Non-random Escape Pathways from a Broadly Neutralizing Human Monoclonal Antibody Map to a Highly Conserved Region on the Hepatitis C Virus E2 Glycoprotein Encompassing Amino Acids 412–423

A challenge for hepatitis C virus (HCV) vaccine development is to define epitopes that are able to elicit protective antibodies against this highly diverse virus. The E2 glycoprotein region located at residues 412–423 is conserved and antibodies to 412–423 have broadly neutralizing activities. However, an adaptive mutation, N417S, is associated with a glycan shift in a variant that cannot be neutralized by a murine but by human monoclonal antibodies (HMAbs) against 412–423. To determine whether HCV escapes from these antibodies, we analyzed variants that emerged when cell culture infectious HCV virions (HCVcc) were passaged under increasing concentrations of a specific HMAb, HC33.1. Multiple nonrandom escape pathways were identified. Two pathways occurred in the context of an N-glycan shift mutation at N417T. At low antibody concentrations, substitutions of two residues outside of the epitope, N434D and K610R, led to variants having improved in vitro viral fitness and reduced sensitivity to HC33.1 binding and neutralization. At moderate concentrations, a S419N mutation occurred within 412–423 in escape variants that have greatly reduced sensitivity to HC33.1 but compromised viral fitness. Importantly, the variants generated from these pathways differed in their stability. N434D and K610R-associated variants were stable and became dominant as the virions were passaged. The S419N mutation reverted back to N419S when immune pressure was reduced by removing HC33.1. At high antibody concentrations, a mutation at L413I was observed in variants that were resistant to HC33.1 neutralization. Collectively, the combination of multiple escape pathways enabled the virus to persist under a wide range of antibody concentrations. Moreover, these findings pose a different challenge to vaccine development beyond the identification of highly conserved epitopes. It will be necessary for a vaccine to induce high potency antibodies that prevent the formation of escape variants, which can co-exist with lower potency or levels of neutralizing activities.     

Highly Conserved Non-Coding Sequences and the 18q Critical Region for Short Stature: A Common Mechanism of Disease?

Background

Isolated growth hormone deficiency (IGHD) and multiple pituitary hormone deficiency (MPHD) are heterogeneous disorders with several different etiologies and they are responsible for most cases of short stature. Mutations in different genes have been identified but still many patients did not present mutations in any of the known genes. Chromosomal rearrangements may also be involved in short stature and, among others, deletions of 18q23 defined a critical region for the disorder. No gene was yet identified.

Methodology/Principal Findings

We now report a balanced translocation X;18 in a patient presenting a breakpoint in 18q23 that was surprisingly mapped about 500 Kb distal from the short stature critical region. It separated from the flanking SALL3 gene a region enriched in highly conserved non-coding elements (HCNE) that appeared to be regulatory sequences, active as enhancers or silencers during embryonic development.

Conclusion

We propose that, during pituitary development, the 18q rearrangement may alter expression of 18q genes or of X chromosome genes that are translocated next to the HCNEs. Alteration of expression of developmentally regulated genes by translocation of HCNEs may represent a common mechanism for disorders associated to isolated chromosomal rearrangements.     

A Conserved Phenylalanine as a Relay between the α5 Helix and the GDP Binding Region of Heterotrimeric Gi Protein α Subunit

G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process.     

Ce−ZSM-5: A Highly Capable Catalyst for the Construction of Acridines in Water and Their Computational Study against DNA Gyrase Protein

Cerium doped ZSM-5 (Ce−ZSM-5) as an environmentally benign and reusable catalyst for the construction of acridines in aqueous medium. This method produced corresponding acridines with good yields and shorter reaction times. Also avoids the use of hazardous solvents and involves a simple work-up process. The solid catalyst was prepared by doping Ce ions with ZSM-5 (Zeolite Socony Mobil-5) and confirmed by XRD, BET SA-PSD and SEM. The synthesised acridine derivatives were confirmed by ¹H-NMR, ¹³C-NMR and FT-IR spectroscopic data. The docking studies of the synthesised compounds are performed by the PyRx auto dock tool against DNA gyrase protein. The products 5a and 6d are found to be the best fit ligands against DNA gyrase protein.     

A Novel Approach to Solve the “Missing Marker Problem” in Marker-Based Motion Analysis That Exploits the Segment Coordination Patterns in Multi-Limb Motion Data

Marker-based human motion analysis is an important tool in clinical research and in many practical applications. Missing marker information caused by occlusions or a marker falling off is a common problem impairing data quality. The current paper proposes a conceptually new gap filling algorithm and presents results from a proof-of-principle analysis. The underlying idea of the proposed algorithm was that a multitude of internal and external constraints govern human motion and lead to a highly subject-specific movement pattern in which all motion variables are intercorrelated in a specific way. Two principal component analyses were used to determine how the coordinates of a marker with gaps correlated with the coordinates of the other, gap-free markers. Missing marker data could then be reconstructed through a series of coordinate transformations. The proposed algorithm was tested by reconstructing artificially created gaps in a 20-step walking trial and in an 18-s one-leg balance trial. The measurement accuracy’s dependence on the marker position, the length of the gap, and other parameters were evaluated. Even if only 2 steps of walking or 1.8 s of postural sway (10% of the whole marker data) were provided as input in the current study, the reconstructed marker trajectory differed on average no more than 11 mm from the originally measured trajectory. The reconstructed result improved further, on average, to distances below 5 mm if the marker trajectory was available more than 50% of the trial. The results of this proof-of-principle analysis supported the assumption that missing marker information can be reconstructed from the intercorrelations between marker coordinates, provided that sufficient data with complete marker information is available. Estimating missing information cannot be avoided entirely in many situations in human motion analysis. For some of these situations, the proposed reconstruction method may provide a better solution than what is currently available.     

