Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

Background  

Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses.     

Hermitian splines for modeling biological soft tissue systems that exhibit nonlinear force-elongation curves

Numerical simulation of soft tissue mechanical properties is a critical step in developing valuable biomechanical models of live organisms. A cubic Hermitian spline optimization routine is proposed in this paper to model nonlinear experimental force-elongation curves of soft tissues, in particular when modeled as lumped elements. Boundary conditions are introduced to account for the positive definiteness and the particular curvature of the experimental curve to be fitted. The constrained least-square routine minimizes user intervention and optimizes fitting of the experimental data across the whole fitting range. The routine provides coefficients of a Hermitian spline or corresponding knots that are compatible with a number of constraints that are suitable for modeling soft tissue tensile curves. These coefficients or knots may become inputs to user-defined component properties of various modeling software. Splines are particularly advantageous over the well-known exponential model to account for the traction curve flatness at low elongations and to allow for more flexibility in the fitting process. This is desirable as soft tissue models begin to include more complex physical phenomena.     

Extracellular and intracellular chemical environments in relation to embryogenesisin vitro

Summary Tissue culture isolated from the root ofDaucus carota readily produced embryos when they were grown on a medium (M_s) containing relatively large amounts of NH₄ ⁺ and nitrate. Embryos were never formed on a second medium (M_w) which contained only nitrate in a low concentration. The cells of M_s-cultures always had a high level of NH₄ ⁺ while it was scarcely detected in M_w-cultures. Addition of either nitrate or glutamate to M_w resulted in the formation of embryos and also in the accumulation of a detectable amount of NH₄ ⁺ in the cells of the tissues. Although the occurrence of NH₄ ⁺ in the medium is not necessary for embryo formationin vitro it appears that a certain level of intracellular NH₄ ⁺ is a prerequisite for this process. Since there is a positive correlation between embryo formation and the contents in the cultures of both soluble and insoluble organic nitrogen, it is probable that NH₄ ⁺ is important for embryo formation because it is an essential substrate for the synthesis of organic nitrogen compounds such as amino acids and proteins. The ability to synthesize organic nitrogen from NH₄ ⁺ decreased conspicuously in the tissues which were cultured on M_s for long periods of time and had lost the capacity to form embryos. A certain level of K⁺ in culture media is necessary for optimal production of embryos on media with NH₄ ⁺, while Na⁺ has no effect on embryo formation.The authors are indebted to Mr. E.Mahn, Miss S.Semenoff, and Mrs. E.Bock for their technical assistances.     

Glycosyl part identified within Balanites aegyptiaca fruit protease

The many milk-clotting proteases from plant are glycosylated; attachment of monosaccharides to enzyme is an advantage for its activity and stability. In this study, gas chromatography coupled to mass spectrometry-electrospray ionization was used to identify glycans bond to proteases purified from Balanites aegyptiaca fruits pulp through cation exchange chromatography. Carbohydrates were identified according to the retention time and the ion at m/z after derivation by heptafluorobutyric acid. The chromatograms obtained from monosaccharides analysis revealed the presence of galactose, mannose, arabinose, xylose, rhamnose and glucuronic acid. The mass spectrometry-electrospray ionization spectra corroborated these findings.     

Osteopontin deficiency aggravates hepatic injury induced by ischemia–reperfusion in mice

Osteopontin (OPN) is a multifunctional protein involved in hepatic steatosis, inflammation, fibrosis and cancer progression. However, its role in hepatic injury induced by ischemia–reperfusion (I–R) has not yet been investigated. We show here that hepatic warm ischemia for 45 min followed by reperfusion for 4 h induced the upregulation of the hepatic and systemic level of OPN in mice. Plasma aspartate aminotransferase and alanine aminotransferase levels were strongly increased in Opn^−/− mice compared with wild-type (Wt) mice after I–R, and histological analysis of the liver revealed a significantly higher incidence of necrosis of hepatocytes. In addition, the expression levels of inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNFα), interleukin 6 (IL6) and interferon-γ were strongly upregulated in Opn^−/− mice versus Wt mice after I–R. One explanation for these responses could be the vulnerability of the OPN-deficient hepatocyte. Indeed, the downregulation of OPN in primary and AML12 hepatocytes decreased cell viability in the basal state and sensitized AML12 hepatocytes to cell death induced by oxygen–glucose deprivation and TNFα. Further, the downregulation of OPN in AML12 hepatocytes caused a strong decrease in the expression of anti-apoptotic Bcl2 and in the ATP level. The hepatic expression of Bcl2 also decreased in Opn^−/− mice versus Wt mice livers after I–R. Another explanation could be the regulation of the macrophage activity by OPN. In RAW macrophages, the downregulation of OPN enhanced iNOS expression in the basal state and sensitized macrophages to inflammatory signals, as evaluated by the upregulation of iNOS, TNFα and IL6 in response to lipopolysaccharide. In conclusion, OPN partially protects from hepatic injury and inflammation induced in this experimental model of liver I–R. This could be due to its ability to partially prevent death of hepatocytes and to limit the production of toxic iNOS-derived NO by macrophages.     

