Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse

Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV) produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA) receptor and non-structural protein 1 (NS1) interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA) variants obtained after 12 or 20-21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA) and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30) suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for studying IAV evolution to increased virulence in the mouse.     

Use of organic acids and salts to control postharvest diseases of lemon fruits in Egypt

Abstract

Postharvest diseases caused by Geotricum candidum (sour rot), Penicillium digitatum (green mould), and P. italicum (blue mould) are the most important negative factors affecting handling and marketing of citrus fruits in Egypt. The effect of organic acids (ascorbic, benzoic, citric and sorbic) as well as organic salts (potassium sorbate and sodium benzoate) were evaluated on the growth of causal agents and their disease incidence under in vitro and in vivo conditions. Complete inhibition was observed in the linear growth of all tested fungi when exposed to benzoic, citric and sorbic organic acids at concentrations of 4% and 2% of either sodium benzoate or potassium sorbate, respectively. Minimizing the tested concentration of organic acid down to 2%, the tested fungi fluctuated in their response such that only benzoic and sorbic acids could completely inhibit the growth of either P. digitatum or P. italicum only. Different organic acids and salts showed various levels of either protective or therapeutic effect for coated lemon fruits against mould infection whatever the time of their artificial inoculation under in vivo conditions. All treated fruits showed reduction in sour rot and green and blue mould diseases when compared with untreated fruits. Complete inhibition of mould incidence was obtained in coated lemon fruits with 4% of water or wax mixtures of sodium benzoate and potassium sorbate 24 hours before inoculation. Also, high reduction in mould incidence was observed in lemon fruits coated with the same concentration at 48 hours after inoculation under the same conditions. On the other hand, the tested organic acids showed a lesser effect on mould incidence. Moreover, they were more effective against mould incidence when dissolved in water than wax, that only 4% of water mixture of sorbic and benzoic acids showed 100% protection against mould incidence. Furthermore, the severity of infection records followed the same trend. The present findings demonstrate that potassium sorbate and sodium benzoate have potential as environmentally friendly products, nontoxic postharvest fungicides against sour rot, green and blue mould incidence of stored citrus fruits and could be suggested for commercial use in packing-houses in consideration to their wide consumption as safely food preservatives.     

A new mathematical evaluation of smoking problem based of algebraic statistical method

Smoking problem is considered as one of the hot topics for many years. In spite of overpowering facts about the dangers, smoking is still a bad habit widely spread and socially accepted. Many people start smoking during their gymnasium period. The discovery of the dangers of smoking gave a warning sign of danger for individuals. There are different statistical methods used to analyze the dangers of smoking. In this study, we apply an algebraic statistical method to analyze and classify real data using Markov basis for the independent model on the contingency table. Results show that the Markov basis based classification is able to distinguish different date elements. Moreover, we check our proposed method via information theory by utilizing the Shannon formula to illustrate which one of these alternative tables is the best in term of independent.     

Aggressive low grade middle ear adenocarcinoma with multiple recurrences: a case report

Background

Special stains, such as reticulin stain and CD34 immunostain, are very helpful in the diagnosis of well differentiated hepatocellular carcinoma (HCC). Most studies have shown that absent or decreased reticulin stain or an abnormal reticulin pattern with widened trabeculae is reliable for the diagnosis of well-differentiated HCC.

Case report

We report here two cases of well differentiated HCC with an unusual reticulin staining pattern. A strongly positive reticulin network was preserved within the tumor, which surrounded individual tumor cells in a monolayered trabecular pattern. At the same time, an increased CD34 stain was present in the tumor.

Conclusions

This unusual reticulin pattern represents part of the diverse reticulin staining patterns seen in HCC. Although this staining pattern is rare, it should be recognized when diagnosing well-differentiated HCC in small samples such as cellblock of fine needle aspiration or small core biopsies.     

