Identification of the DNA damage-responsive elements of therhp51 + gene,arecA andRAD51 homolog from the fission yeastSchizosaccharomyces pombe

TheSchizosaccharomyces pombe rhp51 ⁺ gene encodes a recombinational repair protein that shares significant sequence identities with the bacterial RecA and theSaccharomyces cerevisiae RAD51 protein. Levels ofrhp51 ⁺ mRNA increase following several types of DNA damage or inhibition of DNA synthesis. Anrhp51::ura4 fusion gene was used to identify the cis-acting promoter elements involved in regulatingrhp51 ⁺ expression in response to DNA damage. Two elements, designated DRE1 and DRE2 (fordamage-responsiveelement), match a decamer consensus URS (upstream repressing sequence) found in the promoters of many other DNA repair and metabolism genes fromS. cerevisiae. However, our results show that DRE1 and DRE2 each function as a UAS (upstream activating sequence) rather than a URS and are also required for DNA-damage inducibility of the gene. A 20-bp fragment located downstream of both DRE1 and DRE2 is responsible for URS function. The DRE1 and DRE2 elements cross-competed for binding to two proteins of 45 and 59 kDa. DNase I footprint analysis suggests that DRE1 and DRE2 bind to the same DNA-binding proteins. These results suggest that the DRE-binding proteins may play an important role in the DNA-damage inducibility ofrhp51 ⁺ expression.     

An experimental evaluation of drug‐induced mutational meltdown as an antiviral treatment strategy

The rapid evolution of drug resistance remains a critical public health concern. The treatment of influenza A virus (IAV) has proven particularly challenging, due to the ability of the virus to develop resistance against current antivirals and vaccines. Here, we evaluate a novel antiviral drug therapy, favipiravir, for which the mechanism of action in IAV involves an interaction with the viral RNA‐dependent RNA polymerase resulting in an effective increase in the viral mutation rate. We used an experimental evolution framework, combined with novel population genetic method development for inference from time‐sampled data, to evaluate the effectiveness of favipiravir against IAV. Evaluating whole genome polymorphism data across 15 time points under multiple drug concentrations and in controls, we present the first evidence for the ability of IAV populations to effectively adapt to low concentrations of favipiravir. In contrast, under high concentrations, we observe population extinction, indicative of mutational meltdown. We discuss the observed dynamics with respect to the evolutionary forces at play and emphasize the utility of evolutionary theory to inform drug development.     

Development of species‐specific primers for rapid diagnosis of Tetranychus urticae,T. kanzawai,T. phaselus and T. truncatus (Acari: Tetranychidae)

Species diagnosis is of the utmost importance to both pest management and plant quarantine services. Because of difficulties in the morphological diagnosis of spider mites, molecular techniques are of great value to rapidly and accurately diagnose closely related species. We examined four species of genus Tetranychus (the green and red forms of T. urticae, and T. kanzawai, T. phaselus and T. truncatus), which are found in Korea and are of significance to plant quarantine services. DNA samples isolated from a single egg, larva or adult weighed 64–188 ng. We designed species‐specific primers by performing sequence alignment for 107 sequences of the ribosomal internal transcribed spacer 2 (ITS2) region, which we obtained from GenBank, and sequences generated in this study. Specific nucleotides of each species were selected for designing primers specific for each species. Each species‐specific primer pair, when used to perform PCR analyses, detected only the species from which it originated. However, a T. urticae‐specific primer pair did not discriminate between the green and red forms of this species. These species‐specific primers can be applied in practice for the rapid and accurate diagnosis of spider mite species in plant quarantine and in agricultural fields.     

Imputing Variants in HLA-DR Beta Genes Reveals That HLA-DRB1 Is Solely Associated with Rheumatoid Arthritis and Systemic Lupus Erythematosus

The genetic association of HLA-DRB1 with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) is well documented, but association with other HLA-DR beta genes (HLA-DRB3, HLA-DRB4 and HLA-DRB5) has not been thoroughly studied, despite their similar functions and chromosomal positions. We examined variants in all functional HLA-DR beta genes in RA and SLE patients and controls, down to the amino-acid level, to better understand disease association with the HLA-DR locus. To this end, we improved an existing HLA reference panel to impute variants in all protein-coding HLA-DR beta genes. Using the reference panel, HLA variants were inferred from high-density SNP data of 9,271 RA-control subjects and 5,342 SLE-control subjects. Disease association tests were performed by logistic regression and log-likelihood ratio tests. After imputation using the newly constructed HLA reference panel and statistical analysis, we observed that HLA-DRB1 variants better accounted for the association between MHC and susceptibility to RA and SLE than did the other three HLA-DRB variants. Moreover, there were no secondary effects in HLA-DRB3, HLA-DRB4, or HLA-DRB5 in RA or SLE. Of all the HLA-DR beta chain paralogs, those encoded by HLA-DRB1 solely or dominantly influence susceptibility to RA and SLE.     

Asymptotic method for peristaltic transport

The purpose of this paper is to justify an asymptotic method developed for the study of peristaltic transport in a tube of arbitrary cross section. Within the framework of long wave approximation, the three-dimensional nonlinear Navier-Stokes equations are reduced to a sequence of two-dimensional linear boundary value problems of Laplace and biharmonic operators. It is shown that, if a Reynolds number is less than some constant, the solution of the approximate equations is indeed an asymptotic approximation to the exact solution of the problem as the ratio of the maximum radius of the tube to the wave length of the peristaltic motion of the wall tends to zero, and the error estimates are expressed inL ₂ norms. Furthermore, under the same condition the exact solution is shown to be unique and stable under arbitrary perturbation of spatially periodic disturbance. Application of the stability condition to peristaltic transport in a tube of circular cross section is given.     

The BOS1 gene encodes an essential 27-kD putative membrane protein that is required for vesicular transport from the ER to the Golgi complex in yeast

We recently described the identification of BOS1 (Newman, A., J. Shim, and S. Ferro-Novick. 1990. Mol. Cell. Biol. 10:3405-3414.). BOS1 is a gene that in multiple copy suppresses the growth and secretion defect of bet1 and sec22, two mutants that disrupt transport from the ER to the Golgi complex in yeast. The ability of BOS1 to specifically suppress mutants blocked at a particular stage of the secretory pathway suggested that this gene encodes a protein that functions in this process. The experiments presented in this study support this hypothesis. Specifically, the BOS1 gene was found to be essential for cellular growth. Furthermore, cells depleted of the Bos1 protein fail to transport pro-alpha-factor and carboxypeptidase Y (CPY) to the Golgi apparatus. This defect in export leads to the accumulation of an extensive network of ER and small vesicles. DNA sequence analysis predicts that Bos1 is a 27-kD protein containing a putative membrane-spanning domain. This prediction is supported by differential centrifugation experiments. Thus, Bos1 appears to be a membrane protein that functions in conjunction with Bet1 and Sec22 to facilitate the transport of proteins at a step subsequent to translocation into the ER but before entry into the Golgi apparatus.