Clinical translation of MS-based,quantitative plasma proteomics: status,challenges, requirements,and potential

Introduction: Aided by the advent of advanced mass spectrometry (MS)-based technologies and methodologies, quantitative proteomics has emerged as a viable technique to capture meaningful data for candidate biomarker evaluation. To aid clinical translation, these methods generally utilize a bottom-up strategy with isotopically labeled standards and a targeted form of MS measurement.

Areas covered: This article reviews the status, challenges, requirements, and potential of translating current, MS-based methods to the clinical laboratory. The described methods are discussed and contrasted within a fit-for-purpose approach, while different resources for quality control, quantitative analysis, and data interpretation are additionally provided.

Expert commentary: Although great strides have been made over the past five years in developing reliable quantitative assays for plasma protein biomarkers, it is crucial for investigators to have an understanding of the clinical validation process, a major roadblock in translational research. Continued progress in method design and validation of protein assays is necessary to ultimately achieve widespread adoption and regulatory approval.     

Earth,Air, Fire,and Water: Elements of Art

Abstract

Shoshana Zuboff. In the Age of the Smart Machine: The Future of Work and Power. New York: Basic Books, 1988, 468 pp. $11.95 paperback.

George Gilder. Microcosm: The Quantum Revolution in Economics and Technology. New York: Simon &; Schuster, 1989. 426 pp. $19.95 hardcover.

Loren Baritz. The Good Life. New York: Alfred A. Knopf, Inc., 1988. 361 pp. $19.95 hardcover.

Miles Orville. The Real Thing: Imitation and Authority in American Culture, 1880–1940. Chapel Hill: University of North Carolina Press, 1989. 382 pp. $14.95 paperback.

Peter Shaw. The War Against the Intellect. Iowa City: The University of Iowa Press, 1989. 181 pp. $10.95 paperback.

Robert Alter. The Pleasures of Reading in an Ideological Age. New York: Simon &; Schuster, 1989. 250 pp. $18.95 hardcover.

Ian Crofton. A Dictionary of Art Quotations. New York: Macmillan Publishing Company, 1989. $19.95 hardcover.     

Serologic prevalence of Toxoplasma gondii in field mice, Microtus fortis, from Yuanjiang, Hunan Province, People's Republic of China

Antibodies to Toxoplasma gondii were investigated in serum samples of field mice, Microtus fortis, from Yuanjiang, Hunan Province, People's Republic of China. The modified agglutination test (MAT) incorporating formalin-fixed whole tachyzoites and mercaptoethanol was used to determine antibodies. Antibodies to T. gondii (MAT > or = 1:20) were found in 36 (29%) of 124 trapped mice. The antibody titers of positive sera (percentage in parentheses) were 1:20 (8.9), 1:40 (3.2), 1:80 (3.2), 1:160 (1.6), 1:320 (1.6), 1:640 (1.6), 1:1,280 (1.6), 1: 2,560 (0.8), and > 1:2,560 (6.5). No antibody to T. gondii was found in 104 sera of laboratory-bred M. fortis infected with Schistosoma japonicum between 1 and 45 days after infection.     

Survey of distribution of substance P, vasoactive intestinal polypeptide, cholecystokinin, neurotensin, Met-enkephalin, bombesin and PHI in the spinal cord of cat, dog, sloth and monkey

Levels of substance P (sP), peptide-histidine-isoleucine (PHI), vasoactive intestinal polypeptide (VIP), cholecystokinin (CCK), neurotensin (NT), bombesin (BOM) and methionine-enkephalin (Met-Enk) like immunoreactivity were measured in cat, dog, primate and sloth cervical, thoracic, lumbar and sacral dorsal and ventral horns and dorsal root ganglia. The levels of peptides in the cat sacral cord and the principal peaks of immunoreactivity on a 10-60% acetonitrile gradient on a C18 reverse phase high performance liquid chromatography (HPLC) were sP (sP1-11: 369 ng/g), PHI (PHI: 271 ng/g), VIP (VIP1-28: 210 ng/g), Met-Enk (Met1-5 and extended forms: 257 ng/g), BOM (BOM1-10 and GRP1-27: 20 ng/g), CCK (CCK-8: 15 ng/g) and NT (NT1-13: 10 ng/g). Consideration of the rostrocaudal levels revealed an approximately even distribution with the exception of VIP and PHI which showed sacral/cervical ratios of 79 and 63. For sP, Met-Enk and BOM dorsal/ventral ratios were greater than 1 at all spinal levels. For VIP, PHI and CCK these ratios were greater than 1 only in the sacral cord. Dorsal root ganglion (DRG) levels of sP, VIP, PHI were readily measurable in single ganglia and covaried with the respective levels in the dorsal cord. Pooled samples of spinal ganglia and the trigeminal ganglia revealed that the relative levels of peptide immunoreactivity were: sP (25 ng/g); VIP (26 ng/g); PHI (28 ng/g); Met-Enk (6 ng/g); CCK (2 ng/g); NT (1 ng/g); and BOM (1 ng/g).     