Autotransporter β-domains have a specific function in protein secretion beyond outer-membrane targeting

Autotransporters (ATs) of Gram-negative bacteria contain an N-proximal passenger domain that is transported to the extracellular milieu and a C-terminal β-domain that inserts into the outer membrane (OM) in a β-barrel conformation. This β-domain facilitates translocation of the passenger domain across the OM and has long been considered to be the translocation pore. However, available crystal structures of β-domains show that the β-barrel pore is too narrow for the observed transport of folded elements within the passenger domains. ATs have recently been shown to interact with the β-barrel assembly machinery. These findings questioned a direct involvement of the β-domain in passenger translocation and suggested that it may only target the passenger to the β-barrel assembly machinery pore. To address the function of the β-domain in more detail, we have replaced the β-domain of the Escherichia coli AT hemoglobin protease by β-domains originating from other OM proteins. Furthermore, we have modified the diameter of the β-domain pore. The mutant proteins were analyzed for their capacity to insert into the OM and for surface display of the passenger. Our results show that efficient passenger secretion requires a specific β-domain that not only functions as a targeting device but also is directly involved in the translocation of the passenger to the cell surface.     

Culture of microalgae Chlorella minutissima for biodiesel feedstock production

Microalgae are among the most promising of non‐food based biomass fuel feedstock alternatives. Algal biofuels production is challenged by limited oil content, growth rate, and economical cultivation. To develop the optimum cultivation conditions for increasing biofuels feedstock production, the effect of light source, light intensity, photoperiod, and nitrogen starvation on the growth rate, cell density, and lipid content of Chlorella minutissima were studied. The fatty acid content and composition of Chlorella minutissima were also investigated under the above conditions. Fluorescent lights were more effective than red or white light‐emitting diodes for algal growth. Increasing light intensity resulted in more rapid algal growth, while increasing the period of light also significantly increased biomass productivity. Our results showed that the lipid and triacylglycerol content were increased under N starvation conditions. Thus, a two‐phase strategy with an initial nutrient‐sufficient reactor followed by a nutrient deprivation strategy could likely balance the desire for rapid and high biomass generation (124 mg/L) with a high oil content (50%) of Chlorella minutissima to maximize the total amount of oil produced for biodiesel production. Moreover, methyl palmitate (C16:0), methyl oleate (C18:1), methyl linoleate (C18:2), and methyl linolenate (C18:3) are the major components of Chlorella minutissima derived FAME, and choice of light source, intensity, and N starvation impacted the FAME composition of Chlorella minutissima. The optimized cultivation conditions resulted in higher growth rate, cell density, and oil content, making Chlorella minutissima a potentially suitable organism for biodiesel feedstock production. Biotechnol. Bioeng. 2011;108: 2280–2287. © 2011 Wiley Periodicals, Inc.     

Solution conformation of a pectin fragment disaccharide using molecular modelling and nuclear magnetic resonance

In the present study, the conformational behaviour of methylated pectic disaccharide 4-O-alpha-D-galactopyranurosyl 1-O-methyl-alpha-D-galactopyranuronic 6,6'-dimethyl diester 1 has been completely characterized through combined n.m.r. and molecular modelling studies. The 1H-1H n.O.e. across the glycosidic bond was measured by both steady-state and transient 1D and 2D experiments. In parallel, the complete conformational analysis of the disaccharide has been achieved with the MM3 molecular mechanics method. The conformation of the pyranose ring is confirmed by the excellent agreement between the experimental and calculated intracyclic scalar coupling constants. The iso-energy contours displayed on the 'relaxed' map indicate an important flexibility about the glycosidic linkage. There is no significant influence of the methoxyl group on the conformational behaviour of the disaccharide. The theoretical n.m.r. data were calculated taking into account all the accessible conformations and using the averaging methods appropriate for slow internal motions. 3JC-H coupling constants were calculated using an equation suitable for C-O-C-H segments. The agreement between experimental and theoretical data is excellent. Within the potential energy surface calculated for the disaccharide, several conformers can be identified. When these conformations are extrapolated to a regular polymer structure, they generate pectins with right- and left-handed chirality along with a two-fold helix. These different types of helical structure are the result of small changes in conformation, without any drastic variation of the fibre repeat.