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41.
Background
Modeling of transmembrane domains (TMDs) requires correct prediction of interfacial residues for in-silico modeling and membrane insertion studies. This implies the defining of a target sequence long enough to contain interfacial residues. However, too long sequences induce artifactual polymorphism: within tested modeling methods, the longer the target sequence, the more variable the secondary structure, as though the procedure were stopped before the end of the calculation (which may in fact be unreachable). Moreover, delimitation of these TMDs can produce variable results with sequence based two-dimensional prediction methods, especially for sequences showing polymorphism. To solve this problem, we developed a new modeling procedure using the PepLook method. We scanned the sequences by modeling peptides from the target sequence with a window of 19 residues.Results
Using sequences whose NMR-structures are already known (GpA, EphA1 and Erb2-HER2), we first determined that the hydrophobic to hydrophilic accessible surface area ratio (ASAr) was the best criterion for delimiting the TMD sequence. The length of the helical structure and the Impala method further supported the determination of the TMD limits. This method was applied to the IL-2Rβ and IL-2Rγ TMD sequences of Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus.Conclusions
We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information. 相似文献42.
W. K. Al-Delaimy E. H. J. M. Jansen P. H. M. Peeters J. D. van der Laan P. A. H. van Noord H. C. Boshuizen 《Biomarkers》2013,18(4):370-382
AbstractBiomarkers are widely used in epidemiology, yet there are few reliability studies to assess the appropriateness of using these biomarkers for the assessment of exposure–disease relationships. The aim of the study was to assess the reliability of 20 biomarkers in serum collected from two Dutch centres (Utrecht and Bilthoven) participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) at two points several years apart. Blood samples were collected from 30 men from Bilthoven and 35 women from Utrecht. Ferritin, total iron, total iron-binding capacity, transferrin saturation, transferrin, C-reactive protein, bilirubin, cholesterol, triglycerides, apo lipoprotein-A, apo lipoprotein-B, high-density lipoproteins, low-density lipoproteins, uric acid, creatinine, reactive oxygen metabolites, the ferric-reducing ability of plasma, protein thiol oxidation, fructosamine, and vitamin D biomarkers in serum were analysed from the blood samples at the two points of time. For all biomarkers, except C-reactive protein, there were no substantial changes in the mean levels over time. Uric acid, ferritin, creatinine, HDL, and apo lipoprotein-B levels consistently showed the highest reliability for men and women (intra-class correlation?=?0.69–0.86). Among women, the ferric-reducing ability of plasma, and protein thiol oxidation had poor reliability; and among men iron-related biomarkers (except serum ferritin) had poor reliability. With the exception of a few gender-specific differences, most of the 20 biomarkers performed well and can be considered to have sufficient reliability to be used in future cohort studies. 相似文献
43.
Ellen L. de Hollander Rik P. Bogers Hendriek C. Boshuizen Annika Rosengren Martin J. Shipley Paul Knekt Pierre Ducimetière Alessandro Menotti Lisette CPGM de Groot Wanda J.E. Bemelmans for the BMI‐CHD collaboration investigators 《Obesity (Silver Spring, Md.)》2013,21(5):865-880
Objective:
The association between obesity and coronary heart disease (CHD) may have changed over time, for example due to improved pharmacological treatment of CHD risk factors. This meta‐analysis of 31 prospective cohort studies explores the influence of calendar period on CHD risk associated with body mass index (BMI).Design and Methods:
The relative risks (RRs) of CHD for a five‐BMI‐unit increment and BMI categories were pooled by means of random effects models. Meta‐regression analysis was used to examine the influence of calendar period (>1985 v ≤1985) in univariate and multivariate analyses (including mean population age as a covariate).Results:
The age, sex, and smoking adjusted RR (95% confidence intervals) of CHD for a five‐BMI‐unit increment was 1.28(1.22:1.34). For underweight, overweight and obesity, the RRs (compared to normal weight) were 1.11(0.91:1.36), 1.31(1.22:1.41), and 1.78(1.55:2.04), respectively. The univariate analysis indicated 31% (95%CI: ?56:0) lower RR of CHD associated with a five‐BMI‐unit increment and a 51% (95%CI: ?78: ?14)) lower RR associated with obesity in studies starting after 1985 (n = 15 and 10, respectively) compared to studies starting in or before 1985 (n = 16 and 10). However, in the multivariate analysis, only mean population age was independently associated with the RRs for a five‐BMI‐unit increment and obesity (?29(95%CI: ?55: ?5)) and ?31(95%CI: ?66:3), respectively) per 10‐year increment in mean age).Conclusion:
This study provides no consistent evidence for a difference in the association between BMI and CHD by calendar period. The mean population age seems to be the most important factor that modifies the association between the risk of CHD and BMI, in which the RR decreases with increasing age.44.
