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101.
Nagib Ahsan Luca Fornelli Fares Z. Najar Sanjeewa Gamagedara Mohammad Robiul Hossan R. Shyama Prasad Rao Ujwal Punyamurtula Andrew Bauer Zhibo Yang Steven B. Foster Maureen A. Kane 《Proteomics》2023,23(20):2300150
Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly variable, ranging from 70% to 93%. A pairwise comparison of database search results showed a 10%–19% variation in protein identification among the kits. Immunocapturing-based SAPD kits against IgG and albumin outperformed the others in the removal of these two abundant proteins. Conversely, non-antibody-based methods (i.e., kits using ion exchange resins) and kits leveraging a multi-antibody approach were proven to be less efficient in depleting IgG/albumin from samples but led to the highest number of identified peptides. Notably, our results indicate that different cancer biomarkers could be enriched up to 10% depending on the utilized SAPD kit compared with the undepleted sample. Additionally, functional analysis of the bottom-up proteomic results revealed that different SAPD kits enrich distinct disease- and pathway-specific protein sets. Overall, our study emphasizes that a careful selection of the appropriate commercial SAPD kit is crucial for the analysis of disease biomarkers in serum by shotgun proteomics. 相似文献
102.
Summary The concept of plant available and unavailable soil phosphate has been examined by growing a range of plant species in soils well mixed with carrier free P32.It was found that although activities of 5–100 µC per kg soil caused changes in dry matter and P uptake, they had no influence on the specific activity per unit dose.Only small and agriculturally insignificant differences have been found in the proportion of soil P to added P32 taken up by the different species in the acid and neutral soils employed. It is considered that such differences as there are may be due to exchange of phosphate between seed and soil. Marked differences, however, occurred in the total phosphate absorbed by the crops.These results support the view that a fraction of the soil phosphate exists in a labile pool which will exchange with added P32 and will maintain a definite equilibrium potential in the soil solution. Plants do not appear to have a means of increasing significantly the size of the labile pool under the experimental conditions described. The disparity, however, between the total phosphate uptake especially in very deficient soils does suggest that certain species are more efficient than others in the absorption of soil phosphate at low potential. 相似文献
103.
Internal pH crisis, lysine decarboxylase and the acid tolerance response of Salmonella typhimurium 总被引:10,自引:3,他引:7
Yong-Keun Park Bradley Bearson Seong Ho Bang Iel Soo Bang & John W. Foster 《Molecular microbiology》1996,20(3):605-611
Salmonella typhimurium possesses an adaptive response to acid that increases survival during exposure to extremely low pH values. The acid tolerance response (ATR) includes both log-phase and stationary-phase systems. The log-phase ATR appears to require two components for maximum acid tolerance, namely an inducible pH homeostasis system, and a series of acid-shock proteins. We have discovered one of what appears to be a series of inducible exigency pH homeostasis systems that contribute to acid tolerance in extreme acid environments. The low pH-inducible lysine decarboxylase was shown to contribute significantly to pH homeostasis in environments as low as pH 3.0. Under the conditions tested, both lysine decarboxylase and σs -dependent acid-shock proteins were required for acid tolerance but only lysine decarboxylase contributed to pH homeostasis. The cadBA operon encoding lysine decarboxylase and a lysine/cadaverine antiporter were cloned from S. typhimurium and were found to be 79% homologous to the cadBA operon from Escherichia coli . The results suggest that S. typhimurium has a variety of means of fulfilling the pH homeostasis requirement of the ATR in the form of inducible amino acid decarboxylases. 相似文献
104.
105.
Identification of alcaligin as the siderophore produced by Bordetella pertussis and B. bronchiseptica. 总被引:6,自引:5,他引:1 下载免费PDF全文
C H Moore L A Foster D G Gerbig Jr D W Dyer B W Gibson 《Journal of bacteriology》1995,177(4):1116-1118
The siderophores produced by iron-starved Bordetella pertussis and B. bronchiseptica were purified and were found to be identical. Using mass spectrometry and proton nuclear magnetic resonance, we determined that the siderophore produced by these organisms was identical to alcaligin, a siderophore produced by Alcaligenes denitrificans. 相似文献
106.