An iterative method for faster sum-of-pairs multiple sequence alignment

MOTIVATION: Multiple sequence alignment is an important tool in computational biology. In order to solve the task of computing multiple alignments in affordable time, the most commonly used multiple alignment methods have to use heuristics. Nevertheless, the computation of optimal multiple alignments is important in its own right, and it provides a means of evaluating heuristic approaches or serves as a subprocedure of heuristic alignment methods. RESULTS: We present an algorithm that uses the divide-and-conquer alignment approach together with recent results on search space reduction to speed up the computation of multiple sequence alignments. The method is adaptive in that depending on the time one wants to spend on the alignment, a better, up to optimal alignment can be obtained. To speed up the computation in the optimal alignment step, we apply the alpha(*) algorithm which leads to a procedure provably more efficient than previous exact algorithms. We also describe our implementation of the algorithm and present results showing the effectiveness and limitations of the procedure.     

Cloning, characterization and physical mapping of three cervid satellite DNA families in the genome of the Formosan muntjac (Muntiacus reevesi micrurus)

Due to their high sequence diversity even among closely related species, satellite DNA sequences can be a useful molecular marker for phylogenetic and taxonomic analyses. To characterize the satellite DNA in the genome of a native muntjac species of Taiwan, the Formosan muntjac, satellite DNA clones representing three different cervid satellite DNA families from this species were isolated and analyzed. Genomic organization study of these satellite DNAs was also undertaken. Three Formosan muntjac satellite DNA clones were obtained and designated as FM-satI (1,391 bp), FM-satII (1,143 bp) and FM-satIV (1,103 bp), and found to share approximately 82, 81 and 98% sequence homology with the Chinese muntjac satellite I clone (C5), Indian muntjac satellite II clone (Mmv-0.7) and Chinese muntjac satellite IV clone (MR-1.0), respectively. These three satellite DNA families are organized in a pter<--FM-satII-FM-satIV-FM-satI-->qter orientation in the centromeric region with satII closely associated with the telomeric sequences. Satellite DNA sequence comparison, in combination with chromosome data concludes that the Formosan muntjac is likely a subspecies of M. reevesi, closely related to the Chinese muntjac. With the kinetochore satellite II DNA co-localizing with the telomeric sequences, the Formosan muntjac chromosomes could be truly telocentric.     

Antimicrobial peptide defenses of the Tarahumara frog,Rana tarahumarae

Populations of the Tarahumara frog Rana tarahumarae have decreased markedly in recent years in the northern part of their range. Infection by the chytrid fungus Batrachochytrium dendrobatidis has been implicated in these declines. To determine whether antimicrobial peptides in the skin provide protection against this pathogen, norepinephrine-stimulated skin secretions were tested for their ability to inhibit growth of B. dendrobatidis in vitro. After concentration, crude mixtures of skin peptides inhibited the growth of the chytrid in a concentration-dependent manner. Proteomic analysis led to the identification and characterization of three peptides belonging to the brevinin-1 family of antimicrobial peptides and three belonging to the ranatuerin-2 family. The two most abundant peptides, ranatuerin-2TRa (GIMDSIKGAAKEIAGHLLDNLKCKITGC) and brevinin-1TRa (FLPVIAGIAANVLPKLFCKLTKRC), were active against B. dendrobatidis (MIC of 50 microM for ranatuerin-2TRa and 12.5 microM for brevinin-1TRa against zoospores). These data clearly show that antimicrobial peptides in the skin secretions of the Tarahumara frog are active against B. dendrobatidis and should provide some protection against infection. Therefore, the observed susceptibility of these frogs to this pathogen in the wild may be due to the effects of additional environmental factors that impair this innate defense mechanism, leading to the observed population declines.