Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome

BackgroundThe suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings.Methodology/Principal findingsHigh copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings.Conclusions/SignificanceThis newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests.     

2,2-Bis(ethoxycarbonyl)- and 2-(alkylaminocarbonyl)-2-cyano-substituted 3-(pivaloyloxy)propyl groups as biodegradable phosphate protections of oligonucleotides

Oligonucleotides bearing biodegradable phosphate protecting groups have been synthesized on a solid support. For this purpose, two dimeric building blocks, viz. 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2,2-bis(ethoxycarbonyl)-3-(pivaloyloxy)propyl]-P-thiothymidylyl-(3',5')-thymidine 3'-[O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite] (1) and 5'-O-(4,4'-dimethoxytrityl)-(R(P),S(P))-O(P)-[2-cyano-2-(2-phenylethylaminocarbonyl)-3-(pivaloyloxy)propyl]thymidylyl-(3',5')-thymidine 3'-(H-phosphonate) (2), were prepared. Phosphoramidite 1 was incorporated into an phosphorothioate oligothymidylate sequence on a base-labile hydroquinone-O,O'-diacetic acid linker (Q-linker) and on a photolabile 4-alkoxy-5-methoxy-2-nitrobenzyl carbonate linker (11). H-Phosphonate 2 was, in turn, incorporated into an oligothymidylate sequence only on the photolabile linker. Kinetics of the removal of the protecting groups by porcine liver esterase and subsequent retro aldol condensation/phosphate elimination were then studied. While the pro-oligonucleotide that contained only one phosphate protection gave the deprotected phosphorothioate oligonucleotide in a quantitative yield, the enzymatic step was markedly decelerated upon increasing the number of protection groups, and hence chain cleavage started to compete.     

Three-dimensional structure of the sugar symporter melibiose permease from cryo-electron microscopy

Melibiose permease (MelB) of Escherichia coli is a secondary transporter that couples the uptake of melibiose and various other galactosides to symport of cations that can be Na+, Li+ or H+. MelB belongs to the glycoside-pentoside-hexuronide: cation symporter family of porters and is suggested to have 12 transmembrane helices. We have determined the three-dimensional structure of MelB at 10A resolution in the membrane plane with cryo-electron microscopy from two-dimensional crystals. The three-dimensional map shows a heart-shaped molecule composed of two domains with a large central cavity between them. The structure is constricted at one side of the membrane while it is open to the other. The overall molecular shape resembles those of lactose permease and glycerol-3-phosphate transporter. However, organization of helices in MelB seems less symmetrical than in these two members of the major facilitator superfamily.     

Mature human thymocytes migrate on laminin-5 with activation of metalloproteinase-14 and cleavage of CD44

We have previously shown that laminin-5 is expressed in the human thymic medulla, in which mature thymocytes are located. We now report that laminin-5 promotes migration of mature medullary thymocytes, whereas it has no effect on cortical immature thymocytes. Migration was inhibited by blocking mAbs directed against laminin-5 integrin receptors and by inhibitors of metalloproteinases. Interactions of thymocytes with laminin-5 induced a strong up-regulation of active metalloproteinase-14. However, we found that thymocytes did not cleave the laminin-5 gamma(2) chain, suggesting that they do not use the same pathway as epithelial cells to migrate on laminin-5. Interactions of thymocytes with laminin-5 also induced the release of a soluble fragment of CD44 cell surface molecule. Moreover, CD44-rich supernatants induced thymocyte migration in contrast with supernatants depleted in CD44 by immunoadsorption. CD44 cleavage was recently reported to be due to metalloproteinase-14 activation and led to increased migration in cancer cells. Thus, in this study, we show that laminin-5 promotes human mature thymocyte migration in vitro via a multimolecular mechanism involving laminin-5 integrin receptors, metalloproteinase-14 and CD44. These data suggest that, in vivo, laminin-5 may function in the migration of mature thymocytes within the medulla and be part of the thymic emigration process.     

Defoliation increases carbon limitation in ectomycorrhizal symbiosis of <Emphasis Type="Italic">Betula pubescens</Emphasis>

Boreal forest trees are highly dependent on root-colonizing mycorrhizal fungi. Since the maintenance of mycorrhizal symbiosis implies a significant carbon cost for the host plant, the loss of photosynthetic leaf area due to herbivory is expected to reduce the host investment in mycorrhizae. We tested this hypothesis in a common garden experiment by exposing ectomycorrhizal white birch (Betula pubescens Ehrh.) seedlings to simulated insect defoliation of 50 or 100% intensity during either the previous or the current summer or repeatedly during both seasons before harvest. The shoot and root growth of the seedlings were distinctly reduced by both 100% defoliation and repeated 50% defoliation, and they were more strongly affected by previous-year than current-year defoliation. The root to shoot ratio significantly decreased after 100% defoliation, indicating reduced proportional allocation to the roots. Ergosterol concentration (i.e. fungal biomass) in the fine roots decreased by 100% defoliation conducted either in the year of harvest or in both years. No such decrease occurred following the 100% defoliation conducted in the previous year, indicating the importance of current photosynthates for fungal symbionts. The trend was similar in the colonization percentage of thick-mantled mycorrhizae in the roots, the most marked decline occurring in the repeatedly defoliated seedlings. The present results thus support the prediction that the plant investment in ectomycorrhizae may decline as a response to foliage loss. Moreover, the colonization percentage of thick-mantled mycorrhizae correlated positively with the ratio of leaf to heterotrophic plant biomass in the defoliated birch seedlings, but not in the control ones. This tends to indicate a stronger carbon limitation of ectomycorrhizal colonization in defoliated seedlings.     