S. Gillis B. C. Furie B. Furie H. Patel M. C. Huberty M. Switzer W. B. Foster H. A. Scoble M. D. Bond 《Protein science : a publication of the Protein Society》1997,6(1):185-196
The gamma-carboxyglutamic acid (Gla) domains of the vitamin K-dependent blood coagulation proteins contain 10 highly conserved Gla residues within the first 33 residues, but factor IX is unique in possessing 2 additional Gla residues at positions 36 and 40. To determine their importance, factor IX species lacking these Gla residues were isolated from heterologously expressed human factor IX. Using ion-exchange chromatography, peptide mapping, mass spectrometry, and N-terminal sequencing, we have purified and identified two partially carboxylated recombinant factor IX species; factor IX/gamma 40E is uncarboxylated at residue 40 and factor IX/gamma 36,40E is uncarboxylated at both residues 36 and 40. These species were compared with the fully gamma-carboxylated recombinant factor IX, unfractionated recombinant factor IX, and plasma-derived factor IX. As monitored by anti-factor IX:Ca (II)-specific antibodies and by the quenching of intrinsic fluorescence, all these factor IX species underwent the Ca(II)-induced conformational transition required for phospholipid membrane binding and bound equivalently to phospholipid vesicles composed of phosphatidylserine, phosphatidylcholine, and phosphatidylethanolamine. Endothelial cell binding was also similar in all species, with half-maximal inhibition of the binding of 125I-labeled plasma-derived factor IX at concentrations of 2-6 nM. Functionally, factor IX/gamma 36,40E and factor IX/gamma 40E were similar to fully gamma-carboxylated recombinant factor IX and plasma-derived factor IX in their coagulant activity and in their ability to participate in the activation of factor X in the tenase complex both with synthetic phospholipid vesicles and activated platelets. However, Gla 36 and Gla 40 represent part of the epitope targeted by anti-factor IX:Mg(II)-specific antibodies because these antibodies bound factor IX preferentially to factor IX/gamma 36,40E and factor IX/gamma 40E. These results demonstrate that the gamma-carboxylation of glutamic acid residues 36 and 40 in human factor IX is not required for any function of factor IX examined. 相似文献
107.
108.
Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria 总被引:16,自引:0,他引:16
We show that in animal mitochondria homologous genes that differ in guanine plus cytosine (G + C) content code for proteins
differing in amino acid content in a manner that relates to the G + C content of the codons. DNA sequences were analyzed using
square plots, a new method that combines graphical visualization and statistical analysis of compositional differences in
both DNA and protein. Square plots divide codons into four groups based on first and second position A + T (adenine plus thymine)
and G + C content and indicate differences in amino acid content when comparing sequences that differ in G + C content. When
sequences are compared using these plots, the amino acid content is shown to correlate with the nucleotide bias of the genes.
This amino acid effect is shown in all protein-coding genes in the mitochondrial genome, including cox I, cox II, and cyt b, mitochondrial genes which are commonly used for phylogenetic studies. Furthermore, nucleotide content differences are shown
to affect the content of all amino acids with A + T- and G + C-rich codons. We speculate that phylogenetic analysis of genes
so affected may tend erroneously to indicate relatedness (or lack thereof) based only on amino acid content.
Received: 3 July 1996 / Accepted: 6 November 1996 相似文献
109.
The amphotropic murine leukemia virus receptor gene encodes a 71-kilodalton protein that is induced by phosphate depletion. 总被引:2,自引:2,他引:0 下载免费PDF全文
The amphotropic murine leukemia virus (MuLV) can infect cells from a number of mammals, including humans, via its specific receptor. Basic knowledge of amphotropic MuLV receptor expression is likely to be useful in the development and improvement of gene therapy protocols based on amphotropic-pseudotyped vectors. To investigate the expression of the human receptor for the amphotropic MuLV (GLVR-2, newly termed Pit2), we determined its mRNA levels in several cell lines and found them to vary significantly. Induction of increased levels of mRNA after removal of phosphate from the media was observed in two osteosarcoma cell lines. The increase in GLVR-2 mRNA resulted in a concomitant rise in the levels of a 71-kDa protein specifically recognized by affinity-purified antibodies against GLVR-2. Using these antibodies, we were able to confirm the intracellular topology of the large hydrophilic domain between the proposed sixth and seventh transmembrane domains of the GLVR-2 protein. This assignment is in agreement with the fourth extracellular loop being outside the cell, consistent with the proposal that the fourth extracellular loop of GLVR-2 contains the envelope binding site. 相似文献
110.
The prevalence of obesity among African American women approaches 50% and greatly exceeds rates for Caucasian women. In addition, black women lose less weight than white during obesity treatment and gain more weight when untreated. This study assessed resting energy expenditure (REE) and body composition in obese white (n=122) and black (n=44) women to explore the relationship between biological variables and these observed differences. REE and body composition were assessed by indirect calorimetry and densitometry, respectively, before weight loss. REE was significantly lower in black subjects (1637.6 ± 236.9 kcal/d) than in white (1731.4 ± 262.0) (p=0.04). REE remained significantly lower in blacks than whites after adjusting for body weight (p=0.02). REE, adjusted for fat-free mass, was also significantly lower in blacks than whites (p<0.0001), although the overestimation of fat-free mass by densitometry in blacks may have contributed to this finding. There were no differences between the groups in respiratory quotient. These results suggest that a decreased REE may exist in obese black women, and it may be related to the observed differences between black and white women in the prevalence of obesity and in the response to weight loss treatment. These crosssectional findings await confirmation in longitudinal studies. 相似文献