Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues

While iTRAQ analyses have proved invaluable for the discovery of potential cancer markers, two outstanding issues that remained were its ineffectiveness to consistently detect specific proteins of interest in a complex sample and to determine the absolute abundance of those proteins. These have been addressed by availability of the mTRAQ reagents (Applied Biosystems, Inc., Foster City, CA) a nonisobaric variant of iTRAQ. We have applied this newly emerging technique to quantify one of our potential markers for endometrial cancer, viz. pyruvate kinase M1/M2. The mTRAQ methodolgy relies on multiple reaction monitoring (MRM) to target tryptic peptides from the protein of interest, thus, ensuring maximal opportunity for detection, while the nonisobaric tags enable specific quantification of each version of the labeled peptides through unique MRM transitions conferred by the labels. Known amounts of synthetic peptides tagged with one of the two available mTRAQ labels, when used as quantification standards in a mixture with the oppositely labeled tryptically digested sample, permit determination of the absolute amounts of the corresponding protein in the sample. The ability to label the sample and reference peptides with either one of the two possible combinations is an inherent advantage of this method, as it provides a means for verification of the reported ratios. In this study, we determined that the amount of pyruvate kinase present in the homogenate from a biopsied EmCa tissue sample was 85 nmol/g of total proteins, while the equivalent concentration in the nonmalignant controls was 21-26 nmol/g of total proteins. This approximately 4-fold higher amount of pyruvate kinase in the cancer sample was further confirmed not only by a direct comparison between the cancer sample and one of the nonmalignant controls, but also independently by an enzyme-linked immunosorbant assay (ELISA). Additionally, the 4-fold higher level of pyruvate kinase amount in the cancer homogenate reported in this study is considerably higher than the 2-fold higher ratio reported across 20 cancer samples in the discovery phase with the iTRAQ technique, suggesting that there exists a possibility that the dynamic range of ratios determined by the iTRAQ technique may have been compressed.     

Binding of the human immunodeficiency virus type 1 Gag polyprotein to cyclophilin A is mediated by the central region of capsid and requires Gag dimerization.

The cellular peptidyl-prolyl isomerase cyclophilin A (CyPA) is incorporated into human immunodeficiency virus type 1 (HIV-1) virions via direct contacts with the HIV-1 Gag polyprotein. Disruption of the Gag-CyPA interaction leads to the production of HIV-1 particles lacking CyPA; these virions are noninfectious, indicating that contacts between CyPA and Gag are necessary for HIV-1 replication. Here, we have used the yeast two-hybrid system in conjunction with an in vitro binding assay to identify the minimal domain of Gag required for binding to CyPA. Analysis of a panel of gag deletion mutants in the two-hybrid system indicated that a region spanning the central portion of the capsid (CA) domain was sufficient for interactions with CyPA, but discrepancies between results obtained in different fusion protein contexts suggested that multimerization of Gag might also be necessary for binding to CyPA. Consistent with a requirement for multimerization, the binding of Gag to CyPA in vitro required a region within the nucleocapsid (NC) domain shown previously to be important for Gag self-association. Substitution of a heterologous dimerization motif for the region from NC also promoted specific binding to CyPA, confirming that interactions with CyPA are dependent on Gag multimerization. Fusion of the heterologous dimerization motif to a 100-amino-acid domain from CA was sufficient for binding to CyPA in vitro. These results define the minimal CyPA-binding domain within Gag and provide insight into the mechanism by which CyPA is incorporated into HIV-1 virions.     

Covalent cross-linking of AcVal-tRNA to Tetrahymena thermophila cytoplasmic ribosomes and two of its 17S rRNA mutants

Tetrahymena thermophila 80S ribosomes have been cross-linked to non-enzymatically bound AcVal-tRNA, presumably at the ribosomal P-site. Like the ribosomes from Escherichia coli, yeast, and Artemia salina, cross-linking is exclusively to C-1609, the equivalent of the E. coli C-1400 residue. Mutation of the RNA from G-1707 to A or from U-1711 to C which results in resistance to paromomycin or hygromycin, respectively, failed to affect the rate, yield, or site of cross-linking. The presence of the antibiotics during cross-linking also was without effect. It is concluded that at these two positions the base changes made do not interfere with the tertiary structure of the decoding site.     

A molecular defect in intracellular lipid signaling in human neutrophils in localized aggressive periodontal tissue damage

