The mzIdentML data standard for mass spectrometry-based proteomics results

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.     

Sequence of development of autumn coloration in Euonymus

Low temperature inductive treatment of resting Euonymus plants sequentially resulted in the loss of chlorophyll, an increase in carbohydrate content, an increase in the activity of phenylalanine ammonialyase followed by an accumulation of cinnamic acids and flavonols and finally by the accumulation of flavolans and anthocyanins. These changes were contrasted with changes resulting from low temperature treatments of actively growing plants which are physiologically not capable of the sequence leading to normal autumn coloration.     

Systematic interpolation method predicts protein chromatographic elution with salt gradients,pH gradients and combined salt/pH gradients

A methodology is presented to predict protein elution behavior from an ion exchange column using both individual or combined pH and salt gradients based on high‐throughput batch isotherm data. The buffer compositions are first optimized to generate linear pH gradients from pH 5.5 to 7 with defined concentrations of sodium chloride. Next, high‐throughput batch isotherm data are collected for a monoclonal antibody on the cation exchange resin POROS XS over a range of protein concentrations, salt concentrations, and solution pH. Finally, a previously developed empirical interpolation (EI) method is extended to describe protein binding as a function of the protein and salt concentration and solution pH without using an explicit isotherm model. The interpolated isotherm data are then used with a lumped kinetic model to predict the protein elution behavior. Experimental results obtained for laboratory scale columns show excellent agreement with the predicted elution curves for both individual or combined pH and salt gradients at protein loads up to 45 mg/mL of column. Numerical studies show that the model predictions are robust as long as the isotherm data cover the range of mobile phase compositions where the protein actually elutes from the column.     

Evaluation of testicular toxicology: a synopsis and discussion of the recommendations proposed by the Society of Toxicologic Pathology

BACKGROUND: Detection of chemically induced effects on male fertility and on testicular spermatogenesis in particular, has become of increasing concern. More stringent regulatory guidelines, introduced by ICH, EPA and OECD (Table 1) have raised the awareness of toxicologists and pathologists for the need to conduct sensitive and careful evaluation of the male reproductive tract for potential toxic effects of administered compounds. With it has come confusion and in many cases, inappropriate procedures, often based on misunderstanding of what is required and on inadequate understanding of spermatogenesis. This article summarizes and discusses the main recommendations recently proposed by the Society of Toxicologic Pathology on recommended approaches for the evaluation of testicular and epididymal toxicity [Lanning LL, Creasy DM, Chapin RE, Mann PC, Barlow NJ, Regan KS, Goodman DG. Toxicologic Pathology 30:518-531, 2002]. The major recommendations are: Use sexually mature animals to evaluate effects on spermatogenesis. Sample left and right testes and epididymides and record organ weights. Use modified Davidson's fixative to fix testes from all species from studies of 13 wks duration and less. Examine transverse sections of the testes (including part of the rete), and longitudinal sections of the epididymides. Embed tissues in paraffin wax. For rodent studies up to 28 days, examine periodic acid-Schiff's-hematoxylin stained sections. For all other studies examine hematoxylin and eosin stained sections. Microscopic evaluation of the testis should be a qualitative evaluation carried out with an awareness of the spermatogenic cycle. Quantitative procedures are inappropriate for screening studies. Nomenclature and grading of findings for spermatogenic disturbances will vary on a case by case basis.     

Tetratricopeptide Repeat Domain 9A Negatively Regulates Estrogen Receptor Alpha Activity

Tetratricopeptide repeat domain 9A (TTC9A) is a target gene of estrogen and progesterone. It is over-expressed in breast cancer. However, little is known about the physiological function of TTC9A. The objectives of this study were to establish a Ttc9a knockout mouse model and to study the consequence of Ttc9a gene inactivation. The Ttc9a targeting vector was generated by replacing the Ttc9a exon 1 with a neomycin cassette. The mice homozygous for Ttc9a exon 1 deletion appear to grow normally and are fertile. However, further characterization of the female mice revealed that Ttc9a deficiency is associated with greater body weight, bigger thymus and better mammary development in post-pubertal mice. Furthermore, Ttc9a deficient mammary gland was more responsive to estrogen treatment with greater mammary ductal lengthening, ductal branching and estrogen target gene induction. Since Ttc9a is induced by estrogen in estrogen target tissues, these results suggest that Ttc9a is a negative regulator of estrogen function through a negative feedback mechanism. This is supported by in vitro evidence that TTC9A over-expression attenuated ERα activity in MCF-7 cells. Although TTC9A does not bind to ERα or its chaperone protein Hsp90 directly, TTC9A strongly interacts with FKBP38 and FKBP51, both of which interact with ERα and Hsp90 and modulate ERα activity. It is plausible therefore that TTC9A negatively regulates ERα activity through interacting with co-chaperone proteins such as FKBP38 and FKBP51.     

1H NMR metabolomics reveals increased glutaminolysis upon overexpression of NSD3s or Pdp3 in Saccharomyces cerevisiae

NSD3s, the proline-tryptophan-tryptophan-proline (PWWP) domain-containing, short isoform of the human oncoprotein NSD3, displays high transforming properties. Overexpression of human NSD3s or the yeast protein Pdp3 in Saccharomyces cerevisiae induces similar metabolic changes, including increased growth rate and sensitivity to oxidative stress, accompanied by decreased oxygen consumption. Here, we set out to elucidate the biochemical pathways leading to the observed metabolic phenotype by analyzing the alterations in yeast metabolome in response to NSD3s or Pdp3 overexpression using ¹H nuclear magnetic resonance (NMR) metabolomics. We observed an increase in aspartate and alanine, together with a decrease in arginine levels, on overexpression of NSD3s or Pdp3, suggesting an increase in the rate of glutaminolysis. In addition, certain metabolites, including glutamate, valine, and phosphocholine were either NSD3s or Pdp3 specific, indicating that additional metabolic pathways are adapted in a protein-dependent manner. The observation that certain metabolic pathways are differentially regulated by NSD3s and Pdp3 suggests that, despite the structural similarity between their PWWP domains, the two proteins act by unique mechanisms and may recruit different downstream signaling complexes. This study establishes for the first time a functional link between the human oncoprotein NSD3s and cancer metabolic reprogramming.