The knowledge-integrated network biomarkers discovery for major adverse cardiac events

The mass spectrometry (MS) technology in clinical proteomics is very promising for discovery of new biomarkers for diseases management. To overcome the obstacles of data noises in MS analysis, we proposed a new approach of knowledge-integrated biomarker discovery using data from Major Adverse Cardiac Events (MACE) patients. We first built up a cardiovascular-related network based on protein information coming from protein annotations in Uniprot, protein-protein interaction (PPI), and signal transduction database. Distinct from the previous machine learning methods in MS data processing, we then used statistical methods to discover biomarkers in cardiovascular-related network. Through the tradeoff between known protein information and data noises in mass spectrometry data, we finally could firmly identify those high-confident biomarkers. Most importantly, aided by protein-protein interaction network, that is, cardiovascular-related network, we proposed a new type of biomarkers, that is, network biomarkers, composed of a set of proteins and the interactions among them. The candidate network biomarkers can classify the two groups of patients more accurately than current single ones without consideration of biological molecular interaction.     

Cellular immunity to Coccidioides immitis: In vitro lymphocyte response to spherules,arthrospores, and endospores

In vitro stimulation of incorporation of tritiated thymidine by human peripheral lymphocytes in response to two soluble antigens and three different intact but nonviable fungal forms of Coccidioides immitis was studied. Lymphocytes were obtained from three groups of subjects: healthy skin test positive, healthy skin test negative, and disseminated disease. Dose-response relationships to the intact forms (endospores, arthrospores, and spherules) were determined. Responses of lymphocytes from healthy skin test-positive subjects and subjects with disseminated disease were similar. Ranking of antigens by “potency” gave the following results: endospores = spherulin > mycelial filtrate > arthrospores = spherules. Endospores were the most potent of the intact forms in 10 of 11 subjects. The clear superiority of endospores over spherules is not due to differences in the total particle surface area available for presentation to the leukocytes. All antigens tested except spherules could discriminate between skin test-positive and skin test-negative subjects in this in vitro system. A T-cell-enriched, B-cell- and mono-cyte-depleted cell population demonstrated an active response to spherulin and to endospores. The variance of these finding with animal studies demonstrating spherules to be immunogenically superior when compared to endospores is discussed. This may have importance in future studies in humans of vaccines to C. immitis.     

Bidirectional effect of Wnt signaling antagonist DKK1 on the modulation of anthrax toxin uptake

LRP6,a co-receptor for the morphogen Wnt,aids endocytosis of anthrax complexes.Here we report that Dickkopf1(DKK1)protein,a secreted LRP6 ligand and antagonist,is also a modulator of anthrax toxin sensitivity.shRNA-mediated gene silencing or TALEN-mediated gene knockout of DKK1 reduced sensitivity of cells to PA-dependent hybrid toxins.However,unlike the solely inhibitory effect on Wnt signaling,the effects of DKK1 overexpression on anthrax toxicity were bidirectional,depending on its endogenous expression and cell context.Fluorescence microscopy and biochemical analyses showed that DKK1 facilitates internalization of anthrax toxins and their receptors,an event mediated by DKK1-LRP6-Kremen2 complex.Monoclonal antibodies against DKK1 provided dose-dependent protection to macrophages from killing by anthrax lethal toxin(LT).Our discovery that DKK1 forms ternary structure with LRP6 and Kremen2 in promoting PA-mediated toxin internalization provides a paradigm for bacterial exploitation of mechanisms that host cells use to internalize signaling proteins.     

The Biotransformation of Propylene to Propylene Oxide by Methylococcus capsulatus (Bath): 3. Reactivation of Inactivated Whole Cells to Give a High Productivity System

Methylococcus capsulatus (Bath) possesses methane monooxygenases (soluble - (sMMO) and particulate - (pMMO)) which are able to catalyse the epoxidation of propylene to propylene oxide. In a previous paper we have shown that the production of the epoxide caused a rapid inactivation of the bioconversion process (Stanley et al, 1992). This paper shows that cultures containing pMMO, inactivated by propylene oxide production, could be completely reactivated in the presence of growth substrates within 5 h after the removal of propylene oxide so long as the propylene oxide production rate was below 150 nmol min^-1 [mg dry weight cells]^-1. Reactivation under these conditions was detectable within 30 min of propylene oxide removal. On the other hand, cells inactivated by propylene oxide production rates in excess of 150 nmol min^-1 [mg dry weight]^-1 did not begin to recover activity within the 30 min period. Furthermore a lag period was observed before reactivation began which was dependent upon the initial production rate. Cultures possessing sMMO took twice as long to recover their activity compared with cells containing pMMO.

