Structural insight into antisense gapmer-RNA oligomer duplexes through molecular dynamics simulations

There is an extensive research carrying out on antisense technology and the molecules entering into clinical trials are increasing rapidly. Phosphorothioate (PS) is a chemical modification in which nonbridged oxygen is replaced with a sulfur, consequently providing resistance against nuclease activity. The 2'-4' conformationally restricted nucleoside has the structural features of both 2'-O-methoxy ethyl RNA (MOE), which shows good toxicity profile, and locked nucleic acid (LNA), which shows good binding affinity towards the target RNA. These modifications have been studied and suggested that they can be a potential therapeutic agents in antisense therapy. Mipomersen (ISIS 301012), which contains the novel nucleoside modification has been used to target to apolipoprotein (Apo B), which reduces LDL cholesterol by 6–41%. In this study, classical molecular dynamics (MD) simulations were performed on six different antisense gapmer/target-RNA oligomer duplexes (LNA-PS-LNA/RNA, RcMOE-PS-RcMOE/RNA, ScMOE-PS-ScMOE/RNA, MOE-PS-MOE/RNA, PS-DNA/RNA and DNA/RNA) to investigate the structural dynamics, stability and solvation properties. The LNA, MOE nucleotides present in respective duplexes are showing the structure of A-form and the PS-DNA nucleotides resemble the structure of B-form helix with respect to some of the helical parameters. Free energy calculations suggest that the oligomer, which contains LNA binds to the RNA strongly than other modifications as shown in experimental results. The MOE modified nucleotide, which although had a lower binding affinity but higher solvent accessible surface area (SASA) compared to the other modifications, may be influencing the toxicity and hence may be used it in Mipomersen, the second antisense molecule which is approved by FDA.

Communicated by Ramaswamy H. Sarma     

Adiponectin receptor 1 variants associated with lower insulin resistance in African Americans

Adiponectin has been shown to have a role in insulin resistance. However, little is known about the contribution of genetic variation in the adiponectin receptor 1 gene (ADIPOR1) in this regard. We hypothesized that variation in ADIPOR1 would be associated with significant changes in insulin resistance and tested this hypothesis in a cohort of 483 African-American adolescents. Seven single nucleotide polymorphisms (SNPs) of ADIPOR1 spanning from the promoter to the 3'-untranslated region were genotyped. We analyzed single SNPs and haplotypes for associations with insulin resistance [homeostasis model assessment of insulin resistance (HOMA-IR)] in the full cohort as well as lean (BMI < 85%) and non-lean (BMI >or= 85%) subsets. There was no evidence of ADIPOR1 variant effects on HOMA-IR in the full cohort or in the lean subset. However, in the non-lean subset, SNP +5843 (A allele), and haplotypes including SNPs -8505/-5692/+3002/+5843 (ATTA and AGTG) showed significant associations with decreased HOMA-IR after adjustment for sex, puberty, adiponectin, and waist z-score. Our findings suggest not only that ADIPOR1 variants influence insulin resistance in the presence of adiposity, but also that these variants and haplotypes are protective in African Americans.     

Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChip

Background

Cystic fibrosis (CF) mice, created with a genetically engineered mutation in the Cystic fibrosis transmembrane conductance regulator (Cftr) gene, may develop intestinal plugs which limit their survival past weaning. In a studied population of genetically mixed CF mice differences in allelic ratios at particular loci, between surviving CF mice and mice with the lethal intestinal defect, were used to map cystic fibrosis modifier gene one, Cfm1. Using this approach, we previously identified an X chromosome locus which may influence the survival to weaning of C57BL/6J × BALB/cJ F2 CF mice. We also detected two regions of transmission ratio distortion, independent of Cftr genotype, in a limited dataset. To investigate these findings, in this study we have genotyped 1208 three-week old F2 mice, and 186 day E15.5 embryos, derived from a congenic (C57BL/6J × BALB/cJ) F1 Cftr +/- intercross, for the putative distortion regions.

Results

An excess of homozygous BALB genotypes, compared to Mendelian expectations, was detected on chromosomes 5 (p = 5.7 × 10^-15) and X (p = 3.0 × 10^-35) in three-week old female mice but transmission ratio distortion was not evident in the tested region of chromosome 3 (p = 0.39). Significant pre-weaning lethality of CF mice occurred as 11.3% (137/1208) of the three-week old offspring were identified as CF mice. X chromosome genotypes were not, however, distorted in the female CF mice (p = 0.62), thus the significant non-Mendelian inheritance of this locus was dependent on CF status. The survival of CF embryos to day E15.5 was consistent with Mendelian expectations (42/186 = 23%), demonstrating the loss of CF mice to have occurred between E15.5 and three weeks of age. The excess of X chromosome homozygous BALB genotypes was recorded in female embryos (p = 0.0048), including CF embryos, indicating the distortion to be evident at this age.

