Evaluation of isolation methods for pathogenic Yersinia enterocolitica from pig intestinal content

Aims: The aim of this study was to evaluate the efficiency of four isolation methods for the detection of pathogenic Yersinia enterocolitica from pig intestinal content. Methods and Results: The four methods comprised of 15 isolation steps using selective enrichments (irgasan–ticarcillin–potassium chlorate and modified Rappaport broth) and mildly selective enrichments at 4 or 25°C. Salmonella–Shigella‐desoxycholate–calcium chloride agar, cefsulodin–irgasan–novobiocin agar were used as plating media. The most sensitive method detected 78% (53/68) of the positive samples. Individual isolation steps using cold enrichment as the only enrichment or as a pre‐enrichment step with further selective enrichment showed the highest sensitivities (55–66%). All isolation methods resulted in high numbers of suspected colonies not confirmed as pathogenic Y. enterocolitica. Conclusions: Cold enrichment should be used in the detection of pathogenic Y. enterocolitica from pig intestinal contents. In addition, more than one parallel isolation step is needed. Significance and Impact of the Study: The study shows that depending on the isolation method used for Y. enterocolitica, the detected prevalence of Y. enterocolitica in pig intestinal contents varies greatly. More selective and sensitive isolation methods need to be developed for pathogenic Y. enterocolitica.     

Assignment of protein NMR spectra based on projections,multi-way decomposition and a fast correlation approach

We present an approach for the assignment of protein NMR resonances that combines established and new concepts: (a) Based on published reduced dimensionality methods, two 5-dimensional experiments are proposed. (b) Multi-way decomposition (PRODECOMP) applied simultaneously to all acquired NMR spectra provides the assignment of resonance frequencies under conditions of very low signal-to-noise. (c) Each resulting component characterizes all spin (1/2) nuclei in a (doubly-labeled) CbetaH(n)-CalphaH-C'-NH-CalphaH-CbetaH(n) fragment in an unambiguous manner, such that sequentially neighboring components have about four atoms in common. (d) A new routine (SHABBA) determines correlations for all component pairs based on the common nuclei; high correlation values yield sequential chains of a dozen or more components. (e) The potentially error-prone peak picking is delayed to the last step, where it helps to place the component chains within the protein sequence, and thus to achieve the final backbone assignment. The approach was validated by achieving complete backbone resonance assignments for ubiquitin.     

Analysis of inhibition by H89 of UCP1 gene expression and thermogenesis indicates protein kinase A mediation of beta(3)-adrenergic signalling rather than beta(3)-adrenoceptor antagonism by H89

Although it has generally been assumed that protein kinase A (PKA) is essential for brown adipose tissue function, this has not as yet been clearly demonstrated. H89, an inhibitor of PKA, was used here to inhibit PKA activity. In cell extracts, it was confirmed that norepinephrine stimulated PKA activity, which was abolished by H89 treatment. In isolated brown adipocytes, H89 inhibited adrenergically induced thermogenesis (with an IC(50) of approx. 40 microM), and in cultured cells, adrenergically stimulated expression of the uncoupling protein-1 (UCP1) gene was abolished by H89 (full inhibition with 50 microM). However, H89 has been reported to be an adrenergic antagonist on beta(1)/beta(2)-adrenoceptors (AR). Although adrenergic stimulation of thermogenesis and UCP1 gene expression are mediated via beta(3)-ARs, it was deemed necessary to investigate whether H89 also had antagonistic potency on beta(3)-ARs. It was found that EC(50) values for beta(3)-AR-selective stimulation of cAMP production (with BRL-37344) in brown adipose tissue membrane fractions and in intact cells were not affected by H89. Similarly, the EC(50) of adrenergically stimulated oxygen consumption was not affected by H89. As H89 also abolished forskolin-induced UCP1 gene expression, and potentiated selective beta(3)-AR-induced cAMP production, H89 must be active downstream of cAMP. Thus, no antagonism of H89 on beta(3)-ARs could be detected. We conclude that H89 can be used as a pharmacological tool for elucidation of the involvement of PKA in cellular signalling processes regulated via beta(3)-ARs, and that the results are concordant with adrenergic stimulation of thermogenesis and UCP1 gene expression in brown adipocytes being mediated via a PKA-dependent pathway.     

