Fatal pulmonary acariasis in an aged indoor rhesus macaque (Macaca mulatta)

Pulmonary acariasis is a sporadic, incidental finding in colony‐raised rhesus macaques (Macaca mulatta). Prophylactic treatment in indoor‐raised and indoor‐housed macaques is not routine due to low prevalence, lack of clinical significance, and potential risk of toxicosis. This case is an unusually severe infestation of Pneumonyssus simicola in an indoor‐housed rhesus macaque, which ultimately resulted in this animal's death.     

Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections

Mnt is a repressor from phage P22 that belongs to the ribbon–helix–helix family of DNA binding factors. Four amino acids from the N-terminus of the protein, Arg2, His6, Asn8 and Arg10, interact with the base pairs of the DNA to provide the sequence specificity. Raumann et al. (Nature Struct. Biol., 2, 1115–1122) identified position 6 as a ‘master residue’ that controls the specificity of the protein. Models for the interaction have residue 6 of Mnt interacting directly with position 5 of the operator. In vivo selections demonstrated that protein variants at residue 6 bound specifically to operator mutations at that position. Operators in which the wild-type G at position 5 was replaced by T specifically bound to several different protein variants, primarily hydrophobic residues. The obtained protein variants, plus some others, were used in in vitro selections to determine their preferred binding sites. The results showed that the residue at position 6 influenced the preference for binding site bases predominantly at position 5, but that the effects of altering it can extend over longer distances, consistent with its designation as a ‘master residue’. The similarities of binding sites for different residues do not correlate strongly with common measures of amino acid similarities.     

Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach

Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted repeats are rare and can cause genome instability. Analyses of C. elegans genome identified long, nearly-perfect inverted repeat sequences involving both divergently and convergently oriented homologous gene pairs and complete intergenic sequences. Comparisons with the orthologous regions from the genomes of C. briggsae and C. remanei show that the inverted repeat structures are often far more conserved than the sequences. This observation implies that there is an active mechanism for maintaining the inverted repeat nature of the sequences.     

A novel method combining linkage disequilibrium information and imputed functional knowledge for tagSNP selection

Analyses of high-density SNPs in genetic studies have the potential problems of prohibitive genotyping costs and inflated false discovery rates. Current methods select subsets of representative SNPs (tagSNPs) using information either on potential biologic functionality of the SNPs or on the underlying linkage disequilibrium (LD) structure, but not both. Combining the two types of information may lead to more effective tagSNP selection. The proposed method combines both functional and LD information using a weighted factor analysis (WFA) model. The WFA was applied to the dense SNP collection from 129 genes sequenced by the SeattleSNPs Program for Genomic Application. TagSNPs selected by WFA were compared with those selected by an LD-based method. WFA allowed prioritization of SNPs that would otherwise share equivalent ranking due to underlying LD structure alone. Furthermore, WFA consistently included SNPs not selected by function or by LD alone. A literature review of a subset of genes revealed that SNPs selected by WFA were more likely represented in published reports.