Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish.

BACKGROUND: Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. RESULTS: We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. CONCLUSIONS: Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution.

The LCK-14-3-3ζ-TRPM8 axis regulates TRPM8 function/assembly and promotes pancreatic cancer malignancy.

Transient receptor potential melastatin 8 (TRPM8) functions as a Ca2+-permeable channel in the plasma membrane (PM). Dysfunction of TRPM8 is associated with human pancreatic cancer and several other diseases in clinical patients, but the underlying mechanisms are unclear. Here, we found that lymphocyte-specific protein tyrosine kinase (LCK) directly interacts with TRPM8 and potentiates TRPM8 phosphorylation at Y1022. LCK positively regulated channel function characterized by increased TRPM8 current densities by enhancing TRPM8 multimerization. Furthermore, 14-3-3ζ interacted with TRPM8 and positively modulated channel multimerization. LCK significantly enhanced the binding of 14-3-3ζ and TRPM8, whereas mutant TRPM8-Y1022F impaired TRPM8 multimerization and the binding of TRPM8 and 14-3-3ζ. Knockdown of 14-3-3ζ impaired the regulation of TRPM8 multimerization by LCK. In addition, TRPM8 phosphotyrosine at Y1022 feedback regulated LCK activity by inhibiting Tyr505 phosphorylation and modulating LCK ubiquitination. Finally, we revealed the importance of TRPM8 phosphorylation at Y1022 in the proliferation, migration, and tumorigenesis of pancreatic cancer cells. Our findings demonstrate that the LCK-14-3-3ζ-TRPM8 axis for regulates TRPM8 assembly, channel function, and LCK activity and maybe provide potential therapeutic targets for pancreatic cancer.

The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus.

Hybridization drives rapid speciation by shaping novel genotypic and phenotypic profiles. Genomic incompatibility and transcriptome shock have been observed in hybrids, although this is rarer in animals than in plants. Using the newly sequenced genomes of the blunt snout bream (Megalobrama amblycephala [BSB]) and the topmouth culter (Culter alburnus [TC]), we focused on the sequence variation and gene expression changes in the reciprocal intergeneric hybrid lineages (F1-F3) of BSB × TC. A genome-wide transcriptional analysis identified 145-974 expressed recombinant genes in the successive generations of hybrid fish, suggesting the rapid emergence of allelic variation following hybridization. Some gradual changes of gene expression with additive and dominance effects and various cis and trans regulations were observed from F1 to F3 in the two hybrid lineages. These asymmetric patterns of gene expression represent the alternative strategies for counteracting deleterious effects of the subgenomes and improving adaptability of novel hybrids. Furthermore, we identified positive selection and additive expression patterns in transforming growth factor, beta 1b (tgfb1b), which may account for the morphological variations of the pharyngeal jaw in the two hybrid lineages. Our current findings provide insights into the evolution of vertebrate genomes immediately following hybridization.

Vitexin as an active ingredient in passion flower with potential as an agent for nicotine cessation: vitexin antagonism of the expression of nicotine locomotor sensitization in rats.

CONTEXT: Nicotine, a bioactive component of tobacco, is highly addictive. Numerous therapies have been developed for smoking cessation, and all have met with limited success. Our laboratory has previously shown that an extract of Passiflora incarnata Linn. (Passifloraceae) antagonized the expression of nicotine locomotor sensitization in rats. OBJECTIVE: This study examined the ability of vitexin, a flavonoid found in P. incarnata, to ameliorate the signs of nicotine sensitization in rats. MATERIALS AND METHODS: Male Wistar rats were administered 0.4 mg/kg nicotine or vehicle (n = 16-18 per group) once a day for four consecutive days. Nicotine administration produces sensitization of locomotor activity. On the fifth day, locomotor activity was monitored as rats from each treatment group were administered either 30 or 60 mg/kg vitexin or its vehicle (n = 4-6 per group) 30 min before a challenge dose of 0.4 mg/kg nicotine. RESULTS: The challenge dose of nicotine resulted in locomotor activity in rats sensitized to nicotine for 4 days that was approximately twice that measured in rats treated with vehicle during the sensitization phase. Rats sensitized to nicotine and then treated with 60 mg/kg vitexin prior to the nicotine challenge exhibited a level of locomotor activity equivalent to the vehicle-treated controls. DISCUSSION: Vitexin antagonized the expression of nicotine locomotor sensitization in rats as the whole extract did in the previous study. CONCLUSION: Vitexin should be examined in future studies to evaluate its potential for treating nicotine addiction in humans.

A non-radioactive in vitro CaMKII activity assay using HPLC-MS.

