An integrated cancer biomarker information system

Rapid progress in functional genomics is yielding unparalleled opportunities for cancer biomarker discovery. Several procedures including data collection, analysis, verification, and visualization are necessary to identify cancer biomarkers from continuously updated microarray data, which are derived from multiple tissue sources using various methods. BioMarker is designed to integrate these procedures in a user-friendly manner, for practical application by cancer researcher and clinicians. From the feedback of clinical and research application, BioMarker is the first effort to provide a system that facilitates all aspects of biomarker discovery from microarray datasets.

Proteases and invasion by metastatic tumor-cells - clinical implications for prostate-cancer

Proteases have been widely implicated in tumor invasion and metastases. Likewise, receptors for MMP-2, alpha(2)M, UA and tPA may play a critical regulatory role in modulation protease activity and invasion. These studies have been largely based on in vitro assays with various tumor lines. More recently in situ studies have indicated that metalloproteinases (e.g. MMP-2, UA, tPA) may serve as useful diagnostic or prognostic indicators of tumor progression and metastatic potential. The development of in vitro diagnostic procedures utilizing primary epithelial prostate cultures is considered. Also the potential role of growth factors (PDGF, EGF, TGFB) in the regulation of metalloprotease production is considered. Finally, approaches to drug design and development of chemotherapy regimens are considered which selectively block invasive behavior of metastatically aggressive tumors.

Protection of chickens from infectious laryngotracheitis with a recombinant fowlpox virus expressing glycoprotein B of infectious laryngotracheitis virus

Infectious laryngotracheitis (ILT) is an economically important disease of chickens caused by a type I gallid herpesvirus, infectious laryngotracheitis virus (ILTV). The vaccines currently available are modified live viruses, which are effective in preventing disease outbreaks. However, they have often been associated with a variety of adverse effects including spread of vaccine virus to non-vaccinates, inadequate attenuation, production of latently infected carriers, and increased virulence as a result of in vivo passage. In this study, a recombinant fowlpox virus expressing glycoprotein B (gB) of ILTV (rFPV-ILTVgB) was constructed. Protection of specific pathogen free (SPF) and commercial chickens from ILT with the rFPV-ILTVgB and commercial ILTV vaccine (Nobilis ILT) were compared after challenge with a lethal dose of virulent ILTV.Both the rFPV-ILTVgB- and the Nobilis ILT-vaccinated SPF chickens were completely protected from death, while 90% of the unvaccinated chickens died after challenge. The immunized commercial chickens were also 100% protected with rFPV-ILTVgB, compared with 85% protected with Nobilis ILT. The protective efficacy was also measured by the antibody response to ILTV gB, isolation of challenge virus and polymerase chain reaction amplification of the ILTV thymidine kinase gene after challenge. The results showed that rFPV-ILTVgB could be a potential safe vaccine to replace current modified live vaccines for preventing ILT.

Toxoplasma gondii infection in Bactrian camel (Camelus bactrianus) in China

Camel is important to the economy of many countries. We report Toxoplasma gondii infection in Bactrian camels (Camelus bactrianus), first for this host. Antibodies to T. gondii were found in sera of 7 of 234 C. bactrianus from Qinghai Province, northwestern China. Sera were tested by a commercial indirect hemagglutination test at a cut-off of 1:64. Age or the gender of the camel did not significantly affect the seroprevalence. Results are of public health and economic importance because camel milk and meat are used for human consumption in many countries, including China.

Bioinformatics analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes

BACKGROUND

Lung adenocarcinoma (LAC) is the most frequent histologic type of lung cancer and rates of adenocarcinoma are increasing in most countries. Recently, several molecular markers have been identified to predict LAC. However, more prognostic makers and the underlying role of those makers are still imperative.

AIM

In this study, our objective was to identify a set of discriminating genes that can be used for characterization and prediction of response to LAC.

MATERIALS AND METHODS

Using the bioinformatics analysis method, we merged two LAC datasets-GSE2514 and GSE7670 to find novel target genes and pathways to explain the pathogenicity.

