New antibiotic with typical plant anthraquinone structure obtained studying terrestrial and marine Streptomycetes

In our screening for new antibiotics from bacteria, the streptomycete isolate M097 from Jiaozhou Bay in China was found to produce aloesaponarin II (1a) and 1,6-dihydroxy-8-hydroxymethyl-anthraquinone (2). Similarly, a terrestrial streptomycete GW24/1694 produced 1a and its methyl ether, the new compound 1-hydroxy-6-methoxy-8-methyl-anthraquinone (1b). All structures were derived by spectrochemical analysis and by comparison with reference data. The results showed that the marine streptomycete isolate M097 and the terrestrial streptomycete GW24/1694 could be a promising material for studying the biosynthetic pathway of polyketides.     

Extraction and characterization of chitin and chitosan from local sources

Chitin has been extracted from six different local sources in Egypt. The obtained chitin was converted into the more useful soluble chitosan by steeping into solutions of NaOH of various concentrations and for extended periods of time, then the alkali chitin was heated in an autoclave which dramatically reduced the time of deacetylation. Chitin from squid pens did not require steeping in sodium hydroxide solution and showed much higher reactivity towards deacetylation in the autoclave that even after 15 min of heating a degree of deacetylation of 90% was achieved. The obtained chitin and chitosan were characterized by spectral analysis, X-ray diffraction and thermo gravimetric analysis.     

Maturity assessment of composted olive mill wastes using UV spectra and humification parameters

In this study, two olive mill wastes - exhausted olive cake (EOC) and paste of olive mill wastewater naturally dehydrated (POMW) - were co-composted and mixed with 25% sesame bark (SB). The humification process was evidenced by quantifying the humic substances and the generally accepted humification indices: (i) the ratio of humic acid (HA) carbon to fulvic acid (FA) carbon (CHA/CFA), (ii) the ratio of water soluble organic carbon (CW) to total organic nitrogen (Cw/Norg), (iii) and the ratio of humic acid carbon to total organic carbon CHA/Corg and by determining the absorbance ratios: E2/E4, E2/E6 and E4/E6. The results showed that the time required to reach maturity was dependant on the chemical properties of the initial raw materials used. The compost including EOC had more nitrogen and synthesised more polymerised HA, the POMW compost also had acceptable degrees of stability and maturity at the end of the process. Maturation was confirmed by a decline in Cw below 1.7, an increase in nitrogen, in HA, in CHA/CFA and an elimination of phytotoxicity. Composts produced with olive mill wastes, experimented on potato culture in the field, can be considered beneficial to soils because of their humification indexes and no toxicity.     

C6ORF66 is an assembly factor of mitochondrial complex I

Homozygosity mapping was performed in five patients from a consanguineous family who presented with infantile mitochondrial encephalomyopathy attributed to isolated NADH:ubiquinone oxidoreductase (complex I) deficiency. This resulted in the identification of a missense mutation in a conserved residue of the C6ORF66 gene, which encodes a 20.2 kDa mitochondrial protein. The mutation was also detected in a patient who presented with antenatal cardiomyopathy. In muscle of two patients, the levels of the C6ORF66 protein and of the fully assembled complex I were markedly reduced. Transfection of the patients' fibroblasts with wild-type C6ORF66 cDNA restored complex I activity. These data suggest that C6ORF66 is an assembly factor of complex I. Interestingly, the C6ORF66 gene product was previously shown to promote breast cancer cell invasiveness.     

Standardized generation of fully mature p70 IL-12 secreting monocyte-derived dendritic cells for clinical use