INTRODUCTION: Calcium/Calmodulin-dependent protein kinase II (CaMKII) is a multifunctional protein kinase that phosphorylates and regulates activity of many substrates in various tissues. Traditional CaMKII activity assays rely on incorporation of radioactivity onto a CaMKII substrate by utilizing γ-32P ATP, which has a short half-life and can pose health risks to the researchers. METHODS: An 8-minute HPLC-MS method was developed to measure a CaMKII-specific peptide substrate autocamtide-2 (AC-2) and its phosphorylated form, phosphoautocamtide-2 (PAC-2). Degradation of AC-2 and PAC-2 in solutions and how to stabilize them were studied. The method was validated according to FDA guidelines for bioassays, and applied to determine CaMKII activity in a C2C12 cell lysate and IC50 of KN-93, a known CaMKII inhibitor. RESULTS: Simple acidification with formic acid prevented AC-2 and PAC-2 from undergoing rapid degradation in the CaMKII assay mixture and in diluted water solutions. LLOQ of the HPLC-MS method was 0.26 µM and 0.12 µM for quantification of AC-2 and PAC-2, respectively. Precision was within 15% and accuracy was within 100 ±â€¯15%. Using the developed method, IC50 of KN-93 was measured to be 399 ±â€¯66 nM, which was compatible to reported values. CONCLUSIONS: A validated HPLC-MS method provides precise and accurate determination of AC-2 and PAC-2. This method enabled enzyme activity assay and inhibitor IC50 determination for CaMKII without radioactive labelled reagents.

Developing an Assessment Process for a Master's of Science Degree in a Pharmaceutical Sciences Program.

Objective. To develop a program-level assessment process for a master's of science degree in a pharmaceutical sciences (MSPS) program. Design. Program-level goals were created and mapped to course learning objectives. Embedded assessment tools were created by each course director and used to gather information related to program-level goals. Initial assessment iterations involved a subset of offered courses, and course directors met with the department assessment committee to review the quality of the assessment tools as well as the data collected with them. Insights from these discussions were used to improve the process. When all courses were used for collecting program-level assessment data, a modified system of guided reflection was used to reduce demands on committee members. Assessment. The first two iterations of collecting program-level assessment revealed problems with both the assessment tools and the program goals themselves. Course directors were inconsistent in the Bloom's Taxonomy level at which they assessed student achievement of program goals. Moreover, inappropriate mapping of program goals to course learning objectives were identified. These issues led to unreliable measures of how well students were doing with regard to program-level goals. Peer discussions between course directors and the assessment committee led to modification of program goals as well as improved assessment data collection tools. Conclusion. By starting with a subset of courses and using course-embedded assessment tools, a program-level assessment process was created with little difficulty. Involving all faculty members and avoiding comparisons between courses made obtaining faculty buy-in easier. Peer discussion often resulted in consensus on how to improve assessment tools.

In-depth proteomic analysis of nonsmall cell lung cancer to discover molecular targets and candidate biomarkers.

Advances in proteomic analysis of human samples are driving critical aspects of biomarker discovery and the identification of molecular pathways involved in disease etiology. Toward that end, in this report we are the first to use a standardized shotgun proteomic analysis method for in-depth tissue protein profiling of the two major subtypes of nonsmall cell lung cancer and normal lung tissues. We identified 3621 proteins from the analysis of pooled human samples of squamous cell carcinoma, adenocarcinoma, and control specimens. In addition to proteins previously shown to be implicated in lung cancer, we have identified new pathways and multiple new differentially expressed proteins of potential interest as therapeutic targets or diagnostic biomarkers, including some that were not identified by transcriptome profiling. Up-regulation of these proteins was confirmed by multiple reaction monitoring mass spectrometry. A subset of these proteins was found to be detectable and differentially present in the peripheral blood of cases and matched controls. Label-free shotgun proteomic analysis allows definition of lung tumor proteomes, identification of biomarker candidates, and potential targets for therapy.

Methods for peptide and protein quantitation by liquid chromatography-multiple reaction monitoring mass spectrometry.

Liquid chromatography-multiple reaction monitoring mass spectrometry of peptides using stable isotope dilution (SID) provides a powerful tool for targeted protein quantitation. However, the high cost of labeled peptide standards for SID poses an obstacle to multiple reaction monitoring studies. We compared SID to a labeled reference peptide (LRP) method, which uses a single labeled peptide as a reference standard for all measured peptides, and a label-free (LF) approach, in which quantitation is based on analysis of un-normalized peak areas for detected MRM transitions. We analyzed peptides from the Escherichia coli proteins alkaline phosphatase and ß-galactosidase spiked into lysates from human colon adenocarcinoma RKO cells. We also analyzed liquid chromatography-multiple reaction monitoring mass spectrometry data from a recently published interlaboratory study by the National Cancer Institute Clinical Proteomic Technology Assessment for Cancer network (Addona et al. (2009) Nat. Biotechnol. 27: 633-641), in which unlabeled and isotopically labeled synthetic peptides or their corresponding proteins were spiked into human plasma. SID displayed the highest correlation coefficients and lowest coefficient of variation in regression analyses of both peptide and protein spike studies. In protein spike experiments, median coefficient of variation values were about 10% for SID and 20-30% for LRP and LF methods. Power calculations indicated that differences in measurement error between the methods have much less impact on measured protein expression differences than biological variation. All three methods detected significant (p < 0.05) differential expression of three endogenous proteins in a test set of 10 pairs of human lung tumor and control tissues. Further, the LRP and LF methods both detected significant differences (p < 0.05) in levels of seven biomarker candidates between tumors and controls in the same set of lung tissue samples. The data indicate that the LRP and LF methods provide cost-effective alternatives to SID for many quantitative liquid chromatography-multiple reaction monitoring mass spectrometry applications.

