1,324 research outputs found
The role of Candida albicans in root caries biofilms: an RNA-seq analysis
Objective: This study sought to analyze the gene expression of Candida albicans in sound root surface and root caries lesions, exploring its role in root caries pathogenesis.
Methodology: The differential gene expression of C. albicans and the specific genes related to cariogenic traits were studied in association with samples of biofilm collected from exposed sound root surface (SRS, n=10) and from biofilm and carious dentin of active root carious lesions (RC, n=9). The total microbial RNA was extracted, and the cDNA libraries were prepared and sequenced on the Illumina Hi-Seq2500. Unique reads were mapped to 163 oral microbial reference genomes including two chromosomes of C. albicans SC5314 (14,217 genes). The putative presence of C. albicans was estimated (sum of reads/total number of genes≥1) in each sample. Count data were normalized (using the DESeq method package) to analyze differential gene expression (using the DESeq2R package) applying the Benjamini-Hochberg correction (FDR<0.05).
Results: Two genes (CaO19.610, FDR=0.009; CaO19.2506, FDR=0.018) were up-regulated on SRS, and their functions are related to biofilm formation. Seven genes ( UTP20 , FDR=0.018; ITR1 , FDR=0.036; DHN6 , FDR=0.046; CaO19.7197 , FDR=0.046; CaO19.7838 , FDR=0.046; STT4 , FDR=0.046; GUT1 , FDR=0.046) were up-regulated on RC and their functions are related to metabolic activity, sugar transport, stress tolerance, invasion and pH regulation. The use of alternative carbon sources, including lactate, and the ability to form hypha may be a unique trait of C. albicans influencing biofilm virulence.
Conclusions: C. albicans is metabolically active in SRS and RC biofilm, with different roles in health and disease
Results from the Relativistic Heavy Ion Collider
We describe the current status of the heavy ion research program at the
Relativistic Heavy Ion Collider (RHIC). The new suite of experiments and the
collider energies have opened up new probes of the medium created in the
collisions. Our review focuses on the experimental discoveries to date at RHIC
and their interpretation in the light of our present theoretical understanding
of the dynamics of relativistic heavy ion collisions and of the structure of
strongly interacting matter at high energy density.Comment: 47 pages, 10 figures, submitted to Annual Review of Nuclear and
Particle Science. The authors invite and appreciate feedback about possible
errors and/or inconsistencies in the manuscrip
Three computational approaches to weakly nonlocal Poisson brackets
We compare three different ways of checking the Jacobi identity for weakly nonlocal Poisson brackets using the theory of distributions, pseudo‐differential operators, and Poisson vertex algebras, respectively. We show that the three approaches lead to similar computations and same results
Functional Active Microbiome in Supragingival Biofilms in Health and Caries
The oral microbiome is unique at inter and intra-individual levels at various sites due to physical and biological factors. This study aimed to compare the bacterial composition of supragingival biofilms collected from enamel sites with different caries activity, from active and inactive-caries subjects, and from caries-free (CF) subjects. Twenty-two individuals (aged between 13 and 76 years old; med = 23.5 years old) were allocated into 3 groups: caries-active (CA) (n = 10), caries-inactive (CI) (n = 6), and CF (n = 6). From the CA group, 3 sites were sampled: CA (active non-cavitated lesion), CI (inactive non-cavitated lesion), and sound enamel surface (S). From the subjects of the CI group, biofilm from a CI lesion was collected (INCL), while for the CF subjects, a pool of biofilm from sound enamel surfaces was sampled. The total RNA was extracted, and cDNA libraries were prepared and pairedend sequenced (Illumina HiSeq 3,000). Final dental biofilm samples analysed from CA was 16 (ANCL-CA = 6, INCL-CA = 4, S-CA = 6); from CI, 3 (INCL-CI = 3); and from CF, 6 (S-CF = 6) (some samples were lost by insufficient genetic material). Read sequences were processed and analysed using the Metagenomics RAST server. High-quality sequences (3,542,190) were clustered into operational taxonomic units (97% identity; SILVA SSU), representing 915 genera belonging to 29 phyla (higher abundant: Actinobacteria, Firmicutes, Bacteroidetes, and Fusobacteria). The presence of a core microbiome was observed (123 shared genera). The alpha diversity analysis showed less bacterial diversity in disease (S-CA) compared to health (S-CF). The dominant genera included Actinomyces, Corynebacterium, Capnocytophaga, Leptotrichia, Veillonella, Prevotella, Streptococcus, Eubacterium, and Neisseria. Veillonella and Leptotrichia were related with disease and Prevotella with health. Corynebacterium, Capnocytophaga, and Actinomyces clustered together presenting high abundance in health and disease. The Metric Multidimensional Scaling Ordination analysis shows that sites from active subjects (ANCL-CA, INCL-CA, and S-CA) are closer to each other than either INCL-CI subjects or S-CF subjects. In conclusion, supragingival bacterial communities presented intra-individual similarities, but inter-individual diversity and difference in bacterial composition reveal that the subject’s caries activity status matters more than sites
Low-Energy Theorems from Holography
In the context of gauge/gravity duality, we verify two types of gauge theory
low-energy theorems, the dilation Ward identities and the decoupling of heavy
flavor. First, we provide an analytic proof of non-trivial dilation Ward
