Bacterial Diversity Assessment In Soil Of An Active Brazilian Copper Mine Using High-throughput Sequencing Of 16s Rdna Amplicons

Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.1065879890Altimira, F., Yáñez, C., Bravo, G., González, M., Rojas, L.A., Seeger, M., Characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central Chile (2012) BMC Microbiol, 12, p. 193. , PID: 22950448, COI: 1:CAS:528:DC%2BC3sXjsFWitg%3D%3DAlvarez, A., Benimeli, C.S., Saez, J.M., Fuentes, M.S., Cuozzo, S.A., Polti, M.A., Amoroso, M.J., Bacterial bio-resources for remediation of hexachlorocyclohexane (2012) Int J Mol Sci, 13, pp. 15086-15106. , PID: 23203113, COI: 1:CAS:528:DC%2BC38XhvVequr3KBaker, B.J., Banfield, J.F., Microbial communities in acid mine drainage (2003) FEMS Microbiol Ecol, 44, pp. 139-152. , PID: 19719632, COI: 1:CAS:528:DC%2BD3sXjtFWku7c%3DBaraniecki, C.A., Aislabie, J., Foght, J.M., Characterization of Sphingomonas sp. 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Les zones côtières et le droit communautaire

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments. © 2014 Pereira et al

Comparative Metagenomic Analysis Of Coral Microbial Communities Using A Reference-independent Approach

By comparing the SEED and Pfam functional profiles of metagenomes of two Brazilian coral species with 29 datasets that are publicly available, we were able to identify some functions, such as protein secretion systems, that are overrepresented in the metagenomes of corals and may play a role in the establishment and maintenance of bacteria-coral associations. However, only a small percentage of the reads of these metagenomes could be annotated by these reference databases, which may lead to a strong bias in the comparative studies. For this reason, we have searched for identical sequences (99% of nucleotide identity) among these metagenomes in order to perform a reference-independent comparative analysis, and we were able to identify groups of microbial communities that may be under similar selective pressures. The identification of sequences shared among the metagenomes was found to be even better for the identification of groups of communities with similar niche requirements than the traditional analysis of functional profiles. 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Characterization Of The Storage Protein In Seed Of Coix Lacryma-jobi Var. Adlay

The endosperm of seed of Coix lacryma-jobi var. Adlay contains ca. 20% protein distributed between fraction 1 (albumins and globulins), fraction 2 (prolamins), and fraction 3 (residual proteins) extracts. The major component is prolamin, known as coixin, the amount of which ranged from 8.4% to 78.7% of the total endosperm protein depending upon the concentration of 2-mercaptoethanol in the extraction solvent. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis separated coixin into five components with molecular weights of 27K (C1), 25K (C2), 22K (C3), 17.5K (C4), and 15K (C5). Isoelectric focusing (IEF) of coixin resolved seven major protein bands. Analysis of the individual IEF bands by SDS-PAGE and immunoblotting, using rabbit antibodies raised against C2 and C3, indicated an even greater complexity, with a total of 17 proteins being detected. Amino acid analysis revealed that protein fractions from Coix endosperm have the typical composition of Panicoideae endosperm. The predominant fraction, coixin, is rich in proline and leucine and poor in lysine. © 1990 American Chemical Society.38363163

Fourier Transform Infrared Microspectroscopy As A Bacterial Source Tracking Tool To Discriminate Fecal E. Coli Strains