The content of troponin, tropomyosin, actin, and myosin in rabbit skeletal muscle myofibrils

A stacking sodium dodecyl sulfate polyacrylamide gel electrophoresis system has been used to resolve and quantify all the major myofibrillar protein components (actin, myosin, tropomyosin, and troponin C, T, and I). Quantification was achieved by densitometry of the fast green-stained gels calibrated with the use of purified proteins. The approximate molar ratios of these proteins in rabbit muscle are: actin: myosin: tropomyosin: troponin T: troponin I: troponin C = 7:1:1:1:1:1. On the basis of these results and available structural information one obtains an estimate of 254 myosin molecules per thick filament.     

Cryopreservation of spermatozoa from closed colonies, and inbred, spontaneous mutant, and transgenic strains of rats

We attempted to cryopreserve spermatozoa from closed colonies (Jcl:SD and Jcl:Wistar), and inbred (BN/Crj, F3441 DuCrj, LEW/Crj, Long-Evans and WKY/NCrj), mutant (Zitter [WTC.ZI-zi] and Tremor [TRM]), transgenic (human A-transferase [A], and green fluorescent protein [GFP]) strains of rats. Rat epididymal spermatozoa suspended in cryopreservation solution (23% egg yolk, 8% lactose monohydrate, and 0.7% Equex Stm, pH 7.4, adjusted with 10% Tris [hydroxymethy] aminomethane) were frozen and stored at -196 degrees C. After thawing at 37 degrees C, the spermatozoa were instilled into the tip of each uterine horn of the recipients. A total of five recipient females for each strain were inseminated with cryopreserved spermatozoa, and normal live offspring of all strains (Jcl:SD: 11, Jcl:Wistar: 13, BN/Crj: 9, F344/DuCrj: 28, LEW/Crj: 4, Long-Evans: 6, WKY/NCrj: 8, TRM: 24, WTC.ZI-zi: 27, A: 30 and GFP: 20) were obtained.     

克里雅绿洲旱生芦苇根茎叶C、N、P化学计量特征的季节变化

旱生芦苇在水分限制、元素匮乏的环境条件下,经长期进化适应形成了自身独特的生理生态特征,研究其C、N、P化学计量特征随生长季节的变化规律有助于深入了解该植物生存和适应策略。系统分析了克里雅绿洲旱生芦苇根、茎、叶的C、N、P化学计量特征及其季节动态,深入探讨了不同生长季、不同器官以及两因素的交互作用对以上特征的影响。结果表明:旱生芦苇C、N、P含量均值分别为393.36、12.43、1.25 mg/g,C∶N、N∶P、C∶P均值分别为54.55、9.96、441.27。整个生长季内芦苇各器官间C、N、P平均含量的变化规律一致,为叶茎根,C、N、P化学计量比的变化规律不一致;芦苇C含量随生长季节的变化不断增加,N、P随季节的变化逐渐减少,C、N、P化学计量比随季节的变化规律也不尽相同。对芦苇C、N、P含量及其化学计量比整体变异来源分析显示,生长季节的变化对芦苇C、P、C∶N、C∶P变化的贡献大于器官间差异,器官间差异对芦苇N、N∶P变化的贡献大于生长季节的变化;说明芦苇生长发育过程中各生长季各器官对元素的吸收利用具有特异性。结合N、P元素含量及N∶P值的大小可知,研究区芦苇生长受到N、P共同限制,且更易受N元素的限制。     

Encyclopedia of Precolonial Africa: Archaeology, History, Languages, Cultures, and Environments

Encyclopedia of Precolonial Africa: Archaeology, History, Languages, Cultures, and Environments. Joseph O. Vogel. ed. Walnut Creek, CA: AltaMira Press, 1997.606 pp.     