Thermogenic responses in brown fat cells are fully UCP1-dependent. UCP2 or UCP3 do not substitute for UCP1 in adrenergically or fatty scid-induced thermogenesis

To examine the thermogenic significance of the classical uncoupling protein-1 (UCP1), the thermogenic potential of brown adipocytes isolated from UCP1-ablated mice was investigated. Ucp1(-/-) cells had a basal metabolic rate identical to wild-type; the mitochondria within them were coupled to the same degree. The response to norepinephrine in wild-type cells was robust ( approximately 10-fold increase in thermogenesis); Ucp1(-/-) cells only responded approximately 3% of this. Ucp1(-/-) cells were as potent as wild-type in norepinephrine-induced cAMP accumulation and lipolysis and had a similar mitochondrial respiratory complement. In wild-type cells, fatty acids induced a thermogenic response similar to norepinephrine, but fatty acids (and retinoate) were practically without effect in Ucp1(-/-) cells. It is concluded that no other adrenergically induced thermogenic mechanism exists in brown adipocytes except that mediated by UCP1 and that entopic expression of UCP1 does not lead to overt innate uncoupling, and it is suggested that fatty acids are transformed to an intracellular physiological activator of UCP1. High expression of UCP2 and UCP3 in the tissue was not associated with an overt innate highly uncoupled state of mitochondria within the cells, nor with an ability of norepinephrine or endo- or exogenous fatty acids to induce uncoupled respiration in the cells. Thus, UCP1 remains the only physiologically potent thermogenic uncoupling protein in these cells.     

The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion polymorphisms in the PMEL17 gene

Dominant white, Dun, and Smoky are alleles at the Dominant white locus, which is one of the major loci affecting plumage color in the domestic chicken. Both Dominant white and Dun inhibit the expression of black eumelanin. Smoky arose in a White Leghorn homozygous for Dominant white and partially restores pigmentation. PMEL17 encodes a melanocyte-specific protein and was identified as a positional candidate gene due to its role in the development of eumelanosomes. Linkage analysis of PMEL17 and Dominant white using a red jungle fowl/White Leghorn intercross revealed no recombination between these loci. Sequence analysis showed that the Dominant white allele was exclusively associated with a 9-bp insertion in exon 10, leading to an insertion of three amino acids in the PMEL17 transmembrane region. Similarly, a deletion of five amino acids in the transmembrane region occurs in the protein encoded by Dun. The Smoky allele shared the 9-bp insertion in exon 10 with Dominant white, as expected from its origin, but also had a deletion of 12 nucleotides in exon 6, eliminating four amino acids from the mature protein. These mutations are, together with the recessive silver mutation in the mouse, the only PMEL17 mutations with phenotypic effects that have been described so far in any species.     

Fecal steroid analysis for monitoring reproduction in the sun bear (Helarctos malayanus)

