Computational materials: Multi-scale modeling and simulation of nanostructured materials

The paper provides details on the current approach to multi-scale modeling and simulation of advanced materials for structural applications. Examples are given that illustrate the suggested approaches to predicting the behavior and influencing the design of nanostructured materials such as high-performance polymers, composites, and nanotube-reinforced polymers. Primary simulation and measurement methods applicable to multi-scale modeling are outlined. Key challenges including verification and validation are highlighted and discussed.     

Sequence database searches via de novo peptide sequencing by tandem mass spectrometry

A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.     

Interstitial fluid concentrations of glycerol, glucose, and amino acids in human quadricep muscle and adipose tissue. Evidence for significant lipolysis in skeletal muscle

To determine the relationship between circulating metabolic fuels and their local concentrations in peripheral tissues we measured glycerol, glucose, and amino acids by microdialysis in muscle and adipose interstitium of 10 fasted, nonobese human subjects during (a) baseline, (b) euglycemic hyperinsulinemia (3 mU/kg per min for 3 h) and, (c) local norepinephrine reuptake blockade (NOR). At baseline, interstitial glycerol was strikingly higher (P < 0.0001) in muscle (3710 microM) and adipose tissue (2760 microM) compared with plasma (87 microM), whereas interstitial glucose (muscle 3.3, fat 3.6 mM) was lower (P < 0.01) than plasma levels (4.8 mM). Taurine, glutamine, and alanine levels were higher in muscle than in adipose or plasma (P < 0.05). Euglycemic hyperinsulinemia did not affect interstitial glucose, but induced a fall in plasma glycerol and amino acids paralleled by similar changes in the interstitium of both tissues. Local NOR provoked a fivefold increase in glycerol (P < 0.001) and twofold increase in norepinephrine (P < 0.01) in both muscle and adipose tissues. To conclude, interstitial substrate levels in human skeletal muscle and adipose tissue differ substantially from those in the circulation and this disparity is most pronounced for glycerol which is raised in muscle as well as adipose tissue. In muscle, insulin suppressed and NOR increased interstitial glycerol concentrations. Our data suggest unexpectedly high rates of intramuscular lipolysis in humans that may play an important role in fuel metabolism.     

Silicone elastomer microshards in fluid from a painful metatarsophalangeal implant site. A case report

Histopathologic studies have demonstrated microshards from silicone elastomer metatarsophalangeal joint implants in adjacent tissues in a setting of chronic inflammation and in inguinal lymph nodes. Cytologic smears of synovial fluid from symptomatic implanted joints should show these refractile, nonpolarizing microshards in the reactive inflammatory context. Nonspecific enzymatic inflammatory activity contributes to further destabilization of the implants, eventuating in symptoms and signs requiring prosthesis removal. Cytopathologic examination of aspirated fluid from the vicinity of a symptomatic implanted joint demonstrates foreign body reaction to silicone elastomer, predicting a need for intervention before the local damage is severe and disabling.     

Nature of the metal-support interface in supported metal catalysts: Results from X-ray absorption spectroscopy

X-ray absorption spectra characterizing the metal-support interface in supported metal complexes and supported metal catalysts are summarized and evaluated. Single-metal-atom transition metal complexes on non-reducible metal oxide supports are bonded with metal-oxygen bonds with metal-oxygen distances of approximately 2.15 A; the bonding distance is only weakly sensitive to the oxidation state of the metal. Nearly this same metal-oxygen distance is characteristic of the metal-support interface in metal-oxide-supported metal clusters following high temperature reduction in H₂ (HTR:T > 450 °C). The metals at the interface may be polarized sufficiently that they bond with the oxygen of the support much as the cations in mononuclear complexes bond with it. When the supported metals are treated in H₂ at low temperatures (LTR:T < 350 °C) or are prepared under He with partially hydroxylated supports, a longer metal-support oxygen distance is observed, typically 2.5–2.7 Å. This distance is suggested to characterize interactions between zero-valent metals and support oxygen. Changes in the performance of supported metal catalysts resulting from differences in the temperature of pretreatment in H₂ are attributed to changes in the electronic properties and/or morphology of the metal clusters, which are suggested to be related to the concomitant changes in the structure of the metal-support interface.     

Development of a novel, rapid processing protocol for polymerase chain reaction-based detection of bacterial infections in synovial fluids

We describe the development of a molecular detection system designed for use with synovial fluid (SF)-based infections. The methodology employs a lysis/extraction procedure that effectively disrupts microorganisms allowing for release of the microbial DNA and its amplification by polymerase chain reaction (PCR). We tested the effectiveness of adding a mixed-bed, ion-exchange resin to the extract to remove PCR inhibitory components present in the SF. After centrifugation to separate the resin, DNA contained in the supernatant is subjected to PCR using oligonucleotide primers designed for broad-spectrum microorganism detection. Amplification products are analyzed by agarose gel electrophoresis and/or DNA hybridization methodology. We report here the detection sensitivity and specificity of the protocol using SF inoculated with Escherichia coli and Staphyloccocus aureus. We have applied this new methodology to clinical SF specimens with results superior to standard laboratory culturing assays.