广西大青山杉木人工林碳氮磷生态化学计量特征

为研究杉木人工林生态系统植物、凋落物和土壤碳(C)、氮(N)、磷(P)生态化学计量特征的差异和相互关系,以广西大青山杉木密度试验林为研究对象,测定了5种初植密度下杉木人工林针叶、草本、凋落物和土壤的C、N、P含量及其比值。结果表明:针叶的C、N、P含量最高,凋落物次之,土壤最低。C∶N、C∶P表现为凋落物针叶草本土壤,N∶P表现为凋落物草本针叶土壤。其中针叶的N∶P均值为16.69,凋落物C∶N显著高于N发生释放的C∶N的临界值(30)。杉木人工林针叶和草本N、C∶N呈显著负相关关系,针叶和土壤的C∶N、N∶P,草本和凋落物P含量、C∶P均呈显著正相关关系,体现了杉木生态系统内的C、N、P在针叶、草本、凋落物和土壤之间相互转化和循环。南亚热带杉木人工林植物生长受P限制,凋落物分解慢,土壤有机质的矿化作用慢,养分循环能力低,因此在人工林抚育管理中,应保护林下植被,适当施肥,提高土壤肥力,维持杉木林长期生产力。     

Ceramide dihexosides from the spermatozoa of the starfish, Asterias amurensis, consist of gentiobiosyl- cellobiosyl-, and lactosylceramide

Ceramide dihexoside was obtained from the spermatozoa of the starfish, Asterias amurensis. Gas-liquid chromatography of the methanolysate to determine the sugar composition of the lipid demonstrated an unequal ratio of glucose and galactose, implying that two or more glycolipids are present. They were separated by thin-layer chromatography on a borate-impregnated plate into two bands. From the results of methylation analysis and chromic acid oxidation, one was determined to be lactosylceramide, while the other was suggested to be a mixture of two diglucosylceramides: gentiobiosylceramide (Glc beta 1-6Glc beta 1-1Cer) and cellobiosylceramide (Glc beta 1-4Glc beta 1-1Cer). The molar ratio of gentiobiosyl-, cellobiosyl-, and lactosylceramide was estimated to be 0.7 : 0.3 : 1.0. Ceramide dihexosides obtained from another batch of the spermatozoa, collected at the same place in a different year, consisted almost exclusively of gentiobiosylceramide as confirmed by proton-nuclear magnetic resonance spectroscopy and fast-atom bombardment mass-spectrometry. The fatty acid compositions of these glycolipids were similar and the main acids were 14h:0, 15h:0, 16h:0, 18h:0, and 24h:1 (constituting more than 80% of the total acids). The long-chain base compositions were qualitatively similar and the major constituents were commonly d18:2, d18:3, d19:3, d22:2, and t22:1. Lactosylceramide was rich in t22:1, while diglucosylceramides were rich in d22:2.     

Anti-plasmodial action of de novo-designed, cationic, lysine-branched, amphipathic, helical peptides

ABSTRACT: BACKGROUND: A lack of vaccine and rampant drug resistance demands new anti-malarials. METHODS: In vitro blood stage anti-plasmodial properties of several de novo-designed, chemically synthesized, cationic, amphipathic, helical, antibiotic peptides were examined against Plasmodium falciparum using SYBR Green assay. Mechanistic details of anti-plasmodial action were examined by optical/fluorescence microscopy and FACS analysis. RESULTS: Unlike the monomeric decapeptides {(Ac-GXRKXHKXWA-NH2) (X = F,DeltaF) (Fm, DeltaFm IC50 >100 muM)}, the lysine-branched,dimeric versions showed far greater potency {IC50 (muM) Fd 1.5 , DeltaFd 1.39}. The more helical and proteolytically stable DeltaFd was studied for mechanistic details. DeltaFq, a K-K2 dendrimer of DeltaFm and (DeltaFm)2 a linear dimer of DeltaFm showed IC50 (muM) of 0.25 and 2.4 respectively. The healthy/infected red cell selectivity indices were >35 (DeltaFd), >20 (DeltaFm)2 and 10 (DeltaFq). FITC-DeltaFd showed rapid and selective accumulation in parasitized red cells. Overlaying DAPI and FITC florescence suggested that DeltaFd binds DNA. Trophozoites and schizonts incubated with DeltaFd (2.5 muM) egressed anomalously and Band-3 immunostaining revealed them not to be associated with RBC membrane. Prematurely egressed merozoites from peptide-treated cultures were found to be invasion incompetent. CONCLUSION: Good selectivity (>35), good resistance index (1.1) and low cytotoxicity indicate the promise of DeltaFd against malaria.     

