Antiviral activity of novel 2'-fluoro-6'-methylene-carbocyclic adenosine against wild-type and drug-resistant hepatitis B virus mutants

Novel 2'-fluoro-6'-methylene-carbocyclic adenosine (9) was synthesized and evaluated its anti-HBV activity. The titled compound demonstrated significant antiviral activity against wild-type as well as lamivudine, adefovir and double lamivudine/entecavir resistant mutants. Molecular modeling study indicate that the 2'-fluoro moiety by a hydrogen bond, as well as the van der Waals interaction of the carbocyclic ring with the phenylalanine moiety of the polymerase promote the positive binding, even in the drug resistant mutants.     

16S rDNA-based phylogeny of non-symbiotic bacteria of Entorno-pathogenic nematodes from infected insect cadavers

Using 16S rDNA gene sequencing technique, three different species of non-symbiotic bacteria of entomopatho-genic nematodes (EPNs) (Steinernema sp.and Heterorhabditis sp.) were isolated and identified from infected insect cadavers(Galleria mellonella larvae) after 48-hour post infections.Sequence similarity analysis revealed that the strains SRK3, SRK4 and SRK5 belong to Ochrobactrum cytisi,Schineria larvae and Ochrobactrum anthropi,respectively.The isolates O.anthropi and S.larvae were found to be associated with Heterorhabditis indica strains BDU-17 and Yer-136,respectively,whereas O.cytisi was associated with Steinernema siamkayai strain BDU-87. Phenotypically, temporal EPN bacteria were fairly related to symbiotic EPN bacteria (Photorhabdus and Xenorhabdus genera). The strains SRK3 and SRK5 were phylogeographically similar to several non-symbionts and contaminated EPN bacteria isolated in Germany(LMG3311T) and China (X-14),while the strain SRK4 was identical to the isolates of S.larvae (L1/57,L1/58, L1/68 and L2/11) from Wohlfahrtia magnifica in Hungary.The result was further confirmed by RNA secondary structure and minimum energy calculations of aligned sequences.This study suggested that the non-symbionts of these nematodes are phylogeographically diverged in some extent due to phase variation.Therefore,these strains are not host-dependent, but environment-specific isolates.     

Chimeric anti-staphylococcal enterotoxin B antibodies and lovastatin act synergistically to provide in vivo protection against lethal doses of SEB

Staphylococcal enterotoxin B (SEB) is one of a family of toxins secreted by Staphylococcus aureus that act as superantigens, activating a large fraction of the T-cell population and inducing production of high levels of inflammatory cytokines that can cause toxic shock syndrome (TSS) and death. Extracellular engagement of the TCR of T-cells and class II MHC of antigen presenting cells by SEB triggers the activation of many intracellular signaling processes. We engineered chimeric antibodies to block the extracellular engagement of cellular receptors by SEB and used a statin to inhibit intracellular signaling. Chimeric human-mouse antibodies directed against different neutralizing epitopes of SEB synergistically inhibited its activation of human T-cells in vitro. In the in vivo model of lethal toxic shock syndrome (TSS) in HLA-DR3 transgenic mice, two of these antibodies conferred significant partial protection when administered individually, but offered complete protection in a synergistic manner when given together. Similarly, in vivo, lovastatin alone conferred only partial protection from TSS similar to single anti-SEB antibodies. However, used in combination with one chimeric neutralizing anti-SEB antibody, lovastatin provided complete protection against lethal TSS in HLA-DR3 transgenic mice. These experiments demonstrate that in vivo protection against lethal doses of SEB can be achieved by a statin of proven clinical safety and chimeric human-mouse antibodies, agents now widely used and known to be of low immunogenicity in human hosts.     

SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation That Contributes Markedly to Stability

