Antimicrobial activity of essential oils and structurally related synthetic food additives towards selected pathogenic and beneficial gut bacteria

AIMS: To assess the potential of essential oils and structurally related synthetic food additives in reducing bacterial pathogens in swine intestinal tract. METHODS AND RESULTS: The antimicrobial activity of essential oils/compounds was measured by determining the inhibition of bacterial growth. Among 66 essential oils/compounds that exhibited > or =80% inhibition towards Salmonellatyphimurium DT104 and Escherichia coli O157:H7, nine were further studied. Most of the oils/compounds demonstrated high efficacy against S. typhimurium DT104, E. coli O157:H7, and E. coli with K88 pili with little inhibition towards lactobacilli and bifidobacteria. They were also tolerant to the low pH. When mixed with pig cecal digesta, these oils/compounds retained their efficacy against E. coli O157:H7. In addition, they significantly inhibited E. coli and coliform bacteria in the digesta, but had little effect on the total number of lactobacilli and anaerobic bacteria. CONCLUSIONS: Some essential oils/compounds demonstrated good potential, including efficacy, tolerance to low pH, and selectivity towards bacterial pathogens, in reducing human and animal bacterial pathogens in swine intestinal tract. SIGNIFICANCE AND IMPACT OF THE STUDY: This study has identified candidates of essential oils/compounds for in vivo studies to develop antibiotic substitutes for the reduction of human and animal bacterial pathogens in swine intestinal tract.     

Suppression of human selenium-binding protein 1 is a late event in colorectal carcinogenesis and is associated with poor survival

The purpose of this study was to analyze altered protein expression in cancer tissues and determine its relationship to prognosis in colorectal carcinomas. We performed proteomic expression analysis on 14 colorectal carcinomas and matched nontumorous colonic mucosa by 2-DE and MALDI-TOF-MS. Comparative analysis of the respective spot patterns on 2-DE showed 14 spots that were markedly changed in the colorectal carcinomas. Among them, selenium-binding protein 1 (SELENBP1) was markedly decreased in 12 (85%) carcinomas. The reduced expression of SELENBP1 was further supported by Western blot analysis and immunohistochemistry. Suppression of SELENBP1 was further analyzed in another eight-paired adenomas and carcinomas from the same patients using Western blot analysis and immunohistochemistry, and revealed that one adenoma and seven carcinomas exhibited markedly reduced SELENBP1 expression. Patients with low levels of SELENBP1 expression had significantly lower overall survival rates (72 vs. 85%, p = 0.021) among the 240 stages II and III colorectal carcinomas by using tissue microarray analysis. Our findings indicate that suppression of SELENBP1 is a frequent and late event in colorectal carcinogenesis, and may contribute to the rapid progression of colorectal carcinoma.     

Functional characteristics of shrimp chitosan and its membranes as affected by the degree of deacetylation

The functional properties of three shrimp chitosan preparations with different degrees of deacetylation (75%, 87% and 96% DD) but with a constant molecular weight (about 810 kDa) were investigated. Chitosan with 75% DD had a 1.5 times higher water absorption, probably due to its 20% lower level of crystallinity. Membranes cast from this chitosan also exhibited 1.5 times more water absorption and 2 times higher permeability. However, chitosan with 87% and 96% DD had 1.5-2 times higher absorption of fat and the orange II dye. This is attributed to the higher content of positively charged amine groups in the polymer. Cast into membrane, chitosan of higher degree of deacetylation showed a higher tensile strength and a higher elongation at break, probably due to the higher level of crystallinity.     

