Growth and physiochemical responses of <Emphasis Type="Italic">Camelina sativa</Emphasis> L. under UV-C stress

A study was conducted to estimate the effect of UV-C (200–280 nm) radiation stress on growth and physiochemical responses of Camelina sativa L. cv. Calina (EC643910; a potential bio-fuel crop) for its possible mass multiplication at high-altitude under high radiations. The germination percentage in terms of radicle protrusion and opening of cotyledonary leaves significantly decreased 13.98 and 27.8 %, respectively, as compared to control. However, no significant change was observed in growth parameters including root and shoot lengths and fresh biomass. The relative membrane leakage rate and lipid peroxidation as a malondialdehyde contents significantly increased with the value of ~99 % and 0.17 mM g^?1 FW, respectively, under UV-C stress. Also, the proline, glycine betaine and total soluble sugars contents increased by ~330, ~440, ~144 %, respectively, as compared to control. Among non-enzymatic antioxidants, the ascorbic acid and total phenol contents significantly increased by ~284 and ~537 %, respectively, as compared to control. Likewise, the activity of antioxidant enzyme, ascorbate peroxidase, guaiacol peroxidase and catalase increased under UV-C stress with the value of 1.03, 0.05 and 0.06 µmol mg protein^?1 min^?1, respectively. In addition, the chlorophyll a, b and total (a + b) contents decreased by ~180, ~151 and ~147 %, respectively, as compared to control. In contrast, the total carotenoids and anthocyanin contents increased by ~160 and ~184 %, respectively. Our findings suggest the adaptive growth and physiochemical responses of C. sativa under UV-C stress. Therefore, it may be recommended for large-scale cultivation at high-altitude under intense natural radiations for future bio-fuel production.     

Embedding mRNA stability in correlation analysis of time-series gene expression data

Current methods for the identification of putatively co-regulated genes directly from gene expression time profiles are based on the similarity of the time profile. Such association metrics, despite their central role in gene network inference and machine learning, have largely ignored the impact of dynamics or variation in mRNA stability. Here we introduce a simple, but powerful, new similarity metric called lead-lag R(2) that successfully accounts for the properties of gene dynamics, including varying mRNA degradation and delays. Using yeast cell-cycle time-series gene expression data, we demonstrate that the predictive power of lead-lag R(2) for the identification of co-regulated genes is significantly higher than that of standard similarity measures, thus allowing the selection of a large number of entirely new putatively co-regulated genes. Furthermore, the lead-lag metric can also be used to uncover the relationship between gene expression time-series and the dynamics of formation of multiple protein complexes. Remarkably, we found a high lead-lag R(2) value among genes coding for a transient complex.     

Serum Interferon-Related MicroRNAs as Biomarkers to Predict the Response to Interferon Therapy in Chronic Hepatitis C Genotype 4

MicroRNAs are messengers during interferon-virus interplay and are involved in antiviral immunity, however, little is known about interferon-related microRNAs regarding their detection in serum and their potential use as non-invasive diagnostic and prognostic biomarkers in chronic hepatitis C (CHC). To elucidate some of the molecular aspects underlying failure of pegylated interferon-α/ribavirin therapy, we investigated pretreatment expression profiles of seven selected interferon-related microRNAs (miR-146a, miR-34a, miR-130a, miR-19a, miR-192, miR-195, and miR-296) by quantitative RT-PCR custom array technology in serum of Egyptian CHC genotype 4 patients and whether their pretreatment levels would predict patient response to the combination therapy. One hundred and six CHC patients and forty matched healthy controls were included. Patients were divided into sustained virological response (SVR) and non-responder (NR) groups. Serum miR-34a, miR-130a, miR-19a, miR-192, miR-195, and miR-296 were upregulated, whereas serum miR-146a was downregulated in CHC compared to controls. Significant correlations were found between expression levels of studied microRNAs and also with clinical data. Pretreatment levels of miR-34a, miR-130a, and miR-195 were significantly higher, whereas miR-192 and miR-296 levels were significantly lower in SVR than NR patients. miR-19a and miR-146a levels were not significantly different between the two groups. miR-34a was superior to differentiate CHC from controls, whereas miR-296 was superior to discriminate SVR from NR patients by receiver operating characteristic analysis. Multivariate logistic analysis revealed miR-34a and miR-195 as independent predictors for SVR and miR-192 as an independent variable for non-response. In conclusion, pretreatment expression profiles of five interferon-related microRNAs are associated with treatment outcome in CHC. Of these, miR-34a, miR-195, and miR-192 could predict treatment response. The profiling results could be used as novel non-invasive diagnostic and prognostic pharmacogenetic biomarkers for treatment personalization in CHC and could help to identify new microRNA-based antivirals.     

The gene expression profile of preclinical autoimmune arthritis and its modulation by a tolerogenic disease-protective antigenic challenge

Introduction  

Autoimmune inflammation is a characteristic feature of rheumatoid arthritis (RA) and other autoimmune diseases. In the natural course of human autoimmune diseases, it is rather difficult to pinpoint the precise timing of the initial event that triggers the cascade of pathogenic events that later culminate into clinically overt disease. Therefore, it is a challenge to examine the early preclinical events in these disorders. Animal models are an invaluable resource in this regard. Furthermore, considering the complex nature of the pathogenic immune events in arthritis, microarray analysis offers a versatile tool to define the dynamic patterns of gene expression during the disease course.     