A quantitative linear model accurately (R² = 0.88) describes the thermostabilities of 54 characterized members of a family of fungal cellobiohydrolase class II (CBH II) cellulase chimeras made by SCHEMA recombination of three fungal enzymes, demonstrating that the contributions of SCHEMA sequence blocks to stability are predominantly additive. Thirty-one of 31 predicted thermostable CBH II chimeras have thermal inactivation temperatures higher than the most thermostable parent CBH II, from Humicola insolens, and the model predicts that hundreds more CBH II chimeras share this superior thermostability. Eight of eight thermostable chimeras assayed hydrolyze the solid cellulosic substrate Avicel at temperatures at least 5 °C above the most stable parent, and seven of these showed superior activity in 16-h Avicel hydrolysis assays. The sequence-stability model identified a single block of sequence that adds 8.5 °C to chimera thermostability. Mutating individual residues in this block identified the C313S substitution as responsible for the entire thermostabilizing effect. Introducing this mutation into the two recombination parent CBH IIs not featuring it (Hypocrea jecorina and H. insolens) decreased inactivation, increased maximum Avicel hydrolysis temperature, and improved long time hydrolysis performance. This mutation also stabilized and improved Avicel hydrolysis by Phanerochaete chrysosporium CBH II, which is only 55–56% identical to recombination parent CBH IIs. Furthermore, the C313S mutation increased total H. jecorina CBH II activity secreted by the Saccharomyces cerevisiae expression host more than 10-fold. Our results show that SCHEMA structure-guided recombination enables quantitative prediction of cellulase chimera thermostability and efficient identification of stabilizing mutations.SCHEMA is a computational approach to identifying blocks of sequence that minimize structural disruption when they are recombined in chimeric proteins (1). SCHEMA recombination of eight blocks from three fungal cellobiohydrolase class II (CBH II)² genes was used in our previous work to create a library of 3⁸ = 6,561 chimeric sequences, all having the native Hypocrea jecorina cellulose binding module and linker and observed to feature a degree of glycosylation similar to that found in native CBH IIs secreted by fungi (2). Synthesis and characterization of selected CBH II chimeras expressed in Saccharomyces cerevisiae revealed enzymes with thermostabilities and cellulose hydrolysis performance superior to those of the parent enzymes from Humicola insolens, H. jecorina, and Chaetomium thermophilum.Our prior analysis showed that a qualitative model based on sequence-stability data from 23 functional chimeras (categorizing blocks as destabilizing, stabilizing, or neutral) could identify highly stable chimeras in the SCHEMA library (2). When studying SCHEMA recombination of a bacterial cytochrome P450, we previously estimated that building a quantitative regression model would require stability measurements for at least 35 representative sequences (3). We therefore synthesized an additional 18 CBH II chimeras to further explore the sequences that the qualitative model predicted would encode the most thermostable chimeras. If sequence blocks contribute additively and independently of their context, as was found for SCHEMA chimeras of cytochrome P450 (3), then quantitative stability prediction would be possible based on stability data from a very limited sampling of the thousands of possible chimeras. Here we show that a quantitative CBH II chimera stability model can in fact be constructed and also that it was possible, using site-directed mutagenesis experiments, to pinpoint a single amino acid substitution that is responsible for the large stabilizing contribution of one of the SCHEMA blocks.Highly thermostable fungal CBH IIs are potentially useful for the degradation of cellulosic substrates in biofuels, textile, and other applications (4). High thermostability translates to longer half-lives at elevated hydrolysis temperatures, where viscosity and microbial contamination are reduced (5). We therefore investigated how selected thermostable CBH II chimeras perform in the hydrolysis of crystalline cellulose (Avicel) at elevated temperatures (up to 70 °C). All of the thermostable chimeras tested have specific activities on phosphoric acid swollen cellulose (PASC) at 50 °C that are comparable with the most active parent (H. jecorina CBH II) and hydrolyze Avicel at temperatures higher than any of the three parent enzymes, including the CBH II from the thermophilic fungus H. insolens.     

The impact of tacrolimus on the immunopathogenesis of staphylococcal enterotoxin-induced systemic inflammatory response syndrome and pneumonia

Staphylococcal superantigens (SAg) are a family of potent exotoxins produced by Staphylococcus aureus. They play an important role in the pathogenesis of staphylococcal shock and pneumonia by causing a robust activation of the immune system and eliciting a strong surge in systemic cytokine and chemokine levels. Given the biological functions of SAg, we evaluated the efficacy of tacrolimus, a potent immunosuppressive agent, in the prophylaxis and therapy of staphylococcal TSS and pneumonia using human leukocyte antigen (HLA)-DR3 transgenic mice. Tacrolimus significantly inhibited staphylococcal SAg induced T cell activation in vitro. In vivo, tacrolimus significantly suppressed the SAg-induced elevation in serum cytokine and chemokine levels when given prophylactically, when administered immediately or even 2 h following systemic SAg challenge. Paradoxically, neither the prophylactic nor post-exposure treatment with tacrolimus protected mice from lethal SAg-induced TSS. A closer examination revealed that tacrolimus failed to suppress SAg-induced T cell proliferation and systemic pathology, including gut dysfunction. Tacrolimus also failed to protect from lethal pneumonia induced by a SAg-producing S. aureus strain. Thus, our study showed that even though T cell activation by SAg plays a major role in the immunopathogenesis of TSS and pneumonia, tacrolimus alone has no beneficial effect.     

A study on conventional IMRT and RapidArc treatment planning techniques for head and neck cancers

