PCR-based method for targeting 16S-23S rRNA intergenic spacer regions among Vibrio species

<p>Abstract</p> <p>Background</p> <p>The genus <it>Vibrio </it>is a diverse group of Gram-negative bacteria comprised of 74 species. Furthermore, the genus has and is expected to continue expanding with the addition of several new species annually. Consequently, it is of paramount importance to have a method which is able to reliably and efficiently differentiate the numerous <it>Vibrio </it>species.</p> <p>Results</p> <p>In this study, a novel and rapid polymerase chain reaction (PCR)-based intergenic spacer (IGS)-typing system for vibrios was developed that is based on the well-known IGS regions located between the 16S and 23S rRNA genes on the bacterial chromosome. The system was optimized to resolve heteroduplex formation as well as to take advantage of capillary gel electrophoresis technology such that reproducible analyses could be achieved in a rapid manner. System validation was achieved through testing of 69 archetypal <it>Vibrio </it>strains, representing 48 <it>Vibrio </it>species, from which an 'IGS-type' profile database was generated. These data, presented here in several cluster analyses, demonstrated successful differentiation of the 69 type strains showing that this PCR-based fingerprinting method easily discriminates bacterial strains at the species level among <it>Vibrio</it>. Furthermore, testing 36 strains each of <it>V. parahaemolyticus </it>and <it>V. vulnificus</it>, important food borne pathogens, isolated from a variety of geographical locations with the IGS-typing method demonstrated distinct IGS-typing patterns indicative of subspecies divergence in both populations making this technique equally useful for intraspecies differentiation, as well.</p> <p>Conclusion</p> <p>This rapid, reliable and efficient IGS-typing system, especially in combination with 16S rRNA gene sequencing, has the capacity to not only discern and identify vibrios at the species level but, in some cases, at the sub-species level, as well. This procedure is particularly well-suited for preliminary species identification and, lends itself nicely to epidemiological investigations providing information more quickly than other time-honoured methods traditionally used in these types of analyses.</p

Cube law, condition factor and weight-length relationships: history, meta-analysis and recommendations

This study presents a historical review, a meta-analysis, and recommendations for users about weight–length relationships, condition factors and relative weight equations. The historical review traces the developments of the respective concepts. The meta-analysis explores 3929 weight–length relationships of the type W = aLb for 1773 species of fishes. It shows that 82% of the variance in a plot of log a over b can be explained by allometric versus isometric growth patterns and by different body shapes of the respective species. Across species median b = 3.03 is significantly larger than 3.0, thus indicating a tendency towards slightly positive-allometric growth (increase in relative body thickness or plumpness) in most fishes. The expected range of 2.5 < b < 3.5 is confirmed. Mean estimates of b outside this range are often based on only one or two weight–length relationships per species. However, true cases of strong allometric growth do exist and three examples are given. Within species, a plot of log a vs b can be used to detect outliers in weight–length relationships. An equation to calculate mean condition factors from weight–length relationships is given as Kmean = 100aLb−3. Relative weight Wrm = 100W/(amLbm) can be used for comparing the condition of individuals across populations, where am is the geometric mean of a and bm is the mean of b across all available weight–length relationships for a given species. Twelve recommendations for proper use and presentation of weight–length relationships, condition factors and relative weight are given

Drift or shift? Continuity, change, and international variation in knowledge production in OR/MS

With the aim of contributing to the debate around OR/MS as a discipline, this study provides a historical comparative investigation of publicly available knowledge production in the field. The empirical investigation is based on a content analysis of 300 randomly selected articles from six major journals in the field. We have found: (1) since the late 1950s to the present day there has been no significant change in the types of published research in OR/MS in North America; (2) from the late 1950s to the present day, there have been significant differences in types of published research in OR/MS internationally. The imputed imbalance between theory and applications in published work had already occurred in the early stages of the development of OR/MS in North America and has since remained very much the same. Furthermore, research in the United Kingdom has been distinctly different from that dominant in North America and elsewhere. There are also indications that outside North America and the United Kingdom there is an emerging turn towards applications-oriented research. Over the last two or three decades there has been a significant increase overall in the share of articles published by academic authors

A general scaling relation for the critical current density in Nb3Sn

We review the scaling relations for the critical current density (Jc) in Nb3Sn wires and include recent findings on the variation of the upper critical field (Hc2) with temperature (T) and A15 composition. We highlight deficiencies in the Summers/Ekin relations, which are not able to account for the correct Jc(T) dependence. Available Jc(H) results indicate that the magnetic field dependence for all wires can be described with Kramer's flux shear model, if non-linearities in Kramer plots are attributed to A15 inhomogeneities. The strain (eps) dependence is introduced through a temperature and strain dependent Hc2*(T,eps) and Ginzburg- Landau parameter kappa1(T,eps) and a strain dependent critical temperature Tc(eps). This is more consistent than the usual Ekin unification, which uses two separate and different dependencies on Hc2*(T) and Hc2*(eps). Using a correct temperature dependence and accounting for the A15 inhomogeneities leads to a remarkable simple relation for Jc(H,T,eps). Finally, a new relation for s(eps) is proposed, based on the first, second and third strain invariants.Comment: Accepted Topical Review for Superconductor, Science and Technolog

