Design and evaluation of peptide nucleic acid probes for specific identification of Candida albicans.

Candida albicans is an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiating C. albicans from other Candida species are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel of C. albicans and various nontarget Candida spp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power for C. albicans than P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification of C. albicans in clinical and related applications, especially when combined with FCM

Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags

<p>Abstract</p> <p>Background</p> <p>Nematodes are the dominant soil animals in Antarctic Dry Valleys and are capable of surviving desiccation and freezing in an anhydrobiotic state. Genes induced by desiccation stress have been successfully enumerated in nematodes; however we have little knowledge of gene regulation by Antarctic nematodes which can survive multiple environmental stresses. To address this problem we investigated the genetic responses of a nematode species, <it>Plectus murrayi</it>, that is capable of tolerating Antarctic environmental extremes, in particular desiccation and freezing. In this study, we provide the first insight into the desiccation induced transcriptome of an Antarctic nematode through cDNA library construction and suppressive subtractive hybridization.</p> <p>Results</p> <p>We obtained 2,486 expressed sequence tags (ESTs) from 2,586 clones derived from the cDNA library of desiccated <it>P. murrayi</it>. The 2,486 ESTs formed 1,387 putative unique transcripts of which 523 (38%) had matches in the model-nematode <it>Caenorhabditis elegans</it>, 107 (7%) in nematodes other than <it>C. elegans</it>, 153 (11%) in non-nematode organisms and 605 (44%) had no significant match to any sequences in the current databases. The 1,387 unique transcripts were functionally classified by using Gene Ontology (GO) hierarchy and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results indicate that the transcriptome contains a group of transcripts from diverse functional areas. The subtractive library of desiccated nematodes showed 80 transcripts differentially expressed during desiccation stress, of which 28% were metabolism related, 19% were involved in environmental information processing, 28% involved in genetic information processing and 21% were novel transcripts. Expression profiling of 14 selected genes by quantitative Real-time PCR showed 9 genes significantly up-regulated, 3 down-regulated and 2 continuously expressed in response to desiccation.</p> <p>Conclusion</p> <p>The establishment of a desiccation EST collection for <it>Plectus murrayi</it>, a useful model in assessing the structural, physiological, biochemical and genetic aspects of multiple stress tolerance, is an important step in understanding the genome level response of this nematode to desiccation stress. The type of transcript analysis performed in this study sets the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in nematodes.</p

Co- variation in soil biodiversity and biogeochemistry in northern and southern Victoria Land, Antarctica

Data from six sites in Victoria Land (72–77°S) investigating co-variation in soil communities (microbial and invertebrate) with biogeochemical properties showthe influence of soil properties on habitat suitability varied among local landscapes as well as across climate gradients. Species richness of metazoan invertebrates (Nematoda, Tardigrada and Rotifera) was similar to previous descriptions in this region, though identification of three cryptic nematode species of Eudorylaimus through DNA analysis contributed to the understanding of controls over habitat preferences for individual species. Denaturing Gradient Gel Electrophoresis profiles revealed unexpectedly high diversity of bacteria. Distribution of distinct bacterial communities was associated with specific sites in northern and southern Victoria Land, as was the distribution of nematode and tardigrade species. Variation in soil metazoan communities was related to differences in soil organic matter, while bacterial diversity and community structure were not strongly correlated with any single soil property. There were no apparent correlations between metazoan and bacterial diversity, suggesting that controls over distribution and habitat suitability are different for bacterial and metazoan communities. Our results imply that top-down controls over bacterial diversity mediated by their metazoan consumers are not significant determinants of bacterial community structure and biomass in these ecosystems

Ethnic variations in sexual behaviour in Great Britain and risk of sexually transmitted infections: a probability survey.

BACKGROUND: Ethnic variations in the rate of diagnosed sexually transmitted infections (STIs) have been reported in many developed countries. We used data from the second British National Survey of Sexual Attitudes and Lifestyles (Natsal 2000) to investigate the frequency of high-risk sexual behaviours and adverse sexual health outcomes in five ethnic groups in Great Britain. METHODS: We did a stratified probability sample survey of 11161 men and women aged 16-44 years, resident in Great Britain, using computer-assisted interviews. Additional sampling enabled us to do more detailed analyses for 949 black Caribbean, black African, Indian, and Pakistani respondents. We used logistic regression to assess reporting of STI diagnoses in the past 5 years, after controlling for demographic and behavioural variables. FINDINGS: We noted striking variations in number of sexual partnerships by ethnic group and between men and women. Reported numbers of sexual partnerships in a lifetime were highest in black Caribbean (median 9 [IQR 4-20]) and black African (9 [3-20]) men, and in white (5 [2-9]) and black Caribbean (4 [2-7]) women. Indian and Pakistani men and women reported fewer sexual partnerships, later first intercourse, and substantially lower prevalence of diagnosed STIs than did other groups. We recorded a significant association between ethnic origin and reported STIs in the past 5 years with increased risk in sexually active black Caribbean (OR 2.74 [95% CI 1.22-6.15]) and black African (2.95 [1.45-5.99]) men compared with white men, and black Caribbean (2.41 [1.35-4.28]) women compared with white women. Odds ratios changed little after controlling for age, number of sexual partnerships, homosexual and overseas partnerships, and condom use at last sexual intercourse. INTERPRETATION: Individual sexual behaviour is a key determinant of STI transmission risk, but alone does not explain the varying risk across ethnic groups. Our findings suggest a need for targeted and culturally competent prevention interventions

A prompt neutrino measurement

A test has been made to explore the possibility of beam dump neutrino experiments with short target‐detector separations and modest detectors. Results have given a positive neutrino signal which is interpreted in the context of various charmed‐meson production models. A limit to the lifetime and mass of the axion is also a byproduct of this test.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87326/2/246_1.pd

The Solution Structure, Binding Properties, and Dynamics of the Bacterial Siderophore-binding Protein FepB

The periplasmic binding protein (PBP) FepB plays a key role in transporting the catecholate siderophore ferric enterobactin from the outer to the inner membrane in Gram-negative bacteria. The solution structures of the 34-kDa apo- and holo-FepB from Escherichia coli, solved by NMR, represent the first solution structures determined for the type III class of PBPs. Unlike type I and II PBPs, which undergo large "Venus flytrap" conformational changes upon ligand binding, both forms of FepB maintain similar overall folds; however, binding of the ligand is accompanied by significant loop movements. Reverse methyl cross-saturation experiments corroborated chemical shift perturbation results and uniquely defined the binding pocket for gallium enterobactin (GaEnt). NMR relaxation experiments indicated that a flexible loop (residues 225-250) adopted a more rigid and extended conformation upon ligand binding, which positioned residues for optimal interactions with the ligand and the cytoplasmic membrane ABC transporter (FepCD), respectively. In conclusion, this work highlights the pivotal role that structural dynamics plays in ligand binding and transporter interactions in type III PBPs