Evaluation of plastic composite-supports for enhanced ethanol production in biofilm reactors

Biofilms are a natural form of cell immobilization that result from microbial attachment to solid supports. Biofilm reactors with polypropylene composite-supports containing up to 25% (w/w) of various agricultural materials (corn hulls, cellulose, oat hulls, soybean hulls or starch) and nutrients (soybean flour or zein) were used for ethanol production. Pure cultures ofZymomonas mobilis, ATCC 31821 orSaccharomyces cerevisiae ATCC 24859 and mixed cultures with either of these ethanol-producing microorganisms and the biofilm-formingStreptomyces viridosporus T7A ATCC 39115 were evaluated. An ethanol productivity of 374g L^–1 h^–1 (44% yield) was obtained on polypropylene composite-supports of soybean hull-zein-polypropylene by usingZ. mobilis, whereas mixed-culture fermentations withS. viridosporus resulted in ethanol productivity of 147.5 g L^–1 h^–1 when polypropylene composite-supports of corn starch-soybean flour were used. WithS. cerevisiae, maximum productivity of 40 g L^–1 h^–1 (47% yield) was obtained on polypropylene composite-supports of soybean hull-soybean flour, whereas mixed-culture fermentation withS. viridosporus resulted in ethanol productivity of 190g L^–1 h^–1 (35% yield) when polypropylene composite-supports of oat hull-polypropylene were used. The maximum productivities obtained without supports (suspension culture) were 124 g L^–1 h^–1 and 5 g L^–1 h^–1 withZ. mobilis andS. cerevisiae, respectively. Therefore, forZ. mobilis andS. cerevisiae, ethanol productivities in biofilm fermentations were three- and eight-fold higher than suspension culture fermentations, respectively. Biofilm formation on the chips was detected by weight change and Gram staining of the support material at the end of the fermentation. The ethanol production rate and concentrations were consistently greater in biofilm reactors than in suspension cultures.This is Journal Paper No. J-16356 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa. Project No. 3253     

Associations with habitat versus geographic cohesiveness: size and shape of Bembicium vittatum Philippi (Gastropoda: Littorinidae) in the Houtman Abrolhos Islands

In the Houtman Abrolhos Islands, Western Australia, the direct-developing littorine snail Bembicium vittatum occupies a wide range of habitats, which are replicated across the three major groups of islands. Earlier studies showed that allozyme similarities followed patterns related to gene flow, independent of habitat, providing an excellent opportunity to test for associations with habitat for traits more likely to be adaptively important. As the first test for adaptive divergence, we examined variation in size and shape of shells among 131 populations in the Abrolhos Islands. Two-fold variations were found in width of adults, the allometric coefficient of height with width, and shell height scaled to a standard width. Quantification of habitat characteristics was summarized by principal components analysis. In contrast with the patterns of divergence for allozymes, shell height, adjusted for width, was strongly associated with habitat: flatter shells are found on exposed, vertical shores, while domed, more globose shells predominate in sheltered sites. This association was stronger for shape of adult-sized snails than for height scaled to an arbitrary size, highlighting the importance of using biologically relevant measures. Even highly isolated and allozymically less variable populations in tidal ponds conformed to this association. Because differences in shape are highly heritable in B. vittatum , this association of shape with habitat, independent of patterns of gene flow, indicates local adaptation. Shell size also varied with habitat, but because growth rate is highly plastic, variation in size cannot be interpreted simply in terms of adaptation. Nevertheless, the pattern of variation indicates that, within realized limits, larger size is generally favourable, but may be constrained by local conditions. Thus, variation in size signals the potential for adaptive divergence of life histories among the many, isolated populations of this species.     

Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA

The long (4.6-kb) A+T region of Drosophila melanogaster mitochondrial DNA has been cloned and sequenced. The A+T region is organized in two large arrays of tandemly repeated DNA sequence elements, with nonrepetitive intervening and flanking sequences comprising only 22% of its length. The first repeat array consists of five repeats of 338-373 bp. The second consists of four intact 464-bp repeats and a fifth partial repeat of 137 bp. Three DNA sequence elements are found to be highly conserved in D. melanogaster and in several Drosophila species with short A+T regions. These include a 300-bp DNA sequence element that overlaps the DNA replication origin and two thymidylate stretches identified on opposite DNA strands. We conclude that the length heterogeneity observed in the A+T regulatory region in mitochondrial DNAs from the genus Drosophila results from the expansion (and contraction) of the number of repeated DNA sequence elements. We also propose that the 300-bp conserved DNA sequence element, in conjunction with another primary sequence determinant, perhaps the adjacent thymidylate stretch, functions in the regulation of mitochondrial DNA replication.      

Detection of MET mRNA in gastric cancer in situ. Comparison with immunohistochemistry and sandwich immunoassays

Determination of predictive biomarkers by immunohistochemistry (IHC) relies on antibodies with high selectivity. RNA in situ hybridization (RNA ISH) may be used to confirm IHC and may potentially replace it if suitable antibodies are not available or are insufficiently selective to discriminate closely related protein isoforms. We validated RNA ISH as specificity control for IHC and as a potential alternative method for selecting patients for treatment with MET inhibitors. MET, the HGF receptor, is encoded by the MET proto-oncogene that may be activated by mutation or amplification. MET expression and activity were tested in a panel of control cell lines. MET could be detected in formalin fixed paraffin, embedded (FFPE) samples by IHC and RNA ISH, and this was confirmed by sandwich immunoassays of fresh frozen samples. Gastric cancer cell lines with high MET expression and phosphorylation of tyrosine-1349 respond to the MET inhibitor, BAY-853474. High expression and phosphorylation of MET is a predictive biomarker for response to MET inhibitors. We then analyzed MET expression and activity in a matched set of FFPE vs. fresh frozen tumor samples consisting of 20 cases of gastric cancer. Two of 20 clinical samples investigated exhibited high MET expression with RNA ISH and IHC. Both cases were shown by sandwich immunoassays to exhibits strong functional activity. Expression levels and functional activity in these two cases were in a range that predicted response to treatment. Our findings indicate that owing to its high selectivity, RNA ISH can be used to confirm findings obtained by IHC and potentially may replace IHC for certain targets if no suitable antibodies are available. RNA ISH is a valid platform for testing predictive biomarkers for patient selection.     

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D''. Estimates of D'' from the two approaches were in close agreement (r = 0.91). The mean estimates of D'' for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (~37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.     

Assessment of antioxidant activities in roots of Miswak (Salvadora persica) plants grown at two different locations in Saudi Arabia

Traditionally, in Middle Eastern countries, many cultures use chewing sticks of arak for medicinal purposes especially, for oral cleanliness care. It was used by Muslims for treatment of teeth and highly recommended to be used by Muslims during the whole day. Therefore, the present work aimed to determine the total phenolic content and total flavonoids in two Miswak extracts obtained from arak roots collected from two different localities in Saudi Arabia. They were extracted with aqueous ethanol (80%) and used to estimate in vitro their antioxidative abilities. The new findings showed that the two tested extracts contained significantly different amounts of both total phenolic content and total flavonoids. According to the increase of total phenolic contents and total flavonoids obtained from the two extracts, Miswak collected from the southern region was found to contain more contents than those collected from the middle region. The results of antioxidant activities of Miswak root extract obtained by using different in vitro methods were varied depending on the technique used. According to the malondialdehyde (MDA) method, hydrogen peroxide (H₂O₂) scavenging ability and 1,1-diphenyl-2-picrylhydrazyl (DPPH) methods, the two Miswak extracts exhibited to have high to very high antioxidant activities. Mostly, the values of antioxidant activities of Southern region have been shown to be always the highest.     

