ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

Insect resistance of a full sib family of tetraploid switchgrass \u3ci\u3ePanicum virgatum\u3c/i\u3e L. with varying lignin levels

Little information is available on insect resistance mechanisms and inheritance in biomass grasses. Although reduction of lignin in biomass grasses in order to increase the efficiency of fermentation may result in increased susceptibility to insect feeding, other resistance mechanisms may be more important. Field grown leaves of two tetraploid parent (Kanlow N1, Summer) and 14 progeny switchgrass (Panicum virgatum L.) plant clones selected for a diversity of plant form and ranges in lignin levels were tested for leaf resistance to feeding by the fall armyworm (Spodoptera frugiperda J. E. Smith), a grass feeding insect pest. Although lignin generally appeared important as a resistance mechanism only at early season stages, replicate clones of two low lignin progeny plants generally remained resistant to fall armyworm feeding. Mechanical damaging increased resistance to fall armyworm feeding in several of these plants. Degrees of resistance were sometimes associated with leaf form of progeny. These results indicate there are likely multiple insect resistance mechanisms operating at different stages in switchgrass, and that segregation of some mechanisms appears related to growth form of the plants

Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets

The existing chimera detection programs are not specifically designed for "next generation" sequence data. Technologies like Roche 454 FLX and Titanium have been adapted over the past years especially with the introduction of bacterial tag-encoded FLX/Titanium amplicon pyrosequencing methodologies to produce over one million 250-600 bp 16S rRNA gene reads that need to be depleted of chimeras prior to downstream analysis. Meeting the needs of basic scientists who are venturing into high-throughput microbial diversity studies such as those based upon pyrosequencing and specifically providing a solution for Windows users, the B2C2 software is designed to be able to accept files containing large multi-FASTA formatted sequences and screen for possible chimeras in a high throughput fashion. The graphical user interface (GUI) is also able to batch process multiple files. When compared to popular chimera screening software the B2C2 performed as well or better while dramatically decreasing the amount of time required generating and screening results. Even average computer users are able to interact with the Windows .Net GUI-based application and define the stringency to which the analysis should be done. B2C2 may be downloaded from http://www.researchandtesting.com/B2C2

Expanding the parameters of academia

This paper draws on qualitative data gathered from two studies funded by the UK Leadership Foundation for Higher Education to examine the expansion of academic identities in higher education. It builds on Whitchurch’s earlier work, which focused primarily on professional staff, to suggest that the emergence of broadly based projects such as widening participation, learning support and community partnership is also impacting on academic identities. Thus, academic as well as professional staff are increasingly likely to work in multi-professional teams across a variety of constituencies, as well as with external partners, and the binary distinction between ‘academic’ and ‘non-academic’ roles and activities is no longer clear-cut. Moreover, there is evidence from the studies of an intentionality about deviations from mainstream academic career routes among respondents who could have gone either way. Consideration is therefore given to factors that influence individuals to work in more project-oriented areas, as well as to variables that affect ways in which these roles and identities develop. Finally, three models of academically oriented project activity are identified, and the implications of an expansion of academic identities are reviewed

Cytomegalovirus antibodies in dried blood spots: a minimally invasive method for assessing stress, immune function, and aging

<p>Abstract</p> <p>Background</p> <p>Cytomegalovirus (CMV) is a prevalent herpesvirus with links to both stress and aging. This paper describes and validates a minimally invasive method for assessing antibodies against CMV in finger stick whole blood spot samples for use as an indirect marker of an aspect of cell-mediated immunity.</p> <p>Results</p> <p>Analysis of CMV in dried blood spot samples (DBS) was based on modifications of a commercially available protocol for quantifying CMV antibodies in serum or plasma. The method was evaluated through analysis of precision, reliability, linearity, and correlation between matched serum and DBS samples collected from 75 volunteers. Correlation between DBS and plasma values was linear and high (Pearson correlation <it>R </it>= .96), and precision, reliability, and linearity of the DBS assay were within acceptable ranges.</p> <p>Conclusions</p> <p>The validity of a DBS assay for CMV antibodies will enable its inclusion in population-based surveys and other studies collecting DBS samples in non-clinical settings, increasing scientific understanding of the interaction of social and biological stress and immune function.</p