RESULTS

The results showed that EDNRB (endothelin receptor type B), ADRB2 (beta-adrenergic receptor), S1PR1 (sphingosine-1-phosphate receptor 1), P2RY14 (PsY purinoceptor 14), LEPR (leptin-receptor), GHR (growth hormone receptor), PPM1D (protein phosphatase-1D), and GADD45B (growth arrest and DNA-damage-inducible, beta) have high degrees in response to LAC. Additionally, EDNRB, ADRB2, S1PR1, P2RY14, LEPR, and GHR may be involved in LAC through Neuroactive ligand-receptor interaction, but PPM1D and GADD45B may be through p53 signaling pathway. Some of our prediction had been demonstrated by previous reports, such as ADRB2, S1PR1, GHR, PPM1D, and GADD45B. Therefore, we hope our study could lay a basis for further study of other target genes, such as EDNRB, P2RY14, and LEPR.

CONCLUSIONS

It is effective to identify potential molecular marker for LAC and predict their underlying functions by bioinformatics analysis and graph clustering method. However, further experiments are still indispensable to confirm our conclusion.

Search for a light pseudoscalar Higgs boson in the dimuon decay channel in pp collisions at √s = 7 TeV

The dimuon invariant mass spectrum is searched in the range between 5.5 and 14 GeV for a light pseudoscalar Higgs boson a, predicted in a number of new physics models, including the next-to-minimal supersymmetric standard model. The data sample used in the search corresponds to an integrated luminosity of 1.3 fb(-1) collected in pp collisions at √s = 7 TeV with the CMS detector at the LHC. No excess is observed above the background predictions and upper limits are set on the cross section times branching fraction σ × B(pp→a→μ(+)μ(-)) in the range of 1.5-7.5 pb. These results improve on existing bounds on the abb coupling for m(a) < m(Υ(1S)) and are the first significant limits for m(a) > m(Υ(3S)). Constraints on the supersymmetric parameter space are presented in the context of the next-to-minimal model.

Measurement of the electron charge asymmetry in inclusive W production in pp collisions at sqrt[s]=7 TeV

A measurement of the electron charge asymmetry in inclusive pp→W+X→eν+X production at sqrt[s]=7  TeV is presented based on data recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 840  pb(-1). The electron charge asymmetry reflects the unequal production of W(+) and W(-) bosons in pp collisions. The electron charge asymmetry is measured in bins of the absolute value of electron pseudorapidity in the range of |η|<2.4. The asymmetry rises from about 0.1 to 0.2 as a function of the pseudorapidity and is measured with a relative precision better than 7%. This measurement provides new stringent constraints for parton distribution functions.

Production of muons from heavy flavor decays at forward rapidity in pp and Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV

The ALICE Collaboration has measured the inclusive production of muons from heavy-flavor decays at forward rapidity, 2.5<y<4, in pp and Pb-Pb collisions at sqrt[s(NN)]=2.76  TeV. The p(t)-differential inclusive cross section of muons from heavy-flavor decays in pp collisions is compared to perturbative QCD calculations. The nuclear modification factor is studied as a function of p(t) and collision centrality. A weak suppression is measured in peripheral collisions. In the most central collisions, a suppression of a factor of about 3-4 is observed in 6<p(t)<10  GeV/c. The suppression shows no significant p(t) dependence.

Mass measurements of the neutron-deficient 41Ti, 45Cr, 49Fe, and 53Ni nuclides: first test of the isobaric multiplet mass equation in f p-shell nuclei

Isochronous mass spectrometry has been applied to neutron-deficient 58Ni projectile fragments at the HIRFL-CSR facility in Lanzhou, China. Masses of a series of short-lived T(z)=-3/2 nuclides including 41Ti, 45Cr, 49Fe, and 53Ni have been measured with a precision of 20-40 keV. The new data enable us to test for the first time the isobaric multiplet mass equation (IMME) in fp-shell nuclei. We observe that the IMME is inconsistent with the generally accepted quadratic form for the A=53, T=3/2 quartet. We perform full space shell model calculations and compare them with the new experimental results.

