Base compositional structure of genomes

We model the base compositional structure of the human and Escherichia coli genomes. Three particular properties are first quantified: (1) There is a significant tendency for any region of either genome to have a strand-symmetric base composition. (2) The variation in base composition from region to region, within each genome, is very much larger than expected from common homogeneous stochastic models. (3) A given local base composition tends to persist over a scale of at least kilobases (E. coli) or tens of kilobases (human). Multidomain stochastic models from the literature are reviewed and sharpened. In particular, quantitative measurements of the third property lead us to suggest a significant shift in the style of domain models, in which the variation of A+T content with position is modeled by a random walk with frequent small steps rather than with large quantum jumps. As an application, we suggest a way to reduce the amount of computation in the assembly of large sequences from sequences of randomly chosen fragments.     

Factors Associated with Post-Seasonal Serological Titer and Risk Factors for Infection with the Pandemic A/H1N1 Virus in the French General Population

The CoPanFlu-France cohort of households was set up in 2009 to study the risk factors for infection by the pandemic influenza virus (H1N1pdm) in the French general population. The authors developed an integrative data-driven approach to identify individual, collective and environmental factors associated with the post-seasonal serological H1N1pdm geometric mean titer, and derived a nested case-control analysis to identify risk factors for infection during the first season. This analysis included 1377 subjects (601 households). The GMT for the general population was 47.1 (95% confidence interval (CI): 45.1, 49.2). According to a multivariable analysis, pandemic vaccination, seasonal vaccination in 2009, recent history of influenza-like illness, asthma, chronic obstructive pulmonary disease, social contacts at school and use of public transports by the local population were associated with a higher GMT, whereas history of smoking was associated with a lower GMT. Additionally, young age at inclusion and risk perception of exposure to the virus at work were identified as possible risk factors, whereas presence of an air humidifier in the living room was a possible protective factor. These findings will be interpreted in light of the longitudinal analyses of this ongoing cohort.     

Antihypertensive drug Valsartan promotes dendritic spine density by altering AMPA receptor trafficking

Recent studies demonstrated that the antihypertensive drug Valsartan improved spatial and episodic memory in mouse models of Alzheimer’s Disease (AD) and human subjects with hypertension. However, the molecular mechanism by which Valsartan can regulate cognitive function is still unknown. Here, we investigated the effect of Valsartan on dendritic spine formation in primary hippocampal neurons, which is correlated with learning and memory. Interestingly, we found that Valsartan promotes spinogenesis in developing and mature neurons. In addition, we found that Valsartan increases the puncta number of PSD-95 and trends toward an increase in the puncta number of synaptophysin. Moreover, Valsartan increased the cell surface levels of AMPA receptors and selectively altered the levels of spinogenesis-related proteins, including CaMKIIα and phospho-CDK5. These data suggest that Valsartan may promote spinogenesis by enhancing AMPA receptor trafficking and synaptic plasticity signaling.     

Pharmacological cyclin-dependent kinase inhibitors inhibit replication of wild-type and drug-resistant strains of herpes simplex virus and human immunodeficiency virus type 1 by targeting cellular,not viral,proteins

Pharmacological cyclin-dependent kinase (cdk) inhibitors (PCIs) block replication of several viruses, including herpes simplex virus type 1 (HSV-1) and human immunodeficiency virus type 1 (HIV-1). Yet, these antiviral effects could result from inhibition of either cellular cdks or viral enzymes. For example, in addition to cellular cdks, PCIs could inhibit any of the herpesvirus-encoded kinases, DNA replication proteins, or proteins involved in nucleotide metabolism. To address this issue, we asked whether purine-derived PCIs (P-PCIs) inhibit HSV and HIV-1 replication by targeting cellular or viral proteins. P-PCIs inhibited replication of HSV-1 and -2 and HIV-1, which require cellular cdks to replicate, but not vaccinia virus or lymphocytic choriomeningitis virus, which are not known to require cdks to replicate. P-PCIs also inhibited strains of HSV-1 and HIV-1 that are resistant to conventional antiviral drugs, which target viral proteins. In addition, the anti-HSV effects of P-PCIs and a conventional antiherpesvirus drug, acyclovir, were additive, demonstrating that the two drugs act by distinct mechanisms. Lastly, the spectrum of proteins that bound to P-PCIs in extracts of mock- and HSV-infected cells was the same. Based on these observations, we conclude that P-PCIs inhibit virus replication by targeting cellular, not viral, proteins.     