Confucian Principles: A Study of Chinese Americans’ Interpersonal Relationships in Selected Children’s Picturebooks

[[abstract]]There has not been enough critical analysis of children’s literature by and about Chinese Americans, especially when compared to other minority groups in the United States. In particular, Chinese American historical books lack extensive analysis. It is important to reflect cultural accuracy in literature and to help children develop clear concepts of self and others by providing precise cultural and physical characteristics of people. While cultural authenticity allows children the opportunity to see a reflection of real experiences within a book instead of seeing stereotypes or misrepresentations, obtaining correct information about a certain time period can help children to see images of immigration accurately represented in literature. Using the Confucian delineation of interpersonal relationships as the major criterion of cultural authenticity, this article examines three currently available children’s picturebooks set in the historical period between 1848 and 1885. In addition to exploring how Chinese Americans’ interpersonal relationships are portrayed in these children’s historical books, this article argues for more proactive inclusion of the diversity in selection of picturebooks.[[notice]]補正完

The effect of a 24-hour photoperiod on the survival, growth and swim bladder inflation of pre-flexion yellowfin tuna (Thunnus albacares) larvae

The effects of two different continuous photoperiod regimes on survival, growth and swim bladder inflation of pre-flexion yellowfin tuna (Thunnus albacares) larvae were investigated. Each photoperiod regime was tested twice with a different larval cohort to confirm the observed results. Trials 1 and 2 tested the effect of a reduced night-time light intensity (10-molesm-2s-1=30% of the daytime intensity) and found that those larvae reared for 8days under the 24h lighting (24-L) photoperiod exhibited a slight improvement in survival compared to those reared under the control photoperiod of 12h light (12-L), however these improvements were not significant. In addition, those larvae reared under this photoperiod regime were equal in length to those in the control. Trials 3 and 4 compared the same variables in larvae reared under a continuous photoperiod (24-L) with a constant light intensity of 30-molesm-2s-1, against those reared under the aforementioned 12-L photoperiod. Survival of larvae under the continuous photoperiods were 9±1% (n=2) and 10±2% (n=3) for Trials 3 and 4, respectively, compared to less than 1% in both control treatments; differences that in both cases were highly significant. In addition, in both trials larvae cultured under the 24-L photoperiod were significantly larger and exhibited more advanced development than those reared under the 12-L photoperiod, however swim bladder inflation was significantly lower. We suggest that the improved survival and growth achieved under a continuous photoperiod is due to the extended foraging time combined with the prevention of mortality caused by night-time sinking

Understanding the differential hygienic behavior towards drone brood in Apis mellifera colonies from Argentina