Anne Fages Pietro Ferrari Stefano Monni Laure Dossus Anna Floegel Nicolle Mode Mattias Johansson Ruth C Travis Christina Bamia María-José Sánchez-Pérez Paolo Chiodini Hendriek C Boshuizen Marc Chadeau-Hyam Elio Riboli Mazda Jenab Bénédicte Elena-Herrmann 《Metabolomics : Official journal of the Metabolomic Society》2014,10(6):1074-1083
The key goal of metabolomic studies is to identify relevant individual biomarkers or composite metabolic patterns associated with particular disease status or patho-physiological conditions. There are currently very few approaches to evaluate the variability of metabolomic data in terms of characteristics of individuals or aspects pertaining to technical processing. To address this issue, a method was developed to identify and quantify the contribution of relevant sources of variation in metabolomic data prior to investigation of etiological hypotheses. The Principal Component Partial R-square (PC-PR2) method combines features of principal component and of multivariable linear regression analyses. Within the European Prospective Investigation into Cancer and nutrition (EPIC), metabolic profiles were determined by 1H NMR analysis on 807 serum samples originating from a nested liver cancer case–control study. PC-PR2 was used to quantify the variability of metabolomic profiles in terms of study subjects age, sex, body mass index, country of origin, smoking status, diabetes and fasting status, as well as factors related to sample processing. PC-PR2 enables the evaluation of important sources of variations in metabolomic studies within large-scale epidemiological investigations. 相似文献
45.
Over the past decade, there have been many reports suggesting the presence
of complex carbohydrates on nuclear and cytoplasmic proteins in mammalian
cells. Some of the most often cited of these reports deal with the
glycosylation of the high mobility group (HMG) proteins. These are
relatively abundant chromosomal proteins that are known to be associated
with nucleosomes and actively transcribed regions of chromatin. The
original report describing HMG protein glycosylation presented several
lines of evidence suggesting that these proteins are glycosylated,
including carbohydrate compositional analysis and periodic-acid Schiff
staining. We have attempted to repeat these observations with more highly
purified protein than was utilized in the original study. Using
carbohydrate compositional analysis performed by high pH anion exchange
chromatography coupled to pulsed-amperometric detection, we saw no evidence
for significant glycosylation of these proteins. In addition, we found no
evidence for the presence of O- GlcNAc, a well known form of nuclear
glycosylation. The HMG proteins did react with periodate, suggesting the
presence of a modification containing cis-diols on the protein. Several
tryptic peptides isolated from HMG 14 and 17 which retained the periodate
reactivity had in common lysine residues, suggesting a potential
modification of the straightepsilon-amino groups of lysines such as
nonenzymatic glycation. Western blot analysis of the HMG proteins using
anti-advanced glycation endproducts (AGE) antibodies confirmed the presence
of glycation products on the HMG proteins.
相似文献
46.
