Generation of single-chain Fv antibody fragments against Mu-2-related death-inducing gene in Escherichia coli

Molecular Biology Reports - Mu-2-related death-inducing (MuD) gene is involved in apoptosis in tumor cells. Although we have previously produced mouse monoclonal antibodies (MAbs) that specifically...     

The inhibitory activity of natural products on plant p-hydroxyphenylpyruvate dioxygenase

The inhibitory activity of 34 natural products of various structural classes on hydroxyphenylpyruvate dioxygenase (HPPD), the target site for triketone herbicides, and the mode of interaction of selected natural products were investigated. Recombinant HPPD from arabidopsis is sensitive to several classes of natural compounds including, in decreasing order of sensitivity, triketones, benzoquinones, naphthoquinones and anthraquinones. The triketone natural products acted as competitive tight-binding inhibitors, whereas the benzoquinones and naphthoquinones did not appear to bind tightly to HPPD. While these natural products may not have optimal structural features required for in vivo herbicidal activity, the differences in their kinetic behavior suggest that novel classes of HPPD inhibitors may be developed based on their structural backbones.     

Novel derivatives of 9,10-anthraquinone are selective algicides against the musty-odor cyanobacterium Oscillatoria perornata

Musty "off-flavor" in pond-cultured channel catfish (Ictalurus punctatus) costs the catfish production industry in the United States at least 30 million US dollars annually. The cyanobacterium Oscillatoria perornata (Skuja) is credited with being the major cause of musty off-flavor in farm-raised catfish in Mississippi. The herbicides diuron and copper sulfate, currently used by catfish producers as algicides to help mitigate musty off-flavor problems, have several drawbacks, including broad-spectrum toxicity towards the entire phytoplankton community that can lead to water quality deterioration and subsequent fish death. By use of microtiter plate bioassays, a novel group of compounds derived from the natural compound 9,10-anthraquinone have been found to be much more selectively toxic towards O. perornata than diuron and copper sulfate. In efficacy studies using limnocorrals placed in catfish production ponds, application rates of 0.3 micro M (125 micro g/liter) of the most promising anthraquinone derivative, 2-[methylamino-N-(1'-methylethyl)]-9,10-anthraquinone monophosphate (anthraquinone-59), dramatically reduced the abundance of O. perornata and levels of 2-methylisoborneol, the musty compound produced by O. perornata. The abundance of green algae and diatoms increased dramatically 2 days after application of a 0.3 micro M concentration of anthraquinone-59 to pond water within the limnocorrals. The half-life of anthraquinone-59 in pond water was determined to be 19 h, making it much less persistent than diuron. Anthraquinone-59 appears to be promising for use as a selective algicide in catfish aquaculture.     

Evolution of spore release mechanisms in the saprolegniaceae (Oomycetes): evidence from a phylogenetic analysis of internal transcribed spacer sequences

Classical studies on spore release within the Saprolegniaceae (Oomycetes) led to the proposition that different mechanisms of sporangial emptying represent steps in an evolutionary transition series. We have reevaluated this idea in a phylogenetic framework using internal transcribed spacer sequences of four genera. These data were compared with the response to osmotic stress exhibited by each taxon. Saprolegnia emerges as the most basal genus, sister to Achlya, Thraustotheca, and Dictyuchus. Achlya and Thraustotheca are most closely related, while Dictyuchus appears to have evolved along a separate evolutionary lineage. The resulting phylogenetic framework is consistent with the idea that the mechanism of sporangial emptying exhibited by Saprolegnia represents the plesiomorphic condition from which the other mechanisms were derived independently. These alternative mechanisms of spore release may have resulted from a small number of mutations that inhibited axonemal development and altered the temporal and spatial expression of lytic enzymes that degrade the sporangial wall. Copyright 1998 Academic Press.     

CD47 Promotes Protective Innate and Adaptive Immunity in a Mouse Model of Disseminated Candidiasis

CD47 is a widely expressed receptor that regulates immunity by engaging its counter-receptor SIRPα on phagocytes and its secreted ligand thrombospondin-1. Mice lacking CD47 can exhibit enhanced or impaired host responses to bacterial pathogens, but its role in fungal immunity has not been examined. cd47^-/- mice on a C57BL/6 background showed significantly increased morbidity and mortality following Candida albicans infection when compared with wild-type mice. Despite normal fungal colonization at earlier times, cd47^-/- mice at four days post-infection had increased colonization of brain and kidneys accompanied by stronger inflammatory reactions. Neutrophil and macrophage numbers were significantly elevated in kidneys and neutrophils in the brains of infected cd47^-/- mice. However, no defect in phagocytic activity towards C. albicans was observed in cd47^-/- bone-marrow-derived macrophages, and neutrophil and macrophage killing of C. albicans was not impaired. CD47-deficiency did not alter the early humoral immune response to C. albicans. Th1, Th2, and Th17 population of CD4⁺ T cells were expanded in the spleen, and gene expression profiles of spleen and kidney showed stronger pro-inflammatory signaling in infected cd47^-/- mice. The chemoattractant chemokines MIP-2α and MIP-2β were highly expressed in infected spleens of cd47^-/- mice. G-CSF, GM-CSF, and the inflammasome component NLRP3 were more highly expressed in infected cd47^-/- kidneys than in infected wild-type controls. Circulating pro- (TNF-α, IL-6) and anti-inflammatory cytokines (IL-10) were significantly elevated, but IL-17 was decreased. These data indicate that CD47 plays protective roles against disseminated candidiasis and alters pro-inflammatory and immunosuppressive pathways known to regulate innate and T cell immunity.     

