Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data

We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with similar expression profiles, two basic questions can be asked: 1. Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements. 2. What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways. We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)

Automated Method for the Determination of 5′-Nucleotidase in Serum by Continuous Flow Analysis

Peer Reviewe

Chlamydia muridarum infection differentially alters smooth muscle function in mouse uterine horn and cervix.

Chlamydia trachomatis infection is a primary cause of reproductive tract diseases including infertility. Previous studies showed that this infection alters physiological activities in mouse oviducts. Whether this occurs in the uterus and cervix has never been investigated. This study characterized the physiological activities of the uterine horn and the cervix in a Chlamydia muridarum (Cmu)-infected mouse model at three infection time points of 7, 14, and 21 days postinfection (dpi). Cmu infection significantly decreased contractile force of spontaneous contraction in the cervix (7 and 14 dpi; P < 0.001 and P < 0.05, respectively), but this effect was not observed in the uterine horn. The responses of the uterine horn and cervix to oxytocin were significantly altered by Cmu infection at 7 dpi (P < 0.0001), but such responses were attenuated at 14 and 21 dpi. Cmu infection increased contractile force to prostaglandin (PGF2α) by 53-83% in the uterine horn. This corresponded with the increased messenger ribonucleic acid (mRNA) expression of Ptgfr that encodes for its receptor. However, Cmu infection did not affect contractions of the uterine horn and cervix to PGE2 and histamine. The mRNA expression of Otr and Ptger4 was inversely correlated with the mRNA expression of Il1b, Il6 in the uterine horn of Cmu-inoculated mice (P < 0.01 to P < 0.001), suggesting that the changes in the Otr and Ptger4 mRNA expression might be linked to the changes in inflammatory cytokines. Lastly, this study also showed a novel physiological finding of the differential response to PGE2 in mouse uterine horn and cervix

N, NH, and NH2 radical densities in a remote Ar-NH3-SiH4 plasma and their role in silicon nitride deposition

The densities of N, NH, and NH2 radicals in a remote Ar-NH3-SiH4 plasma used for high-rate silicon nitride deposition were investigated for different gas mixts. and plasma settings using cavity ringdown absorption spectroscopy and threshold ionization mass spectrometry. For typical deposition conditions, the N, NH, and NH2 radical densities are on the order of 1012 cm-3 and the trends with NH3 flow, SiH4 flow, and plasma source current are reported. We present a feasible reaction pathway for the prodn. and loss of the NHx radicals that is consistent with the exptl. results. Furthermore, mass spectrometry revealed that the consumption of NH3 was typically 40%, while it was over 80% for SiH4. On the basis of the measured N densities we deduced the recombination and sticking coeff. for N radicals on a silicon nitride film. Using this sticking coeff. and reported surface reaction probabilities of NH and NH2 radicals, we conclude that N and NH2 radicals are mainly responsible for the N incorporation in the silicon nitride film, while Si atoms are most likely brought to the surface in the form of SiHx radicals. [on SciFinder (R)

Iron abundances from optical Fe III absorption lines in B-type stellar spectra

The role of optical Fe III absorption lines in B-type stars as iron abundance diagnostics is considered. To date, ultraviolet Fe lines have been widely used in B-type stars, although line blending can severely hinder their diagnostic power. Using optical spectra, covering a wavelength range ~ 3560 - 9200 A, a sample of Galactic B-type main-sequence and supergiant stars of spectral types B0.5 to B7 are investigated. A comparison of the observed Fe III spectra of supergiants, and those predicted from the model atmosphere codes TLUSTY (plane-parallel, non-LTE), with spectra generated using SYNSPEC (LTE), and CMFGEN (spherical, non-LTE), reveal that non-LTE effects appear small. In addition, a sample of main-sequence and supergiant objects, observed with FEROS, reveal LTE abundance estimates consistent with the Galactic environment and previous optical studies. Based on the present study, we list a number of Fe III transitions which we recommend for estimating the iron abundance from early B-type stellar spectra.Comment: 3 figures and 8 tables. Table 3 is to be published online only (included here on last page). Accepted for publication in MNRA

Phase behaviour of charged colloidal sphere dispersions with added polymer chains

We study the stability of mixtures of highly screened repulsive charged spheres and non-adsorbing ideal polymer chains in a common solvent using free volume theory. The effective interaction between charged colloids in an aqueous salt solution is described by a screened-Coulomb pair potential, which supplements the pure hard-sphere interaction. The ideal polymer chains are treated as spheres that are excluded from the colloids by a hard-core interaction, whereas the interaction between two ideal chains is set to zero. In addition, we investigate the phase behaviour of charged colloid-polymer mixtures in computer simulations, using the two-body (Asakura-Oosawa pair potential) approximation to the effective one-component Hamiltonian of the charged colloids. Both our results obtained from simulations and from free volume theory show similar trends. We find that the screened-Coulomb repulsion counteracts the effect of the effective polymer-mediated attraction. For mixtures of small polymers and relatively large charged colloidal spheres, the fluid-crystal transition shifts to significantly larger polymer concentrations with increasing range of the screened-Coulomb repulsion. For relatively large polymers, the effect of the screened-Coulomb repulsion is weaker. The resulting fluid-fluid binodal is only slightly shifted towards larger polymer concentrations upon increasing the range of the screened-Coulomb repulsion. In conclusion, our results show that the miscibility of dispersions containing charged colloids and neutral non-adsorbing polymers increases, upon increasing the range of the screened-Coulomb repulsion, or upon lowering the salt concentration, especially when the polymers are small compared to the colloids.Comment: 25 pages,13 figures, accepted for publication on J.Phys.:Condens. Matte