RS Redman 《Biotechnic & histochemistry》2013,88(3-4):103-130
Radiation therapy for cancer of the head and neck can devastate the salivary glands and partially devitalize the mandible and maxilla. As a result, saliva production is drastically reduced and its quality adversely altered. Without diligent home and professional care, the teeth are subject to rapid destruction by caries, necessitating extractions with attendant high risk of necrosis of the supporting bone. Innovative techniques in delivery of radiation therapy and administration of drugs that selectively protect normal tissues can reduce significantly the radiation effects on salivary glands. Nonetheless, many patients still suffer severe oral dryness. I review here the functional morphology and development of salivary glands as these relate to approaches to preventing and restoring radiation-induced loss of salivary function. The acinar cells are responsible for most of the fluid and organic material in saliva, while the larger ducts influence the inorganic content. A central theme of this review is the extent to which the several types of epithelial cells in salivary glands may be pluripotential and the circumstances that may influence their ability to replace cells that have been lost or functionally inactivated due to the effects of radiation. The evidence suggests that the highly differentiated cells of the acini and large ducts of mature glands can replace themselves except when the respective pools of available cells are greatly diminished via apoptosis or necrosis owing to severely stressful events. Under the latter circumstances, relatively undifferentiated cells in the intercalated ducts proliferate and redifferentiate as may be required to replenish the depleted pools. It is likely that some, if not many, acinar cells may de-differentiate into intercalated duct-like cells and thus add to the pool of progenitor cells in such situations. If the stress is heavy doses of radiation, however, the result is not only the death of acinar cells, but also a marked decline in functional differentiation and proliferative capacity of all of the surviving cells, including those with progenitor capability. Restoration of gland function, therefore, seems to require increasing the secretory capacity of the surviving cells, or replacing the acinar cells and their progenitors either in the existing gland remnants or with artificial glands. 相似文献
47.
K Ramamoorthy Subramanian Raghunandhakumar RS Anand A Paramasivam S Kamaraj S Nagaraj Devaraj Ezhilarasan Thangavelu Lakshmi Kamal Dua Dinesh Kumar Chellappan Ashokkumar Veeramuthu 《Bioinformation》2020,16(11):965
Astaxanthin (AXN) is known to have health benefits by epidemiological studies. Therefore, it is of interest to assess the effect of AXN (derived from indigenous unicellular green alga Haematococcus lacustris) to modulate cell cycle arrest, lysosomal acidification and eventually apoptosis using in vitro in A549 lung cancer cells. Natural extracts of astaxanthin were obtained by standardized methods as reported earlier and characterized by standard HPLC and MS. Treatment of A549 cells with AXN (purified fraction) showed significant reduction in cell viability (about 50%) as compared to crude extract at 50µM concentration. Thus, we show the anticancer effects and lysosomal acidification in A549 cells by Astaxanthin from Haematococcus lacustris for further consideration. Together, our results demonstrated the anticancer potential of AXN from Haematococcus lacustris, which is found to be mediated via its ability to induce cell cycle arrest, lysosomal acidification and apoptotic induction. 相似文献
48.
Youn Tae Kwak Alexa Raney Lillian S Kuo Sarah J Denial Brenda RS Temple J Victor Garcia John L Foster 《Retrovirology》2010,7(1):1-22
Background
The HIV-1 pathogenic factor, Nef, is a multifunctional protein present in the cytosol and on membranes of infected cells. It has been proposed that a spatial and temporal regulation of the conformation of Nef sequentially matches Nef's multiple functions to the process of virion production. Further, it has been suggested that dimerization is required for multiple Nef activities. A dimerization interface has been proposed based on intermolecular contacts between Nefs within hexagonal Nef/FynSH3 crystals. The proposed dimerization interface consists of the hydrophobic B-helix and flanking salt bridges between R105 and D123. Here, we test whether Nef self-association is mediated by this interface and address the overall significance of oligomerization.Results
By co-immunoprecipitation assays, we demonstrated that HIV-1Nef exists as monomers and oligomers with about half of the Nef protomers oligomerized. Nef oligomers were found to be present in the cytosol and on membranes. Removal of the myristate did not enhance the oligomerization of soluble Nef. Also, SIVNef oligomerizes despite lacking a dimerization interface functionally homologous to that proposed for HIV-1Nef. Moreover, HIV-1Nef and SIVNef form hetero-oligomers demonstrating the existence of homologous oligomerization interfaces that are distinct from that previously proposed (R105-D123). Intracellular cross-linking by formaldehyde confirmed that SF2Nef dimers are present in intact cells, but surprisingly self-association was dependent on R105, but not D123. SIVMAC239Nef can be cross-linked at its only cysteine, C55, and SF2Nef is also cross-linked, but at C206 instead of C55, suggesting that Nefs exhibit multiple dimeric structures. ClusPro dimerization analysis of HIV-1Nef homodimers and HIV-1Nef/SIVNef heterodimers identified a new potential dimerization interface, including a dibasic motif at R105-R106 and a six amino acid hydrophobic surface.Conclusions
We have demonstrated significant levels of intracellular Nef oligomers by immunoprecipitation from cellular extracts. However, our results are contrary to the identification of salt bridges between R105 and D123 as necessary for self-association. Importantly, binding between HIV-1Nef and SIVNef demonstrates evolutionary conservation and therefore significant function(s) for oligomerization. Based on modeling studies of Nef self-association, we propose a new dimerization interface. Finally, our findings support a stochastic model of Nef function with a dispersed intracellular distribution of Nef oligomers. 相似文献49.