The aim of this work was to use the FT-IR microspectroscopy technique, a union of a FT-IR spectrometer with a microscope, to discriminate fecal Escherichia coli strains from cows, chickens and humans and to compare the efficiency of this method with the genomic fingerprinting method, BOX-PCR. The obtained BOX-PCR profiles were able to correctly discriminate 93.75% of the chicken strains, 80% of the cow strains and 65% of the human strains. An efficient PLS-DA model was developed, using orthogonal signal correction and the second derivate of the FT-IR spectra. This model allowed the correct discrimination, according to the animal source, of all the E. coli strains analyzed. The bands in the FT-IR spectra that were responsible for the strains discrimination were in the region between 2816 and 3026cm -1 wavenumber, described as fatty acids. It was demonstrated that FT-IR microspectroscopy can be a suitable tool for fecal E. coli discrimination, because it is fast, easy to carry out and presents a flexible discrimination power. © 2011 Elsevier B.V.9911519Leclerc, H., Mossel, D.A.A., Edberg, S.C., Struijk, C.B., Advances in the bacteriology of the coliform group: their suitability as markers of microbial water safety (2001) Annu. Rev. Microbiol., 55, pp. 201-234(2004) Microbial Source Tracking Guide Document, , EPA Office of Water, Washington, U.S.Environmental Protection AgencyMeays, C.L., Broersma, K., Nordin, R., Mazumder, A., Source tracking fecal bacteria in water: a critical review of current methods (2004) J. Environ. Manage., 73, pp. 71-79Jiang, S.C., Chu, W., Olson, B.H., He, J.W., Choi, S., Zhang, J., Le, J.Y., Gedalanga, P.B., Microbial source tracking in a small southern California urban watershed indicates wild animals and growth as the source of fecal bacteria (2007) Appl. Microbiol. Biotechnol., 76, pp. 927-934Price, B., Venso, E., Frana, M., Greenberg, J., Ware, A., A comparison of ARA and DNA data for microbial source tracking based on source-classification models developed using classification trees (2007) Water Res., 16, pp. 3575-3584Harwood, V.J., Wiggins, B., Hagedorn, C., Ellender, R.D., Gooch, J., Kern, J., Samadpour, M., Robinson, B.J., Phenotypic library-based microbial source tracking methods: efficacy in the California collaborative study (2003) J. Water Health, 1, pp. 153-166Moussa, S.H., Massengale, R.D., Identification of the sources of Escherichia coli in a watershed using carbon-utilization patterns and composite data sets (2008) J. Water Health, 6, pp. 197-207Siegrist, T.J., Anderson, P.D., Huen, W.H., Kleinheinz, G.T., McDermott, C.M., Sandrin, T.R., Discrimination and characterization of environmental strains of Escherichia coli by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) (2007) J. Microbiol. Meth., 68, pp. 554-562Parveen, S., Portier, K.M., Robinson, K., Edmiston, L., Tamplin, M.L., Discriminant analysis of ribotype profiles of Escherichia coli for differentiating human and nonhuman sources of fecal pollution (1999) Appl. Environ. Microbiol., 65, pp. 3142-3147Nelson, M., Jones, S.H., Edwards, C., Ellis, J.C., Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping (2008) Dis. Aquat. Organ., 81, pp. 53-63Casarez, E.A., Pillai, S.D., Mott, J.B., Vargas, M., Dean, K.E., Di Giovanni, G.D., Direct comparison of four bacterial source tracking methods and use of composite data sets (2007) J. Appl. Microbiol., 103, pp. 350-364D'Edlia, T.V., Cooper, C.R., Johnston, C.G., Source tracking of Escherichia coli by 16S-23S intergenic spacer region denaturing gradient gel electrophoresis (DGGE) of the rrnB ribosomal operon (2007) Can. J. Microbiol., 53, pp. 1174-1184Dombek, P.E., Johnson, L.K., Zimmerley, S.T., Sadowsky, M.J., Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources (2000) Appl. Environ. Microbiol., 66, pp. 2572-2577Mohapatra, B.R., Broersma, K., Nordin, R., Mazumder, A., Evaluation of repetitive extragenic palindromic-PCR for discrimination of fecal Escherichia coli from humans, and different domestic- and wild-animals (2007) Microbiol. Immunol., 51, pp. 733-740Versalovic, J., Koeuth, T., Lupski, J.R., Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes (1991) Nucleic Acids Res., 19, pp. 6823-6831Vesalovic, J., Schneider, M., de Bruijn, F.J., Lupski, L.R., Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction (1994) Meth. Mol. Cell. Biol., 5, pp. 25-40Mohapatra, B.R., Mazumder, A., Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments (2008) Water Sci. Technol., 58, pp. 537-547Naumann, D., Helm, D., Labischinski, H., Microbiological characterizations by FT-IR spectroscopy (1991) Nature, 351, pp. 81-82Mouwen, D.J.M., Weijtens, M.J.B.M., Capita, R., Alonso-Calleja, C., Prieto, M., Discrimination of enterobacterial repetitive intergenic consensus PCR types of Campylobacter coli and Campylobacter jejuni by Fourier transform infrared spectroscopy (2005) Appl. Environ. Microbiol., 71, pp. 4318-4324Gilbert, M.K., Frick, C., Wodowski, A., Vogt, F., Spectroscopy imaging for detection and discrimination of different E. coli strains (2009) Appl. Spectrosc., 63, pp. 6-13Clarke, F.C., Hammond, S.V., Jee, R.D., Moffat, A.C., Determination of the information depth and sample size for the analysis of pharmaceutical materials using reflectance near-infrared microscopy (2002) Appl. Spectrosc., 56, p. 1475Gomes, T.A.T., Vieira, M.A.M., Abe, C.A., Rodrigues, D., Griffin, P.M., Ramos, S.R.T.S., Adherence patterns and adherence-related DNA sequences in Escherichia coli isolates from children with and without diarrhea in São Paulo City, Brazil (1998) J. Clin. Microbiol., 36, pp. 3609-3613Vicente, H.I.G., Amaral, L.A., Cerqueira, A.M.F., Shigatoxigenic Escherichia coli serogroup O157, O111 and O113 in feces, water and milk samples from dairy farms (2005) Braz. J. Microbiol., 36, pp. 217-222Silveira, W.D., Ferreira, A., Brocchi, M., Hollanda, L.M., Castro, A.F.P., Yamada, A.T., Lancelloti, M., Biological characteristics and pathogenicity of avian Escherichia coli strains (2002) Vet. 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Phylogenetic Group Distribution Among Escherichia Coli Isolated From Rivers In São Paulo State, Brazil

