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Dogs diagnosed with chronic enteropathy (CE) or small-cell lymphoma (SCL) exhibit marked differences in faecal microbiota and organic acid profiles compared with healthy dogs, as well as immune abnormalities in intestinal mucosal tissue. However, few studies have analysed trace organic acids, such as succinic acid, which have been suggested to be associated with IBD in humans. Therefore, in this study, we compared the faecal microbiota and organic acid profiles as well as serum inflammatory markers between dogs with disease (n = 11; 6 with CE and 5 with SCL) and healthy controls (n = 16). We also performed machine learning and correlation analysis to obtain more detailed insights into the characteristics of affected dogs. These results revealed that dogs with CE and SCL had lower levels of Erysipelotrichaceae (e.g. Turicibacter and Allobaculum), exhibited abnormalities in the succinic acid metabolism (i.e. succinic acid accumulation and decreased levels of Phascolarctobacterium as succinic acid-utilising bacteria) and increased levels of pathobiont bacteria such as Escherichia-Shigella. Additionally, the presence of Dubosiella was significantly negatively correlated with Canine Inflammatory Bowel Disease Activity Index scores. These findings are expected to aid the development of microbiome-based medications and/or supplements, although further verification is needed. [ABSTRACT FROM AUTHOR]

During coevolution with the host, HIV-1 developed the ability to hijack the cellular ubiquitin/proteasome degradation pathway to counteract the antiviral activity of APOBEC3G (A3G), a host cytidine deaminase that can block HIV-1 replication. Abrogation of A3G function involves the HIV-1 Vif protein, which binds A3G and serves as an adapter molecule to recruit A3G to a Cullin5-based E3 ubiquitin ligase complex. Structure-guided mutagenesis of A3G focused on the 14 most surface-exposed Lys residues allowed us to identify four Lys residues (Lys-297, 301, 303, and 334) that are required for Vif-mediated A3G ubiquitination and degradation. Substitution of Arg for these residues confers Vif resistance and restores A3G's antiviral activity in the presence of Vif. In our model, the critical four Lys residues cluster at the C terminus, opposite to the known N-terminal Vif-interaction region in the protein. Thus, spatial constraints imposed by the E3 ligase complex may be an important determinant in Vif-dependent A3G ubiquitination. structure model | deaminase | antiviral www.pnas.org/cgi/doi/10.1073/pnas.0906652106

Reporting the theoretical analysis of YBCO growth during post annealing in the TFA-MOD process considering the diffusion in the boundary layer as well as the growth kinetics at the precursor/YBCO interface is reviewed. The results show that the mass transfer in the gas boundary layer limited the growth rate.

Processing temperature dependencies of the preferred orientation axis of REBa2Cu3O7-y films prepared on various substrates by chemical solution deposition using metal naphthenates were investigated. Four high density points with four-fold symmetry were given by the (102) pole figures of the films, indicating in plane-aligned axes. Rare-earth mixed Yb1-xErxBa2Cu3O7-y and Sm1-xNd(sub x)Ba2Cu3O7-y films were prepared to confirm the relationship between a/b-axis oriented growth and ionic radius of RE elements. At certain average R(sub i, RE's), orientation of the films critically changed.

Abstract Background Analysis of within-patient HIV evolution under anti-HIV therapy is crucial to a better understanding the possible mechanisms of HIV drug-resistance acquisition. The high evolutionary rate of HIV allows us to trace its evolutionary process in real time by analyzing virus samples serially collected from the same patient. However, such studies are still uncommon due to the lack of powerful computational methods designed for serial virus samples. In this study, we develop a computational method, vSPA (viral Sequential Pathway Analysis), which groups viral sequences from the same sampling time into clusters and traces the evolution between clusters over sampling times. The method makes use of information of different sampling times and traces the evolution of important amino acid mutations. Second, a permutation test at the codon level is conducted to determine the threshold of the correlation coefficient for clustering viral quasispecies. We applied vSPA to four large data sets of HIV-1 protease and reverse transcriptase genes serially collected from two AIDS patients undergoing anti-HIV therapy over several years. Results The results show that vSPA can trace within-patient HIV evolution by detecting many amino acid changes, including important drug-resistant mutations, and by classifying different viral quasispecies coexisting during different periods of the therapy. Conclusion Given that many new anti-HIV drugs will be available in the near future, vSPA may be useful for quickly providing information on the acquisition of HIV drug-resistant mutations by monitoring the within-patient HIV evolution under anti-HIV therapy as a computational approach.

In metalorganic deposition using trifluoroacetates (TFA-MOD), CuO nanocrystallites in calcined film, which influence the critical current density (J[sub c]) of the resulting film, have seldom been considered before. CuO nanocrystallites ripen and grow during the calcining process at 200-250°C and grow into large CuO grains in the YBa[sub 2]Cu[sub 3]O[sub 7-x] (YBCO) film. The final diameter of the grains is about 0.1 µm. When highly purified coating solution is used, suppressing the creation of nanocrystallites in the precursor film is an effective way to obtain high-J[sub c] YBCO film because the nanocrystallites consist only of CuO. We obtained the highest-J[sub c] YBCO film on LaA1O[sub 3] single crystal with a calcining process of 9h43m at 200-250°C. It was 141 nm thick and had a J[sub c] of 7.5 MA/cm² (77 K, 0 T), as measured by the four-probe method. The firing process of TFA-MOD still has several unsolved problems; why can H[sub 2]O and HF gas diffuse quickly within the film? These phenomena can be explained by a model with a quasiliquid consisting of Y, Ba, Cu, O, H, and F. The H[sub 2]O and HF can move quickly in the quasiliquid network within the film during the firing process. According to the model, we can get more conversion of CuO nanocrystallites into quasiliquid by increasing the amount of water vapor. J[sub c] of the film was increased from 3.3 to 4.5 MA/cm² (77 K, 0 T) by increasing the humidity from 4.2% to 12.1% during the long calcining profile of 66h40m at 200-250°C. These results confirm the above model. CuO nanocrystallites in precursor films induce nonstoichiometric metal contents in the quasiliquid. Isolated CuO grains in YBCO film indirectly cause nonstoichiometric quasiliquid in other areas. Such nonstoichiometric quasiliquid leads to non-YBCO materials such as BaO, Y[sub 2]O[sub 3], and Y[sub 2]Cu[sub 2]O[sub 5]. Thus, films derived from non-highly purified coating solution and ones prepared with an... [ABSTRACT FROM AUTHOR]