Performance evaluation of a new fourth-generation HIV combination antigen-antibody assay

Education and diagnostic tests capable of early detection represent our most effective means of preventing transmission of human immunodeficiency virus (HIV). The importance of early detection is underlined by studies demonstrating increased life expectancy following early initiation of antiviral treatment. The Elecsys(®) HIV combi PT assay is a fourth-generation antigen-antibody combination assay developed to allow earlier detection of seroconversion, and to have increased sensitivity and improved specificity. We aimed to determine how early the assay could detect infection compared with existing assays; whether all HIV variants could be detected; and the assay's specificity using samples from blood donors, routine specimens, and patients with potential cross-reacting factors. Samples were identified as positive by the Elecsys(®) assay 4.9 days after a positive polymerase chain reaction result (as determined by the panel supplier), which was earlier than the 5.3-7.1 days observed with comparators. The analytical sensitivity of the Elecsys(®) HIV combi PT assay for the HIV-1 p24 antigen was 1.05 IU/mL, which compares favorably with the comparator assays. In addition, the Elecsys(®) assay identified all screened HIV subtypes and displayed greater sensitivity to HIV-2 homologous antigen and antibodies to HIV-1 E and O and HIV-2 than the other assays. Overall, the specificity of the Elecsys(®) assay was 99.88 % using samples from blood donors and 99.81 % when analyzing unselected samples. Potential cross-reacting factors did not interfere with assay performance. The Elecsys(®) HIV combi PT assay is a sensitive and specific assay that has been granted the CE mark according to Directive 2009/886/EC

Tuberculosis research in South Africa over the past 30 years: From bench to bedside

The South African Medical Research Council Centre for Tuberculosis Research has a rich history of high-impact research that has influenced our understating of this hyper-epidemic which is further exacerbated by the emergence and spread of drug-resistant forms of the disease. This review aims to summarise the past 30 years of research conducted in the Centre which has influenced the way that tuberculosis (TB) is diagnosed and treated. The review includes the development of new technologies for rapid screening of people with probable TB and the repurposing of human diagnostics for wildlife conservation

Radiographic Predictors of Conversion to Total Knee Arthroplasty After Tibial Plateau Fracture Surgery:Results in a Large Multicenter Cohort

Background: Radiographic measurements of initial displacement of tibial plateau fractures and of postoperative reduction are used to determine treatment strategy and prognosis. We assessed the association between radiographic measurements and the risk of conversion to total knee arthroplasty (TKA) at the time of follow-up.Methods: A total of 862 patients surgically treated for tibial plateau fractures between 2003 and 2018 were eligible for this multicenter cross-sectional study. Patients were approached for follow-up, and 477 (55%) responded. The initial gap and step-off were measured on the preoperative computed tomography (CT) scans of the responders. Condylar widening, residual incongruity, and coronal and sagittal alignment were measured on postoperative radiographs. Critical cutoff values for gap and step-off were determined using receiver operating characteristic curves. Postoperative reduction measurements were categorized as adequate or inadequate on the basis of cutoff values in international guidelines. Multivariable analysis was performed to assess the association between each radiographic measurement and conversion to TKA.Results: Sixty-seven (14%) of the patients had conversion to TKA after a mean follow-up of 6.5 ± 4.1 years. Assessment of the preoperative CT scans revealed that a gap of &gt;8.5 mm (hazard ratio [HR] = 2.6, p &lt; 0.001) and step-off of &gt;6.0 mm (HR = 3.0, p &lt; 0.001) were independently associated with conversion to TKA. Assessment of the postoperative radiographs demonstrated that residual incongruity of 2 to 4 mm was not associated with increased risk of TKA compared with adequate fracture reduction of &lt;2 mm (HR = 0.6, p = 0.176). Articular incongruity of &gt;4 mm resulted in increased risk of TKA. Coronal (HR = 1.6, p = 0.05) and sagittal malalignment (HR = 3.7 p &lt; 0.001) of the tibia were strongly associated with conversion to TKA.Conclusions: Substantial preoperative fracture displacement was a strong predictor of conversion to TKA. Postoperative gaps or step-offs of &gt;4 mm as well as inadequate alignment of the tibia were strongly associated with an increased risk of TKA.Level of Evidence: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.</p