Mapping of the Gene Encoding the Regulatory Subunit RIIα of cAMP-Dependent Protein Kinase (Locus PRKAR2A) to Human Chromosome Region 3p21.3–p21.2

We have determined the chromosomal localization of the gene for the regulatory subunit RIIα of cAMP-dependent protein kinase (locus PRKAR2A) to human chromosome 3 using polymerase chain reaction (PCR) and Southern blot analysis of two different somatic cell hybrid mapping panels. Furthermore, PCR analysis of a chromosome 3 mapping panel revealed the presence of a human RIIα-specific amplification product only in cell lines containing the region 3p21.3–p21.2. The localization of PRKAR2A was confirmed by PCR mapping using the Stanford G3 Radiation Hybrid Panel as template. The results from this analysis demonstrated that PRKAR2A is most closely linked to D3S3334 (lod score 12.5) and flanked by D3S1322E and D3S1581.     

“Beijing Region” (3pter-D3S3397) of the Human Genome: Complete sequence and analysis

The Human Genome Project (HGP), undoubtedly one of the greatest endeavors in the history of natural sciences, aims at determining the DNA sequence of the 3-billion-basepair human genome that holds an extraordinary trove of information about evolution, growth, and development of humans. China officially joined HGP and became one of the six member states of the International Human Genome Sequencing Con-sortium (IHGSC), alongside France, Germany, Japan, United Kingdom, and United State…     

“Beijing Region” (3pter-D3S3397) of the Human Genome: Complete sequence and analysis

The goal of the Human Genome Project (HGP) is to determine a complete and high-quality sequence of the human genome. China, as one of the six member states, takes a region between 3pter and D3S3397 of the human chromosome 3 as its share of this historic project, referred as “Beijing Region”. The complete sequence of this region comprises of 17.4 megabasepairs (Mb) with an average GC content of 42% and an average recombination rate of 2.14 cM/Mb. Within Beijing Region, 122 known and 20 novel genes are identified, as well as 42607 single nucleotide polymorphisms (SNPs). Comprehensive analyses also reveal: (i) gene density and GC-content of Beijing Region are in agreement with human cytogenetic maps, i.e. G-minus bands are GC-rich and of a high gene density, whereas G-plus bands are GC-poor and of a relatively low gene density; (ii) the average recombination rate within Beijing Region is relatively high compared with other regions of chromosome 3, with the highest recombination rate of 6.06 cM/Mb in the subtelomeric area; (iii) it is most likely that a large gene, associated with the mammary gland, may reside in the 1.1 Mb gene-poor area near the telomere; (iv) many disease-related genes are genetically mapped to Beijing Region, including those associated with cancers and metabolic syndromes. All make Beijing Region an important target for in-depth molecular investigations with a purpose of medical applications.     

A Water Mediated Electrostatic Interaction Gives Thermal Stability to the “Tail” Region of the GrpE Protein from <Emphasis Type="Italic">E. coli</Emphasis>

The GrpE protein from E. coli is a homodimer with an unusual structure of two long paired α-helices from each monomer interacting in a parallel arrangement to form a “tail” at the N-terminal end. Using site-directed mutagenesis, we show that there is a key electrostatic interaction involving R57 (mediated by a water molecule) that provides thermal stability to this “tail” region. The R57A mutant showed a drop in T _m of 8.5°C and a smaller ΔH _u (unfolding) compared to wild-type for the first unfolding transition, but no significant decrease in dimer stability as shown through equilibrium analytical ultracentrifugation studies. Another mutant (E94A) at the dimer interface showed a decrease in ΔH _u but no drop in T _m for the second unfolding transition and a slight increase in dimer stability.     

A Novel Adeno-Associated Virus–Based Genetic Vaccine Encoding the Hepatitis C Virus NS3/4 Protein Exhibits Immunogenic Properties in Mice Superior to Those of an NS3-Protein-Based Vaccine

More than 170 million individuals worldwide are infected with hepatitis C virus (HCV), and up to an estimated 30% of chronically infected individuals will go on to develop progressive liver disease. Despite the recent advances in antiviral treatment of HCV infection, it remains a major public health problem. Thus, development of an effective vaccine is urgently required. In this study, we constructed novel adeno-associated virus (AAV) vectors expressing the full-length NS3 or NS3/4 protein of HCV genotype 1b. The expression of the NS3 or NS3/4 protein in HepG2 cells was confirmed by western blotting. C57BL/6 mice were intramuscularly immunised with a single injection of AAV vectors, and the resultant immune response was investigated. The AAV2/rh32.33.NS3/4 vaccine induced stronger humoral and cellular responses than did the AAV2/rh32.33.NS3 vaccine. Our results demonstrate that AAV-based vaccines exhibit considerable potential for the development of an effective anti-HCV vaccine.     

Separating the Noise from the Noise: A Finding in Support of the “Niche Hypothesis,” That Birds are Influenced by Human-Induced Noise in Natural Habitats

ABSTRACT

Controlling for the confounding influence of physical disturbance, it was possible to test the hypothesis that ambient noise alone would play a role in structuring bird communities in riparian habitats in Boulder, Colorado, USA. Point counts of birds were conducted in open space/minimally disturbed, residential, commercial and industrial neighborhoods. Within the same disturbance parameters and land use, species richness and PIF scores (a weighted value based on species' importance) consistently and significantly decreased as ambient noise increased. These results can be viewed as support for the “Niche Hypothesis” (Krause 1987, 1998), that wildlife species' acoustic niches are adversely affected by human-induced noise pollution.