The phylogenetic group distribution of Escherichia coli strains isolated from the Sorocaba and Jaguari Rivers located in the State of São Paulo, Brazil, is described. E. coli strains from group D were found in both rivers while one strain from group B2 was isolated from the Sorocaba river. These two groups often include strains that can cause extraintestinal diseases. Most of the strains analyzed were allocated into the phylogenetic groups A and B1, supporting the hypothesis that strains from these phylogenetic groups are more abundant in tropical areas. Though both rivers are located in urbanized and industrialized areas where the main source of water pollution is considered to derive from domestic sewage, our results suggest that the major sources of contamination in the sampling sites of both rivers might have originated from animals and not humans. © 2008 Springer Science+Business Media B.V.24815731577Carson, C.A., Shear, B.L., Ellersieck, M.R., Schnell, J.D., Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals (2003) Appl Environ Microbiol, 69, pp. 1836-1839. , 3(2004) Relatório de Qualidade de Águas Interiores Do Estado de São Paulo - 2003, , http://www.cetesb.sp.gov.br, CETESB, São PauloClermont, O., Bonacorsi, S., Bingen, E., Rapid and simple determination of the Escherichia coli phylogenetic group (2000) Appl Environ Microbiol, 66, pp. 4555-4558. , 10Dixit, S.M., Gordon, D.M., Wu, X.Y., Chapman, T., Kailasapathy, K., Chin, J.J.C., Diversity 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Heterogeneity Of Coix, Maize, And Teosinte Prolamins Detected By Isoelectric Focusing

The prolamins of maize, teosinte, and Coix strains were extracted and analysed by isoelectric focusing. Each strain analysed showed a distinct prolamin profile. The extensive charge heterogeneity observed in the Coix profiles suggests that multiple genes encode for the prolamins, as previously reported for maize and teosinte prolamins. Among the prolamin bands that characterize the maize genotypes, a group of four bands with pI between 6.55 and 6.27 and a band with pI 5.56 were found in every maize strain. Some of the teosinte strains analysed also had bands distributed in the pI range of 6.55 to 6.27. The band with pI 5.56 was observed in every teosinte strain analysed. Based on the observed homologies, it can be inferred that the isoelectric focusing profiles of the maize strains are more homologous to the profiles of teosintes than to those of Coix.13231332

The Effects Of Copper Ions On The Synthesis Of Periplasmic And Membrane Proteins In Acidithiobacillus Ferrooxidans As Analyzed By Sds-page And 2d-page

