Prediction of sequential antigenic regions in proteins

Prediction of antigenic regions in a protein will be helpful for a rational approach to the synthesis of peptides which may elicit antibodies reactive with the intact protein. Earlier methods are based on the assumption that antigenic regions are primarily hydrophilic regions at the surface of the protein molecule. The method presented here is based on the amino acid composition of known antigenic regions in 20 proteins which is compared with that of 314 proteins [(1978) Atlas of Protein Sequence and Structure, vol. 5, suppl. 3, 363-373]. Antigenicity values were derived from the differences between the two data sets. The method was applied to bovine ribonuclease, the B-subunit of cholera toxin and herpes simplex virus type 1 glycoprotein D. There was a good correlation between the predicted regions and previously determined antigenic regions.     

The oxidation of the calcium probe quin2 and its analogs by prostaglandin H synthase

Quin2 and its analogs BAPTA, 5,5'-dimethyl BAPTA, 5,5'-difluoro BAPTA, fura-2, and indo-1 were developed to measure intracellular calcium concentrations. In this study we investigated whether quin2 and its analogs are susceptible to peroxidase-catalyzed oxidation. The hydroperoxidase activity of prostaglandin H synthase, like other peroxidases, is capable of oxidizing a wide variety of substrates. It was found that quin2 and its analogs served as reducing cofactors for the hydroperoxidase activity of prostaglandin H synthase, undergoing oxidation in the process. Furthermore, arachidonic acid metabolism was stimulated. Oxidation of quin2 and its analogs resulted in the formation of a carbon-centered radical, as could be detected by ESR, and in the formation of formaldehyde. Quin2 fluorescence decreased upon addition of arachidonic acid and prostaglandin H synthase. Furthermore, addition of calcium no longer resulted in an increase in quin2 fluorescence, as was observed prior to the addition of arachidonic acid and the enzyme. This indicates that one or more of the -N-CH2-COOH groups, which are responsible for the binding of calcium, were oxidized by the hydroperoxidase. Since prostaglandin H synthase is present in many cellular systems in which calcium concentrations are modulated, oxidation of the calcium probe might not only affect the measurement of intracellular calcium but could activate arachidonic acid metabolism as well.     

Toxigenic fungi associated with stored corn

A total of 246 fungal isolates were obtained from 25 moldy corn samples collected in central Iowa. Either water or ether extracts of all corn samples except one exhibited some degree of toxicity in mice and/or ducklings. At least one toxigenic isolate was obtained from each corn sample. Extracts of cultures of 99 of the fungal isolates, involving 13 genera, produced death in one or more of the assay animals. The majority of the toxigenic isolates belonged to the generaAspergillus andPenicillium. Three isolates ofTrichothecium roseum were highly toxic to ducklings and mice. The ducklings exhibited a flaccid paralysis shortly after receiving an oral dose of extracts of these three isolates. Death frequently occurred following a second oral dose given 24 hr later. Mice given intraperitoneal injections of extracts ofT. roseum first exhibited lethargy and intermittent tremors, then hyperemotivity, roughening of the hair coat, abdominal respirations, incoordination, dyspnea and clonic convulsions with death occurring usually within 10 to 20 min.

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Zusammenfassung Insgesamt sind 246 Pilzisolierungen von 25 verschimmelten Getreideproben, die in Zentral-Iowa gesammelt worden sind, erhalten worden. Sowohol Wasser- wie Aether-Extrakte von allen Getreideproben zeigten eine gewisse Toxizität in Mäusen als auch in Entchen außer einer einzigen Probe. Kulturextrakte von 99 der Pilzisolierungen, die 13 Gattungen umfaßten, verursachten den Tod in einem oder in mehreren Versuchstieren. Die Mehrheit der toxischen Isolierungen gehörte den GattungenAspergillus undPenicillium an. Drei Isolierungen vonTrichothecium roseum waren hoch toxisch für Entchen und Mäuse. Die Entchen zeigten eine schlaffe Paralyse kurz nachdem sie eine orale Dosis der Auszüge dieser drei Isolierungen erhalten hatten. Tod erfolgte häufig nach der zweiten oralen Dosis innerhalb 24 Stunden. Mäuse, die eine intraperitoneale Injektion der Auszüge vonT. roseum erhielten, zeigten erst eine Lethargie und einen intermittierenden Tremor, dann eine Hyperemotivität, aufgerauhte Haarbedeckung, abdominale Atmung, Inkoordination, Dyspnoe, klonische Zuckungen und Tod gewöhnlich innerhalb 10 bis 20 Minuten.