MicroRNA expression patterns in the bovine mammary gland are affected by stage of lactation

The objective of this work was to determine the expression pattern of microRNA (miR) associated with cellular proliferation, lipid metabolism, and innate immunity in dairy cow mammary gland tissue at different stages of lactation. The expression of miR-10a, miR-15b, miR-16, miR-21, miR-31, miR-33b, miR-145, miR-146b, miR-155, miR-181a, miR-205, miR-221, and miR-223 was studied by real-time reverse-transcription PCR in tissue (n=7/stage) harvested via repeated biopsies during the dry period (-30 d prepartum), the fresh period (7 d postpartum), and early lactation (30 d postpartum). Except for miR-31, all miR studied increased in expression between the dry and fresh periods. Among those upregulated, the expression of miR-221 increased further at early lactation, suggesting a role in the control of endothelial cell proliferation or angiogenesis, whereas the expression of miR-223 decreased at early lactation but to a level that was greater than in the dry period, suggesting it could play a role in the mammary response to pathogens soon after parturition. The expression of miR-31, a hormonally regulated miR that inhibits cyclin gene expression, was greater at early lactation compared with the dry period. From a metabolic standpoint, the consistent upregulation of miR-33b during early lactation compared with the dry period suggests that this miR may exert some control over lipogenesis in mammary tissue. Overall, results indicate that expression of miR associated with transcriptional regulation of genes across diverse biological functions is altered by stage of lactation. The specific roles of these miR during lactation will require further research.

Effects of maternal protein or energy restriction during late gestation on antioxidant status of plasma and immune tissues in postnatal goats

Maternal malnutrition can have temporary or long-lasting effects on development and physiological function of offspring. Our objective was to investigate whether maternal protein or energy restriction in late gestation affects the antioxidant status of plasma, immune organs (thymus and spleen), and natural barrier organs (jejunum) in neonatal goats and whether the effects could be reversed after nutritional recovery. Forty-five pregnant goats (Liuyang Blacks) of similar age (2.0 ± 0.3 yr) and BW (22.2 ± 1.5 kg at d 90 of gestation) were assigned to 3 dietary treatments during late gestation: control (ME = 9.34 MJ/kg and CP = 12.5%, DM basis), 40% protein restricted (PR), and 40% energy restricted (ER) until parturition, after which offspring received the normal diet for nutritional recovery. Plasma and tissues of kids were sampled to determine antioxidant enzymes [superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC), and catalase (CAT)] and gene expression of antioxidant enzymes (Cu/Zn-SOD [SOD1], CAT, and peroxiredoxin 2 [PRDX2]). Maternal protein or energy restriction decreased (P < 0.05) SOD activities in plasma, liver, thymus, and spleen and SOD1 expression in thymus, and maternal energy restriction also decreased (P < 0.05) plasma GSH-Px activity and expressions of SOD1 and CAT in liver at birth. After nutritional recovery of 6 wk, SOD activities in thymus (both in PR and ER) and spleen (only in PR) were greater (P < 0.05), but CAT activity of thymus (both in PR and ER) and CAT expression (only in ER) were less (P < 0.01) than those in control. After nutritional recovery of 22 wk, SOD1 and PRDX2 expression in thymus (both in PR and ER) and SOD1 expression in liver (only in ER) were greater (P < 0.05) whereas CAT expression in thymus (both in PR and ER) was less (P < 0.001) than in control. The current results indicate that maternal protein or energy restriction can decrease the antioxidant capacity of the neonatal kids and result in an imbalance of SOD and hydrogen peroxide-inactivating systems in thymus, even after 6 or 22 wk of nutritional recovery.

Search for new physics with same-sign isolated dilepton events with jets and missing transverse energy

A search for new physics is performed in events with two same-sign isolated leptons, hadronic jets, and missing transverse energy in the final state. The analysis is based on a data sample corresponding to an integrated luminosity of 4.98 fb(-1) produced in pp collisions at a center-of-mass energy of 7 TeV collected by the CMS experiment at the LHC. This constitutes a factor of 140 increase in integrated luminosity over previously published results. The observed yields agree with the standard model predictions and thus no evidence for new physics is found. The observations are used to set upper limits on possible new physics contributions and to constrain supersymmetric models. To facilitate the interpretation of the data in a broader range of new physics scenarios, information on the event selection, detector response, and efficiencies is provided.