identities for a theory holographically dual to a background with gluon
condensate (the self-dual Liu--Tseytlin background). In this way an important
class of low-energy theorems for correlators of different operators with the
trace of the energy-momentum tensor is established, which so far has been
studied in field theory only. Another low-energy relationship, the so-called
decoupling theorem, is numerically shown to hold universally in three
holographic models involving both the quark and the gluon condensate. We show
this by comparing the ratio of the quark and gluon condensates in three
different examples of gravity backgrounds with non-trivial dilaton flow. As a
by-product of our study, we also obtain gauge field condensate contributions to
meson transport coefficients.Comment: 32 pages, 4 figures, two references added, typos remove
Non-perturbative computation of double inclusive gluon production in the Glasma
The near-side ridge observed in A+A collisions at RHIC has been described as
arising from the radial flow of Glasma flux tubes formed at very early times in
the collisions. We investigate the viability of this scenario by performing a
non-perturbative numerical computation of double inclusive gluon production in
the Glasma. Our results support the conjecture that the range of transverse
color screening of correlations determining the size of the flux tubes is a
semi-hard scale, albeit with non-trivial structure. We discuss our results in
the context of ridge correlations in the RHIC heavy ion experiments.Comment: 25 pages, 11 figures, uses JHEP3.cls V2: small clarifications,
published in JHE
JunctionViewer: customizable annotation software for repeat-rich genomic regions
<p>Abstract</p> <p>Background</p> <p>Repeat-rich regions such as centromeres receive less attention than their gene-rich euchromatic counterparts because the former are difficult to assemble and analyze. Our objectives were to 1) map all ten centromeres onto the maize genetic map and 2) characterize the sequence features of maize centromeres, each of which spans several megabases of highly repetitive DNA. Repetitive sequences can be mapped using special molecular markers that are based on PCR with primers designed from two unique "repeat junctions". Efficient screening of large amounts of maize genome sequence data for repeat junctions, as well as key centromere sequence features required the development of specific annotation software.</p> <p>Results</p> <p>We developed JunctionViewer to automate the process of identifying and differentiating closely related centromere repeats and repeat junctions, and to generate graphical displays of these and other features within centromeric sequences. JunctionViewer generates NCBI BLAST, WU-BLAST, cross_match and MUMmer alignments, and displays the optimal alignments and additional annotation data as concise graphical representations that can be viewed directly through the graphical interface or as PostScript<sup>® </sup>output.</p> <p>This software enabled us to quickly characterize millions of nucleotides of newly sequenced DNA ranging in size from single reads to assembled BACs and megabase-sized pseudochromosome regions. It expedited the process of generating repeat junction markers that were subsequently used to anchor all 10 centromeres to the maize map. It also enabled us to efficiently identify key features in large genomic regions, providing insight into the arrangement and evolution of maize centromeric DNA.</p> <p>Conclusions</p> <p>JunctionViewer will be useful to scientists who wish to automatically generate concise graphical summaries of repeat sequences. It is particularly valuable for those needing to efficiently identify unique repeat junctions. The scalability and ability to customize homology search parameters for different classes of closely related repeat sequences make this software ideal for recurring annotation (e.g., genome projects that are in progress) of genomic regions that contain well-defined repeats, such as those in centromeres. Although originally customized for maize centromere sequence, we anticipate this software to facilitate the analysis of centromere and other repeat-rich regions in other organisms.</p
Vaccines against toxoplasma gondii : challenges and opportunities
Development of vaccines against Toxoplasma gondii infection in humans is of high priority, given the high burden of disease in some areas of the world like South America, and the lack of effective drugs with few adverse effects. Rodent models have been used in research on vaccines against T. gondii over the past decades. However, regardless of the vaccine construct, the vaccines have not been able to induce protective immunity when the organism is challenged with T. gondii, either directly or via a vector. Only a few live, attenuated T. gondii strains used for immunization have been able to confer protective immunity, which is measured by a lack of tissue cysts after challenge. Furthermore, challenge with low virulence strains, especially strains with genotype II, will probably be insufficient to provide protection against the more virulent T. gondii strains, such as those with genotypes I or II, or those genotypes from South America not belonging to genotype I, II or III. Future studies should use animal models besides rodents, and challenges should be performed with at least one genotype II T. gondii and one of the more virulent genotypes. Endpoints like maternal-foetal transmission and prevention of eye disease are important in addition to the traditional endpoint of survival or reduction in numbers of brain cysts after challenge
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