Reactivation of propylene oxide production could occur without growth, but the process required the presence of a carbon and energy source (methane or methanol), sulphur, nitrogen and oxygen, although copper (which is normally involved in pMMO activity) was not required. It was shown that de novo protein synthesis was required for reactivation of activity.

Production rates of 12 g 1^-1 d^-1 could be maintained for longer than three weeks in a single phase production process and rates up to 30 g 1^-1 d^-1 were achieved in a two stage process. Using Methylocystis parvus (OBBP) rates of up to 90 g 1^-1 d^-1 were attained over a one week period.     

Method of Melanin Bleaching in MIB1-Ki67 Immunostaining of Pigmented Lesions: A Quantitative Evaluation in Malignant Melanomas

The effect of melanin bleaching on the immunoreactivity of the MIB1-Ki67 antigen in pigmented melanocytic lesions was investigated. Eight paired non-pigmented and heavily pigmented malignant melanomas (6 primary melanomas and 2 secondary melanomas) were selected. Avidin–biotin immunoperoxidase complex (ABC) and microwave antigen retrieval were used in immunostaining. Sections were incubated with 10% H2O2 for 24h before immunostaining with primary antibody MIB1, or after the completion of immunostaining. Non-bleached controls were obtained by conducting the identical staining but omitting the bleaching procedure. In all heavily pigmented lesions bleached by 10% H2O2 before or after immunostaining, the melanin was bleached effectively and MIB1-positively stained cells were clearly seen. Cell counting in the non-pigmented group found that there were no significant differences in the percentage of MIB1-positive melanoma cells (%MIB1) between non-bleached controls and those sections which had been bleached by 10% H2O2 either before or after the immunostaining. The results suggest that hydrogen peroxide can effectively bleach melanin in pigmented melanocytic lesions without significantly affecting MIB1-Ki67 immunolabelling.     

Golgi Complex Organization in Skeletal Muscle: A Role for Golgi‐Mediated Glycosylation in Muscular Dystrophies?

The Golgi complex (GC) is the central organelle of the classical secretory pathway, and it receives, modifies and packages proteins and lipids en route to their intracellular or extracellular destinations. Recent studies of congenital muscular dystrophies in skeletal muscle suggest an exciting new role for an old and well-established function of the GC: glycosylation. Glycosylation is the exquisitely regulated enzymatic addition of nucleotide sugars to proteins and lipids mediated by glycosyltransferases (GTs). Mutations in putative Golgi-resident GTs, fukutin, fukutin-related protein and large1 cause these progressive muscle-wasting diseases. The appropriate localization of GTs to specific subcompartments of the Golgi is critical for the correct assembly line-like addition of glycan groups to proteins and lipids as they pass through the GC. Consequently, these studies of congenital muscular dystrophies have focused attention on the organization and function of the GC in skeletal muscle. In contrast to other cells and tissues, the GC in skeletal muscle has received relatively little attention; however, in recent years, several studies have shown that GC distribution in muscle is highly dynamic or plastic and adopts different distributions in muscle cells undergoing myogenesis, denervation, regeneration and maturation. Here, we review the current understanding of the dynamic regulation of GC organization in skeletal muscle and focus on the targeting of fukutin, fukutin-related protein and large1 to the GC in muscle cells.     

Bioarchaeological investigation of ancient Maya violence and warfare in inland northwest Yucatan,Mexico

This study investigates evidence of changes and continuities in ancient Maya violence and warfare in inland northwest Yucatan, Mexico from the Middle Preclassic (600–300 BC) to the Postclassic (AD 1050–1542) through bioarchaeological analysis of cranial and projectile trauma. It is hypothesized that the frequency of violence increases before the Classic Maya collapse and remains high during the Postclassic period. It is also hypothesized that the flat, open terrain was conducive to warfare and resulted in higher trauma frequencies than in other parts of the Maya area. Results show that the frequency of cranial trauma decreases before the Classic collapse and increases in the Postclassic, partially matching the expected chronological trends. The frequency of cranial trauma does not differ significantly from other Maya regions but the pattern does: for all periods, males have more healed injuries than females and they are concentrated on the left side of the anterior of the skull. Some injuries appear to be from small points hafted in wooden clubs. In addition, projectile trauma is evident in a scapula with an embedded arrowhead tip, the first such case reported in a Maya skeleton. Overall, these results suggest greater reliance on open combat and less on raids in this region compared with other parts of the Maya area, possibly due to the flat, open terrain, though the identification of perimortem trauma in both women and men indicates surprise raids on settlements were also practiced. Am J Phys Anthropol 154:140–151, 2014. © 2014 Wiley Periodicals, Inc.