Self-compatibility and incompatibility in tetraploid sour cherry (Prunus cerasus L.)

. Gametophytic self-incompatibility (GSI) typically "breaks down" due to polyploidy in many Solanaceous species, resulting in self-compatible (SC) tetraploid individuals. However, sour cherry (Prunus cerasus L.), a tetraploid species resulting from hybridization of the diploid sweet cherry (P. avium L.) and the tetraploid ground cherry (P. fruticosa Pall.), is an exception, consisting of both self-incompatible (SI) and SC individuals. Since sweet cherry exhibits GSI with 13 S-ribonucleases (S-RNases) identified as the stylar S-locus product, the objectives were to compare sweet and sour cherry S-allele function, S-RNase sequences and linkage map location as initial steps towards understanding the genetic basis of SI and SC in sour cherry. S-RNases from two sour cherry cultivars that were the parents of a linkage mapping population were cloned and sequenced. The sequences of two S-RNases were identical to those of sweet cherry S-RNases, whereas three other S-RNases had unique sequences. One of the S-RNases mapped to the Prunus linkage group 6, similar to its location in sweet cherry and almond, whereas two other S-RNases were linked to each other but were unlinked to any other markers. Interspecific crosses between sweet and sour cherry demonstrated that GSI exists in sour cherry and that the recognition of common S-alleles has been maintained in spite of polyploidization. It is hypothesized that self-compatibility in sour cherry is caused by the existence of non-functional S-RNases and pollen S-genes that may have arisen from natural mutations.     

Identification of Novel Small Molecule Inhibitors of Oncogenic RET Kinase

Oncogenic mutation of the RET receptor tyrosine kinase is observed in several human malignancies. Here, we describe three novel type II RET tyrosine kinase inhibitors (TKI), ALW-II-41-27, XMD15-44 and HG-6-63-01, that inhibit the cellular activity of oncogenic RET mutants at two digit nanomolar concentration. These three compounds shared a 3-trifluoromethyl-4-methylpiperazinephenyl pharmacophore that stabilizes the ‘DFG-out’ inactive conformation of RET activation loop. They blocked RET-mediated signaling and proliferation with an IC50 in the nM range in fibroblasts transformed by the RET/C634R and RET/M918T oncogenes. They also inhibited autophosphorylation of several additional oncogenic RET-derived point mutants and chimeric oncogenes. At a concentration of 10 nM, ALW-II-41-27, XMD15-44 and HG-6-63-01 inhibited RET kinase and signaling in human thyroid cancer cell lines carrying oncogenic RET alleles; they also inhibited proliferation of cancer, but not non-tumoral Nthy-ori-3-1, thyroid cells, with an IC50 in the nM range. The three compounds were capable of inhibiting the ‘gatekeeper’ V804M mutant which confers substantial resistance to established RET inhibitors. In conclusion, we have identified a type II TKI scaffold, shared by ALW-II-41-27, XMD15-44 and HG-6-63-01, that may be used as novel lead for the development of novel agents for the treatment of cancers harboring oncogenic activation of RET.     

Spatial and temporal patterns of urea content in a eutrophic stream continuum on the Northern Great Plains

Biogeochemistry - Urea can degrade water quality and stimulate toxic phytoplankton in P-rich lakes, yet little is known of its sources, abundance, or transportation in lotic systems, particularly...