Identification of peptides within a known protein sequence using COMSEQ analysis of data containing multiple sequences

Modern methods of automated protein sequence analysis can provide high-quality data with which unambiguous amino-acid sequences can be determined, but analyses are more difficult when the sample is not pure. COMSEQ and auxillary programs were written to facilitate reconciliation of multiple amino-acid sequences potentially contained in noisy data with the known amino-acid sequence of the parent protein. The COMSEQ program prints a matrix in which the first vertical column represents the known amino-acid sequence of a selected protein. Each row of the matrix contains the sequencer yield corresponding to the amino acid in the first column, with each column corresponding to the sequencing reaction cycle. A diagonal which contains net increases of amino acids for each amino acid in the known sequence identifies a peptide potentially contained within the data. The number of matches for each diagonal over the entire known sequence are tabulated and presented as an aid to locating comparisons of greatest interest. The RNDSEQ program conducts multiple analyses using randomized versions of the known amino-acid sequence and tabulates the cumulative frequencies of potential sequence matches irrespective of the true known sequence. TRANSEQ is a utility program that translates edited sequence data from common databases into files that can be used by COMSEQ and RNDSEQ. The programs have been used successfully to identify two co-sequenced peptides from bovine serum albumin, an albumin peptide sequence in the presence of hemoglobin, and to identify two sequences of rat alpha-2u-globulin that differ in their amino termini.     

Construction experiences with SSC collider dipole magnets atFermilab

Full length and short model SSC (Superconducting Super Collider) 50 mm bore dipoles are being built and tested at Fermilab. The mechanical design of these magnets has been determined from experience with the construction of previous superconducting magnets. Construction experience includes coil fabrication, ground insulation, instrumentation, collaring, and yoke assembly. Fabrication techniques are explained, and construction problems and their solutions are reviewed. The relationship of short to long model construction is discussed     

Human and monkey trabecular meshwork accumulate alpha B-crystallin in response to heat shock and oxidative stress

PURPOSE: Oxidative stress and other forms of injury to trabecular meshwork (TM) cells may contribute to changes seen with age and primary open-angle glaucoma. This study was designed to investigate if TM expresses alpha B-crystallin, a small heat-shock protein with chaperone activity, and whether it might be overexpressed under stress conditions. METHODS: The TM from human and monkey eyes, as well as organ and primary cell cultures derived from these eyes, were investigated for alpha B-crystallin by immunohistochemistry, two-dimensional gel electrophoresis, Northern and Western blot analysis. The TM cell cultures were stressed by heat shock (44 degrees C for 15 minutes) or hydrogen peroxide (200 mumol for 1 hour). Semiquantitation of alpha B-crystallin messenger RNA (mRNA) or protein was obtained by densitometry. RESULTS: In both species, alpha B-crystallin could be detected in fresh and cultured TM by two-dimensional gel electrophoresis in conjunction with Western blot analysis. Immunohistochemistry of fresh samples showed that alpha B-crystallin was expressed predominantly in the cribriform area. Protein expression was enhanced in 4- to 7-day organ cultures. Primary cultures from human TM cells expressed two sizes (approximately 0.8 and 1.1 kb) of alpha B-crystallin mRNA in Northern blots. In monkey TM cultures, a 0.8-kb band was observed, which comigrated with lens alpha B-crystallin. In both species, heat shock caused a significant increase in alpha B-crystallin mRNA with a peak after 4 hours. An increase in alpha B-crystallin mRNA also was observed after oxidative stress; however, the onset of mRNA induction was slower. After heat shock, but not after oxidative stress, a transient change in mRNA mobility was observed. Western dot blot analysis showed a 3.4-fold increase in protein 24 hours after heat shock and a 20-fold increase after 48 hours. No constitutive mRNA expression and only a minimal increase 4 hours after heat shock could be observed in simian virus 40 transformed cell lines from human TM. CONCLUSIONS: Overexpression of alpha B-crystallin might be an important mechanism for TM to prevent cellular damage associated with various stress conditions.     