中国大陆的腐霉属菌物

综述了中国大陆腐霉属的研究进展,内容包括腐霉属菌物的发生、分布、分类鉴定、致病性、所致植物病害防治及腐霉的利用等方面.至今,中国已报道的腐霉属菌物有64个种,其中有13个种作为世界新种进行了描述,这13个新种分别为:顶生腐霉Pythium acrogynum,孤雌腐霉P.amasculinum,百色腐霉P.baisense,北方腐霉P.boreale,短枝腐霉P.breve,壁合腐霉P.connatum,镰雄腐霉P.falciforme,贵阳腐霉P.guiyangense,广西腐霉P.guangxiense,下雄腐霉P.hypoandrum,昆明腐霉P.kummingense,南宁腐霉尸nanningense和中国腐霉P.sinensis.瓜果腐霉Pythium aphanidermatum为优势种,在全国普遍引起多种植物严重的猝倒病和根、茎、叶、果腐烂病.其中,大多数腐霉种对植物具有致病性,44个种寄生植物,1个种:紫菜腐霉P.porphyrae寄生红藻和紫菜,2个种:卡地腐霉P.carolinianum 和贵阳腐霉P.guiyangense寄生蚊子幼虫,2个种:努氏腐霉P.nunn和寡雄腐霉P.oligandrum 是真菌的重寄生菌.相比之下,台湾报道的腐霉种有48种(其中新种1个:四季腐霉P.sukuiense),海南报道的腐霉种有28种.对中国大陆腐霉属的研究前景也进行了讨论.     

Metabolites of cis,trans, and trans,cis isomers of linoleic acid in mice and incorporation into tissue lipids

Metabolism of octadecadienoic acid isomers in weanling mice was studied by feeding fat-free diets supplemented with 2% by weight of cis-9,trans-12-octadecadienoic acid (c,t-18:2-d0), tetradeuterated trans-9,cis-12-octadecadienoic acid (t,c-18:2-d4) or dideuterated cis-9,cis-12-octadecadienoic acid (c,c-18:2-d2). Rates for conversion of c,t-18:2-d0 and c,c-18:2-d2 to c,t-20:4-d0 and c,c-20:4-d2 were identical and both were 5-times higher than conversion of t,c-18:2-d4 to t,c-20:4-d4. Accumulation of t,c-18:2-d4 in liver lipids was 2-4-times higher than for c,t-18:2-d0 or c,c-18:2-d2. The t,c-18:2 diet significantly increased with the 20:3(n-9) and total lipid concentrations in liver but not in heart, plasma or brain. The 20:3(n-9)/20:4(n-6) ratio in the liver lipids was 2-4-times higher for t,c-18:2-d4 than c,c-18:2-d2 fed mice. The position of the trans bond had a marked influence on the distribution of the various intermediate desaturation and elongation products. Intermediate metabolite data for the liver lipids indicated t,c-18:2-d4 was preferentially converted to 5c,11c,14t-20:3 ('dead end' product) rather than to t,c-20:4. Concentration of the 18:3(n-6) metabolite of c,t-18:2-d0 was about 10-times greater than the 18:3(n-6) metabolite of c,c-18:2-d2. Conversely, the concentration of the normal 20:3(n-6) metabolite from c,c-18:2-d2 was 4-times higher than the 20:3(n-6) metabolite of c,t-18:2-d0. Compared to the c,c-18:2 diet, the t,c- and c,t-18:2 diets significantly increased the total n-3, but not the total n-6 fatty acid content of heart lipids. These results illustrate that the position of the trans double-bond influences a variety of enzyme activities and the isomers differ in their physiological effects.     

Effects of phenylephrine on tissue gas tension, bleeding, infection, and lidocaine absorption

In an attempt to find a vasoconstrictor with less detrimental local and systemic effects than epinephrine, the effects of phenylephrine, a pure alpha agonist, on tissue gas tension, bleeding, infection rates, and lidocaine absorption were studied. All concentrations of phenylephrine significantly reduced tissue PO2 within 10 minutes of injection, and reduction of PO2 was dose-dependent. Phenylephrine 1:10,000 produced significant bacterial growth when simultaneously injected with 6 X 10(6) Staphylococcus aureus. Bacterial growth was insignificant with 1:20,000 phenylephrine and absent with 1:40,000 phenylephrine. Blood loss from a standard wound was significantly reduced at all concentrations of phenylephrine. Lidocaine absorption was significantly reduced with 1:20,000 and 1:40,000 phenylephrine. In a rat model, 1:40,000 phenylephrine significantly reduced blood loss and lidocaine absorption, produced minimal reduction of tissue PO2, and did not enhance bacterial invasion.     