AimTo evaluate the performance of volumetric arc modulation with RapidArc against conventional IMRT for head and neck cancers.BackgroundRapidArc is a novel technique that has recently been made available for clinical use. Planning study was done for volumetric arc modulation with RapidArc against conventional IMRT for head and neck cancers.Materials and methodsTen patients with advanced tumors of the nasopharynx, oropharynx, and hypopharynx were selected for the planning comparison study. PTV was delineated for two different dose levels and planning was done by means of simultaneously integrated boost technique. A total dose of 70 Gy was delivered to the boost volume (PTV boost) and 57.7 Gy to the elective PTV (PTV elective) in 35 equal treatment fractions. PTV boost consisted of the gross tumor volume and lymph nodes containing visible macroscopic tumor or biopsy-proven positive lymph nodes, whereas the PTV elective consisted of elective nodal regions. Planning was done for IMRT using 9 fields and RapidArc with single arc, double arc. Beam was equally placed for IMRT plans. Single arc RapidArc plan utilizes full 360° gantry rotation and double arc consists of 2 co-planar arcs of 360° in clockwise and counter clockwise direction. Collimator was rotated from 35 to 45° to cover the entire tumor, which reduced the tongue and groove effect during gantry rotation. All plans were generated with 6 MV X-rays for CLINAC 2100 Linear Accelerator. Calculations were done in the Eclipse treatment planning system (version 8.6) using the AAA algorithm.ResultsDouble arc plans show superior dose homogeneity in PTV compared to a single arc and IMRT 9 field technique. Target coverage was almost similar in all the techniques. The sparing of spinal cord in terms of the maximum dose was better in the double arc technique by 4.5% when compared to the IMRT 9 field and single arc techniques. For healthy tissue, no significant changes were observed between the plans in terms of the mean dose and integral dose. But RapidArc plans showed a reduction in the volume of the healthy tissue irradiated at V_15 Gy (5.81% for single arc and 4.69% for double arc) and V_20 Gy (7.55% for single arc and 5.89% for double arc) dose levels when compared to the 9-Field IMRT technique. For brain stem, maximum dose was similar in all the techniques. The average MU (±SD) needed to deliver the dose of 200 cGy per fraction was 474 ± 80 MU and 447 ± 45 MU for double arc and single arc as against 948 ± 162 MU for the 9-Field IMRT plan. A considerable reduction in maximum dose to the mandible by 6.05% was observed with double arc plan. Double arc shows a reduction in the parotid mean dose when compared with single arc and IMRT plans.ConclusionRapidArc using double arc provided a significant sparing of OARs and healthy tissue without compromising target coverage compared to IMRT. The main disadvantage with IMRT observed was higher monitor units and longer treatment time.     

Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins

Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic diversity and fitness through iterative directed evolution will accelerate improvements in engineered protein therapeutics.     

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

Background

Production of proteins as therapeutic agents, research reagents and molecular tools frequently depends on expression in heterologous hosts. Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the corresponding physical DNA. Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles.

Principal Findings

To identify sequence features that affect protein expression we synthesized and expressed in E. coli two sets of 40 genes encoding two commercially valuable proteins, a DNA polymerase and a single chain antibody. Genes differing only in synonymous codon usage expressed protein at levels ranging from undetectable to 30% of cellular protein. Using partial least squares regression we tested the correlation of protein production levels with parameters that have been reported to affect expression. We found that the amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids. Favorable codons were predominantly those read by tRNAs that are most highly charged during amino acid starvation, not codons that are most abundant in highly expressed E. coli proteins. Finally we confirmed the validity of our models by designing, synthesizing and testing new genes using codon biases predicted to perform well.

Conclusion

The systematic analysis of gene design parameters shown in this study has allowed us to identify codon usage within a gene as a critical determinant of achievable protein expression levels in E. coli. We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology should allow similar design algorithms to be empirically derived for any expression system.     

Identification of VP1/2A and 2C as virulence genes of hepatitis A virus and demonstration of genetic instability of 2C

Fourteen different chimeric virus genomes were constructed from two infectious cDNA clones encoding a virulent and an attenuated isolate, respectively, of the HM175 strain of hepatitis A virus. The ability of each recombinant virus to infect tamarins and to cause acute hepatitis was determined. Comparisons of the genotype and phenotype of each virus suggested that VP1/2A and 2C genes were responsible for virulence. The 2C gene derived from the attenuated parent virus was unstable, and one or more mutations arose in this gene during the first passage in tamarins.     

Expression and function of transgenic HLA-DQ molecules and lymphocyte development in mice lacking invariant chain

Invariant chain (Ii) is a non-MHC-encoded molecule, which plays an accessory role in the proper assembly/expression of functional MHC class II molecules and there by plays an important role in Ag processing/presentation. The phenotype of mice lacking Ii depends on the allotype of the MHC class II molecule. In some mice strains, Ii deficiency results in reduction in expression of class II molecules accompanied by defective CD4(+) T cell development. Responses to conventional Ags/superantigens are also compromised. In this study, we describe for the first time the functionality of human class II molecules, HLA-DQ6 and HLA-DQ8, in transgenic mice lacking Ii. HLA transgenic Ii(-/-) mice expressed very low levels of surface DQ6 and DQ8 accompanied by severe reduction in CD4(+) T cells both in the thymus and periphery. In vitro proliferation and cytokine production to an exogenous superantigen, staphylococcal enterotoxin B (SEB) was diminished in HLA-transgenic Ii(-/-) mice. However, SEB-induced in vivo expansion of CD8(+) T cells expressing TCR Vbeta8 family in DQ8.Ii(-/-) mice was comparable with that of DQ8.Ii(+/+) mice. Systemic IFN-gamma production following in vivo challenge with SEB was reduced in DQ8.Ii(-/-) mice and were also protected from SEB-induced toxic shock. Although the T cell response to a known peptide Ag was diminished in DQ8.Ii(-/-) mice, DQ8.Ii(-/-) APCs were capable of presenting that peptide to primed T cells from wild-type DQ8 mice as well as to a specific T cell hybridoma. Differentiation of mature B cells was also affected to a certain extent in DQ8.Ii(-/-) mice.