The effects of 200 mM copper ions on the synthesis of membrane and periplasmic proteins were investigated in iron-grown cells of Acidithiobacillus ferrooxidans (At. ferrooxidans). Total membrane protein profiles of cells grown in the absence of copper ions (unadapted cells) and in the presence of copper ions (copper-adapted cells) were compared by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Crude preparations of outer membrane and periplasmic proteins were analyzed by SDS-PAGE. The synthesis of proteins was diminished or increased in the presence of copper ions. Low molecular weight proteins (<14 kDa) were significantly repressed by copper. These proteins are probably acidic proteins located in the outer membrane. An over-expression of a periplasmic protein of about 17 kDa was detected in the copper-adapted cells and was assumed to be rusticyanin, a 16.5-kDa periplasmic copper protein present in At. ferrooxidans cells and involved in the electron-transport chain of the iron oxidation pathway. To our knowledge, this is the first report of a possible involvement of the rusticyanin and outer membrane proteins in the mechanism of copper resistance in At. ferrooxidans. © 2003 Elsevier B.V. All rights reserved.7101/02/15165171Achouak, W., Heulin, T., Pagès, J.M., Multiple facets of bacterial porins (2001) FEMS Microbiol. Lett., 199, pp. 1-7Amaro, A.M., Chamorro, D., Seeger, M., Arredondo, R., Peirano, I., Jerez, C.A., Effect of external pH perturbations on in vivo protein synthesis by the acidophilic bacteria Thiobacillus ferrooxidans (1991) J. Bacteriol., 173, pp. 910-915Benz, R., Structure and function of porins from Gram-negative bacteria (1988) Ann. Rev. Microbiol., 42, pp. 359-393Booth, B.R., Curtis, N.A.C., Separation of the cytoplasmic and outer membrane of Pseudomonas aeruginosa PAO1 (1977) Biochem. Biophys. Res. Commun., 74, pp. 1168-1176Bradford, M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding (1976) Anal. Biochem., 72, pp. 248-254Brierley, J.A., Brierley, C.L., Present and future commercial applications of biohydrometallurgy (1999) Biohydrometallurgy and the Environment Toward the Mining of the 21st Century, (PART A), pp. 81-90. , R. Amils, & A. Ballester. Amsterdam: ElsevierButcher, B.G., Deane, S.M., Rawlings, D.E., The chromosomal arsenic resistance genes of Thiobacillus ferrooxidans have unusual arrangement and confer increased arsenic and antimony resistance to Escherichia coli (2000) Appl. Environ. Microbiol., 66, pp. 1826-1833Cha, J.S., Cooksey, D.A., Copper resistance in Pseudomonas syringae mediated by periplasmic and outer membrane proteins (1991) Proc. Natl. Acad. Sci., 88, pp. 8915-8919Cox, J.C., Boxer, D.H., The purification and some properties of rusticyanin, a blue copper protein involved in iron (II) oxidation from T. ferrooxidans (1978) Biochem. J., 174, pp. 497-502Das, A., Modak, J.M., Natarajan, K.A., Surface chemical studies of Thiobacillus ferrooxidans with reference to copper tolerance (1998) Antonie van Leeuwenhoek, 73, pp. 215-222De Mot, R., Vanderleyden, J., Application of two-dimensional protein analysis for strain fingerprinting and mutant analysis of Azospirillum species (1989) Can. J. Microbiol., 35, pp. 960-967Garcia O., Jr., Isolation and purification of Thiobacillus ferrooxidans and Thiobacillus thiooxidans from some coal and uranium mines of Brazil (1991) Rev. Microbiol., 22, pp. 1-6De, G.C., Oliver, D.J., Pesic, B.M., Effect of heavy metals on the ferrous iron oxidizing ability of Thiobacillus ferrooxidans (1997) Hydrometallurgy, 44, pp. 