     

Analysis of pipecolic acid in biological fluids using capillary gas chromatography with electron-capture detection and [H11]pipecolic acid as internal standard

A sensitive and accurate stable isotope dilution assay was developed for the measurement of pipecolic acid in body fluids using capillary gas chromatography with electron-capture detection. The method utilizes [²H₁₁]pipecolic acid as the internal standard. Sample preparation consisted of derivatization in aqueous solution (pH 11.5) of the amine moiety with methyl chloroformate to the N-methylcarbamate, followed by acidic ethyl acetate extraction at pH ≤ 2 and further derivatization of the carboxyl moiety with pentafluorobenzyl bromide, the excess of which was removed by solid-phase extraction. Control values have been determined in the plasma of at-term infants, age > 1 week (n = 21, mean = 1.36 μM, range = 0.47–3.27 μM). The utility of the method was demonstrated by quantitating pipecolic acid in biological fluids derived from patients with peroxisomal disorders. The method was validated against an established electron-capture negative ion mass fragmentographic technique.     

Enaminones 9. Further studies on the anticonvulsant activity and potential type IV phosphodiesterase inhibitory activity of substituted vinylic benzamides

Structure-activity relationship studies were employed to synthesize a series of 3- and 3,4-substituted benzamides from 3-amino-2-cyclohexenones. An improved method for the synthesis of benzamides from 3-amino-2-cyclohexenones is presented which provided significantly higher yields (71-79%) for the reported compounds. NMR and X-ray structural analyses were undertaken to note the possible intra- and intermolecular interactions of the synthesized analogs. Molecular modeling studies were used to determine the minimized configuration and were compared to their X-ray structures for correlation. These new entities were evaluated as potential anticonvulsants and type IV phosphodiesterase inhibitors (PDE4).     

Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia

Epigenetic modifications, such as aberrant DNA promoter methylation, are frequently observed in cervical cancer. Identification of hypermethylated regions allowing discrimination between normal cervical epithelium and high-grade cervical intraepithelial neoplasia (CIN2/3), or worse, may improve current cervical cancer population-based screening programs. In this study, the DNA methylome of high-grade CIN lesions was studied using genome-wide DNA methylation screening to identify potential biomarkers for early diagnosis of cervical neoplasia. Methylated DNA Immunoprecipitation (MeDIP) combined with DNA microarray was used to compare DNA methylation profiles of epithelial cells derived from high-grade CIN lesions with normal cervical epithelium. Hypermethylated differentially methylated regions (DMRs) were identified. Validation of nine selected DMRs using BSP and MSP in cervical tissue revealed methylation in 63.2–94.7% high-grade CIN and in 59.3–100% cervical carcinomas. QMSP for the two most significant high-grade CIN-specific methylation markers was conducted exploring test performance in a large series of cervical scrapings. Frequency and relative level of methylation were significantly different between normal and cancer samples. Clinical validation of both markers in cervical scrapings from patients with an abnormal cervical smear confirmed that frequency and relative level of methylation were related with increasing severity of the underlying CIN lesion and that ROC analysis was discriminative. These markers represent the COL25A1 and KATNAL2 and their observed increased methylation upon progression could intimate the regulatory role in carcinogenesis. In conclusion, our newly identified hypermethylated DMRs represent specific DNA methylation patterns in high-grade CIN lesions and are candidate biomarkers for early detection.     

Expression of Telomerase and Telomere Length Are Unaffected by either Age or Limb Regeneration in Danio rerio

Background

The zebrafish is an increasingly popular model for studying many aspects of biology. Recently, ztert, the zebrafish homolog of the mammalian telomerase gene has been cloned and sequenced. In contrast to humans, it has been shown that the zebrafish maintains telomerase activity for much of its adult life and has remarkable regenerative capacity. To date, there has been no longitudinal study to assess whether this retention of telomerase activity equates to the retention of chromosome telomere length through adulthood.

Methodology/Principal Findings

We have systematically analyzed individual organs of zebrafish with regard to both telomere length and telomerase activity at various time points in its adult life. Heart, gills, kidney, spleen, liver, and intestine were evaluated at 3 months, 6 months, 9 months, and 2 years of age by Southern blot analysis. We found that telomeres do not appreciably shorten throughout the lifespan of the zebrafish in any organ. In addition, there was little difference in telomere lengths between organs. Even when cells were under the highest pressure to divide after fin-clipping experiments, telomere length was unaffected. All aged (2 year old) tissues examined also expressed active amounts of telomerase activity as assessed by TRAP assay.

Conclusions/Significance

In contrast to several other species including humans, the retention of lifelong telomerase and telomeres, as we have reported here, would be necessary in the zebrafish to maintain its tremendous regenerative capacity. The ongoing study of the zebrafish''s ability to maintain telomerase activity may be helpful in unraveling the complexity involved in the maintenance (or lack thereof) of telomeres in other species such the mouse or human.     

Studies on adventive embryo formation in the petiole expiants of coriander (Coriandrum sativum)

Summary The petiole expiants of coriander when cultured on a solid or liquid Murashige and Skoog's medium supplemented with 0.5 mg/l 2,4-D developed a large number of meristemoids. These meristemoids could then be induced to form adventive embryos when transferred into a liquid MS-medium without 2,4-D. The development of the expiants leading to the formation of meristemoids was followed anatomically and by using SDS-polyacrylamide gel electrophoresis of soluble proteins at various days of culture.