Conclusion

Two of three previously suggested loci of transmission ratio distortion were replicated as distorted in this mouse cross. The non-Mendelian inheritance of X chromosome genotypes implicates this region in the survival to weaning of non-CF mice.     

An early event in the herpes simplex virus type-2 replication cycle is sufficient to induce Chlamydia trachomatis persistence

Epidemiological studies have demonstrated that co-infections of herpes simplex virus type 2 (HSV-2) and Chlamydia trachomatis occur in vivo. Data from a tissue culture model of C. trachomatis/HSV-2 co-infection indicate that viral co-infection stimulates the formation of persistent chlamydiae. Transmission electron microscopic (TEM) analyses demonstrated that in both HeLa and HEC-1B cells, co-infection caused developing chlamydiae to exhibit swollen, aberrantly shaped reticulate bodies (RBs), characteristically observed in persistence. Additionally, HSV-2 co-infection suppressed production of infectious chlamydial elementary bodies (EBs) in both host cell types. Co-infection with HSV type 1 (HSV-1) produced similar morphologic alterations and abrogated infectious EB production. These data indicate that virus-induced chlamydial persistence was neither host cell- nor virus strain-specific. Purification of crude HSV-2 stocks demonstrated that viral particles were required for coinfection-induced chlamydial persistence to occur. Finally, co-infection with either UV-inactivated, replication-incompetent virus or replication-competent HSV-2 in the presence of cyclohexamide reduced chlamydial infectivity without altering chlamydial genomic DNA accumulation. These data demonstrate that productive viral replication is not required for the induction of chlamydial persistence and suggest that HSV attachment and entry can provide the necessary stimulus to alter C. trachomatis development.     

Production and characterization of monoclonal antibodies against a local isolate of classical swine fever virus

Monoclonal antibodies (mAbs) against a classical swine fever virus (CSFV; subgenogroup 1:1) isolate from Assam, India were produced and characterized. Four fusions of myeloma cells (SP2/0Ag) were made with spleenocytes of 8-10 weeks old BALB/C mice immunized with the viral antigen. Several hybridoma clones secreting antibodies to the virus were obtained after four fusions, but five hybridoma clones secreting antibody specific to the virus could be stabilized. All the mAbs belong to the IgG2a isotype. Except one, none of the four mAbs showed cross reaction with bovine viral diarrhoea virus and border disease virus (BDV). One mAb showed cross reaction with BDV. All the four mAbs specific to CSFV showed reactivity with the parental virus in immunoperoxidase test (IPT) and with a single protein band (molecular weight 55 kD approximately) of the virus in western blotting. In neutralization peroxidase linked assay (NPLA) all the mAbs reacted with 13 CSFV local isolates as well as with the cell culture adapted lapinized vaccine virus strain belonging to the subgenogroup 1:1. This is the first report on production and characterization of mAbs against CSFV in India.     

Genetic structure of native circumpolar populations based on autosomal,mitochondrial, and Y chromosome DNA markers

This study investigates the genetic structure of the present‐day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a “ubiquitous” allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non‐native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the “ubiquitous” allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935‐GQ922973. Am J Phys Anthropol 143:62–74, 2010. © 2010 Wiley‐Liss, Inc.     

Isolation of two antifungal compounds fromNeolitsea cuipala and their activity against some plant pathogenic fungi

Zeylanidine and zeylanicine isolated fromNeolitsea cuipala fruit peels are found to be potential antifungal agents againstHelminthosporium oryzae, Fusarium oxysporum, Alternaria solani, Curvularia varuciformis andColletotrichum gleosporioides.     

Studies on thermal degradation and termite resistant properties of chemically modified wood

A series of experiments were carried out to examine the resistant capacity of a chemically treated hard wood, Anthocephalus cadamba (Roxb) Miq. to thermal and termite degradation. The treatment with thermosetting resins viz. urea formaldehyde (UF), melamine formaldehyde (MF) and phenol formaldehyde (PF) at 31-33 levels of weight percent gain (WPG) increased the strength property i.e. modulus of rupture (MOR) by 7.50-21.02% and stiffness i.e. modulus of elasticity (MOE) by 9.50-12.18% over the untreated one with no remarkable effect on specific gravity. The treated samples were found resistant to termite attack, while the untreated one was badly damaged by termites on 12 months' exposure to a termite colony. The thermal degradations of untreated and treated wood samples were studied using thermogravimetric (TGA) and differential thermogravimetric (DTG) techniques at heating rates 20 and 30 degrees C min(-1) in temperature range 30-650 degrees C. The treated wood was found to be thermally more stable than the untreated one.