53-63Holmes, D.S., Barreto, M., Valdes, J., Dominguez, C., Arriagada, C., Silver, S., Bueno, S., Jedlicki, E., Whole genome sequence of Acidithiobacillus ferrooxidans: Metabolic reconstruction, heavy metal resistance and other characteristics (2001) Proceedings of the International Biohydrometallurgy Symposium, (PART A), pp. 237-251. , V.S.T. Ciminelli, & O. Jr. Garcia. Biohydrometallurgy: Fundamentals, Technology and Sustainable Development. Amsterdam: ElsevierJerez, C.A., Seeger, M., Amaro, A.M., Phosphate starvation affects the synthesis of outer membrane proteins in Thiobacillus ferrooxidans (1992) FEMS Microbiol. Lett., 98, pp. 29-34Kelly, D.P., Wood, A.P., Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov (2000) Int. J. Syst. Evol. Microbiol., 50, pp. 511-516Laemmli, U.K., Cleavage of structural proteins during the assembly of the head of bacteriophage T4 (1970) Nature, 227, pp. 680-685Leduc, L.G., Ferroni, G.D., Trevors, J.T., Resistance to heavy metals in different strains of Thiobacillus ferrooxidans (1997) World J. Microbiol. Biotechnol., 13, pp. 453-455Li, X.Z., Nikaido, H., Williams, K.E., Silver-resistant mutants of Escherichia coli display active efflux of Ag+ and are deficient in porins (1997) J. Bacteriol., 179, pp. 6127-6132Lutkenhaus, J.F., Role of a major outer membrane protein in Escherichia coli (1977) J. Bacteriol., 131, pp. 631-637McCready, R.G.L., Gould, W.D., Bioleaching of uranium (1990) Microbial Mineral Recovery, pp. 107-126. , H.L. Ehrlich, & C.L. Brierley. New York: McGraw-HillNovo, M.T.M., Da Silva, A.C., Moreto, R., Cabral, P.C.P., Costacurta, A., Garcia O., Jr., Ottoboni, L.M.M., Thiobacillus ferrooxidans response to copper and other heavy metals: Growth, protein synthesis and protein phosphorylation (2000) Antonie van Leeuwenhoek, 77, pp. 187-195Nyashanu, R.M., Monhemius, A.J., Buchanan, D.L., The effect of ore mineralogy on the speciation of arsenic in bacterial oxidation of refractory arsenical gold ores (1999) Biohydrometallurgy and the Environment Toward the Mining of the 21st Century, (PART A), pp. 431-442. , R. Amils, & A. Ballester. Amsterdam: ElsevierPugsley, A.P., Schnaitman, C.A., Outer membrane proteins of Escherichia coli: VII. Evidence that bacteriophage-directed protein 2 functions as a pore (1978) J. Bacteriol., 133, pp. 1181-1189Rawlings, D.E., The molecular genetics of Thiobacillus ferrooxidans and other mesophilic, acidophilic, chemolithotrophic, iron- or sulfur-oxidizing bacteria (2001) Hydrometallurgy, 59, pp. 187-201Shiratori, T., Inoue, C., Sugawara, K., Kusano, T., Kitagawa, Y., Cloning and expression of Thiobacillus ferrooxidans mercury ion resistance genes in Escherichia coli (1989) J. Bacteriol., 171, pp. 3458-3464Sugio, T., Kuwano, H., Negishi, A., Maeda, T., Takeuchi, F., Kamimura, K., Mechanism of growth inhibition by tungsten in Acidthiobacillus ferrooxidans (2001) Biosci. Biotechnol. Biochem., 65, pp. 555-562Tuovinen, O.H., Kelly, D.P., Studies on the growth of Thiobacillus ferrooxidans: I. Use of membrane filters and ferrous iron agar to determine viable number and comparison with 14CO2 fixation and iron oxidation as measures of growth (1973) Arch. Microbiol., 88, pp. 285-298Van der Westen, H.M., Mayhew, S.G., Veeger, C., Separation of hydrogenase from intact cells from Desulfovibrio vulgaris (1978) FEBS Lett., 86, pp. 122-126Yarzábal, A., Brasseur, G., Ratouchniak, J., Lund, K., Lemes le-Meunier, D., DeMoss, J.A., Bonnefoy, V., The high molecular weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein (2002) J. Bacteriol., 184, pp. 313-31