Protein targets of reactive electrophiles in human liver microsomes.

Liver microsomes are widely used to study xenobiotic metabolism in vitro, and covalent binding to microsomal proteins serves as a surrogate marker for toxicity mediated by reactive metabolites. We have applied liquid chromatography-tandem mass spectrometry (LC-MS-MS) to identify protein targets of the biotin-tagged model electrophiles 1-biotinamido-4-(4'-[maleimidoethylcyclohexane]-carboxamido)butane (BMCC) and N-iodoacetyl-N-biotinylhexylenediamine (IAB) in human liver microsomes. The biotin-tagged peptides resulting from in-gel tryptic digestion were enriched by biotin-avidin chromatography and LC-MS-MS was used to identify 376 microsomal cysteine thiol targets of BMCC and IAB in 263 proteins. Protein adduction was selective and reproducible, and only 90 specific cysteine sites in 70 proteins (approximately 25% of the total) were adducted by both electrophiles. Differences in adduction selectivity correlated with different biological effects of the compounds, as IAB- but not BMCC-induced ER stress in HEK293 cells. Targeted LC-MS-MS analysis of microsomal glutathione-S-transferase cysteine 50, a target of both IAB and BMCC, detected time-dependent adduction by the reactive acetaminophen metabolite N-acetyl-p-benzoquinoneimine during microsomal incubations. The results indicate that electrophiles selectively adduct microsomal proteins, but display differing target selectivities that correlate with differences in toxicity. Analysis of selected microsomal protein adduction reactions thus could provide a more specific indication of potential toxicity than bulk covalent binding of radiolabeled compounds.

A rapid method for the purification of methanol dehydrogenase from Methylobacterium extorquens.

Methanol dehydrogenase (MDH) is a water soluble quinoprotein that catalyzes the oxidation of methanol as an important carbon source in methylotrophic bacteria. A rapid method for the purification of MDH from Methylobacterium extorquens AM1 was developed using a single cation exchange chromatographic step, followed by ultrafiltration for final purification, enzyme concentration, and buffer exchange. MDH was obtained in an excellent overall yield with a final enzyme purity of greater than 97%. Storage at -80 degrees C in 20mM phosphate buffer, pH 7.0, showed only a negligible loss of enzyme activity after six months.

Evaluation of chiral discrimination of highly negatively charged enantiomers by quaternary ammonium beta-cyclodextrin using 1H NMR.

The positively charged quaternary ammonium cyclodextrin, QA-beta-CD, was previously used as a chiral selector to achieve baseline resolution of two of the dianionic enantiomers of disodium 3-(p-isothiocyanatophenoxy)-3-(p-isothiocyanatophenyl)propane-1,2-disulfate by capillary electrophoresis. The basis of the chiral discrimination between QA-beta-CD and the enantiomers was investigated by (1)H NMR spectroscopy. COSY and NOESY spectra were used to infer the role that molecular interactions and the stereocenters have upon association of QA-beta-CD with the enantiomers. A parallel two-step complexation model is used to rationalize the NMR and the chiral discrimination observed during separation of the enantiomers.

Chiral separation of highly negatively charged enantiomers by capillary electrophoresis.

The separation of two highly negatively charged enantiomeric organic disulfates containing two chiral centers was investigated by capillary electrophoresis using cyclodextrin based chiral selectors added to the run buffer. The optimum separation for the enantiomers was achieved in less than 3 min at 25 degrees C with a run buffer of 10 mM glycine pH 2.4 and 5 mM QA-beta-CD, which is a positively charged quaternary ammonium beta-cyclodextrin derivative. The method resulted in baseline resolution, excellent linearity, and highly reproducible migration times allowing facile evaluation of the enantiomeric purity of the individual isomers. Detection limits for the enantiomeric pair were determined to be 0.3 ng/microl (S/N = 3). The nature of the selector-enantiomer interaction and a quantitative measurement of the apparent stability constants that governed chiral discrimination of the enantiomers with QA-beta-CD were also investigated by UV-Vis spectroscopy and electrospray ionization mass spectrometry.