Fecal steroid analyses were conducted on captive (n = 10) and free-ranging (n = 2) sun bears (Helarctos malayanus) in order to establish a noninvasive technique for monitoring endocrine profiles during the estrous cycle and pregnancy. Secondly, the effect of the contraceptive porcine zona pellucida protein (PZP) on reproductive function was studied. Finally, we investigated whether the sun bear, naturally living in the aseasonal tropical forests of Southeast Asia, is a seasonal breeder. Fecal samples were collected over periods of 7-48 months in captive untreated (n = 8) and PZP-treated (n = 2) female sun bears. In addition samples were collected over a period of 12 months from radio-collared free-ranging females (n = 2) in their natural habitat in Indonesian Borneo. Androgens, precursors of estrogens, were found to be reliable indicators of the follicular phase, whereas estrogens were found unsuitable. Pregnanediol assay was found to be a reliable indicator of luteal function. Results indicate that sun bears are polyestrous, nonseasonal breeders. Interestrus intervals in nonpregnant animals (n = 2), which were monitored for 27 months, were between 140 and 216 days. Luteal phases (89.6 +/- 3.7 days; n = 9) were preceded by androgen peaks of 15.2 +/- 1.0 days (n = 10). Hormonal profiles of two females treated with PZP indicated missing ovarian activity in one, and persistent follicular and luteal activity in another animal. However, extended periods of missing ovarian, and persistent follicular and luteal activity were also observed in other sun bears studied.     

Alignment of chain-like molecules

The steric obstruction model, that describes the enhanced alignment of folded proteins by anisotropic medium, is extended to account for the residual dipolar couplings of chain-like polypeptides. The average alignment of each chain segment is calculated from an ensemble of conformations represented by a spatial probability distribution. The segmental alignment depends on chain length, flexibility and segment's position in the chain. Residual dipolar couplings in turn depend on internuclear vector directions within each fragment. The results of calculations and simulations explain salient features of the experimental data. With this insight residual dipolar couplings can be interpreted to assess the degree of denaturation, local structures and spatial organization of weakly structured proteins.     

There exist at least 30 human G-protein-coupled receptors with long Ser/Thr-rich N-termini

We report six novel members of the superfamily of human G-protein coupled receptors (GPCRs) found by searches in the human genome databases, termed GPR123, GPR124, GPR125, GPR126, GPR127, and GPR128. Phylogenetic analysis demonstrates that these are additional members of the family of GPCRs with long N-termini, previously termed EGF-7TM, LNB-7TM, B2 or LN-7TM, showing that there exist at least 30 such GPCRs in the human genome. Three of these receptors form their own phylogenetic cluster, while two other places in a cluster with the previously reported HE6 and GPR56 (TM7XN1) and one with EMR1-3. All the novel receptors have a GPS domain in their N-terminus, except GPR123, as well as long Ser/Thr rich regions forming mucin-like stalks. GPR124 and GPR125 have a leucine rich repeat (LRR), an immunoglobulin (Ig) domain, and a hormone-binding domain (HBD). The Ig domain shows similarities to motilin and titin, while the LRR domain shows similarities to LRIG1 and SLIT1-2. GPR127 has one EGF domain while GPR126 and GPR128 do not contain domains that are readily recognized in other proteins beyond the GPS domain. We found several human EST sequences for most of the receptors showing differential expression patterns, which may indicate that some of these receptors participate in central functions while others are more likely to have a role in the immune or reproductive systems.     

A set of HA-detected experiments for measuring scalar and residual dipolar couplings

A new set of HCACO based three-dimensional NMR experiments for measuring residual dipolar couplings in proteins is presented. Using spin-state selection and editing in three dimensions, the experiments allow accurate measurement of intraresidual , and scalar and residual dipolar couplings of ¹⁵N/¹³C labeled proteins in D₂O and dilute liquid crystals with minimal spectral crowding. The presented experiments are especially suitable for small or medium sized proline-rich proteins, or proteins that require high pH solvent conditions, making ¹H^N detected experiments unattractive. In addition, the tetrahedral coordination of C is superior to the planar peptide bond for determination of local alignments in partially structured polypeptides. For the efficient use of spectrometer time and to avoid complications arising from the varying magnitude of the alignment tensor during relatively long experiments, the and couplings can also be measured simultaneously in an E.COSY like manner with high accuracy. The pulse sequences are balanced for cross-correlation effects and minimized for relaxation losses. The pulse sequences are tested with a sample of ¹⁵N/¹³C human ubiquitin. We find internuclear vector directions determined from the dipolar couplings to have an excellent correlation with those of ubiquitins refined solution structure.