Comparative analysis of multiple protein-sequence alignment methods [published erratum appears in Mol Biol Evol 1994 Sep;11(5):811]

We have analyzed a total of 12 different global and local multiple protein-sequence alignment methods. The purpose of this study is to evaluate each method's ability to correctly identify the ordered series of motifs found among all members of a given protein family. Four phylogenetically distributed sets of sequences from the hemoglobin, kinase, aspartic acid protease, and ribonuclease H protein families were used to test the methods. The performance of all 12 methods was affected by (1) the number of sequences in the test sets, (2) the degree of similarity among the sequences, and (3) the number of indels required to produce a multiple alignment. Global methods generally performed better than local methods in the detection of motif patterns.      

Protein enrichment of sweet potato residue by solid-state cultivation with mono- and co-cultures of amylolytic fungi

The degree of protein enrichment of sweet potato residue by different amylolytic moulds in solid-state cultivation was much greater than that obtained using amylolytic yeasts. The optimum initial moisture content for protein enrichment was about 65% (w/w). Adding nitrogen sources to the culture twice (at the start of the incubation and after 24 h) considerably improved the final protein content. A co-culture of amylolytic mycelial fungi yielded a product with 32% (w/w) crude protein after 4 days' incubation at 30°C. In a column reactor, the highest temperatures reached were 42°C and 40°C and the minimum O₂ concentrations were 1.5% and 2.5% of full saturation in the central and bottom layers, respectively.     

Stabilized bubbles in the body: pressure-radius relationships and the limits to stabilization

Van Liew, Hugh D., and Soumya Raychaudhuri. Stabilizedbubbles in the body: pressure-radius relationships and the limits tostabilization. J. Appl. Physiol.82(6): 2045-2053, 1997.We previously outlined the fundamentalprinciples that govern behavior of stabilized bubbles, such as themicrobubbles being put forward as ultrasound contrast agents. Ourpresent goals are to develop the idea that there are limits to thestabilization and to provide a conceptual framework for comparison ofbubbles stabilized by different mechanisms. Gases diffuse in or out ofstabilized bubbles in a limited and reversible manner in response tochanges in the environment, but strong growth influences will cause thebubbles to cross a threshold into uncontrolled growth. Also, bubblesstabilized by mechanical structures will be destroyed if outsideinfluences bring them below a critical small size. The in vivo behaviorof different kinds of stabilized bubbles can be compared by using plotsof bubble radius as a function of forces that affect diffusion of gasesin or out of the bubble. The two ends of the plot are the limits forunstabilized growth and destruction; these and the curve's slopepredict the bubble's practical usefulness for ultrasonic imaging orO₂ carriage to tissues.

     

Mechanisms of acquired immunity in leishmaniasis

Self-curing cutaneous leishmaniasis depends on T cell-mediated immune activation of infected macrophages. Failure of immune control in inbred mouse models of metastasizing mucocutaneous and visceralizing forms of the disease involves, respectively, insusceptibility of the parasite and the generation of T cells that suppress a potentially curative response. Prophylactic immunization in man has so far been restricted to cutaneous leishmaniasis and based on inducing infection under controlled conditions with virulent Leishmania tropica major promastigotes. The feasibility of immunization against visceral leishmaniasis merits reconsideration. BALB/c mice are genetically vulnerable to L. tropica major, which produces a fatal visceralizing type of disease involving specific suppression of cell-mediated immunity. Potent and lasting protection can be induced by repeated intravenous immunization with irradiated promastigotes. The efficacy of this 'vaccine' is relatively heat-stable (1 h at 56 degrees C). Immunity is not attributable to antibody but to the generation of Lyt-1+2- T cells which, although possessing helper and macrophage-activating functions, do not express classical delayed-type hypersensitivity. The immunological features of this system and its relevance to the possibility of protection against human Leishmania donovani infection are considered.     

Studies on humoral immunity against Taenia taeniaeformis infection in rats

Rats were infected with doses of 100, 1000, 5000 and 10 000 eggs of Taenia taeniaeformis. Haemagglutinating antibody to cysticerus antigen was detected at the 4th week of infection. The appearance and levels of antibody titre did not vary greatly with the infective dose. An IgM peak appeared at the 6th week, with IgG appearing slightly later and continuing to rise. Transfer of serum from the 1st week onwards from infections with 1000 eggs however could confer significant protection. Dilutions of hyperimmune serum (1 ml volumes) of up to 1/32 conferred significant protection on normal recipients. Hyperimmune serum transferred up to 4 days before challenge could confer 80% protection whereas serum transferred 4 days after challenge was totally non-protective. The significance of this finding is discussed in the light of current knowledge of metacestode immunity.     