Birch PR-10c interacts with several biologically important ligands

PR-10c is a unique member of PR-10 proteins in birch, since it is the only one known to be post-translationally modified by glutathione and is not constitutively expressed in pollen. Both reduced and S-glutathiolated forms of PR-10c show low ribonuclease activity. However, the major function of the protein is apparently not yet resolved. Our protein-ligand interaction studies with saturation transfer difference (STD) NMR revealed that PR-10c interacts with several biologically important molecules, including cytokinin, flavonoid glycosides, sterols and emodin. Competition study with deoxycholate and kinetin revealed no statistically significant binding interference, indicating that these ligands have different binding sites in PR-10c. Ligand docking studies with a molecular model of PR-10c support the STD NMR results of ligand binding and binding epitopes, suggesting that there are three potential binding sites in PR-10c: two in the hydrophobic cavity and one in the glycine-rich loop. Our docking calculations suggested that only kinetin interacts with the glycine-rich loop, the binding occurring through its adenine moiety. Clear ligand specificity could be observed in the binding of nucleotide derivatives. S-glutathiolation of PR-10c did not affect kinetin binding. The present results suggest that birch PR-10c is a multifunctional protein, which has diverse roles in plant stress responses.     

The dissections of craniocervical arteries

Dissection of craniocervical arteries internal carotid artery (ICA), or vertebral artery (VA) is an increasingly recognized entity and infrequent cause of stroke. We investigated 8 patients (4 women and 4 men) with dissections of the craniocervical arteries. Diagnostic procedures for detection of craniocervical dissection included: extracranial ultrasound-color Doppler flow imaging (CDFI) of carotid and vertebral arteries, transcranial Doppler sonography (TCD) and radiological computed tomography (CT) and digital subtractive angiography (DSA) examinations. Ultrasound findings (CDFI of carotid and vertebral arteries) were positive for vessel dissection in seven patients (or 87.5 per cent) and negative in one patient. DSA was consistent with dissection in five patients (or 62.5 per cent), negative in one, while in two patients the examination was not performed due to known allergy to contrast media. Five patients (62.5 per cent) were treated with anticoagulants, one with suppressors of platelet aggregation, and two patients were operated. Six patients (75 per cent) after the treatment showed partial recovery of neurological defects, and an improvement of ultrasound finding of dissected arteries. In one patient, following operation, stroke developed with deterioration of motor deficit, and one patient was readmitted three months later due to a newly developed stroke and soon died. The diagnosis should be suspected in any young or middle-age patient with new onset of otherwise unexplained unremitting headache or neck ache, especially in association with transient or permanent focal neurological deficits.     

Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35

Biological membranes control the flow of molecules into and out of cells, and they transmit information about the milieu. Structural studies of membrane-containing viruses provide one way to study these membranes in situ. Cryo-electron microscopy and image reconstruction of bacteriophage Bam35 to 7.3 A resolution revealed a membrane bilayer constrained within an icosahedrally symmetric pseudo T = 25 capsid. A total of 60 large transmembrane protein complexes affect the curvature and thickness of the membrane. Here, we describe these membrane parameters quantitatively. Furthermore, we show that Bam35 differs from bacteriophage PRD1 in these parameters, even though the two viruses share the same principles of capsid architecture. Most notably, each virus possesses a tape measure protein suggesting a general mechanism for capsid size determination in icosahedral viruses.     

Alloethic efficiency in the patrolling networks of a polymorphic ant,Tapinoma nigerrimum (hymenoptera: Formicidae)

This study analyses some aspects of the role of alloethism in the networks of patrolling workers of a polymorphic ant species (Tapinoma nigerrimum) in the nest surroundings. We focus on the analysis of movement and distribution patterns of different-sized individuals, and their relationship to the potential transfer of information between each other via contacts during patrolling activities. Our results suggest that small workers are potentially more efficient in these kind of activities (information discovery and transfer), because they contact each other more than could be expected by a random process based on their proportions and, also, because their deduced energetic expenditure per unit of information found or transferred is lower than that of large workers. These differences in the contacts between patrolling ants for small and large workers cannot be explained by their movement patterns (velocity, time spend in movement, turning angles), which do not differ between both groups but, rather, seem to be a consequence of their resulting distribution patterns (overdispersed for large ants and random for small ones).