Modeling the Role of Negative Cooperativity in Metabolic Regulation and Homeostasis

A significant proportion of enzymes display cooperativity in binding ligand molecules, and such effects have an important impact on metabolic regulation. This is easiest to understand in the case of positive cooperativity. Sharp responses to changes in metabolite concentrations can allow organisms to better respond to environmental changes and maintain metabolic homeostasis. However, despite the fact that negative cooperativity is almost as common as positive, it has been harder to imagine what advantages it provides. Here we use computational models to explore the utility of negative cooperativity in one particular context: that of an inhibitor binding to an enzyme. We identify several factors which may contribute, and show that acting together they can make negative cooperativity advantageous.     

Identification two novel nacrein-like proteins involved in the shell formation of the Pacific oyster Crassostrea gigas

Nacrein-like proteins have carbonic anhydrase (CA)-like domains, but their coding regions are flanked by inserted repeat sequence, such as Gly-X-Asn. Reportedly, nacrein-like proteins show the highest similarity to human carbonic anhydrase 1(α-CA1), possess CA catalytic functions, and play a key role in shell biomineralization. In the present study, two novel nacrein-like proteins were firstly identified from the shell-forming mantle of the Pacific oyster Crassostrea gigas. With numerous analyses, it was identified and characterized that both the nacrein-like proteins F1 and F2 were secreted and most closely related to the nacrein-like protein of California mussel Mytilus californianus via phylogenetic analysis. RT-PCR analysis showed that the nacrein-like proteins F1 and F2 were expressed in multiple tissues and the expression levels remarkably rose after entering the spat stage, which were basically consistent with the increase of calcite fractions in the total shell volume. Surprisingly, the Gly-X-Asn repeat domain, which is distinctive in most nacrein-like proteins, was absent in the two newly identified nacrein-like proteins in C. gigas and replaced with a series of acidic amino acids (D/E). Regardless, nacrein-like proteins in mollusks seem to be vital to the deposition of calcium carbonate and likely perform diverse functions.     

Comparative study on the surface ultrastructures of fertilized eggs of three Sebastes species

Fertilized eggs of Sebastes schlegelii, Sebastes pachycephalus and Sebastes hubbsi are morphologically similar under stereomicroscope. However, under the scanning electron microscope, significant differences in the ultrastructures of the egg surface among the three species were observed, and herein, a taxonomic key was proposed for future applications. A clustering analysis based on the ultrastructures of the egg surface and the diameter of the oil globule suggested that among the three species, S. hubbsi and S. pachycephalus were more genetically similar, while S. schlegelii had diverged earlier. The results agree with the conclusions drawn from morphological and molecular analyses on adult samples of the same species.     

Multiple-Interval Mapping for Quantitative Trait Loci With a Spike in the Trait Distribution

For phenotypic distributions where many individuals share a common value—such as survival time following a pathogenic infection—a spike occurs at that common value. This spike affects quantitative trait loci (QTL) mapping methodologies and causes standard approaches to perform suboptimally. In this article, we develop a multiple-interval mapping (MIM) procedure based on mixture generalized linear models (GLIMs). An extended Bayesian information criterion (EBIC) is used for model selection. To demonstrate its utility, this new approach is compared to single-QTL models that appropriately handle the phenotypic distribution. The method is applied to data from Listeria infection as well as data from simulation studies. Compared to the single-QTL model, the findings demonstrate that the MIM procedure greatly improves the efficiency in terms of positive selection rate and false discovery rate. The method developed has been implemented using functions in R and is freely available to download and use.     

Efficient flow cytometric assay for platelet-leukocyte aggregates in whole blood using fluorescence signal triggering.

BACKGROUND: Platelet-leukocyte aggregates (PLAs) may be important in thrombotic and inflammatory disease states, but accurate assessment of PLA formation in vivo is hampered by the propensity for in vitro artefacts caused by sample manipulation. A whole blood flow cytometric assay for circulating PLAs, based on minimal sample manipulation, was thus developed. METHODS: Citrated whole blood was labeled with a RPE-CD45 MAb (leukocyte marker) and an FITC-CD42a (GPIX) MAb (platelet marker). The latter was used to avoid possible influences of platelet glycoprotein proteolysis by neutrophil-derived proteases. The samples were mildly fixed with 0.5% formaldehyde saline. The cytometer was triggered by RPE-CD45 fluorescence. Leukocyte subpopulations were separated according to their typical light scattering and CD45 expression. RESULTS: Minimal sample manipulation and mild sample fixation resulted in minor in vitro artefacts and good sample stability. Fluorescence triggering increased the efficiency of the flow cytometric analysis approximately 5-fold compared with triggering with light scatter, and allowed discrimination of leukocyte subpopulations. The majority of PLAs involved monocytes and neutrophils, rather than lymphocytes, both without and with in vitro stimulation by ADP or thrombin. A cocktail of blocking MAbs to CD62P, CD15, GPIIb/IIIa and the CD11b/CD18 complex had no effect on unstimulated samples, whilst totally inhibiting aggregation induced by 10(-5) M ADP, suggesting that the PLAs in unstimulated blood were preformed in vivo. CONCLUSIONS: This whole blood flow cytometric assay for PLAs is simple and efficient, and appears to reflect closely platelet-leukocyte aggregates in circulating blood in vivo.