Unexpected drop of dynamical heterogeneities in colloidal suspensions approaching the jamming transition

As the glass (in molecular fluids\cite{Donth}) or the jamming (in colloids and grains\cite{LiuNature1998}) transitions are approached, the dynamics slow down dramatically with no marked structural changes. Dynamical heterogeneity (DH) plays a crucial role: structural relaxation occurs through correlated rearrangements of particle ``blobs'' of size $\xi$\cite{WeeksScience2000,DauchotPRL2005,Glotzer,Ediger}. On approaching these transitions, $\xi$ grows in glass-formers\cite{Glotzer,Ediger}, colloids\cite{WeeksScience2000,BerthierScience2005}, and driven granular materials\cite{KeysNaturePhys2007} alike, strengthening the analogies between the glass and the jamming transitions. However, little is known yet on the behavior of DH very close to dynamical arrest. Here, we measure in colloids the maximum of a ``dynamical susceptibility'', $\chi^*$, whose growth is usually associated to that of $\xi$\cite{LacevicPRE}. $\chi^*$ initially increases with volume fraction $\phi$, as in\cite{KeysNaturePhys2007}, but strikingly drops dramatically very close to jamming. We show that this unexpected behavior results from the competition between the growth of $\xi$ and the reduced particle displacements associated with rearrangements in very dense suspensions, unveiling a richer-than-expected scenario.Comment: 1st version originally submitted to Nature Physics. See the Nature Physics website fro the final, published versio

Time-dependent suppression of oscillatory power in evolving solar magnetic fields

Oscillation amplitudes are generally smaller within magnetically active regions like sunspots and plage when compared to their surroundings. Such magnetic features, when viewed in spatially resolved power maps, appear as regions of suppressed power due to reductions in the oscillation amplitudes. Employing high spatial- and temporal-resolution observations from the Dunn Solar Telescope (DST) in New Mexico, we study the power suppression in a region of evolving magnetic fields adjacent to a pore. By utilizing wavelet analysis, we study for the first time how the oscillatory properties in this region change as the magnetic field evolves with time. Image sequences taken in the blue continuum, G-band, Ca ii K, and Hα filters were used in this study. It is observed that the suppression found in the chromosphere occupies a relatively larger area, confirming previous findings. Also, the suppression is extended to structures directly connected to the magnetic region, and is found to get enhanced as the magnetic field strength increased with time. The dependence of the suppression on the magnetic field strength is greater at longer periods and higher formation heights. Furthermore, the dominant periodicity in the chromosphere was found to be anti-correlated with increases in the magnetic field strength

Credit bureaus between risk-management, creditworthiness assessment and prudential supervision

"This text may be downloaded for personal research purposes only. Any additional reproduction for other purposes, whether in hard copy or electronically, requires the consent of the author. If cited or quoted, reference should be made to the full name of the author, the title, the working paper or other series, the year, and the publisher."This paper discusses the role and operations of consumer Credit Bureaus in the European Union in the context of the economic theories, policies and law within which they work. Across Europe there is no common practice of sharing the credit data of consumers which can be used for several purposes. Mostly, they are used by the lending industry as a practice of creditworthiness assessment or as a risk-management tool to underwrite borrowing decisions or price risk. However, the type, breath, and depth of information differ greatly from country to country. In some Member States, consumer data are part of a broader information centralisation system for the prudential supervision of banks and the financial system as a whole. Despite EU rules on credit to consumers for the creation of the internal market, the underlying consumer data infrastructure remains fragmented at national level, failing to achieve univocal, common, or defined policy objectives under a harmonised legal framework. Likewise, the establishment of the Banking Union and the prudential supervision of the Euro area demand standardisation and convergence of the data used to measure debt levels, arrears, and delinquencies. The many functions and usages of credit data suggest that the policy goals to be achieved should inform the legal and institutional framework of Credit Bureaus, as well as the design and use of the databases. This is also because fundamental rights and consumer protection concerns arise from the sharing of credit data and their expanding use

Gender Differences in Russian Colour Naming

In the present study we explored Russian colour naming in a web-based psycholinguistic experiment (http://www.colournaming.com). Colour singletons representing the Munsell Color Solid (N=600 in total) were presented on a computer monitor and named using an unconstrained colour-naming method. Respondents were Russian speakers (N=713). For gender-split equal-size samples (NF=333, NM=333) we estimated and compared (i) location of centroids of 12 Russian basic colour terms (BCTs); (ii) the number of words in colour descriptors; (iii) occurrences of BCTs most frequent non-BCTs. We found a close correspondence between females’ and males’ BCT centroids. Among individual BCTs, the highest inter-gender agreement was for seryj ‘grey’ and goluboj ‘light blue’, while the lowest was for sinij ‘dark blue’ and krasnyj ‘red’. Females revealed a significantly richer repertory of distinct colour descriptors, with great variety of monolexemic non-BCTs and “fancy” colour names; in comparison, males offered relatively more BCTs or their compounds. Along with these measures, we gauged denotata of most frequent CTs, reflected by linguistic segmentation of colour space, by employing a synthetic observer trained by gender-specific responses. This psycholinguistic representation revealed females’ more refined linguistic segmentation, compared to males, with higher linguistic density predominantly along the redgreen axis of colour space