Dendritic cells (DC) have been shown to be efficient antigen-presenting cells (APC) and, as such, could be considered ideal candidates for cancer immunotherapy. Immature DC (iDC) efficiently capture surrounding antigens; however, only mature DC (mDC) prime naive T lymphocytes. Clinical trials using DC-based tumor vaccines have achieved encouraging, but limited, success, possibly due to the use of immature or incompletely mature DC. Thus, it was apparent that a method capable of generating large numbers of fully functional iDC, their pulsing with desired form of tumor antigens and the subsequent complete and reproducible maturation of iDC is needed. Therefore, we compared two different methods of producing large numbers of iDC. Both protocols yielded comparable numbers of cells with an iDC phenotype with phagocytic function. We next determined which of the clinically applicable activators could induce the complete and reproducible maturation of DC, in order to define the most suitable combination for future clinical trials. Only a combination of TNFalpha + Poly (I:C), or a previously described cytokine cocktail of TNFalpha + IL-1beta + IL-6 + prostaglandin E2, induced the complete activation of the whole DC population, as assessed by the cell surface expression of CD83 and costimulatory molecules. The matured DC were functionally superior to iDC in their ability to stimulate the proliferation of allogeneic lymphocytes and autologous keyhole limpet hemocyanin (KLH)-specific T lymphocytes. Furthermore, only the combination of TNFalpha + Poly (L:C) activated DC to produce large amounts of biologically active p70 IL-12. Thus DC maturation by TNFalpha + Poly (I:C) could efficiently bias T cell response towards Th1 response. Implementation of our results into clinical protocols used for DC generation could be beneficial for future immunotherapy trials.     

Sedimentology of the Late Quaternary Wadi Hasa Marl Formation of Central Jordan: a record of climate variability

The sedimentary features and fossils within the Wadi Hasa Marl Formation coupled with optical luminescence chronology indicate alternating wet and dry periods have occurred on the Jordanian plateau since the last interglacial. The Jurf Ed Darawish Member rests unconformably on the Maastrichtian Muwaqqar Chalk Marl Formation and is composed predominantly of poorly sorted, clast-supported conglomerate. Palaeocurrents and clast composition indicate provenance from Cretaceous sedimentary rocks and Tertiary basalts to the west and southwest of the study site and the facies suggest a flashy alluvial depositional environment probably similar to the modern wadis. The overlying Burma Member consists of bedded grey-green clayey silts and marls with calcrete profiles, up to 1.2 m thick, and isolated gravel lenses. The fine-grained sediments contain charophytes, ostracods, bivalves and various species of gastropod indicating normal freshwater lacustrine conditions. The calcretes contain a poorly preserved fauna suggesting lacustrine deposition followed by subaerial exposure and pedogenesis. Three optical luminescence ages have been obtained from the Burma Member which suggest that the member ranges in age from >111 ka through to <40 ka. The facies variations are indicative of climatic fluctuations in Jordan during this period and human artefacts are found embedded in the sediments. This preliminary study suggests that the Late Quaternary central Jordan sedimentary record may preserve valuable evidence of complex climatic variation which will supplement the data from the Jordan Valley where tectonic activity complicates the sedimentary record.     

Single and Combined Effects of Deoxynivalenol Mycotoxin and a Microbial Feed Additive on Lymphocyte DNA Damage and Oxidative Stress in Broiler Chickens

The immune and intestinal epithelial cells are particularly sensitive to the toxic effects of deoxynivalenol (DON). The aim of this experiment was to study the effects of DON and/or a microbial feed additive on the DNA damage of blood lymphocytes and on the level of thiobarbituric acid reactive substance (TBARS) as an indicator of lipid peroxidation and oxidative stress in broilers. A total of forty 1-d-old broiler chicks were randomly assigned to 1 of 4 dietary treatments (10 birds per group) for 5 wk. The dietary treatments were 1) basal diet; 2) basal diet contaminated with 10 mg DON/kg feed; 3) basal diet contaminated with 10 mg DON/kg feed and supplemented with 2.5 kg/ton of feed of Mycofix Select; 4) basal diet supplemented with Mycofix Select (2.5 kg/ton of feed). At the end of the feeding trial, blood were collected for measuring the level of lymphocyte DNA damage of blood and the TBARS level was measured in plasma, heart, kidney, duodenum and jejunum. The dietary exposure of DON caused a significant increase (P = 0.001) of DNA damage in blood lymphocytes (31.99±0.89%) as indicated in the tail of comet assay. Interestingly addition of Mycofix Select to DON contaminated diet decreased (P = 0.001) the DNA damage (19.82±1.75%) induced by DON. In order to clarify the involvement of lipid peroxidation in the DNA damage of DON, TBARS levels was measured. A significant increase (P = 0.001) in the level of TBARS (23±2 nmol/mg) was observed in the jejunal tissue suggesting that the lipid peroxidation might be involved in the DNA damage. The results indicate that DON is cytotoxic and genotoxic to the chicken intestinal and immune cells and the feed additive have potential ability to prevent DNA damage induced by DON.     

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

Background  

Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.