Biosynthesis of lipid resorcinols and benzoquinones in isolated secretory plant root hairs

The primary functions of root hairs are to increase the root surface area and to aid plants in water and nutrient uptake. However, some root hairs also have secretory functions and exude bioactive secondary metabolites. Sorghum (Sorghum bicolor) root hairs release a substantial amount of phenolic lipids including sorgoleone, a 3-pentadecatriene benzoquinone. The activity of the key enzymes involved in the biosynthesis of lipid resorcinols and benzoquinones was measured directly in isolated root hair preparations obtained from 6-d-old roots. The purified root hair preparation readily converted long-chain acyl-CoA starter units to their corresponding lipid resorcinols and decanoyl-CoA was the best substrate, yielding a 5-n-nonyl-resorcinol. The isolated root hair preparation also had high S-adenosyl-L-methionine-dependent O-methyltransferase activity, which catalyses the methylation of several 5-n-alkyl-resorcinols. Optimum activity was with 5-n-pentyl-resorcinol. Isolated root hairs also exhibited hydroxylase activity (putatively a P450 mono-oxygenase) that reacted with the lipophilic 5-pentadecyl-resorcinol substrate. The in situ hydroxylase activity was low relative to the other enzymes studied, but was still detectable in isolated root hairs. Thus, sorghum root hairs possess the entire metabolic machinery necessary for the biosynthesis of lipid resorcinols and benzoquinones. This will have implications for the genetic engineering of bioactive lipid resorcinols and benzoquinones in sorghum and in other plant species. It also demonstrates that some root hairs can function as specialized cells for the production of bioactive secondary metabolites.     

I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data

MOTIVATION: DNA microarray technology typically generates many measurements of which only a relatively small subset is informative for the interpretation of the experiment. To avoid false positive results, it is therefore critical to select the informative genes from the large noisy data before the actual analysis. Most currently available filtering techniques are supervised and therefore suffer from a potential risk of overfitting. The unsupervised filtering techniques, on the other hand, are either not very efficient or too stringent as they may mix up signal with noise. We propose to use the multiple probes measuring the same target mRNA as repeated measures to quantify the signal-to-noise ratio of that specific probe set. A Bayesian factor analysis with specifically chosen prior settings, which models this probe level information, is providing an objective feature filtering technique, named informative/non-informative calls (I/NI calls). RESULTS: Based on 30 real-life data sets (including various human, rat, mice and Arabidopsis studies) and a spiked-in data set, it is shown that I/NI calls is highly effective, with exclusion rates ranging from 70% to 99%. Consequently, it offers a critical solution to the curse of high-dimensionality in the analysis of microarray data. AVAILABILITY: This filtering approach is publicly available as a function implemented in the R package FARMS (www.bioinf.jku.at/software/farms/farms.html).     

Types of the cerebral arterial circle (circle of Willis) in a Sri Lankan Population

Background  

The variations of the circle of Willis (CW) are clinically important as patients with effective collateral circulations have a lower risk of transient ischemic attack and stroke than those with ineffective collaterals. The aim of the present cadaveric study was to investigate the anatomical variations of the CW and to compare the frequency of prevalence of the different variations with previous autopsy studies as variations in the anatomy of the CW as a whole have not been studied in the Indian subcontinent.     

Antimicrobial activity of the extract and isolated compounds from Baccharis dracunculifolia D. C. (Asteraceae)

Baccharis dracunculifolia D.C. (Asteraceae) is the most important plant source of the Brazilian green propolis. Since propolis is known for its antimicrobial activity, the aim of this work was to evaluate the antimicrobial activities of B. dracunculifolia and some of its isolated compounds. The results showed that the leaves extract of B. dracunculifolia (BdE) presents antifungal and antibacterial activities, especially against Candida krusei and Cryptococcus neoformans, for which the BdE showed IC50 values of 65 microg mL(-1) and 40 microg mL(-1), respectively. In comparison to the BdE, it was observed that the green propolis extract (GPE) showed better antimicrobial activity, displaying an IC50 value of 9 microg mL(-1) against C. krusei. Also, a phytochemical study of the BdE was carried out, affording the isolation of ursolic acid (1), 2a-hydroxy-ursolic acid (2), isosakuranetin (3), aromadendrin-4'-methylether (4), baccharin (5), viscidone (6), hautriwaic acid lactone (7), and the clerodane diterpene 8. This is the first time that the presence of compounds 1, 2, and 8 in B. dracunculifolia has been reported. Among the isolated compounds, 1 and 2 showed antibacterial activity against methicillin-resistant Staphylococcus aureus, displaying IC50 values of 5 microg mL(-1) and 3 microg mL(-1), respectively. 3 was active against C. neoformans, showing an IC50 value of 15 microg mL(-1) and a MIC value of 40 microg mL(-1), while compounds 4-8 were inactive against all tested microorganisms. The results showed that the BdE, similar to the GPE, displays antimicrobial activity, which may be related to the effect of several compounds present in the crude extract.     

A consolidated approach to analyzing data from high-throughput protein microarrays with an application to immune response profiling in humans.

Motivation: DNA microarrays are a well-known and established technology in biological and pharmaceutical research providing a wealth of information essential for understanding biological processes and aiding drug development. Protein microarrays are quickly emerging as a follow-up technology, which will also begin to experience rapid growth as the challenges in protein to spot methodologies are overcome. Like DNA microarrays, their protein counterparts produce large amounts of data that must be suitably analyzed in order to yield meaningful information that should eventually lead to novel drug targets and biomarkers. Although the statistical management of DNA microarray data has been well described, there is no available report that offers a successful consolidated approach to the analysis of high-throughput protein microarray data. We describe the novel application of a statistical methodology to analyze the data from an immune response profiling assay using human protein microarray with over 5000 proteins on each chip.