Proteomics FASTA Archive and Reference Resource

A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to properly cite FASTA files used in a study, and to publicly access such FASTA files post-publication. An extension to the Tranche data sharing network has been developed that includes web-pages, documentation, and tools for facilitating the use of FASTA files. These include conversion to the new HUPO-PSI format, and provisions for both citing and publicly archiving FASTA files. This new resource is available immediately, free of charge, and can be accessed at http://www.proteomecommons.org/data/fasta/. Source-code for related tools is also freely available under the BSD license.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58584/1/1756_ftp.pd

Synthesis and structural characterisation of bismuth(III) hydroxamates and their activity against Helicobacter pylori

Seven new bismuth(III) hydroxamate complexes derived from the hydroxamic acids N-methylfurohydroxamic acid (H-MFHA), N-benzoyl-N-phenylhydroxamic acid (H-BPHA), salicylhydroxamic acid (H2-SHA), benzohydroxamic acid (H2-BHA), and acetohydroxamic acid (H2-AHA) have been synthesized and characterized. The complexes formed are either tris-hydroxamato complexes containing only mono-anionic ligands, [Bi(H-SHA)3], [Bi(MFHA)3] and [Bi(BPHA)3]; mixed-anion complexes, [Bi(SHA)(H-SHA)] and [Bi(AHA)(H-AHA)]; and potassium bismuthate complexes, K[Bi(SHA)2] and K[Bi(BHA)2]. The solid-state structure of three complexes has been determined through single crystal X-ray diffraction; [Bi(MFHA)3]2·Me2C[double bond, length as m-dash]O, {[Bi(SHA)(H-SHA)(DMSO)2][Bi(SHA)(H-SHA)(DMSO)]·DMSO}∞ and [Bi(BPHA)3]2·2EtOH. All the complexes and their parent acids were assessed for the bactericidal activity against three strains of Helicobacter pylori (26695, B128 and 251). Of the acids, only acetohydroxamic acid showed any activity at low concentrations (MIC 6.25 μg mL−1; 83.26 µM) while the others were not toxic below 25 μg mL−1. In contrast, their bismuth(III) complexes all showed excellent activity across all three strains (e.g. 0.28 μM for [Bi(H-SHA)3] to 6.01 μM for K[Bi(BHA)2] against strain 251) with only minor variations in activity being both ligand and composition dependant

Thick blood film examination for Plasmodium falciparum malaria has reduced sensitivity and underestimates parasite density

BACKGROUND: Thick blood films are routinely used to diagnose Plasmodium falciparum malaria. Here, they were used to diagnose volunteers exposed to experimental malaria challenge. METHODS: The frequency with which blood films were positive at given parasite densities measured by PCR were analysed. The poisson distribution was used to calculate the theoretical likelihood of diagnosis. Further in vitro studies used serial dilutions to prepare thick films from malaria cultures at known parasitaemia. RESULTS: Even in expert hands, thick blood films were considerably less sensitive than might have been expected from the parasite numbers measured by quantitative PCR. In vitro work showed that thick films prepared from malaria cultures at known parasitaemia consistently underestimated parasite densities. CONCLUSION: It appears large numbers of parasites are lost during staining. This limits their sensitivity, and leads to erroneous estimates of parasite density

Early events of Bacillus anthracis germination identified by time-course quantitative proteomics

Germination of Bacillus anthracis spores involves rehydration of the spore interior and rapid degradation of several of the protective layers, including the spore coat. Here, we examine the temporal changes that occur during B. anthracis spore germination using an isobaric tagging system. Over the course of 17 min from the onset of germination, the levels of at least 19 spore proteins significantly decrease. Included are acid-soluble proteins, several known and predicted coat proteins, and proteins of unknown function. Over half of these proteins are small (less than 100 amino acids) and would have been undetectable by conventional gel-based analysis. We also identified 20 proteins, whose levels modestly increased at the later time points when metabolism has likely resumed. Taken together, our data show that isobaric labeling of complex mixtures is particularly effective for temporal studies. Furthermore, we describe a rigorous statistical approach to define relevant changes that takes into account the nature of data obtained from multidimensional protein identification technology coupled with the use of isobaric tags. This study provides an expanded list of the proteins that may be involved in germination of the B. anthracis spore and their relative levels during germination.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55849/1/5199_ftp.pd

Multifunctional hybrid materials based on transparent poly(methyl methacrylate) reinforced by lanthanoid hydroxo clusters