Recognition of oxidatively modified bases within the biotin-binding site of avidin

Oxidative damage of DNA results in the formation of many products, including 8-oxodeoxyguanosine, which has been used as a marker to quantify DNA damage. Earlier studies have demonstrated that avidin, a protein prevalent in egg-white and which has high affinity for the vitamin biotin, binds to 8-oxodeoxyguanosine and related bases. In this study, we have determined crystal structures of avidin in complex with 8-oxodeoxyguanosine and 8-oxodeoxyadenosine. In each case, the base is observed to bind within the biotin-binding site of avidin. However, the mode of association between the bases and the protein varies and, unlike in the avidin:biotin complex, complete ordering of the protein in this region does not accompany binding. Fluorescence studies indicate that in solution the individual bases, and a range of oligonucleotides, bind to avidin with micromolar affinity. Only one of the modes of binding observed is consistent with recognition of oxidised purines when incorporated within a DNA oligomer, and from this structure a model is proposed for the selective binding of avidin to DNA containing oxidatively damaged deoxyguanosine. These studies illustrate the molecular basis by which avidin might act as a marker of DNA damage, although the low levels of binding observed are inconsistent with the recognition of oxidised purines forming a major physiological role for avidin.     

A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps

The accuracy of the secondary structure element (SSE) identification from volumetric protein density maps is critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM). It is still challenging to detect the SSE automatically and accurately from the density maps at medium resolutions (～5-10 ?). We present a machine learning approach, SSELearner, to automatically identify helices and β-sheets by using the knowledge from existing volumetric maps in the Electron Microscopy Data Bank. We tested our approach using 10 simulated density maps. The averaged specificity and sensitivity for the helix detection are 94.9% and 95.8%, respectively, and those for the β-sheet detection are 86.7% and 96.4%, respectively. We have developed a secondary structure annotator, SSID, to predict the helices and β-strands from the backbone Cα trace. With the help of SSID, we tested our SSELearner using 13 experimentally derived cryo-EM density maps. The machine learning approach shows the specificity and sensitivity of 91.8% and 74.5%, respectively, for the helix detection and 85.2% and 86.5% respectively for the β-sheet detection in cryoEM maps of Electron Microscopy Data Bank. The reduced detection accuracy reveals the challenges in SSE detection when the cryoEM maps are used instead of the simulated maps. Our results suggest that it is effective to use one cryoEM map for learning to detect the SSE in another cryoEM map of similar quality.     

Recycling and adaptation of Klebsormidium flaccidum microalgae for the sustained production of gold nanoparticles

Targeting the development of cell-based bioreactors for the production of metal nanoparticles, the possibility to perform the sustained synthesis of colloidal gold using Klebsormidium flaccidum green algae was studied. A first strategy relying on successive growth/reduction/reseeding recycling steps demonstrated maintained biosynthesis capability of the microalgae but limitation in metal content due to toxic effects. An alternative approach consisting of progressive gold salt addition revealed to be suitable to favor cell adaptation to larger metal concentrations and supported particle release over month periods.     

Late Cretaceous biostratigraphy and paleoenvironmental reconstruction based on non-marine ostracodes from well SK1 (south), Songliao Basin,northeast China

High-resolution biostratigraphy has been established on the basis of fossil ostracodes from cores of the Cretaceous Continental Scientific Drilling borehole-Songke 1 (south) (SK1(s)) in the Songliao Basin, northeast China. More than 80 species belonging to 13 genera have been identified and 15 ostracode assemblage zones have been recognized. On the basis of ostracode paleoecological analysis, paleoenvironments, for example lake levels and salinity, have been reconstructed. Two inferred deep-water phases occurred during the deposition of the lower Qingshankou and lower Nenjiang formations, whereas shallower water phases probably occurred during deposition of the upper Quantou and uppermost Qingshankou to Yaojia formations. The salinity of paleo-Songliao lake is interpreted as predominantly freshwater to oligohaline. Oligohaline to mesohaline water environments may have occurred during the first and middle third members of the Qingshankou formation and the lower first and lower second members of the Nenjiang formation.     

Variation,Sex, and Social Cooperation: Molecular Population Genetics of the Social Amoeba Dictyostelium discoideum

Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell–cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. discoideum across these strains, with a mean nucleotide diversity (π) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter ρ. The SNP data indicate that recombination is widespread within D. discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle.     

