Identification of T-cell epitopes on E2 protein of rubella virus, as recognized by human T-cell lines and clones.

T-cell epitopes on the E2 protein of rubella virus were studied by using 15 overlapping synthetic peptides covering the E2 protein sequence. The most frequently recognized epitopes on E2 were E2-4 (residues 54 to 74), with 5 of 10 tested T-cell lines responding to it. Two CD4+ cytotoxic T-cell cloned isolated from one T-cell line responded strongly in proliferation assays with peptide E2-4 and were cytotoxic to target cells presenting the E2-4 determinant. Truncated peptides contained within the E2-4 peptide sequence were used to define the T-cell determinants. Results indicated that amino acid residues 54 to 65 were directly involved. Human cell lines with different HLA phenotypes were tested for the capacity to present the antigenic determinants. The results suggested that recognition of peptide E2-4 by T-cell clones was associated with HLA DR7.     

Predicting protein secondary structure using neural net and statistical methods.

A comparison of neural network methods and Bayesian statistical methods is presented for prediction of the secondary structure of proteins given their primary sequence. The Bayesian method makes the unphysical assumption that the probability of an amino acid occurring in each position in the protein is independent of the amino acids occurring elsewhere. However, we find the predictive accuracy of the Bayesian method to be only minimally less than the accuracy of the most sophisticated methods used to date. We present the relationship of neural network methods to Bayesian statistical methods and show that, in principle, neural methods offer considerable power, although apparently they are not particularly useful for this problem. In the process, we derive a neural formalism in which the output neurons directly represent the conditional probabilities of structure class. The probabilistic formalism allows introduction of a new objective function, the mutual information, which translates the notion of correlation as a measure of predictive accuracy into a useful training measure. Although a similar accuracy to other approaches (utilizing a mean-square error) is achieved using this new measure, the accuracy on the training set is significantly and tantalizingly higher, even though the number of adjustable parameters remains the same. The mutual information measure predicts a greater fraction of helix and sheet structures correctly than the mean-square error measure, at the expense of coil accuracy, precisely as it was designed to do. By combining the two objective functions, we obtain a marginally improved accuracy of 64.4%, with Matthews coefficients C alpha, C beta and Ccoil of 0.40, 0.32 and 0.42, respectively. However, since all methods to date perform only slightly better than the Bayes algorithm, which entails the drastic assumption of independence of amino acids, one is forced to conclude that little progress has been made on this problem, despite the application of a variety of sophisticated algorithms such as neural networks, and that further advances will require a better understanding of the relevant biophysics.     

Relationship between rate of gluconeogenesis and content of nicotinamide adenine dinucleotide in renal cortex

Gluconeogenesis in rat renal cortex was measured using tissue slices incubated with or without appropriate substrates. Immediately after incubation the tissue slices were snap-frozen and the content of oxidized nicotinamide adenine dinucleotide (NAD⁺) was determined. Incubation with 10 mM α-ketoglutarate or L-glutamate led to enhanced glucose production and an increase in tissue content of NAD⁺. Quinolinate and 3-mercaptopicolinate inhibited the rate of gluconeogenesis from L-glutamate and α-ketoglutarate respectively, and decreased the tissue levels of NAD⁺. The enhanced rate of gluconeogenesis was associated with an increase of NAD⁺ in the cytosol fraction (10⁵ × g supernatant) but not in the particulate fraction (10⁵ × g pellet) of renal cortex homogenate. Present results indicate that NAD⁺ content changes in parallel with the rate of gluconeogenesis in renal cortical tissue.     

Role of surface exclusion genes in lethal zygosis in Escherichia coli K12 mating

Summary We find that diaminopimelic acid in the recipient membrane is released into the medium during bacterial matings, indicating that membrane damage was inflicted on the recipient by the donor, probably for forming a channel for DNA transfer. When the damage is extensive, as in matings with an excess of Hfr bacteria, the F^- bacteria are killed (lethal zygosis). The transfer of a large amount of DNA in Hfr matings appears to enhance the killing. In analogous F⁺xF^- (Nal^r) matings, on the other hand, killing of F^- bacteria does not occur unless F plasmid transfer is inhibited by a substance like nalidixic acid. The F^- bacteria are killed, suggesting that F plasmids contain genes that express immunity to lethal zygosis in the recipient. For example, bacteria containing surface exclusion-deficient mutants of F plasmids, such as traS ^- and traT ^-, induce lethal zygosis in F^- bacteria and are susceptible to it. Various tra ^- polar mutants that abolish surface exclusion are also susceptible to lethal zygosis when mated with Hfr bacteria. Kinetic experiments indicate that in F⁺ (wild type) x F^- matings, immunity to lethal zygosis is expressed in the F^- recipient within 1/4 division time, whereas a complete expression of surface exclusion requires more than 1 division time. Thus, a complete change in all receptor sites seems to be required for the expression of surface exclusion.     

Enzyme assay in cultures of Escherichia coli by a continuous flow method based on lysis from without by a phage ghost.

Lysis of Escherichia coli from without by excess of phage ghost has been shown to give excellent yield of several enzymes. The application of lysis from without to a continuous determination of enzymes in growing cultures of E. coli is illustrated with β-galactosidase. This application can be used in studies on changes of a large number of enzymes during metabolic perturbation (induction, repression, etc.) of growing cultures of E. coli.     

Effect of 1,10-phenanthroline on bacterial conjugation in Escherichia coli K-12: inhibition of maturation from preliminary mates into effective mates.

The addition of 1 mM orthophenanthroline (OP) into a mating mixture drastically reduced the production of recombinants. Examination of the effect of OP on each step of conjugation showed that the effect on the following steps could not account for the up to 500-fold reduction of recombinant formation: (i) preliminary mate formation and (ii) deoxyribonucleic acid transfer and integration. Taking these results and additional experiments together, we conclude that OP inhibits the maturation of preliminary mates into effective mates. Kinetic experiments showed that there were two phases in the maturation of preliminary (OP-sensitive) mates into effective (OP-resistant) mates. The half-time (the time required to reach 50% OP-resistant mates) was 2.5 min for the first phase and 4 min for the second phase, with an overall half-time of 7.5 min. In contrast, only 3 min was required to reach 50% Zn2+-resistant mates. The difference in half-time suggests that there is an intermediate step involved to form an effective mate from a preliminary mate.     

Modeling the Transmission of Middle East Respirator Syndrome Corona Virus in the Republic of Korea

The 2015 epidemic of Middle East respiratory syndrome (MERS) in the Republic of Korea has been the largest outbreak outside Middle East. This epidemic had caused 185 laboratory-confirmed cases and 36 deaths in the Republic of Korea until September 2, 2015, which attracted public’s attention. Based on the detailed data of patients released by World Health Organization (WHO) and actual propagation of the epidemic, we construct two dynamical models to simulate the propagation processes from May 20 to June 8 and from June 9 to July 10, 2015, respectively and find that the basic reproduction number R ₀ reaches up to 4.422. The numerical analysis shows that the reasons of the outbreak spread quickly are lack of self-protection sense and targeted control measures. Through partial correction analysis, the parameters β ₁ and γ have strong correlations with R ₀, i.e., the infectivity and proportion of the asymptomatic infected cases have much influence on the spread of disease. By sensitivity analysis, strengthening self-protection ability of susceptible and quickly isolating or monitoring close contacts are effective measures to control the disease.