Evaluating Peptide Mass Fingerprinting-based Protein Identification

Identification of proteins by mass spectrometry (MS) is an essential step in pro- teomic studies and is typically accomplished by either peptide mass fingerprinting (PMF) or amino acid sequencing of the peptide. Although sequence information from MS/MS analysis can be used to validate PMF-based protein identification, it may not be practical when analyzing a large number of proteins and when high- throughput MS/MS instrumentation is not readily available. At present, a vast majority of proteomic studies employ PMF. However, there are huge disparities in criteria used to identify proteins using PMF. Therefore, to reduce incorrect protein identification using PMF, and also to increase confidence in PMF-based protein identification without accompanying MS/MS analysis, definitive guiding principles are essential. To this end, we propose a value-based scoring system that provides guidance on evaluating when PMF-based protein identification can be deemed sufficient without accompanying amino acid sequence data from MS/MS analysis.     

Phylogeography and domestication of Indian river buffalo

Background  

The water buffalo- Bu balus bubalis holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poorly understood. Therefore, to understand the relationship among the maternal lineages of Indian river buffalo breeds and their domestication process, we analysed mitochondrial D-loop region of 217 animals representing eight breeds from eight different locations in India along with published sequences of Mediterranean buffalo.     

TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12

Pulsed-field gel electrophoresis (PFGE) revealed three previously uncharacterized megaplasmids in the genome of Rhodococcus erythropolis AN12. These megaplasmids, pREA400, pREA250, and pREA100, are approximately 400, 250, and 100kb, respectively, based on their migration in pulsed-field gels. Genetic screening of an AN12 transposon insertion library showed that two megaplasmids, pREA400, and pREA250, are conjugative. Mobilization frequencies of these AN12 megaplasmids to recipient R. erythropolis SQ1 were determined to be approximately 7x10(-4) and 5x10(-4) events per recipient cell, respectively. It is known for other bacterial systems that a relaxase encoded by the traA gene is required to initiate DNA transfer during plasmid conjugation. Sequences adjacent to the transposon insertion in megaplasmid pREA400 revealed a putative traA-like open reading frame. A targeted gene disruption method was developed to generate a traA mutation in AN12, which allowed us to address the role of the traA gene product for Rhodococcus megaplasmid conjugation. We found that the AN12 traA mutant is no longer capable of transferring the pREA400 megaplasmid to SQ1. Furthermore, we confirmed that the conjugation defect was specifically due to the disruption of the traA gene, as pREA400 megaplasmid conjugation defect is restored with a complementing copy of the traA gene.     

Pressurized water versus ethanol as a Silybum marianum extraction solvent for inhibition of low-density lipoprotein oxidation mediated by copper and J774 macrophage cells

Silybum marianum contains flavonolignans, termed silymarin (SM), that are therapeutic agents for many inflammation-based diseases including atherosclerosis. Oxidation of human low-density lipoprotein was induced by CuSO4 or J774 macrophage cells and measured by the formation of thiobarbituric acid reactive substances (TBARS). SM was extracted by pressurized hot water (PHWE) or ethanol, and the effects of these extracts on TBARS formation were evaluated in comparison with those of SM preparations made from blending masses of individual flavonolignan standards in ratios identical to those of the water and ethanol extracts. Ethanol-extracted SM and its blended counterpart inhibited the generation of TBARS by 82% and 43%, respectively, at 150 mumol/L doses. TBARS levels in the presence of 150 micromol/L of the PHWE and its blended SM counterpart were reduced by 84% and 38%, respectively. Extracts from milk thistle fruit displayed higher protective effects than blended SM solutions of the same concentration with an identical compositional makeup. The appearance of degradation peaks in the water extract did not create any cytotoxic effects. Results of this study confirm that PHWE can be used to extract flavonolignans from milk thistle and that these extracts may possess therapeutic potential different from or beyond that of traditional organic solvent preparations.     

Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo

Water buffalo (Bubalus bubalis) is broadly classified into river and swamp categories, but it remains disputed whether these two types were independently domesticated, or if they are the result of a single domestication event. In this study, we sequenced the mitochondrial D-loop region and cytochrome b gene of 217 and 80 buffalo respectively from eight breeds/locations in northern, north-western, central and southern India and compared our results with published Mediterranean and swamp buffalo sequences. Using these data, river and swamp buffalo were distinguished into two distinct clades. Based upon the existing knowledge of cytogenetic, ecological and phenotypic parameters, molecular data and present-day distribution of the river and swamp buffalo, we suggest that these two types were domesticated independently, and that classification of the river and swamp buffalo as two related subspecies is more appropriate.     

Nitric oxide: a possible mediator of ovulation and postovulatory follicle regression in chicken

Nitric oxide (NO) has recently emerged as a regulator of functional and structural regression in mammalian reproductive tissues. However, the role of NO in ovulation and postovulatory follicles (POF) that undergo regression in laying birds is unclear. In the present investigation, the expression profiles of iNOS mRNA, tissue NO levels and the percentage of apoptotic cells were studied in the regressing chicken postovulatory follicle (POF). The postovulatory follicles gradually lost weight during its regression and reached the lowest weight on POF5. The number of apoptotic cells was increased significantly during the regression of POF. The mRNA expression of iNOS was noticed in the second largest preovulatory follicle (F2) that subsequently increased in the largest preovulatory follicle (F1). However, the level of iNOS mRNA was declined immediately after ovulation and thereafter upregulated again to reach a peak in POF3 with a subsequent reduction in POF5 to below the basal level. The tissue NO levels followed a similar pattern except with a peak production in POF4. The gross regression and apoptosis in POFs were well associated with iNOS expression and NO production. In conclusion, NO appears to play a role in ovulation and regression of postovulatory follicle in chicken.     

A luminal breast cancer genome atlas: progress and barriers

The challenge of developing an atlas that catalogs all the functionally important genomic changes associated with the development of luminal-type breast cancer is discussed in this article. The development of genome-wide techniques such as expression profiling, array-based comparative genomic hybridization and unbiased sequencing have put a cancer genome atlas within reach. However these techniques have revealed that the somatic DNA alterations associated with the development of a common solid tumor such as breast cancer are extremely complex. For example, large scale tumor DNA resequencing projects, focused on a small number of cell lines and the analysis of many genes, suggest that as many as 100 somatic mutations may have accumulated by the time a diagnosis is made. Similarly, array comparative hybridization experiments have uncovered multiple gene amplification and deletion events. Dealing with this complexity requires access to tumor and matched normal DNA from a large number of cases, with sufficient material to complete a spectrum of analytical techniques. Second, an acceptable approach to patient consent or sample de-identification must be in place if DNA sequencing traces are to be entered into public databases. Third, samples must be linked to detailed information on disease outcomes in order to identify lesions associated with aggressive clinical behavior. We conclude that samples from neoadjuvant endocrine therapy clinical protocols offer the best sample sets to initiate a luminal breast cancer genome atlas because these studies are amongst the few in which investigators have obtained high quality frozen tumor samples associated with both short term information on the estrogen dependence of individual ER+ tumors, as well as conventional data on long-term cancer survival.     

Structure-activity relationships of novel, highly potent, selective, and orally active CCR1 antagonists

Design and synthesis of a series of 3-amino-4-(2-(2-(4-benzylpiperazin-1-yl)-2-oxoethoxy)phenylamino)cyclobutenedione derivatives as novel CCR1 antagonists are described. Structure-activity relationship studies led to the identification of compound 22, which demonstrated potent binding activity, functional antagonism of CCR1 as well as good species cross-reactivity. In addition, compound 22 also showed desirable pharmacokinetic profiles and was selected for in vivo studies in the mouse collagen-induced arthritis model.     

Induction of gamma-glutamyl transpeptidase by hexachlorocyclohexane

Hexachlorocyclohexane (BHC) induced gamma-Glutamyl transpeptidase in rat liver. The enzyme was partially purified from normal BHC fed and fetal liver and also from hepatoma. The gel filtration and electrophoretic properties of the BHC-induced enzyme was compared against that of the other three. Chemical induced hepatoma showed an additional peak of activity in Sephadex G-200 filtration. The other enzymes could be cleaved by papain to give a fraction which cochromatographed with the additional peak of hepatoma enzyme. BHC-induced enzyme and normal enzyme had similar electrophoretic mobility but differed from that of hepatoma and fetal liver enzyme which showed a slightly slower movement.