Prediction of protein signal sequences and their cleavage sites

Protein signal sequences play a central role in the targeting and translocation of nearly all secreted proteins and many integral membrane proteins in both prokaryotes and eukaryotes. The knowledge of signal sequences has become a crucial tool for pharmaceutical scientists who genetically modify bacteria, plants, and animals to produce effective drugs. However, to effectively use such a tool, the first important thing is to find a fast and effective method to identify the "zipcode" entity; this is also evoked by both the huge amount of unprocessed data available and the industrial need to find more effective vehicles for the production of proteins in recombinant systems. In view of this, a sequence-encoded algorithm was developed to identify the signal sequences and predict their cleavage sites. The rate of correct prediction for 1,939 secretory proteins and 1,440 nonsecretory proteins by self-consistency test is 90.14% and that by jackknife test is 90.13%. The encouraging results indicate that the signal sequences share some common features although they lack similarity in sequence, length, and even composition and that they are predictable to a considerably accurate extent.     

The adsorption of Congo red and vacuum pump oil by rice hull ash

Rice hull ash (RHA) of large surface area was obtained by acid wash and then calcination at 600 degrees C for 4 h. The white ash was then mixed with kaolin and starch to make pellet adsorbents with reasonable strength to be utilized in a packed column. Both ash and pellet samples showed good adsorption capacities toward the organic substances in wastewater. Furthermore, the surface nature of the white ash and pellet adsorbent could be modified through either hydration or esterification reactions. Corresponding changes in silanol concentrations were successfully correlated to changes in adsorption capacity toward either Congo red or vacuum pump oil molecules.     

The 300-kDa intermediate filament-associated protein (IFAP300) is a hamster plectin ortholog

Plectin is a high-molecular-weight cytoskeleton-associated protein that was initially identified in intermediate filament (IF)-enriched fractions of rat C6 glioma cells. At the cellular level, plectin has been found to associate with IF networks and IF-associated structures that are involved in cell-cell and cell-substrate adhesions. IFAP300 is an IF-associated protein that was initially identified in hamster cells by a monoclonal antibody directed against a high molecular weight protein present in IF-enriched cytoskeletal preparations. Plectin and IFAP300 display similar distribution patterns within cells as determined by immunofluorescence. Based upon this and the finding that their biochemical properties are similar, it has been suggested that they may actually be orthologous proteins. In this paper we demonstrate that this is the case. Cloning and sequencing of most of the hamster plectin cDNA demonstrates that plectin is found in hamster cells and that its sequence is highly conserved between species. Using immunological cross-reactivity, epitope mapping, and immunoelectron microscopy, we show that IFAP300 is actually the hamster ortholog of plectin.     

Effect of Piper betle L. and its extracts on the growth and aflatoxin production by Aspergillus parasiticus

Ground powder of the leaf and fruit of Piper betle L., a tropical spice plant grown in Southeast Asia, was prepared and extracted by chloroform, ethanol and water with one solvent only or with 3 solvents in sequence. The betel powder and various extracts were added to YES broth to determine their effects on the growth and aflatoxin production by Aspergillus parasiticus. Results showed that betel leaf powder exhibited higher antimycotic activity than fruit. One half percent of ground leaf powder completely inhibited the growth and aflatoxin production by A. parasiticus. Among the solvent extracts, chloroform and ethanol extracts of betel leaf prepared from a single solvent extraction showed more antimycotic activity. The ethanol extract of betel leaf at the level of 450 micrograms/ml would eliminate A. parasiticus growth and aflatoxin production. The antimycotic activity of this ethanol extract was most pronounced at pH 4.     