Toll-Like Receptor 4-Mediated Activation of p38 Mitogen-Activated Protein Kinase Is a Determinant of Respiratory Virus Entry and Tropism

Respiratory viruses exert a heavy toll of morbidity and mortality worldwide. Despite this burden there are few specific treatments available for respiratory virus infections. Since many viruses utilize host cell enzymatic machinery such as protein kinases for replication, we determined whether pharmacological inhibition of kinases could, in principle, be used as a broad antiviral strategy for common human respiratory virus infections. A panel of green fluorescent protein (GFP)-expressing recombinant respiratory viruses, including an isolate of H1N1 influenza virus (H1N1/Weiss/43), was used to represent a broad range of virus families responsible for common respiratory infections (Adenoviridae, Paramyxoviridae, Picornaviridae, and Orthomyxoviridae). Kinase inhibitors were screened in a high-throughput assay that detected virus infection in human airway epithelial cells (1HAEo-) using a fluorescent plate reader. Inhibition of p38 mitogen-activated protein kinase (MAPK) signaling was able to significantly inhibit replication by all viruses tested. Therefore, the pathways involved in virus-mediated p38 and extracellular signal-regulated kinase (ERK) MAPK activation were investigated using bronchial epithelial cells and primary fibroblasts derived from MyD88 knockout mouse lungs. Influenza virus, which activated p38 MAPK to approximately 10-fold-greater levels than did respiratory syncytial virus (RSV) in 1HAEo- cells, was internalized about 8-fold faster and more completely than RSV. We show for the first time that p38 MAPK is a determinant of virus infection that is dependent upon MyD88 expression and Toll-like receptor 4 (TLR4) ligation. Imaging of virus-TLR4 interactions showed significant clustering of TLR4 at the site of virus-cell interaction, triggering phosphorylation of downstream targets of p38 MAPK, suggesting the need for a signaling receptor to activate virus internalization.Respiratory virus infections cause considerable morbidity and mortality worldwide; it was recently reported that hospitalizations due to respiratory syncytial virus (RSV) exceed 2 million per year in the Unites States alone (16). An H1N1 swine influenza pandemic took place during the 2009-2010 winter season (14), and there is the lingering threat of an H5N1 avian influenza pandemic, with mortality due to direct bird-to-human H5N1 infection in hospitalized patients between 30 and 100% (3). The severe acute respiratory syndrome (SARS)-associated coronavirus, isolated in 2003, resulted in devastating respiratory tract infections with few treatment options (40). For most common respiratory viruses, treatment is symptomatic, and for pathogens such as influenza viruses for which specific treatments are available, oseltamivir (Tamiflu)- and amantidine-resistant strains are emerging and being transmitted globally (33).All functions within a cell are triggered and regulated by cell signaling cues. Since viruses are obligate intracellular parasites, they rely upon cell signaling to regulate all processes within the cell that drive virus replication. In this study we investigated the effects of kinase inhibitors as a therapeutic strategy and to investigate the roles played by some kinases during virus replication. The extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinases (MAPKs) have been shown by us and others to play important roles during virus replication in vitro (19, 20, 26, 30, 42), and we have recently reported that inhibition of p38 MAPK activation is an effective and novel antiviral strategy in vivo (29). The significance of p38 MAPK activity in vivo is such that inadvertent and coincident activation of this kinase by some pharmaceutical agents enhances virus replication (29). Antiviral strategies may exist whereby inhibition of host cell kinases may stem the spread and replication of numerous different viral species. Such broad antiviral strategies would permit administration of kinase inhibitors to patients suspected of having respiratory viral infection, and to health care workers or inhabitants within the locale of a viral outbreak, prior to the availability of results from laboratory diagnostic testing.The activation of p38 MAPK by pattern recognition receptors (PRRs) has been studied in the context of the antiviral immune response (reviewed in reference 22). We report here that viruses usurp these responses for the benefit of virus replication through activation of p38 MAPK, mediated by a PRR (Toll-like receptor 4 [TLR4]) and MyD88, providing the basis for a broad-spectrum antiviral.