陕西省森林群落乔灌草叶片和凋落物C、N、P生态化学计量特征

研究陕西省121个森林群落中乔叶、灌叶、草叶和凋落物4个层次的C、N、P化学计量学特征及其变异性,分析了各层次间及其与地理因子间的关系.结果表明： 乔叶C、N含量最高,草叶P含量最高,凋落物C、N、P含量均最低.乔叶、灌叶、草叶和凋落物的C∶N∶P分别为439.4∶14.2∶1、599.2∶13.5∶1、416.5∶13.3∶1、504.8∶15.5∶1,乔叶、灌叶、草叶N∶P值差异不显著,但均与凋落物N∶P值差异显著,表明不同生活型活体植物叶片的N∶P值具有一定的稳定性.与N含量相比,C和P含量在各层次间表现出更好的相关性;C、N、P含量及其比值在草叶与乔叶之间较在灌叶与乔叶之间表现出更好的相关性;凋落物与乔叶和草叶之间C、N、P含量均表现出显著正相关,与灌叶只在P含量之间存在显著正相关.灌叶N、P含量随纬度增加而增加,草叶N、P含量随经度增加而降低,海拔对叶片和凋落物C、N、P含量及其比值的影响较小,只有乔叶N∶P与海拔之间存在显著负相关.各地理因子对草叶的影响大小表现为经度>纬度>海拔,对乔叶、灌叶和凋落物的影响大小表现为纬度>经度>海拔.     

Hydrobiological Studies on Suraj Kund and Chandrama Kund,Hot Springs of Rajgir,Bihar, India

The hot water of Rajgir springs is used for drinking and bathing purposes by tourists. Certain physico-chemical characteristics (temperature, pH, NO, PO, etc.) of the water along with phycological parameters viz. community composition, species diversity, standing crop etc. were measured from June 1986 to April 1987. The water was deficient in Na, NO and PO ions. The hot springs were mainly dominated by algae belonging to Cyanophyceae and Bacillariophyceae. The algal community comprised 18 species, with dominance of Cyanophyceae over Bacillariophyceae. While Mastigocladus laminosus and species of Phormidium were dominant in Suraj Kund, species of Oscillaroria and Synechococcus dominated in Chandrama Kund. Diatoms comprised about 10 % of the algal community. Though there was a considerable seasonal change in species diversity of the algal community the total biomass (chlorophyll a extracted per unit area from the algal mat) remained constant.     

Neutral lipids, their fatty acids, and the sterols of the marine ciliated protozoon, Parauronema acutum

The neutral lipids and their fatty acids and the sterol fractions of the marine ciliated protozoon, Parauronema acutum, were characterized. The neutral lipids consisted of triglycerides (30%), sterols (29%), free fatty acids (24%), steryl esters (9%), and diglycerides (8%) and small amounts of fatty alcohols. The fatty acid profiles of these lipids were very similar although quantitative differences were detected. Saturated fatty acids, primarily 14:0, 16:0, and 18:0 constituted 20-30% of the total. Unsaturated fatty acids containing one to three double bonds, primarily 18:1(9), 18:2 (9,12), 18:3 (9, 12, 15) and 20:3 (11, 14, 17), constituted 35-50% of the total. Highly unsaturated fatty acids, 18:4 (6, 9, 12, 15), 20:5 (5, 8, 11, 14, 17) and 22:6 (4, 7, 10, 16, 19), constituted 16-25% of the total. The fatty alcohols consisted of 14:0 (2%), 16:0 (66%), 18:0 (3%), 20:0 (8%), and 22:0 (21%). The sterols of Parauronema acutum consisted of cholesterol (53%), campesterol (32%), desmosterol (7%), and beta-sitosterol (8%).     

Crossing, Creolization, and the African Roots of American Culture

Group Harmony: The Black Urban Roots of Rhythm and Blues. Stuart L. Goosman. Philadelphia: University of Pennsylvania Press, 2005. 291 pp.
Right to Rock: The Black Rock Coalition and the Cultural Politics of Race. Maureen Mahon. Durham, NC: Duke University Press, 2004. 317 pp.
Crossovers: Essays on Race, Music, and American Culture. John Szwed. Philadelphia: University of Pennsylvania Press, 2005. 283 pp.     

Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA

Potassium can stabilize the formation of chair- or edge-type quadruplex DNA structures and appears to be the only naturally occurring cation that can do so. As quadruplex DNAs may be important in the structure of telomere, centromere, triplet repeat and other DNAs, information about the details of the potassium–quadruplex DNA interactions are of interest. The structures of the 1:1 and the fully saturated, 2:1, potassium–DNA complexes of d(GGTTGGTGTGGTTGG) have been determined using the combination of experimental NMR results and restrained molecular dynamics simulations. The refined structures have been used to model the interactions at the potassium binding sites. Comparison of the 1:1 and 2:1 potassium:DNA structures indicates how potassium binding can determine the folding pattern of the DNA. In each binding site potassium interacts with the carbonyl oxygens of both the loop thymine residues and the guanine residues of the adjacent quartet.