Social Network Analysis Metrics And Their Application In Microbiological Network Studies

In the last decade, several researchers have been using interaction networks resources to investigate of the role of biologic interactions in biodiversity maintenance. The conceptual foundations are the same as in Social Networks (such as Facebook), that have brought a set of metrics to study the network structure and the function of each node in the network. Thus, the aim of this work was to assess the application of Social Network Analysis (SNA) concepts and metrics in microbiological interaction networks, to identify patterns of cohesive subgroups, besides discovering new knowledge regarding the underlying structure of subgroups. We built a bipartite microbiological interaction database containing frequency of phylogenetic subgroups in water bodies and applied the following SNA metrics: dependence distribution, strength, betweenness centrality and clique. The sna package for the R program, Pajek, Dieta and Ucinet programs were the tools used. Among the results, we found that SNA concepts and metrics are extremely useful in microbiological studies to understand the correlation between each node in the network (the generalist and the predominant nodes), as well as to analyze the co-occurrence pattern of microorganisms in the network (cohesive subgroups). © 2014 Springer International Publishing Switzerland.549251260Araújo, M.S., Guimarães, P.R., Svanbäck, R., Pinheiro, A., Guimarães, P., Reis, S.F., Bol-Nick, D.I., Network analysis reveals contrasting effects of intraspecific competition on indi-vidual vs. Population diets (2008) Ecology, 89, pp. 1981-1993Bapteste, E., Bicep, C., Lopez, P., Evolution of genetic diversity using networks: The human gut microbiome as a case study (2012) Clin. Microbiol. Infect., 18, pp. 40-43Bascompte, J., Jordano, P., Plant-animal mutualistic networks: The architecture of biodiversity (2007) Annu. Rev. Ecol. Evol. Syst., 38, pp. 567-593Batagelj, V., Mrvar, A., Pajek - Program for large network analysis (1998) Connections, 21, pp. 47-57Blüthgen, N., Fründ, J., Vázquez, D.P., Menzel, F., What do interaction network metrics tell us about specialization and biological traits (2008) Ecology, 89, pp. 3387-3399. , http://dx.doi.org/10.1890/07-2121.1Borgatti, S.P., Everett, M.G., Freeman, L.C., (1999) UCINET 5 for Windows: Software for Social Network Analysis (USER'S GUIDE), , http://www.analytictech.com/ucinet6/Ucinet_Guide.doc, (accessed in November 15, 2012)Borgatti, S.P., Everett, M.G., Freeman, L.C., (2002) Ucinet for Windows: Software for Social Network Analysis, , Analytic Technologies, HarvardButts, C.T., Social Network Analysis with sna (2008) Journal of Statistical Software, 24, pp. 1-51Carlos, C., Pires, M.M., Stoppe, N.C., Hachich, E.M., Sato, M.I.Z., Gomes, T.A.T., Amaral, L.A., Ottoboni, L.M.M., Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination (2010) BMC Microbiol., 10, p. 161Chen, M., Cho, J., Zhao, H., Incorporating biological pathways via a Markov random field model in genome-wide association studies (2011) PLoS Genet., 7, pp. e1001353Clermont, O., Bonacorsi, S., Bingen, E., Rapid and simple determination of the Escherichia coli phylogenetic group (2000) Appl. Environ. Microbiol., 66, pp. 4555-4558Escobar-Páramo, P., Grenet, K., Lemenac'h, A., Rode, L., Salgado, E., Amorin, C., Gouriou, S., Ruimy, R., Largescale population structure of human commensal Escherichia coli isolates (2004) Appl. Environ. Micro-Biol., 70, pp. 5698-5700Freeman, L.C., Centrality in social networks: Conceptual clarification (1979) Social Networks, 1 (3), pp. 215-239Hagedorn, C., Blanch, A.R., Harwood, V.J., (2011) Microbial Source Tracking: Methods, Application, and Case Studies, p. 642. , Springer, New YorkHanneman, R.A., Riddle, M., (2005) Introduction to Social Network Methods, , http://faculty.ucr.edu/~hanneman/, University of California, Riverside, Riverside, CA, published in digital form atHansen, D.L., Shneiderman, B., Smith, M.A., (2011) Analysing Social Media Networks with NodeXL: Insights from A Connected World, p. 284. , Morgan Kaufmann, AmsterdanJordano, P., Patterns of mutualistic interactions in pollination and seed dispersal: Connec- tance, dependence asymmetries, and coevolution (1987) American Naturalist, 129, pp. 657-677Jordano, P., Vázquez, D., Bascompte, J., Redes complejas de interacciones mutualistas planta-animal (2009) Ecología y Evolución de Interacciones Planta-Animal, pp. 17-41. , Mendel, R., Aizen, M.A., Zamora, R. (eds.) 1a ed., Universitaria, Santiago de ChileJostins, L., Ripke, S., Weersma, R.K., Duerr, R.H., McGovern, D.P., Hui, K.Y., Lee, J.C., Sharma, Y., Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease (2012) Nature, 491, pp. 119-124Kumar, K., Novak, J., Tomkins, A., Structure and evolution of online social networks (2006) Proc. of ACM SIGKDD Intl. Conf. of Knowledge Discovery and Data Mining, pp. 611-617. , New YorkLee, J.E., Lee, S., Sung, J., Ko, G.P., Analysis of human and animal fecal microbiota for microbial source tracking (2011) The ISME J., 5, pp. 362-365Ley, R.E., Hamady, M., Lozupone, C., Turnbaough, P.J., Ramey, R.R., Bircher, S., Schlegel, M., Gordon, J.I., Evolution of mammals and their gut microbes (2008) Science, 320, pp. 1647-1651Mello, M.A.R., (2013) Guia Para Análise de Redes Ecológicas, , http://marcomello.casadosmorcegos.org/Redes.html, Version March 3 (accessed in April 1, 2013)Nooy, W., Mrvar, A., Batagelj, V., (2005) Exploratory Network Analysis with Pajek, p. 334. , Cambridge University PressRoesch, L.F.W., Fulthorpe, R.R., Pereira, A.B., Pereira, C.K., Lemos, J.N., Barbosa, A.D., Suleiman, A.K.A., Costa, E.M., Soil bacteria community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica (2012) Appl. Soil Ecol., 61, pp. 7-15Scott, J., (2000) Social Network Analysis: A Handbook, , 2nd edn Sage, LondonStoppe, N.C., Silva, J.S., Torres, T.T., Carlos, C., Hachich, E.M., Sato, M.I.Z., Saraiva, A.M., Ottoboni, L.M.M., Clustering of water bodies in unpolluted and polluted environments based on Escherichia coli phylogroup abundance using a simple interaction database BMC Microbiology, , unpublishedVázquez, D.P., Morris, W.F., Jordano, P., Interaction frequency as a surrogate for the total effect of animal mutualists on plants (2005) Ecology Letters, 8, pp. 1088-1094Vázquez, D.P., Blüthgen, N., Cagnolo, L., Chacoff, N.P., Uniting pattern and process in plant-animal mutualistic networks: A review (2009) Annals of Botany, 103, pp. 1445-1457Wootton, J.T., Emmerson, M., Measurement of interaction strength in nature (2005) Annual Review of Ecology, Evolution and Systematics, 36, pp. 419-444Yamada, T., Bork, P., Evolution of biomolecular networks - Lessons from metabolic and protein interactions (2009) Nature Rev. Mol. Cell Biol., 10, pp. 791-80