Brood diseases of Apis mellifera colonies constitute a main problem of beekeeping worldwide. Worker bees display a social health mechanism that consists in detecting, uncapping and removing dead or diseased brood from the hive: the hygienic behavior (CH). These activities are induced by olfactory cues and have been described as associated to hygiene of brood parasitized by Varroa destructor. This mite have preference for drone brood, but the efficiency of CH towards their cells is significantly lower compared with cells of worker brood, being left uninspected by workers. Some authors suggest that a possible cause of the CH differences is due to the cell wax cap of drone brood (thicker than worker cells) acting as a barrier to volatile compounds and obstructing disease detection. The aims of this research were to study the differential CH towards worker and drone brood belonging to highly hygienic colonies from Argentina, and to explore the importance of drone cell wax cap as an interfering factor in the transmission of chemical signals. To this end, removal percentages of pin-killed worker and drone brood were recorded and an innovative cell wax cap exchange was implemented in three different treatments: pin-killed worker pupa with a healthy drone cell wax cap; a healthy worker pupa with a pin-killed drone cell wax cap; and a healthy worker pupa covered with a healthy drone cell wax cap (control). Results showed a greater removal towards worker cells than drone cells. For the cell wax cap exchange experiment, we found that the removal of pin-killed worker pupae covered with healthy drone cell wax cap was significantly high, while the removal of healthy worker pupae covered with pin-killed drone opercula was low. These preliminary results confirms a differential behavior between both type of brood cells and suggests that the cell wax cap of drone brood is not interfering the detection of chemical compounds from the diseased brood by worker bees, regardless the thickness. This work contributes to a better understanding of the detection activity of different types of diseased brood and provides information useful to control strategies of varroosis and other brood diseases.Fil: Dowd, D. Duggan. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Muntaabski, Irina. Instituto Nacional de Tecnologia Agropecuaria. Centro de Investigacion En Ciencias Veterinarias y Agronomicas. Instituto de Agrobiotecnologia y Biologia Molecular. Grupo Vinculado Instituto de Genetica "ewald A. Favret" Al Iabimo | Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Pque. Centenario. Instituto de Agrobiotecnologia y Biologia Molecular. Grupo Vinculado Instituto de Genetica "ewald A. Favret" Al Iabimo.; ArgentinaFil: Russo, R. M.. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Landi, L.. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; ArgentinaFil: Lanzavecchia, S. B.. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Cladera, J. L.. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Palacio, M. A.. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Bedascarrabure, E.. Instituto Nacional de Tecnologia Agropecuaria. Centro de Investigacion de Agroindustria. Instituto de Ingeniería Rural.; ArgentinaFil: Scannapieco, Alejandra Carla. Instituto Nacional de Tecnologia Agropecuaria. Centro de Investigacion En Ciencias Veterinarias y Agronomicas. Instituto de Agrobiotecnologia y Biologia Molecular. Grupo Vinculado Instituto de Genetica "ewald A. Favret" Al Iabimo | Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Pque. Centenario. Instituto de Agrobiotecnologia y Biologia Molecular. Grupo Vinculado Instituto de Genetica "ewald A. Favret" Al Iabimo.; ArgentinaFil: Liendo, María Clara. Instituto Nacional de Tecnologia Agropecuaria. Centro de Investigacion En Ciencias Veterinarias y Agronomicas. Instituto de Agrobiotecnologia y Biologia Molecular. Grupo Vinculado Instituto de Genetica "ewald A. Favret" Al Iabimo | Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Pque. Centenario. Instituto de Agrobiotecnologia y Biologia Molecular. Grupo Vinculado Instituto de Genetica "ewald A. Favret" Al Iabimo.; Argentina46th Apimondia International Apicultural Congress: Beekeeping together within agricultureQuébecCanadáInternational Federation of Beekeepers' AssociationsCanadian Honey Counci

Persistent Herpesvirus Infections and Telomere Attrition Over 3 Years in the Whitehall II Cohort

The determinants of telomere attrition, a potential marker of cellular aging, are not well understood. Persistent herpesvirus infections including cytomegalovirus (CMV) infection may be particularly important for telomere dynamics via mechanisms such as inflammation, oxidative stress, and their impact on peripheral blood lymphocyte composition. This study examined the association of 4 human herpesviruses (CMV, herpes simplex virus type 1, human herpesvirus type 6, and Epstein-Barr virus) with change in leukocyte telomere length (LTL) over 3 years in 400 healthy individuals (aged 53–76 years) from the Whitehall II cohort. CMV, herpes simplex virus type 1, and human herpesvirus 6 infection were independently associated with greater 3-year LTL attrition, with no association found for Epstein-Barr virus. The magnitudes of these associations were large, for example, the equivalent of almost 12 years of chronological age for those CMV seropositive. Seropositivity to more herpesviruses was additively associated with greater LTL attrition (3 herpesviruses vs none, β = −0.07 and P = .02; 4 infections vs none, β = −0.14 and P < .001). Higher immunoglobulin G antibody levels among those seropositive to CMV were also associated with shorter LTL at follow-up. These associations were robust to adjustment for age, sex, employment grade, body mass index, and smoking status. These results suggest that exposure to infectious agents should be an important consideration in future studies of telomere dynamics