The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

Chronic administration of Abarema cochliacarpos attenuates colonic inflammation in rats

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Inflammatory bowel diseases are characterized by a chronic clinical course of relapse and remission associated with self-destructive inflammation of the gastrointestinal tract. Active extracts from plants have emerged as natural potential candidates for its treatment. Abarema cochliacarpos (Gomes) Barneby & Grimes, Fabaceae (Barbatimao), is a native medicinal plant in to Brazil. Previously we have demonstrated in an acute colitis model a marked protective effect of a butanolic extract, so we decided to assess its anti-inflammatory effect in a chronic ulcerative colitis model induced by trinitrobenzensulfonic acid (TNBS). Abarema cochliacarpos (150 mg/day, v.o.) was administered for fourteen consecutive days. This treatment decreased significantly macroscopic damage as compared with TNBS. Histological analysis showed that the extract improved the microscopic structure. Myeloperoxidase activity (MPO) was significantly decreased. Study of cytokines showed that TNF-alpha was diminished and IL-10 level was increased after Abarema cochliacarpos treatment. In order to elucidate inflammatory mechanisms, expression of cyclooxygenase (COX)-2 and nitric oxide synthase (iNOS) were studied showing a significant downregulation. In addition, there was reduction in the JNK and p-38 activation. Finally, I kappa B degradation was blocked by Abarema cochliacarpos treatment being consistent with an up-regulation of the NF-kappaB-binding activity. These results reinforce the anti-inflammatory effects described previously suggesting that Abarema cochliacarpos could provide a source for the search for new anti-inflammatory compounds useful in ulcerative colitis treatment.214680690Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Estadual de Alagoas, BrazilInstituto Federal de Educacao Ciencia e Tecnologia-Sergipe, BrazilCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture

(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

BACKGROUND: The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. RESULTS: We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome. CONCLUSIONS: In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied

Cytology Microarrays

The use of high throughput genetic and expression platforms are generating many candidate diagnostic markers and therapeutic targets for a wide variety of clinical conditions. Tissue microarrays can be used for the evaluation of the utility of many of these markers. However, tissue microarrays can suffer from the limitations associated with sampling and sectioning tissues. We introduce a novel microarray technique based on cell suspensions. Multiple slides can be made, all of which are equally representative of the initial sample. A robotic device was designed that can deposit 60 distinct spots of cytological material on a glass slide. Each spot of cells deposited in this manner may correspond to a unique source. Controlling the number of cells per spot, their distribution within the spot and the size of the spot can be achieved by modifying the viscosity of the cell solution or regulating the amount of fluid deposited. A fully automated analysis of quantitatively stained microarray samples has been performed to quantify the number of cells per spot, the size of spots and the DNA amount per cell in each spot. The reproducibility of these parameters was found to be high

Anti-inflammatory intestinal activity of Abarema cochliacarpos (Gomes) Barneby & Grimes in TNBS colitis model

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Aim of the study To assess the anti-inflammatory effect of butanolic fraction of methanolic extract from bark of Abarema cochliacarpos in acute ulcerative colitis model induced by intracolonic administration of trinitrobenzene sulfonic acid (TNBS) in Wistar rats Materials and methods: Abarema cochliacarpos (100 and 150 mg/kg/day) was administered by gavage 48, 24 and 1 h prior to the induction of colitis with 10 mg/kg of TNBS and, 24 h later Results: Phytochemical studies by mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) revealed that catechins were a major component into condensate class of tannins Treatment with Abarema cochliacarpos decreased significantly macroscopic damage as compared with TNBS (p <0.05) Histological analysis showed that both doses of the extract improved the microscopic structure and preserved some areas of the colonic mucosa structure In addition, myeloperoxidase activity (MPO), as a marker of neutrophil infiltration, was decreased in a dose-dependent way (p < 0 01 and p < 0.001 respectively), TNF-alpha level was also diminished with the highest dose of the extract (p < 0 001) and, IL-10 level obtained no significant results In order to elucidate some of the mechanisms, expression of inducible inflammatory enzymes, such as cyclooxygenase (COX)-2 and nitric oxide synthase (iNOS), were studied showing a significant reduction Finally, the involvement of c-Jun N-terminal kinase (JNK) signalling demonstrated a reduction in the JNK activation with the highest dose (p < 005 vs TNBS) Conclusions We have shown for the first time that the extracts obtained from Abarema cochliacarpos bark possess active substances, which exert marked protective effects in acute experimental colitis, confirming and justifying. at least in part, the popular use of this plant to treat gastrointestinal diseases (C) 2010 Elsevier Ireland Ltd All rights reserved1282467475Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Estadual de Alagoas (UNEAL, Brazil)Institut Federal de Educacao Ciencia e Tecnologia-Sergipe (IFS, Brazil)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Abarema Cochliacarpos Reduces Lps-induced Inflammatory Response In Murine Peritoneal Macrophages Regulating Ros-mapk Signal Pathway