Host defense mechanisms are impaired in patients with congenital neutrophil (polymorphonuclear neutrophils (PMN)) defects. Impaired PMN chemotaxis is observed in localized aggressive periodontitis (LAP), a familial disorder characterized by destruction of the supporting structures of dentition. In the present studies, we sought evidence for molecular events underlying this aberrant human PMN phenotype. To this end, PMN transendothelial migration and superoxide anion generation were assessed with LAP patients and asymptomatic family members, as well as patients with other chronic mucosal inflammation. PMN from LAP patients showed decreased transmigration across vascular endothelial monolayers (18 +/- 12% of control, n = 4) and increased superoxide anion generation (358 +/- 37%, p = 0.003). Gene expression was analyzed using oligonucleotide microarrays and fluorescence-based kinetic PCR. cDNA microarray and kinetic-PCR analysis revealed diminished RNA expression of leukocyte-type diacylglycerol (DAG) kinase alpha in PMN from LAP patients (4.6 +/- 1.7 relative units, n = 6, p = 0.007) compared with asymptomatic individuals (51 +/- 27 relative units, n = 7). DAG kinase activity was monitored by DAG phosphorylation and individual DAG molecular species were quantified using liquid chromatography and tandem mass spectrometry-based lipidomics. DAG kinase activity was also significantly decreased (73 +/- 2%, p = 0.007) and correlated with increased accumulation of 1,2-diacyl-sn-3-glycerol substrates (p = 0.01). These results implicate defects in both PMN transendothelial migration and PMN DAG kinase alpha signaling as disordered functions in LAP. Moreover, they identify a potential molecular lesion in PMN signal transduction that may account for their aberrant responses and tissue destruction in this disease.     

Playback of colony sound alters the breeding schedule and clutch size in zebra finch (Taeniopygia guttata) colonies

The hypothesis that social stimulation, derived from the presence and activities of conspecifics, can hasten and synchronize breeding in colonies of birds was tested. A modified playback/recorder system was used to continuously exaggerate the amount of colony sound available to zebra finches throughout their courtship period. Males that heard 'sound supplements' generated from their own colony sang more than males in control colonies that did not receive playback; males that heard samples from a different colony, sang at an intermediate level. Females that were exposed to the vocalizations of their mate and playback from a colony other than their own, laid eggs earlier and more synchronously than females in control colonies. Females that heard the vocalizations of their mate along with playback samples generated from their own colony, laid eggs more synchronously but not earlier than control females. Both acoustic treatments caused females to lay larger clutches. Social stimulation influences the breeding schedule and clutch size in zebra finch colonies. If there are advantages associated with these effects, social stimulation may contribute to the maintenance of colonial breeding systems.     

Developmental changes in the isoenzymes controlling glycolysis in the acridine grasshopper,Caledia captiva

Summary In this paper is reported an example of extensive developmental changes in the isoenzymes controlling a biochemical pathway: more than half of the glycolytic enzymes of the grasshopper,Caledia captiva differ in electrophoretic phenotype between embryonic and adult stages. A similar pattern of changes is found in each of the taxa ofC. captiva, which is actually a species complex. The present example of developmental variation differs from that described for glycolytic enzymes in vertebrates in two main points. Firstly, the changes between the phenotypes of the embryos and adults are co-incident in time, occurring near hatching. Secondly, in contrast to vertebrates where embryospecific isoenzymes are rare, there exist inC. captiva isoenzymes of trehalase, glucosephosphate isomerase, aldolase, pyruvate kinase, lactate dehydrogenase and 6-phosphogluconate dehydrogenase which are found in the embryo but not in the adult. Some of the variable enzymes also exhibit tissue specificity in the adult. The existence of the changes, whatever their basis, shows that the theory that the expression of housekeeping genes is developmentally invariant is not generally correct.     

The role of learning in fish behaviour

Summary The behavioural patterns of fish are the result of innate (built-in) patterns of maturation (developmental changes) and of learning processes (imprinting and trial-and-error learning). Innate behavioural patterns are considered to be hard-wired and inflexible. However, through learning, fish can adapt to environmental change. For instance, the homing behaviour of fish may be partly the result of the development of specific parts of the brain and partly because of changes in behaviour with experience. Similarly, one can assume that the feeding mode of fish involving snap-responses is innate, but learning enables fish to modify their foraging behaviour in response to a fluctuating environment. By reviewing these and other examples, such as the role of recognition learning and socially transmitted behaviour, one can illustrate the importance of learning in the everyday life of fishes. Although learning plays a large role in the behaviour of fishes, the learning capacity of fishes may also be useful to fisheries research and hatchery operations.     

Predator biomass and vegetation influence the coastal distribution of threespine stickleback morphotypes

Intraspecific niche differentiation can contribute to population persistence in changing environments. Following declines in large predatory fish, eutrophication, and climate change, there has been a major increase in the abundance of threespine stickleback (Gasterosteus aculeatus) in the Baltic Sea. Two morphotype groups with different levels of body armor—completely plated and incompletely plated—are common in coastal Baltic Sea habitats. The morphotypes are similar in shape, size, and other morphological characteristics and live as one apparently intermixed population. Variation in resource use between the groups could indicate a degree of niche segregation that could aid population persistence in the face of further environmental change. To assess whether morphotypes exhibit niche segregation associated with resource and/or habitat exploitation and predator avoidance, we conducted a field survey of stickleback morphotypes, and biotic and abiotic ecosystem structure, in two habitat types within shallow coastal bays in the Baltic Sea: deeper central waters and shallow near‐shore waters. In the deeper waters, the proportion of completely plated stickleback was greater in habitats with greater biomass of two piscivorous fish: perch (Perca fluviatilis) and pike (Esox lucius). In the shallow waters, the proportion of completely plated stickleback was greater in habitats with greater coverage of habitat‐forming vegetation. Our results suggest niche segregation between morphotypes, which may contribute to the continued success of stickleback in coastal Baltic Sea habitats.