Effects of elevated CO2 and O3 on the rate and duration of grain growth and harvest index in spring wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) cv. Minaret was grown in open-top chambers (OTCs) in 1995 and 1996 under three carbon dioxide (CO₂) and two ozone (O₃) levels. Plants were harvested regularly between anthesis and maturity to examine the rate of grain growth (dG/dt; mg d^–1) and the rate of increase in harvest index (dHI/dt;% d^–1). The duration of grain filling was not affected by elevated CO₂ or O₃, but was 12 days shorter in 1995, when the daily mean temperature was over 3 °C higher than in 1996. Season-long exposure to elevated CO₂ (680 μmol mol^–1) significantly increased the rate of grain growth in both years and mean grain weight at maturity (MGW) was up to 11% higher than in the chambered ambient air control (chAA; 383 μmol mol^–1). However, the increase in final yield obtained under elevated CO₂ relative to the chAA control in 1996 resulted primarily from a 27% increase in grain number per unit ground area. dG/dt was significantly reduced by elevated O₃ under ambient CO₂ conditions in 1995, but final grain yield was not affected because of a concurrent increase in grain number. Neither dG/dt nor dHI/dt were affected by the higher mean O₃ concentrations applied in 1996 (77 vs. 66 nmol mol^–1); the differing effects of O₃ on grain growth in 1995 and 1996 observed in both the ambient and elevated CO₂ treatments may reflect the contrasting temperature environments experienced. Grain yield was nevetheless reduced under elevated O₃ in 1996, primarily because of a substantial decrease in grain number. The data obtained show that, although exposure to elevated CO₂ and O₃ individually or in combination may affect both dG/dt and dHI/dt, the presence of elevated CO₂ does not protect against substantial O₃-induced yield losses resulting from its direct deleterious impact on reproductive processes. The implications of these results for food production under future climatic conditions are considered.     

Defining leaf area index for non-flat leaves

To eliminate the confusion in the definition of leaf area index (L) for non-flat leaves, the projection coefficients of several objects including spheres, cylinders, hemicircular cylinders, and triangular and square bars are investigated through mathematical derivation and numerical calculation for a range of ellipsoidal angular distributions. It is shown that the projection coefficient calculated based on half the total intercepting area is close to a constant of 0.5 when the inclination angle of the objects is randomly (spherically) distributed, whereas the calculated results based on the object's largest projected area are strongly dependent on the shape of the objects. Therefore, it is suggested that the leaf area index of non-flat leaves be defined as half the total intercepting area per unit ground surface area and that the definition of L based on the projected leaf area be abandoned.     

Contrasting evolutionary rates in the duplicate chaperonin genes of Mycobacterium tuberculosis and M. leprae

A phylogenetic analysis of chaperonin (heat shock protein 60) sequences from prokaryotes and eukaryotes indicated that a single gene duplication event in the common ancestor of Mycobacterium tuberculosis, M. leprae, and Streptomyces albus gave rise to the duplicate chaperonin genes found in these species (designated HSP65 and GroEL in the mycobacterial species). Comparison of rates of synonymous and nonsynonymous nucleotide substitution in different gene regions suggested that the 5' end of the HSP65 gene was homogenized by an ancient recombination event between M. tuberculosis and M. leprae. In S. albus, the two duplicated chaperonin genes have evolved at essentially the same rate. In both M. tuberculosis and M. leprae, however, the GroEL gene has evolved considerably more rapidly at nonsynonymous nucleotide sites than has the HSP65 gene. Because this difference is not seen at synonymous sites, it must be due to a difference in selective constraint on the proteins encoded by the two genes, rather than to a difference in mutation rate. The difference between GroEL and HSP65 is striking in regions containing epitopes recognized by T cells of the vertebrate host; in certain cross-reactive epitopes conserved across all organisms, nonsynonymous sites in GroEL have evolved twice as fast as those in HSP65. It is suggested that these differences are correlated with differences in the way in which the duplicate chaperonins of M. tuberculosis and M. leprae interact with the host immune system.