The relative efficiency of penetrance estimators for sib pairs

Here we present analytical studies to evaluate the relative efficiency of commonly used penetrance estimators using linkage designs. We investigated three different methods of estimating penetrance using sib pairs: Maximum likehood estimation (MLE) with trait information alone, MLE with both trait and marker information and the MOD score approach. Modeling sib pairs with unknown phase, we evaluated the asymptotic relative efficiency between estimators under either random sampling or single ascertainment for an autosomal dominant or recessive disease. We then provide plots of the asymptotic relative efficiency, enabling researchers to easily determine regions where the MOD score or segregation alone performs with comparable efficiency relative to joint segregation and linkage.     

The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant

Understanding of the ecological factors that shape intraspecific variation of insect microbiota in natural populations is relatively poor. In Lepidopteran caterpillars, microbiota is assumed to be mainly composed of transient bacterial symbionts acquired from the host plant. We sampled Glanville fritillary (Melitaea cinxia) caterpillars from natural populations to describe their gut microbiome and to identify potential ecological factors that determine its structure. Our results demonstrate high variability of microbiota composition even among caterpillars that shared the same host plant individual and most likely the same genetic background. We observed that the caterpillars harboured microbial classes that varied among individuals and alternated between two distinct communities (one composed of mainly Enterobacteriaceae and another with more variable microbiota community). Even though the general structure of the microbiota was not attributed to the measured ecological factors, we found that phylogenetically similar microbiota showed corresponding responses to the sex and the parasitoid infection of the caterpillar and to those of the host plant's microbial and chemical composition. Our results indicate high among-individual variability in the microbiota of the M. cinxia caterpillar and contradict previous findings that the host plant is the major driver of the microbiota communities of insect herbivores.     

Role of loops in the folding and stability of yeast phosphoglycerate kinase.

Yeast phosphoglycerate kinase (yPGK) is a monomeric two domain protein used as folding model representative of large proteins. We inserted short unstructured sequences (four Gly or four Thr) into the connections between secondary structure elements and studied the consequences of these insertions on the folding process and stability of yPGK. All the mutated proteins can refold efficiently. The effect per residue on stability is larger for the first inserted residue. Insertion in two long betaalpha loops (at residue positions 71 and 129) is more destabilizing than an insertion in a short alphabeta loop (at residue position 89) located on the opposite side of the N-terminal domain. The effect on stability is mainly due to a large increase of the unfolding rate rather than a decrease of the folding rate. This suggests that these connections between secondary structure elements do not play an active role in directing the folding process. Insertion into the short alphabeta loop (position 89) has limited effects on stability and results in the detection of a kinetic phase not previously seen with the wild-type protein, suggesting that insertions in this particular loop do qualitatively affect the folding process without a large effect on folding efficiency. For the two long betaalpha loops (positions 71 and 129) located in the inner surface of the N-terminal domain, the effects on stability are possibly associated with decoupling of the two domains as observed by differential scanning calorimetry during thermal unfolding.     

Whole-genome sequence of Wolbachia strain wAlbB, an endosymbiont of tiger mosquito vector Aedes albopictus

Although bacteria of the genus Wolbachia induced significant extended phenotypes to infected hosts, most molecular mechanisms involved are still unknown. To gain insight into the bacterial genetic determinants, we sequenced the whole genome of Wolbachia wAlbB strain, a commensal obligate intracellular of the tiger mosquito Aedes albopictus.     

Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase

The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined.     

Asymmetric diphenol formation by a fungal laccase.

A laccase isolated from the fungus Rhizoctonia praticola catalyzed the cross-coupling of two differently halogenated phenols. When 2,4-dichlorophenol and 4-bromo-2-chlorophenol were incubated together with the enzyme, three dimers were formed and isolated by thin-layer chromatography. The molecular weights of these compounds were determined by mass spectrometry as 322, 410, and 366, which correspond with the respective dimers of each of the phenols and with a hybrid formed from both, tentatively assigned the structure 3,3',5'-trichloro-5-bromo-2,2'-diphenol. Gas chromatography-mass spectrometry analysis of these products and of their methylated derivatives lent support to these structural assignments.     

Differences in cuticular lipid composition of the antennae of Helicoverpa zea, Heliothis virescens, and Manduca sexta

Analyses of the hexane washes of antennae, forelegs and whole bodies of Helicoverpa zea, Heliothis virescens, and Manduca sexta revealed notable differences in the components of the cuticular coatings of each species. Most striking were the differences between the cuticular coatings of male and female antennae of both H. zea and H. virescens. Novel esters of short-chain acids (C2-C4) and long-chain secondary alcohols (C25-C32) were identified in the hexane washes of the male antenna and forelegs of H. zea and H. virescens. These compounds were found in only small amounts or were completely absent on the female antennae of both species. In H. zea, butyrates of 7- and 8-pentacosanol and 8- and 9-heptacosanol were found, whereas, in the foreleg extracts of H. virescens, acetates and propionates were detected in addition to butyrates. While cholesterol is a major component of antennal washes (10-15%), only traces were found in the foreleg extracts. Although the composition of the cuticular coating of M. sexta differed greatly from that of the other two species, the extractable coatings of the antennae of male and female M. sexta were nearly identical.     

Amphipol-Mediated Screening of Molecular Orthoses Specific for Membrane Protein Targets

Specific, tight-binding protein partners are valuable helpers to facilitate membrane protein (MP) crystallization, because they can i) stabilize the protein, ii) reduce its conformational heterogeneity, and iii) increase the polar surface from which well-ordered crystals can grow. The design and production of a new family of synthetic scaffolds (dubbed αReps, for “artificial alpha repeat protein”) have been recently described. The stabilization and immobilization of MPs in a functional state are an absolute prerequisite for the screening of binders that recognize specifically their native conformation. We present here a general procedure for the selection of αReps specific of any MP. It relies on the use of biotinylated amphipols, which act as a universal “Velcro” to stabilize, and immobilize MP targets onto streptavidin-coated solid supports, thus doing away with the need to tag the protein itself.