New Calicivirus isolated from walrus

The nucleotide sequence and genome organization of a new member of Caliciviridae was determined. Cell culture inoculated with fecal matter from walrus was used to recover fragments of a new virus by Suppression Subtractive Hybridization (SSH). The isolate was identified as a member of the Vesivirus genus of Caliciviridae and designated the name Walrus Calicivirus (WCV). Sets of PCR primers spanning the entire putative genome were designed using known sequences of other vesiviruses. The assembled genome was 8289 nucleotides (nt) long and shared no more than 87% identity with sequences of the other members of the genus Vesivirus. The largest open reading frame (ORF1) between positions 4-5646 encoded a polyprotein. ORF2, found at position 5652-7778, encoded a putative capsid protein. ORF3 overlapped ORF2 and encoded a small basic protein. Comparative analysis of multiple caliciviral capsid proteins was performed to propose a uniform capsid structural organization for this viral family.     

Antigenic heterogeneity of the hepatitis C virus NS4 protein as modeled with synthetic peptides

The effect of sequence heterogeneity on the immunologic properties of two strong antigenic regions of the hepatitis C virus (HCV) NS4 protein was studied by using a set of 443 overlapping 20-mer synthetic peptides. One antigenic region comprising the cleavage site between NS4a and NS4b (region 5-1-1) was modeled with peptides derived from 73 different known sequences, representing HCV genotypes 1-6. The other antigenic region, designated region 59 and located at the C-terminus of the NS4b protein, was modeled with peptides from 7 known sequences representing genotypes 1-3. All peptides were tested for antigenic reactivity by enzyme immunoassay with a panel of anti-HCV-positive serum specimens representing genotypes 1-5. The data demonstrated that immunoreactive peptides fell into two groups. One group, represented by N-terminal peptides, demonstrated genotype-independent immunoreactivity; the other group, from the central part of region 5-1-1, showed strict genotype specificity. Nineteen peptides from the genotype-independent group strongly immunoreacted with a wide range of serum samples containing antibodies to all 5 HCV genotypes. Twenty-five peptides from the genotype-specific group were found to strongly react with serum containing antibodies only to the genotype from which the peptides were derived. Similar to the N-terminal part of region 5-1-1, peptides derived from region 59 did not show genotype-specific immunoreactivity. Some peptides derived from the central part of region 59 showed very strong and broad antigenic reactivity. Thus, after examining two antigenic regions of the NS4 protein, we identified short sequences that can be used for the efficient detection of either genotype-independent or genotype-specific HCV antibodies.     

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus

To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.     

Impact of amino acid sequence variation of a determinant(s) on the antigenic properties of hepatitis B virus HBsAg

Impact of amino acid sequence variation on the antigenic properties of the surface hepatitis B virus antigen HBsAg was studied. Eleven recombinant HBsAg variants of wild (adr, ayw2, adw2, adw4, aywl, adw2) and vaccine escape (adw2 T126S, adw2 Q129L, adw2 Q129R, adw2 T143K, adw2 Q145R, aywl Q145A) were obtained. All the recombinant antigens were tested on a panel of 43 monoclonal antibodies (MAb) specific to different HBsAg determinants. Amino acid sequence variation of the a-determinant of HBsAg was shown to significantly affect its immunological responsiveness and antigenic properties. Amino acid substitution in different positions or in the same position, but for various amino acids may differently affect these properties.     

A new method for preservation of viable leukocytes at near-zero temperatures

We propose a new effective, available, and economic method for preservation of leukocytes at near-zero temperatures for 6 days using an original protecting solution. __________ Translated from Byulleten’ Eksperimental’noi Biologii i Meditsiny, Vol. 144, No. 9, pp. 358–360, September, 2007     

Use of Choline Chloride for Leukocyte Cryopreservation (-40°C)

Choline chloride in complex with the main cryophylactic (1,2-propanediol) preserves morphological integrity and functional activity of blood nuclears after freezing to -40°C by the exponential program.     

The molecular epidemiology of hepatitis E virus infection

Molecular characterization of various hepatitis E virus (HEV) strains circulating among humans and animals (particularly swine, deer and boars) in different countries has revealed substantial genetic heterogeneity. The distinctive four-genotype distribution worldwide of mammalian HEV and varying degrees of genetic relatedness among local strains suggest a long and complex evolution of HEV in different geographic regions. The population expansion likely experienced by mammalian HEV in the second half of the 20th century is consistent with an extensive genetic divergence of HEV strains and high prevalence of HEV infections in many parts of the world, including developed countries. The rate and mechanisms of human-to-human transmission and zoonotic transmission to humans vary geographically, thus contributing to the complexity of HEV molecular evolution.     

Serological diagnostics of hepatitis E virus infection

Development of accurate diagnostic assays for the detection of serological markers of hepatitis E virus (HEV) infection remains challenging. In the course of nearly 20 years after the discovery of HEV, significant progress has been made in characterizing the antigenic structure of HEV proteins, engineering highly immunoreactive diagnostic antigens, and devising efficient serological assays. However, many outstanding issues related to sensitivity and specificity of these assays in clinical and epidemiological settings remain to be resolved. Complexity of antigenic composition, viral genetic heterogeneity and varying epidemiological patterns of hepatitis E in different parts of the world present challenges to the refinement of HEV serological diagnostic assays. Development of antigens specially designed for the identification of serological markers specific to acute infection and of IgG anti-HEV specific to the convalescent phase of infection would greatly facilitate accurate identification of active, recent and past HEV infections.