The biological functions of low-frequency vibrations (phonons) 5. A phenomenological theory

Low-frequency internal motions of a biomacromolecule are thought to possess significant biological function from the dynamic point of view. In this paper, a general phenomenological theory is established by which it is clearly verified that low-frequency resonance plays a central role in the energy transmission required during the cooperative interaction between subunits in a protein oligomer. According to the present theory, it is found that the energy transmission between a pair of diagonal subunits in a protein oligomer with a polygon arrangement is the most efficient, so as to in a sense further predict that after a ligand is bound to a subunit by random collision, its diagonal subunit in the same protein oligomer will possess the greatest probability of binding with the next ligand. Furthermore, based on the concept of the 'resonance-controlled trigger' derived from the phenomenological theory, it is feasible to estimate the lower time limit of allosteric transition from one subunit to the other. Such a time limit depends on the dominant low-frequency mode of each subunit, the ratio of the coupling force constant to the corresponding inherent force constant, as well as the geometrical arrangement of subunits in a protein oligomer. So far none of the allosteric transitions observed in proteins has exceeded the time limit as defined here, indicating a logical consistency between our theory and the experiments.     

Cellular fatty acid composition of Oerskovia species,CDC Coryneform groups A-3, A-4, A-5, Corynebacterium aquaticum,Listeria denitrificans and Brevibacterium acetylicum

Twenty four strains representing eight species of gram positive yellow-pigmented rods (Oerskovia turbata, Oerskovia xanthineolytica, CDC Coryneform groups A-3, A-4, A-5, Listeria denitrificans, Corynebacterium aquaticum and Brevibacterium acetylicum) were divided into two major groups based on the relative amounts of 12 methyltetradecanoate (15:0^a) obtained by capillary gas liquid chromatography. O. turbata, O. xanthineolytica, CDC groups A-3 and A-4, L. denitrificans and C. aquaticum were placed in the first group due to the presence of a higher percentage (29–47%) of 15:0^a, than CDC group A-5 and B. acetylicum. The latter contained 2–6% of this fatty acid, and were placed in the second group.All species in the two groups except C. aquaticum and CDC group A-4, were further separated from each other based on the qualitative and quantitative differences in their fatty acid compositions. In addition, the eight strains of CDC group A-5 revealed four different patterns and were further divided into four subgroups. This study supports the importance of the composition of cellular fatty acids in differentiating some closely related organisms.     

A therapeutic trial of bezafibrate on patients with hyperlipidemia with or without diabetes mellitus

Bezalip (bezafibrate), at an oral dosage of 200 mg three times a day, has been used on 12 patients with idiopathic hyperlipidemia, and on 12 patients with hyperlipidemia superimposed with diabetes mellitus. Each patient received bezafibrate for 3 months and placebo for 3 months. Blood glycosylated hemoglobin (HbA1) and fasting plasma glucose (FPG) were used as indices of diabetic control. Serum triglyceride (TG), total cholesterol (TC), high density lipoprotein-cholesterol (HDL-C), and TC/HDL-C ratio were measured and calculated in order to compare the antilipemic effects of bezafibrate with that of placebo. Non-parametric Wilcoxon test was used for statistical analysis. In both the idiopathic group and diabetic group, bezafibrate significantly lowered the serum levels of TG and TC/HDL-C, as well as elevated the level of HDL-C. The serum TC levels were not significantly altered in either of the groups. These effects could not be ascribed to an improved diabetic control, since the percent changes of HbA1 were not different between the bezafibrate periods and the placebo periods. There were no significant facial flushing, nor other side effects during the treatment with bezafibrate. It is concluded that bezafibrate has antilipemic effects, and may be helpful in reducing the atherogenic risks.     

The major site of guinea-pig myelin basic protein encephalitogenic in Lewis rats.

In the Lewis rat, fragment 43–88 of the highly encephalitogenic guinea-pig basic protein has been previously shown to retain the full activity of the parent protein. In the present studies this fragment was subjected to controlled chymotryptic digestion so that cleavage occurred only at tyrosine 67, generating two peptides, residues 43-67 and residues 68-88. When compared on an equimolar basis peptide 68-88 had the same encephalitogenic activity as the intact fragment and induced the same degree of immunologically specific cell response as measured by the in vitro lymphocyte stimulation test. Peptide 68-88 was further fragmented by selective tryptic cleavage at arginine 78 after blocking lysine 73 with citraconic anhydride. The two peptides, residues 68-78 and residues 79-88, were not encephalitogenic, indicating that residues adjacent to the point of cleavage contribute to the active site.