The performance of fungal xylan-degrading enzyme preparations in elemental chlorine-free bleaching for Eucalyptus pulp 总被引:2,自引:0,他引:2
Medeiros RG Silva FG Salles BC Estelles RS Filho EX 《Journal of industrial microbiology & biotechnology》2002,28(4):204-206
Cellulase-free xylan-degrading enzyme preparations from Acrophialophora nainiana, Humicola grisea var. thermoidea and two Trichoderma harzianum strains were used as bleaching agents for Eucalyptus kraft pulp, prior to a chlorine dioxide and alkaline bleaching sequence. In comparison to the control sequence (performed
without xylanase pretreatment), the sequence incorporating enzyme treatment was more effective. Removal of residual lignin
was indicated by a reduction in kappa number. Overall, enzyme preparations from T. harzianum were marginally more effective in reducing pulp viscosity and chlorine chemical consumption and improving the brightness
of the kraft pulp. However, the highest reduction in pulp viscosity was mediated by the xylanase preparation from A. nainiana. Xylanase pretreatment compares very favorably with that of chemical pulping. Journal of Industrial Microbiology & Biotechnology (2002) 28, 204–206 DOI: 10.1038/sj/jim/7000227
Received 27 April 2001/ Accepted in revised form 03 November 2001 相似文献
50.
Regier JC; Fang QQ; Mitter C; Peigler RS; Friedlander TP; Solis MA 《Molecular biology and evolution》1998,15(9):1172-1182
Evolution and phylogenetic utility of the period gene are explored through
sequence analysis of a relatively conserved 909-bp fragment in 26
lepidopteran species. Taxa range from tribes to superfamilies, primarily
within the putative clade Macrolepidotera plus near outgroups, and include
both strongly established and problematic groupings. Their divergence dates
probably range from the late Cretaceous through much of the Tertiary.
Comparisons within the same set of closely related species show that amino
acid substitutions in period occur 4.9 and 44 times as frequently as they
do in two other nuclear genes--dopa decarboxylase and elongation factor-1
alpha, respectively. In contrast, rates of observed synonymous substitution
are within 60% of each other for these three genes. Synonymous changes in
period approach saturation by the family level, whereas nonsynonymous and
amino acid divergences across the Macrolepidoptera are less than half the
maximal values reported for this gene. Phylogenetic analyses of period
strongly supported groupings at the family level and below. In contrast to
previous analyses at this level with other nuclear genes, much of the
information lies in nonsynonymous change. Relationships up to the
superfamily level were recovered with decreasing effectiveness, and little,
if any, signal was apparent regarding relationships among superfamilies.
This could reflect rapid radiation of the superfamilies, however, rather
than saturation in the period locus; thus, period, in combination with
other genes, remains a plausible candidate for approaching the difficult
problems of lepidopteran family and superfamily relationships.
相似文献