Expression of human IL-1 beta in Salmonella typhimurium. A model system for the delivery of recombinant therapeutic proteins in vivo.

The feasibility of using Salmonella typhimurium aroA mutant (SL3261) to deliver protein therapeutic agents was investigated in a murine model system. We have constructed an Escherichia coli expression plasmid designed to express the human protein IL-1 beta. This plasmid expresses IL-1 beta to high levels (greater than 30% total cell protein) in E. coli. In Salmonella the IL-1 beta is expressed constitutively to about 10% total cell protein, as verified by Western blotting analysis using polyclonal rabbit anti-IL-1 beta antibody. The protein is produced in a soluble and biologically active form. BALB/c mice administered orally or i.v. with S. typhimurium aroA mutants carrying the plasmid produced highly significant antibody responses against human IL-1 beta as determined by a solid-phase RIA. Furthermore, mice injected with the construct were significantly protected against lethal gamma-irradiation (850 rad). This study therefore demonstrates that the vaccine strain of Salmonella mutants can also be used effectively to deliver therapeutic proteins in vivo.     

Effect of thyrotropin on the phosphorylation of thyroid chromosomal proteins.

Thyrotropin (TSH) stimulated the phosphorylation of histone H1 in calf thyroid slices but had no effect on other classes of histones. Phosphorylation of total phenol-soluble nonhistone chromosomal proteins was not affected by incubation with TSH. However, when these phenol-soluble nonhistone chromosomal proteins were analysed by two-dimensional gels involving isoelectrofocusing and dodecyl sulfate-polyacrylamide gel electrophoresis, TSH was shown to stimulate the phosphorylation of two specific groups of phosphoproteins with molecular weights between 35,000 and 45,000 and isoelectric points at pH values of 5.4-6.0. This increase in phosphorylation with TSH stimulation was confirmed by quantitative analysis of one-dimensional isoelectrofocusing gels.     

Characterization of proteins associated with nuclear ribonucleoprotein particles by two-dimensional polyacrylamide gel electrophoresis.

Rat liver nuclear ribonucleoprotein particles were prepared by two different methods and defined as 40S ribonucleoprotein (40S RNP) and heterogeneous nuclear ribonucleoprotein (HnRNP) particles. The RNP particles were either solubilized in 8 M urea--6 mM 2-mercaptoethanol--20 mM glycine--20 mM Tris--HCl (pH 8.4) or subjected to removal of RNA by phenol extraction prior to solubilizing the proteins in the urea buffer. The proteins associated with 40S RNP and HnRNP were heterogeneous and very similar in their electrophoretic patterns when analyzed by two-dimensional PAGE, except a protein with molecular weight of 62 000 and an isoelectric point (pI) of 6.2 was present only in HnRNP particles. At least 12 major and 22 minor components could be identified in both preparations. The major proteins were found at pI values varying from 6.0 to 8.5 and with molecular weights from 32 000 to 42 000, and a group of proteins with molecular weight approximately 65 000 were more prominent in HnRNP than in 40S RNP. The other components were found mainly at pI ranges from 5.0 to 6.5 with molecular weights from 43 000 to 65 000. The phenol method extracted essentially all proteins associated with either 40S RNP and HnRNP, but was less effective in extracting a group of proteins with pI values from 5.0 to 5.5 and more efficient for proteins with pI values from 7.5 to 8.5. When chromatin proteins isolated by phenol extraction were compared with HnRNP particle proteins isolated by the same method, the electrophoretic mobilities of the HnRNP particle proteins were found to be identical with a fraction nonhistone chromatin proteins. The 40S RNP particles were further purified by metrizamide isopycnic density gradient centrifugation. The electrophoretic patterns of these proteins were very similar to those prepared by sucrose density gradient centrifugation. Therefore, we concluded that the proteins of RNP particles constituted part of the chromatin proteins.     

Purification of a phosphoprotein from chromatin of rat liver.

A simple and effective method to purify a phosphoprotein (B2) (Mr 68,000, pI 6.2-8) from phenol-soluble non-histone chromatin proteins of rat liver is described. The purification involved only two steps, CM-cellulose chromatography and preparative SDS/polyacrylamide (10%)-gel electrophoresis. The purified phosphoprotein B2 was shown to be homogeneous by SDS/polyacrylamide-gel electrophoresis. The yield was 2% of total non-histone chromatin proteins. The acidic to basic amino acid ratio of phosphoprotein B2 was less than 1, with high contents of glutamic acid, aspartic acid, arginine, lysine, glycine and alanine. The phosphate content of this protein is 0.3%.