云中基于蚁群算法改进的负载均衡策略

针对云计算虚拟化资源中,提高资源利用率、负载均衡度的问题,在蚁群算法的基础上,提出云中节点间负载均衡的改进算法。前向蚂蚁检测节点的类型、记录节点信息,遇到负载节点时留下觅食信息素;后向蚂蚁依据循迹信息素追溯回负载节点,合理分配超载节点任务。所有蚂蚁不再更新自己的结果集,而是致力于更新单个结果集,在搜索过程中依据节点类型动态地修改路径信息素。在Cloudsim平台下进行的仿真实验验证了改进算法的有效性。     

Predictors of long-term smoking cessation in head and neck cancer patients

Cigarette smoking is a major risk factor for head and neck cancer, and individuals who continue to smoke past diagnosis and treatment are at elevated risk for further disease. In a randomized controlled trial, a state of the art provider-delivered smoking cessation intervention was compared to a usual care advice control condition. The intervention consisted of surgeon- or dentist-delivered advice to stop smoking, a contracted quit date, tailored written materials, and booster advice sessions. Subjects were 186 patients with newly diagnosed first primary squamous cell carcinomas of the upper aerodigestive tract who had smoked cigarettes within the past year. At randomization, 88.2% of subjects were current smokers. At 12-month follow-up, 70.2% of subjects completing the trial (n = 114) were continuous abstainers; among baseline smokers alone the continuous abstinence (CA) rate was 64.6%. The cotinine validation rate at 12 months was 89.6%. Modeling techniques were utilized in order to derive expected CA rates, which included noncompleter subjects (n = 72). The CA rate expected at 1 year for the entire patient population was 64.2%, and for smokers alone the expected CA rate was 59.4%. Logistic regression analysis carried out on baseline smokers identified predictors of 12-month CA status. These included medical treatment, stage of change, age, nicotine dependence, and race. The intervention effect was not significant, although the sign of the effect was positive. Based on these findings, we recommend systematic brief advice to stop smoking for head and neck cancer patients, with a stepped care approach for patients less able to quit.     

Effect of alendronate treatment on the osteoclastogenic potential of bone marrow cells in mice

The expression of cytokeratins (CK), involucrin, vimentin, CD34, and alpha-smooth-muscle actin was studied in fetal and adult hair follicles. The first stage of the developing hair follicle is characterized by palisaded, elongated epithelial cells budding from the epidermal basal layer. These cells express CK5/6, CK14, CK17, CK19, and vimentin. During the following weeks of gestation, different structures in the developing hair follicle can be identified and characterized. The matrical cells display only CK19. The keratinocytes of the outer root sheath express CK5/6, CK14, CK17, CK19, and involucrin; those of the inner root sheath, CK4, CK18, and involucrin; those of the isthmus, the same profile as the ORS. In the infundibulum, the basal-layer keratinocytes express CK5/6, CK14, CK17, and CK19, whereas in the suprabasal layers CK1, CK4, CK10, CK14, and CK17 are seen. The adult hair follicle in anagen fails to express CK19 in the matrical cells and isthmus and both CK17 and CK19 in the infundibulum. These profiles of intermediate filaments and other markers appear to be potentially useful in categorizing neoplasms with apparent follicular differentiation.     

Structural characterization of the cyanelle peptidoglycan of Cyanophora paradoxa by 252Cf plasma desorption mass spectrometry and fast atom bombardment/tandem mass spectrometry

A strategy for the structural characterization of the four major NaBH4-reduced peptidoglycan monomers derived from muramidase-digested peptidoglycan from the cyanelles of the flagellate Cyanophora paradoxa Korschikoff is described. Initial molecular weight determination of these glycopeptides was performed by positive and negative ion plasma desorption mass spectrometry. Due to the presence of two pairs of disaccharide tripeptide and disaccharide tetrapeptide monomers differing in mass by 112 units, respectively, an as yet unknown peptidoglycan modification either at the carbohydrate or at the peptide moiety was assumed. beta-Elimination of the disaccharide unit from the unreduced peptidoglycan monomers yielded the corresponding (modified) N1-lactyltripeptides and -tetrapeptides, respectively. These peptides, N-terminally blocked with lactic acid, unambiguously showed the modification to be located on the peptide moiety. By positive ion fast atom bombardment/hybrid tandem mass spectrometry of the reduced peptidoglycan monomers as well as of the corresponding deglycosylated monomers (= N1-lactylpeptides) the modification was determined to be linked to the glutamic acid moiety. Based on combined data from plasma desorption mass spectrometry, tandem mass spectrometry, accurate mass measurement and amino acid analysis of the acid hydrolysate after derivatization with o-phthaldialdehyde by high-performance liquid chromatography we could establish the structure of the modification as N-acetylputrescine. Finally, the confirmation of the linkage of the glutamic acid to diaminopimelic acid via the gamma-COOH was based on the presence of a-type peptide backbone fragment ions in the positive ion plasma desorption mass spectra of the modified N1-lactylpeptides.