Synthesis And Deposition Of Coixin In Seeds Of Coix Lacryma-jobi

The synthesis and assembly of prolamins into protein bodies of Coix lacryma-jobi seeds were investigated. Coixins, the Coix prolamins, are grouped into two distinct classes namely α- and γ-coixins. Alpha-coixins are constituted by four size classes, while γ-coixins comprise only one molecular weight class. SDS-PAGE and western blot analysis of prolamins extracted from endosperm during seed development showed that α-coixins are synthesized at earlier developmental stages than γ-coixin. In vitro translation of polysomal RNA attached to protein bodies isolated from mid-maturation endosperm showed that these polyribosomes are highly enriched in coixin messages. Polysomal RNAs isolated from all developmental stages were electrophoresed and probed with cDNA clones representing α- and γ-coixins. The results confirmed the earlier expression of α-coixins and also demonstrated that coixin RNA accumulation in the endosperm occurs mainly at seed mid maturation. Protein bodies isolated from immature endosperm contained all coixin components as determined by SDS-PAGE and western blot analyses. Immunocytochemical analysis by electron and light microscopy revealed that the coixin components are spread all over the protein bodies. The protein bodies are localized in the starchy endosperm cells filling the spaces left by the starch granules. They are surrounded by continuous membranes and are larger than the protein bodies described for maize. © 1992.832169180Osborne, Our present knowledge of plant proteins (1908) Science, 28, pp. 417-427Miflin, Shewry, The biology and biochemistry of cereal seed prolamins (1979) Seed Protein Improvement in Cereals and Grain Legumes, 1, pp. 137-158. , 3rd edn, IAEA, ViennaLarkins, Seed storage proteins: characterization and biosynthesis (1981) The Biochemistry of Plants, 6, pp. 449-489. , 3rd edn, P.K. Stumpf, E.E. Conn, Academic, New YorkKhoo, Wolf, Origin and development of protein granules in maize endosperm (1970) American Journal of Botany, 57, pp. 1042-1050Burr, Burr, Zein synthesis in maize endosperm by polyribosomes attached to protein bodies (1976) Proc. Natl. Acad. Sci. U.S.A., 73, pp. 515-519. , 3rd ednLarkins, Hurkman, Synthesis and deposition of zein in protein bodies of maize endosperm (1978) PLANT PHYSIOLOGY, 62, pp. 256-263Pernollet, The protein bodies of seeds: ultrastructure, biochemistry, biosynthesis and degradation (1978) Phytochemistry, 17, pp. 1473-1480Marks, Lindell, Larkins, Quantitative analysis of the accumulation of zein mRNA during maize endosperm development (1985) J. Biol. Chem., 260, pp. 16445-16450Clayton, The awnless species of Andropogoneae (1973) Kew Bulletin, 28, pp. 49-58Clayton, Notes on tribe Andropogoneae (Gramineae) (1983) Kew Bulletin, 35, pp. 813-818Jain, Banerjee, Preliminary observations on the ethnobotany of the genus Coix (1974) Econ. Bot., 28, pp. 38-42Arora, Job's tears (Coix lacryma-jobi) — a minor food and fooder crop from North Eastern India (1977) Econ. Bot., 31, pp. 358-366Shaaffhausen, Adlay or Job's tears — a cereal of potentially greater economic importance (1952) Economic Botany, 6, pp. 216-227Raimo, Leme, Contribuiçao para o estudo dos substitutos do farelo de trigo na alimentaçao das aves: I cereal Adlay (1950) Bot. Ind. Anim., 11, pp. 85-89Torres, Bergamin, O cereal do Adlay Estudo de seu valor agricola e nutricional para aves (1951) Anais da Escola Superior de Agricultura Luiz de Queiroz, 8, pp. 669-685Venkateswarlu, Chaganti, Job's Tears (Coix lacryma-jobi