external training load and dietary food intake were also similar. COL showed a significant increase in fat-free mass (FFM) compared with the placebo group (p < 0.05). Body fat mass (BFM) was unchanged in COL, whereas a significant increase in BFM was observed in PLA. Both groups showed significant increases in all strength tests, with a trend for a slightly more pronounced effect in COL. The fCSA of type II muscle fibers increased significantly in both groups without differences between the two groups. We firstly demonstrated improved body composition in healthy, recreationally active men subsequent to prolonged CP supplementation in combination with RET. As the observed increase in FFM was not reflected in differences in fCSA hypertrophy between groups, we assume enhanced passive connective tissue adaptations in COL due to CP intake.

scholarly journals Adsorption and Absorption of Collagen Peptides to Polydimethlysiloxane and Its Influence on Platelet Adhesion Flow Assays

Micromachines ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 62
Author(s):  
Matthew G. Sorrells ◽  
Keith B. Neeves
Keyword(s):  
Platelet Adhesion ◽  
Amino Acid Sequences ◽  
Poloxamer 407 ◽  
Silicon Substrates ◽  
Force Microscopy ◽  
Glycoprotein Vi ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Peptide Adsorption ◽  
Von Willebrand

Collagen peptides are an alternative to animal derived collagens for platelet function studies under flow. The purpose of this study was to examine the use of collagen peptides in polydimethylsiloxane (PDMS) devices. Three collagen peptides with amino acid sequences and structures that capture von Willebrand factor and bind it with the platelet receptors integrin α2β1 and glycoprotein VI were patterned on glass, silicon, and PDMS. Each of these surfaces was also functionalized with tridecafluoro-1,1,2,2-tetrahydrooctyltrichlorosilane (FOTS). Surfaces were characterized by their ability to support platelet adhesion, topology by atomic force microscopy, contact angle, and peptides absorption. PDMS readily absorbs collagen peptides, depleting them from solution, thus reducing their adsorption to glass and silicon substrates when used for micropatterning. Treatment of PDMS with FOTS, but not bovine serum albumin or poloxamer 407, inhibits collagen peptide absorption and supports adsorption and platelet adhesion at venous and arterial shear rates. Similarly, FOTS treatment of glass or silicon supports collagen peptide adsorption even in the presence of untreated PDMS. In conclusion, PDMS acts as an absorptive sink for collagen peptides, rendering a non-adhesive surface for platelet adhesion and competing for peptides when used for micropatterning. The absorption of collagen peptides can be overcome by functionalization of PDMS with a fluorinated alkyl silane, thus allowing its use as a material for micropatterning or as a surface for platelet adhesion flow assays.

scholarly journals Collagen survival and its use for species identification in Holocene-lower Pleistocene bone fragments from British archaeological and paleontological sites

Antiqua ◽  
2011 ◽  
Vol 1 (1) ◽  
pp. 1 ◽  
Author(s):  
Mike Buckley ◽  
Matthew James Collins
Keyword(s):  
Species Identification ◽  
Collagen Type I ◽  
Systematic Investigation ◽  
Type I ◽  
Structural Protein ◽  
Collagen Peptides ◽  
Collagen Peptide ◽  
Peptide Mass ◽  
Lower Pleistocene ◽  
Bone Fragments

Proteins have long been known to persist in Quaternary bone fossils and are often targeted as a source of carbon used in radiocarbon dating and stable isotope analyses for determining provenance and obtaining dietary information. We have previously reported a technique using the dominant structural protein collagen (type I) as a source of genetic information for species identification in modern and relatively young (Holocene) archaeological samples. We report a systematic investigation of amino acid composition and collagen peptide mass fingerprints (PMF), for a range of samples dating back approximately 1.5 million years. Extrapolation from high temperature experimental decomposition rates predict that at a constant 10°C (the approximate mean annual air temperature in Britain today) it will take between 0.2 and 0.7 Ma for levels of collagen to fall to 1% of their original concentration in an optimal burial environment. Even when the glacial intervals of the British Quaternary are factored into the temperature calculations, the more conservative of these two estimates extends the range for collagen sequencing to the Lower Pleistocene as confirmed by the presence of collagen peptides in bones from the Weybourne Crag (~1.5 Ma). Collagen fingerprinting can extend the range of identifiable taxa present at sites with large assemblages of fragmentary bone material such as that encountered at the ~900 Ka site at Happisburgh (Norfolk, UK) recently identified as showing signs of the earliest humans in Britain.

scholarly journals Analysis of peptide binding patterns in different major histocompatibility complex/T cell receptor complexes using pigeon cytochrome c-specific T cell hybridomas. Evidence that a single peptide binds major histocompatibility complex in different conformations.

1989 ◽  
Vol 170 (5) ◽  
pp. 1609-1625 ◽  
Author(s):  
H Bhayani ◽  
Y Paterson
Keyword(s):  
Major Histocompatibility Complex ◽  
T Cell ◽  
Cytochrome C ◽  
Peptide Sequence ◽  
Single Amino Acid ◽  
Major Histocompatibility ◽  
Peptide Antigens ◽  
Receptor Complexes ◽  
Histocompatibility Complex ◽  
Single Peptide

The interaction of TCR, antigen, and MHC complex has been analyzed using synthetic peptide antigens and a series of single amino acid-substituted analogues. Two similar antigens, mouse cytochrome c (mcyt c) and pigeon cytochrome c (pcyt c), elicit T cell responses in strains of mice bearing MHC class II Ek beta Ek alpha (B10.A), Eb beta Ek alpha [B10.A(5R)], and Es beta Ek alpha [B10.S(9R)]. The immunogenic regions of these antigens are located in the peptide sequence p88-104 for pcyt c and m88-103 for mcyt c. The limited T cell repertoire for these antigens is comprised of four groups of T cell phenotypes that have very few differences in their TCR gene make up. In this paper, we examine the diversity in their fine specificity for each of the antigens, m88-103 and p88-104, complexed with each of the I-Ek haplotypes. Epitopes, i.e., residues that interact with the TCR, and agretopes, i.e., residues in the MHC-binding site, were assigned for the two peptide antigens in the presence of APC bearing E beta kEk alpha, Eb beta Ek alpha, or Eb beta Ek alpha using T cell hybridomas of the phenotypes I, IIIa, and IV. From our results, we conclude that first, the substitution of any residue between 95 and 104 of the cytochrome c peptide changed the antigenic potency of the peptide for at least one of the hybridomas. Second, each T cell type has a different recognition pattern of epitopes and agretopes for a particular antigen-MHC complex, thus, ruling out a static model of T cell recognition, which assigns certain, invariant agretopic residues to the peptide by which it interacts with the MHC molecule independently of the TCR. Third, the same T cell hybridoma responded to the antigens differently when presented on various MHC molecules, implying that overall changes in the MHC groove, as displayed by the three haplotypes, may affect the efficiency in binding the peptide. Fourth, since most of the residues are used as epitopes by at least one of the T cell specificities, the peptide appears to be recognized in a different conformation by each T cell hybridoma phenotype; and, finally, the epitopic and agretopic residues do not segregate, for any one of the T cell specificities, in such a way that suggests they are recognized in a helical conformation. In summary, our results suggest that a single peptide may generate diversity in the T cell response by virtue of its conformational flexibility within the TCR-MHC-antigen complex.

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