J/ψ suppression at forward rapidity in Pb-Pb collisions at √s(NN) = 2.76 TeV

The ALICE experiment has measured the inclusive J/ψ production in Pb-Pb collisions at √s(NN) = 2.76 TeV down to zero transverse momentum in the rapidity range 2.5 < y < 4. A suppression of the inclusive J/ψ yield in Pb-Pb is observed with respect to the one measured in pp collisions scaled by the number of binary nucleon-nucleon collisions. The nuclear modification factor, integrated over the 0%-80% most central collisions, is 0.545 ± 0.032(stat) ± 0.083(syst) and does not exhibit a significant dependence on the collision centrality. These features appear significantly different from measurements at lower collision energies. Models including J/ψ production from charm quarks in a deconfined partonic phase can describe our data.

The M-T hook structure is critical for design of HIV-1 fusion inhibitors

CP621-652 is a potent HIV-1 fusion inhibitor peptide derived from the C-terminal heptad repeat of gp41. We recently identified that its N-terminal residues Met-626 and Thr-627 adopt a unique hook-like structure (termed M-T hook) thus stabilizing the interaction of the inhibitor with the deep pocket on the N-terminal heptad repeat. In this study, we further demonstrated that the M-T hook structure is a key determinant of CP621-652 in terms of its thermostability and anti-HIV activity. To directly define the structure and function of the M-T hook, we generated the peptide MT-C34 by incorporating Met-626 and Thr-627 into the N terminus of the C-terminal heptad repeat-derived peptide C34. The high resolution crystal structure (1.9 Å) of MT-C34 complexed by an N-terminal heptad repeat-derived peptide reveals that the M-T hook conformation is well preserved at the N-terminal extreme of the inhibitor. Strikingly, addition of two hook residues could dramatically enhance the binding affinity and thermostability of 6-helix bundle core. Compared with C34, MT-C34 exhibited significantly increased activity to inhibit HIV-1 envelope-mediated cell fusion (6.6-fold), virus entry (4.5-fold), and replication (6-fold). Mechanistically, MT-C34 had a 10.5-fold higher increase than C34 in blocking 6-helix bundle formation. We further showed that MT-C34 possessed higher potency against T20 (Enfuvirtide, Fuzeon)-resistant HIV-1 variants. Therefore, this study provides convincing data for our proposed concept that the M-T hook structure is critical for designing HIV-1 fusion inhibitors.

A possible biomechanical role of occlusal cusp-fossa contact relationships

Biomechanical features of occlusal contacts are important in understanding the role of the occlusion contributing to masticatory function. Cusp-fossa contact is the typical pattern of occlusion between upper and lower teeth. This includes static relations, such as that during clenching, and dynamic relations when mandibular teeth contact in function along the maxillary occlusal pathways, as during mastication. During clenching in the maximum intercuspal position (ICP), cuspal inclines may take the role of distributing the occlusal forces in multi-directions thus preventing excessive point pressures on the individual tooth involved. During chewing movement on the functional side, the mandible moves slightly from buccal through the maximum ICP to the contralateral side. The part of the chewing cycle where occlusal contacts occur and the pathways taken by the mandible with teeth in occlusal contacts are determined by the morphology of the teeth. The degree of contact is associated with the activity of the jaw muscles. To obtain repeatable static and dynamic occlusal contact information provided by the morphology of the teeth, maximum voluntary clenching and chewing movements with maximum range are needed. In conclusion, in addition to the standard occlusal concepts of centric relation/centric occlusion and group function/cuspid protection relation, biomechanics in static and dynamic cusp-fossa relationships should be included to develop an understanding of occlusal harmony which includes no interfering or deflective contacts in functional occlusal contact.

PaxDb, a database of protein abundance averages across all three domains of life

Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels. These extend from a few molecules per cell for signaling proteins, to millions of molecules for structural proteins. When addressing fundamental questions related to protein evolution, translation and folding, but also in routine laboratory work, a simple rough estimate of the average wild type abundance of each detectable protein in an organism is often desirable. Here, we introduce a meta-resource dedicated to integrating information on absolute protein abundance levels; we place particular emphasis on deep coverage, consistent post-processing and comparability across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. By aggregating and averaging over the various samples, conditions and cell-types, the resulting integrated data set achieves increased coverage and a high dynamic range. We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually. The current PaxDb-release 2.1 (at http://pax-db.org/) presents whole-organism data as well as tissue-resolved data, and covers 85,000 proteins in 12 model organisms. All values can be seamlessly compared across organisms via pre-computed orthology relationships.