JAPANESE DEMAND FOR WHEAT PROTEIN QUANTITY AND QUALITY

Ladd and Martin's hedonic pricing model is extended to include the interactive effect of noncontracted characteristics on the value of contracted characteristics. Marginal values of wheat protein in the Japanese import market are estimated using the interactive effects of noncontracted dough/flour characteristics typically proxied by protein. Protein value is linked positively to farinograph stability, a prime factor in blending different flours. Three high protein wheats maintained about the same marginal value of protein. The marginal value for the two low protein wheats appear more end-use dependant. They varied in a $2.00/ton range depending on protein absorption, stability, and extensibility.Demand and Price Analysis,

One way to Characterize the compact structures of lattice protein model

On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact structure. The Partnum is compared with the concept Designability of protein structures emerged recently. It is shown that the highly designable structures have, on average, an atypical number of local degree of freedom. The statistical property of Partnum and its dependence on sequence length is also studied.Comment: 10 pages, 5 figure

Quality control by a mobile molecular workshop: quality versus quantity

Ribosome is a molecular machine that moves on a mRNA track while, simultaneously, polymerizing a protein using the mRNA also as the corresponding template. We define, and analytically calculate, two different measures of the efficiency of this machine. However, we arugue that its performance is evaluated better in terms of the translational fidelity and the speed with which it polymerizes a protein. We define both these quantities and calculate these analytically. Fidelity is a measure of the quality of the products while the total quantity of products synthesized in a given interval depends on the speed of polymerization. We show that for synthesizing a large quantity of proteins, it is not necessary to sacrifice the quality. We also explore the effects of the quality control mechanism on the strength of mechano-chemical coupling. We suggest experiments for testing some of the ideas presented here.Comment: Final version published in Physical Review

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

Background: Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results: Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion: Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots

Law of Genome Evolution Direction : Coding Information Quantity Grows

The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, and gene transfer from outside. The function-coding information quantity of a genome consists of two parts, p-coding information quantity which encodes functional protein and n-coding information quantity which encodes other functional elements except amino acid sequence. The evidences on the evolutionary law about the function-coding information quantity are listed. The needs of function is the motive force for the expansion of coding information quantity and the information quantity expansion is the way to make functional innovation and extension for a species. So, the increase of coding information quantity of a genome is a measure of the acquired new function and it determines the directionality of genome evolution.Comment: 16 page

Biosynthesis, structure, and biological activities of envelope protein gp65 of murine coronavirus.

We have previously shown that gp65 (E3) is a virion structural protein which varies widely in quantity among different strains of mouse hepatitis virus (MHV). In this study, the biosynthetic pathway and possible biological activities of this protein were examined. The glycosylation of gp65 in virus-infected cells was inhibited by tunicamycin but not by monensin, suggesting that it contains an N-glycosidic linkage. Glycosylation is cotranslational and appears to be complete before the glycoprotein reaches the Golgi complex. Pulse-chase experiments showed that this protein decreased in size after 30 min of chase, suggesting that the carbohydrate chains of gp65 undergo trimming during its transport across the Golgi. This interpretation is supported by the endoglycosidase treatment of gp65, which showed that the peptide backbone of gp65 did not decrease in size after pulse-chase periods. This maturation pathway is distinct from that of the E1 or E2 glycoproteins. Partial endoglycosidase treatment indicated that gp65 contains 9 to 10 carbohydrate side chains; thus, almost all of the potential glycosylation sites of gp65 were glycosylated. In vitro translation studies coupled with protease digestion suggest that gp65 is an integral membrane protein. The presence of gp65 in the virion is correlated with the presence of an acetylesterase activity. No hemagglutinin activity was detected

Extracting protein-protein interaction based on discriminative training of the Hidden Vctor State model

The knowledge about gene clusters and protein interactions is important for biological researchers to unveil the mechanism of life. However, large quantity of the knowledge often hides in the literature, such as journal articles, reports, books and so on. Many approaches focusing on extracting information from unstructured text, such as pattern matching, shallow and deep parsing, have been proposed especially for extracting protein-protein interactions (Zhou and He, 2008). A semantic parser based on the Hidden Vector State (HVS) model for extracting protein-protein interactions is presented in (Zhou et al., 2008). The HVS model is an extension of the basic discrete Markov model in which context is encoded as a stack-oriented state vector. Maximum Likelihood estimation (MLE) is used to derive the parameters of the HVS model. In this paper, we propose a discriminative approach based on parse error measure to train the HVS model. To adjust the HVS model to achieve minimum parse error rate, the generalized probabilistic descent (GPD) algorithm (Kuo et al., 2002) is used. Experiments have been conducted on the GENIA corpus. The results demonstrate modest improvements when the discriminatively trained HVS model outperforms its MLE trained counterpart by 2.5% in F-measure on the GENIA corpus