L.) (1973) ICAR Tech. Bull. (Agric.), 43-44, pp. 1-54Ottoboni, Leite, Targon, Crozier, Arruda, Characterization of the storage protein in seed of Coix lacryma-jobi var Adlay Journal of Agricultural and Food Chemistry, 38, pp. 631-635Leite, Ottoboni, Targon, Silva, Turcinelli, Arruda, Phylogenetic relationship of zeins and coixins as determined by immunological cross-reactivity and Southern blot analysis (1990) Plant Molecular Biology, 14, pp. 734-751Ottoboni, Leite, Targon, Silva, Arruda, Heterogeneity of Coix, maize and teosinte prolamins detected by isoelectric focusing (1990) Rev. Bras. Genet., 13, pp. 313-322Laemmli, Cleavage of structural proteins during the assembly of the head of bacteriophage T4 (1970) Nature, 227, pp. 680-684Naito, Dubé, Beachy, Differential expression of conglycinin α- and β-subunit genes in transgenic plants (1988) Plant Mol. Biol., 11, pp. 109-123Maniatis, Fritsch, Sambrook, (1982) Molecular Cloning: A Laboratory Manual, , 3rd edn, Cold Spring Harbor Laboratory, Cold Spring Harbor, NYMechler, Isolation of messenger RNA from membrane bound polysomes (1987) Methods Enzymol., 152, pp. 241-248Ludevid, Torrent, Martinez-Izquierdo, Puigdomenech, Palau, Subcellular localization of glutenin-2 in maize (Zea mays L.) endosperm (1984) Plant Mol. Biol., 3, pp. 227-234Benner, Phillips, Messing, Genetic analysis of methionine-rich storage protein accumulation in maize (1989) Theor. Appl. Genet., 78, pp. 761-767Burr, Burr, Rubenstein, Simon, Purification and translation of zein messenger RNA from maize endosperm protein bodies (1978) Proc. Natl. Acad. Sci. U.S.A., 75, pp. 696-700. , 3rd ednDonovan, Lee, Longhurst, Cell-free synthesis of wheat prolamins (1982) Australian Journal of Plant Physiology, 9, pp. 59-68Matthews, Miflin, In vitro synthesis of barley storage proteins (1980) Planta, 149, pp. 262-268Torrent, Poca, Campos, Ludevid, Palau, In maize, glutelin-2 and low molecular weight zeins are synthesized by membrane-bound polyribosomes and translocated into microsomal membranes (1986) Plant Mol. Biol., 7, pp. 393-403Brineagar, Paterson, Synthesis of oat globulin precursor Analogy to legume 11S storage protein synthesis (1982) PLANT PHYSIOLOGY, 70, pp. 1767-1769Viotti, Sala, Marotta, Alberi, Balducci, Soave, Genes and mRNAs coding for zein polypeptides in Zea mays (1979) Eur. J. Biochem., 102, pp. 211-222Park, Lewis, Rubenstein, Heterogeneity of zein mRNA and protein in maize (1980) PLANT PHYSIOLOGY, 65, pp. 98-106Pérez-Grau, Cortadas, Puigdomenech, Palau, Accumulation and subcellular localization of glutelin-2 transcripts during maturation of maize endosperm (1986) FEBS Lett., 202, pp. 145-148Taylor, Schussler, Liebonberg, Protein body formation in the starchy endosperm of developing Sorghum bicolor (L.) Moench seeds (1985) S. Afr. J. Bot., 51, pp. 35-40Pernollet, Moose, Structure and location of legume and cereal seed storage proteins (1983) Seed Proteins, pp. 155-191. , J. Daussant, J. Mosse, J. Vaughan, Academic Press, LondonLending, Larkins, Changes in the zein composition of protein bodies during maize endosperm development (1989) Plant Cell, 1, pp. 1011-1023Lending, Chesnut, Shaw, Larkins, Structure of maize protein bodies and immunocytochemical localization of zeins (1988) Protoplasma, 143, pp. 51-62Bechtel, Juliano, Formation of protein bodies in the starchy endosperm of rice (Oryza sativa L.): a reinvestigation (1980) Ann. Bot., 45, pp. 503-509Oparka, Harris, Rice protein body formation: all types are initiated by dilation of the endosplasmic reticulum (1982) Planta, 154, pp. 184-18