Effects of Isoform-selective Phosphatidylinositol 3-Kinase Inhibitors on Osteoclasts: ACTIONS ON CYTOSKELETAL ORGANIZATION,SURVIVAL, AND RESORPTION*

Phosphatidylinositol 3-kinases (PI3K) participate in numerous signaling pathways, and control distinct biological functions. Studies using pan-PI3K inhibitors suggest roles for PI3K in osteoclasts, but little is known about specific PI3K isoforms in these cells. Our objective was to determine effects of isoform-selective PI3K inhibitors on osteoclasts. The following inhibitors were investigated (targets in parentheses): wortmannin and {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 (pan-p110), PIK75 (α), GDC0941 (α, δ), TGX221 (β), AS252424 (γ), and IC87114 (δ). In addition, we characterized a new potent and selective PI3Kδ inhibitor, GS-9820, and explored roles of PI3K isoforms in regulating osteoclast function. Osteoclasts were isolated from long bones of neonatal rats and rabbits. Wortmannin, {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002, GDC0941, IC87114, and GS-9820 induced a dramatic retraction of osteoclasts within 15–20 min to 65–75% of the initial area. In contrast, there was no significant retraction in response to vehicle, PIK75, TGX221, or AS252424. Moreover, wortmannin and GS-9820, but not PIK75 or TGX221, disrupted actin belts. We examined effects of PI3K inhibitors on osteoclast survival. Whereas PIK75, TGX221, and GS-9820 had no significant effect on basal survival, all blocked RANKL-stimulated survival. When studied on resorbable substrates, osteoclastic resorption was suppressed by wortmannin and inhibitors of PI3Kβ and PI3Kδ, but not other isoforms. These data are consistent with a critical role for PI3Kδ in regulating osteoclast cytoskeleton and resorptive activity. In contrast, multiple PI3K isoforms contribute to the control of osteoclast survival. Thus, the PI3Kδ isoform, which is predominantly expressed in cells of hematopoietic origin, is an attractive target for anti-resorptive therapeutics.     

Synonymous codon usage in forty staphylococcal phages identifies the factors controlling codon usage variation and the phages suitable for phage therapy

The immergence and dissemination of multidrug-resistant strains of Staphylococcus aureus in recent years have expedited the research on the discovery of novel anti-staphylococcal agents promptly. Bacteriophages have long been showing tremendous potentialities in curing the infections caused by various pathogenic bacteria including S. aureus. Thus far, only a few virulent bacteriophages, which do not carry any toxin-encoding gene but are capable of eradicating staphylococcal infections, were reported. Based on the codon usage analysis of sixteen S. aureus phages, previously three phages were suggested to be useful as the anti-staphylococcal agents. To search for additional S. aureus phages suitable for phage therapy, relative synonymous codon usage bias has been investigated in the protein-coding genes of forty new staphylococcal phages. All phages appeared to carry A and T ending codons. Several factors such as mutational pressure, translational selection and gene length seemed to be responsible for the codon usage variation in the phages. Codon usage indeed varied phage to phage. Of the phages, phages G1, Twort, 66 and Sap-2 may be extremely lytic in nature as majority of their genes possess high translational efficiency, indicating that these phages may be employed in curing staphylococcal infections.     

Seasonal courses of nutrients and heavy metals in water,sediment and above- and below-ground Typha domingensis biomass in Lake Burullus (Egypt): Perspectives for phytoremediation

The present study was carried out in natural stands of Typha domingensis in Lake Burullus, Egypt, to investigate (1) nutrient dynamics and heavy metals accumulation in its organs, (2) the phytoextractive potential of its organs and (3) the amount of nutrients and heavy metals released back into the water after decomposition of the dead tissues. Nitrogen concentrations were higher in the shoot than in the root and rhizome, while P, Ca, Cu, Fe, Zn and ash concentrations were higher in the root than in the rhizome and shoot. Significant differences in the concentrations of Mg, Cd, Cu and ash were assessed during the growing season of T. domingensis. The content of most nutrients and heavy metals in the shoot increased rapidly during the early growing season in February, reached maximal values in July and then decreased again. The nutrient and heavy metal contents in the below-ground portion of the plant showed an opposite trend compared to the shoot; they decreased sharply during the spring, when they were translocated, supporting the heterotrophic phase of shoot growth. However, they increased slightly from July to September and then decreased again. The transfer factors of all nutrients and heavy metals from the sediment to the below-ground organs were greater than unity. The higher translocation ratio of N in T. domingensis shoots makes it suitable for N phytoextraction from water and sediment, while the lower translocation ratios for Cd, Cu, Fe, Pb and Zn make it suitable for metal ion phytostabilisation. The dead shoot biomass of the stands at the end of 2010 amounted to 1950 g DM m⁻², when the seasonal decomposition process began. With a decay rate of 0.0049 day⁻¹, 1624 g DM m⁻² is decomposed in the lake in a year. This is equivalent to releasing the following nutrient and heavy metals into the surrounding water (in g m⁻²): 23.4 N, 0.8 P, 19.2 Ca, 1.8 Mg, 5.6 Na, 32.8 K, 0.01 Cd, 0.01 Cu, 0.84 Fe, 0.12 Pb and 0.03 Zn.     

Effect of exogenous circulating anti-bPL antibodies on bovine placental lactogen measurements in foetal samples

Background  

The involvement of placental lactogen (PL) in the regulation of foetal growth has been investigated in different species by in vivo immunomodulation techniques. However, when circulating antibodies are present together with the hormone, the procedure for hormonal measurement becomes considerably complex. The aim of this study was the immunoneutralization of bovine placental lactogen (bPL) concentrations in bovine foetal circulation by direct infusion of rabbit anti-bPL purified immunoglobulins (IgG) via a foetal catheter (in vivo study). The ability of a RIA based on guinea pig anti-bPL antiserum, for the measurement of bPL concentrations in samples containing exogenous rabbit anti-bPL immunoglobulins, was also analyzed in in vitro and in vivo conditions.