Microcapsules on Streptococcus mutans Serotypes by Electron Microscopy

Extracellular microcapsules have been demonstrated on cells of most serotypes of Streptococcus mutans by electron microscopy, using bacterial strains of the various serotypes and peroxidase labeled or unlabeled immune serum. A correlation was noted between the amount of capsular substance on the strains of S mutans examined and degree of antigenicity as expressed by the indirect fluorescent antibody (FA) title. A serotype d strain was shown to lose both antigenicity as determined by the FA reaction and capsular material as seen by electron microscopy with repeated in vitro passage. When 10% unheated rabbit serum was added to the medium, antigenicity and capsular material were restored.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68107/2/10.1177_00220345770560021101.pd

Identification of Streptococcus mutans serotypes in dental plaque by fluorescent antibody techniques

The presence of Streptococcus mutans in dental plaque may be related to human dental caries. The cultural identification of this organism in plaque is not likely to be used routinely in a clinical or epidemiological situation. In an effort to develop a simpler diagnostic means of identifying Strep. mutans in plaque, antisera were prepared for the 5 known serotypes of Strep. mutans. These immune sera were conjugated with fluorescein isothiocyanate, fractionated to obtain the gamma globulin and titrated against their homologous antigens to obtain working titres. These antisera were compared with cultural methods for their ability to detect Strep. mutans in plaque samples. Nonspecific fluorescent antibody reactions and weak cross-reactions were essentially eliminated by applying eriochrome black as a counterstain, after plaque and conjugated antiserum had been incubated. The results suggest that the fluorescent antibody is more sensitive than cultural methods in the detection of Strep. mutans in dental plaque.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33874/1/0000135.pd

Regulatory modules controlling maize inflorescence architecture

Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures

Making sense of policy choices: understanding the roles of value predispositions, mass media, and cognitive processing in public attitudes toward nanotechnology

Using a nationally representative telephone survey of 1,015 adults in the United States, this study examines how value predispositions, communication variables, and perceptions of risks and benefits are associated with public support for federal funding of nanotechnology. Our findings show that highly religious individuals were less supportive of funding of nanotech than less religious individuals, whereas individuals who held a high deference for scientific authority were more supportive of funding of the emerging technology than those low in deference. Mass media use and elaborative processing of scientific news were positively associated with public support for funding, whereas factual scientific knowledge had no significant association with policy choices. The findings suggest that thinking about and reflecting upon scientific news promote better understanding of the scientific world and may provide a more sophisticated cognitive structure for the public to form opinions about nanotech than factual scientific knowledge. Finally, heuristic cues including trust in scientists and perceived risks and benefits of nanotech were found to be associated with public support for nanotech funding. We conclude with policy implications that will be useful for policymakers and science communication practitioners

Watching People Making Decisions: A Gogglebox on Online Consumer Interaction

This paper presents a research study, using eye tracking technology, to measure participant cognitive load when encountering micro-decision. It elaborates and improves on a pilot study that was used to test the experiment design. Prior research that led to a taxonomy of decision constructs faced in online transactional processes is discussed. The main findings relate to participants’ subjective cognitive load and task error rates

Socially networked heterogeneity : the influence of WhatsApp as a social networking site on polarisation in Kenya

Using a cross-sectional survey of two sampled counties in Kenya, this article analyses whether social networking sites reflect social network heterogeneity. It then examines how social network heterogeneity influences polarisation in Kenya. Three types of polarisation are examined: party, ethnic and ideological (around county resources). The study focuses specifically on the public WhatsApp platform (the most popular SNS in Kenya). To assess this empirical data, theoretical perspectives are drawn from the literatures on incidental and selective exposure and their impact on political polarisation. The findings indicate that the randomised composition of a WhatsApp group through public links indeed reflects social network heterogeneity. The findings further show that posting political news, obtaining political news and commenting on political news influence social network heterogeneity to some degree. This social network heterogeneity was also found to influence all three (party, ideological and ethnic) types of polarisation in varying but significant degrees

Cytological changes related to Brucella canis variants uptake in vitro

In this study, evidence for in vitro uptake, invasion, and cytopathogonomic effects of normal and variant strains of B. canis on tissue culture, is presented. B. canis L-phase were penicillin-induced and these microorganisms produced revertants on penicillin-free media. Tissue culture (LLC-MK 2 ) cells were divided into different normal and variant-infected groups (I–IV), including controls. Bright-field and electron microscopic observations indicated uptake of all the strains and recognizable host cell damage (CPE) to varying degrees. At 72 h after infection, the extent of damage by L-phase was the least (55.5% CPE). The L-phase-derived revertants resulted in 80% damage; this approximates the adverse effect of normal B. canis (85%). In addition to these gross changes, various structural abnormalities, including pyknosis, nuclear disorganization, vacuolation, and karyorrhexis, were apparent. The implications of these findings and the indirect role of the L-phase in brucellosis due to B. canis are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47529/1/430_2005_Article_BF02123560.pd

Comparing de novo assemblers for 454 transcriptome data

<p>Abstract</p> <p>Background</p> <p>Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode <it>Litomosoides sigmodontis</it>.</p> <p>Results</p> <p>Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs.</p> <p>Conclusions</p> <p>Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended.</p

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein

Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In Gram-negative bacteria, ∼30–60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties. © 2011 Blanca et al; licensee BioMed Central Ltd.Blanca Postigo, JM.; Cañizares Sales, J.; Roig Montaner, MC.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Picó Sirvent, MB. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 12:104-117. doi:10.1186/1471-2164-12-104S1041171