Three pentanuclear lanthanoid hydroxo clusters of composition [Ln(OH)5(abzm)10], where Ln = Eu, Tb,Ho and abzm = di(4-allyloxy)benzoylmethanide, have been prepared. The structures have beencharacterised by means of IR, Raman, elemental analyses and X-ray diffraction, showing a pyramidalsquare-based cluster core. The clusters (Tb and Ho) exhibit Curie?Weiss Law behaviour, displayingantiferromagnetic ordering at low temperatures. The emission properties of the Eu cluster demonstratethe abzm- ligand is an efficient antenna (lex = 420 nm) only for the sensitisation of Eu luminescence inthe visible range, via energy transfer to the 5D0 state of the trivalent metal. The clusters have beenreacted in the presence of methyl methacrylate and azobisisobutyronitrile to prepare reinforcedpolymers via radical polymerisation. The obtained materials exhibit swelling upon immersion intoorganic solvents up to 110% of their original size, in agreement with the presence of cluster-crosslinked polymeric chains. Also, no loss of transparency was observed in the preparation of the materials. The characteristic red emission of the Eu cluster in also retained in the polymeric material

Synthesis and characterization of cyclic pseudopeptide libraries containing thiomethylene and thiomethylene-sulfoxide amide bond surrogates

We describe the first examples of a series of cyclic pseudopeptide libraries that have been prepared in a systematic approach in order to facilitate both synthesis and subsequent deconvolution attempts. Our synthetic strategy involved the attachment of a trifunctional amino acid (Asp, Asn or Glu) to a polystyrene resin via its side chain, and stepwise chain elongation using either protected amino acids or a pseudodipeptide building block. Head to tail cyclic peptides were formed by removal of the temporary N- and C-terminal protecting groups followed by ring closure by amide formation. Cyclization of the hexa, hepta, and octapseudopeptides on the resin avoided dimer formation, as monitored by mass spectrometry. We utilized a ‘psi-scan’ approach in which a second fixed position was serially addressed by stepping a dipeptide surrogate, Proψ[CH 2 S]Gly around the rings to generate a group of cyclic pseudopeptide sub-libraries. Oxidation of ψ[CH 2 S] to ψ[CH 2 SO] helped validate the synthesis and also provides a strategy for forming a new set of pseudopeptide libraries (previously described as ‘libraries from libraries’). Our results suggest that libraries of cyclic pseudopeptides are an efficient method of preparing and assaying these synthetically more challenging entities as potential drug leads.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43245/1/11030_2004_Article_169023.pd

A novel protamine variant reversal of heparin anticoagulation in human blood in vitro

AbstractPurpose: Protamine reversal of heparin anticoagulation during cardiovascular surgery may cause severe hypotension and pulmonary hypertension. A novel protamine variant, [+18RGD], has been developed that effectively reverses heparin anticoagulation without toxicity in canine experiments. Heretofore, human studies have not been undertaken. This investigation hypothesized that [+18RGD] would effectively reverse heparin anticoagulation of human blood in vitro. Methods: Fifty patients who underwent anticoagulation therapy during vascular surgery had blood sampled at baseline and 30 minutes after receiving heparin (150 IU/kg). Activated clotting times were used to define specific quantities of [+18RGD] or protamine necessary to completely reverse heparin anticoagulation in the blood sample of each patient. These defined amounts of [+18RGD] or protamine were then administered to the heparinized blood samples, and percent reversals of activated partial thromboplastin time, thrombin clotting time, and antifactor Xa/IIa levels were determined. In addition, platelet aggregation assays, as well as platelet and white blood cell counts were performed. Results: [+18RGD] and protamine were equivalent in reversing heparin as assessed by thrombin clotting time, antifactor Xa, antifactor IIa levels, and white blood cell changes. [+18RGD], when compared with protamine, was superior in this regard, as assessed by activated partial thromboplastin time (94.5 ± 1.0 vs 86.5 ± 1.3%δ, respectively; p < 0.001) and platelet declines (–3.9 ± 2.9 vs –12.8 ± 3.4 per mm3, respectively; p = 0.048). Platelet aggregation was also decreased for [+18RGD] compared with protamine (23.6 ± 1.5 vs 28.5 ± 1.9%, respectively; p = 0.048). Conclusions: [+18RGD] was as effective as protamine for in vitro reversal of heparin anticoagulation by most coagulation assays, was statistically more effective at reversal than protamine by aPTT assay, and was associated with lesser platelet reductions than protamine. [+18RGD], if less toxic than protamine in human beings, would allow for effective clinical reversal of heparin anticoagulation. (J Vasc Surg 1997;26:1043-8.