Ethnopharmacological relevance Abarema cochliacarpos (Gomes) Barneby and Grimes (Fabaceae), known by the vulgar name of Babatenã, has been traditionally used in Northeast Brazil, as an anti-inflammatory remedy. Previous studies have demonstrated its anti-inflammatory and antiulcer effects in skin lesion, alcohol gastric ulcer and acute and chronic colitis. Aims The present study was designed to evaluate the antioxidant and anti-inflammatory effects of the butanolic fraction from A. cochliacarpos (BFAC) and its major flavonoid, (+)-catechin, in LPS-stimulated murine peritoneal macrophages. Moreover, we studied the role of mitogen-activated protein kinase (MAPK)s and NF-kB signaling pathways possibly involved in the beneficial effects. Materials and methods The quantification of the extract was carried out by ultra-performance liquid chromatography analysis. Cell viability was determined using SRB assay. Nitric oxide (NO) production was analyzed by Griess method and intracellular reactive oxygen species (ROS) by fluorescence analysis. In addition, cyclooxygenase (COX-2) and inducible nitric oxide synthase (iNOS) expression, MAPK activation and IkappaBalpha (IKBα) degradation, were determined by Western blot. Results After BFAC characterization, (+)-catechin was revealed as its major constituent. Both BFAC and (+)-catechin, exerted significant anti-oxidant and anti-inflammatory effects inhibiting LPS-induced intracellular ROS and NO production in peritoneal macrophages. Additionally, the extract but also its major component reduced pro-inflammatory proteins expression probably through c-Jun N-terminal kinase and p38 MAPK signaling pathways. Conclusion These data suggest that the beneficial effects of BFAC might be mediated, at least in part, by the presence of (+)-catechin. Conclusively our findings confirm the potential of A. cochliacarpos as a new therapeutic strategy for the management of inflammatory and oxidative stress-related diseases. © 2013 Elsevier Ireland Ltd.1491140147Adler, V., Yin, Z., Tew, K.D., Ronai, Z., Role of redox potential and reactive oxygen species in stress signaling (1999) Oncogene, 18, pp. 6104-6111Albuquerque, U.P., Medeiros, P.M., Almeida, A.L.S., Monteiro, J.M., Neto, E.M.F.L., Melo, J.G., Santos, J.P., Medicinal plants of the caatinga (semi-arid) vegetation of NE Brazil: A quantitative approach (2007) Journal of Ethnopharmacology, 114, pp. 325-354Alleva, D.G., Johnson, E.B., Lio, F.M., Boehme, S.A., Conlon, P.J., Crowe, P.D., Regulation of murine macrophage proinflammatory and anti-inflammatory cytokines by ligands for peroxisome proliferator-activated receptor-gamma: Counter-regulatory activity by IFN-gamma (2002) Journal of Leukocyte Biology, 71, pp. 677-685Altavilla, D., Squadrito, F., Bitto, A., Polito, F., Burnett, B.P., Di Stefano, V., Minutoli, L., Flavocoxid, a dual inhibitor of cyclooxygenase and 5-lipoxygenase, blunts pro-inflammatory phenotype activation in endotoxin-stimulated macrophages (2009) British Journal of Pharmacology, 157, pp. 1410-1418Barton, G.M., Medzhitov, R., Toll-like receptor signaling pathways (2003) Science, 300, pp. 1524-1525Blackwell, T.S., Black, T.R., Holden, E.P., Christman, B.W., Christman, J.W., In vivo antioxidant treatment suppresses nuclear factor-κB activation and neutrophilic lung inflammation (1996) The Journal of Immunology, 157, pp. 1630-1637Bowie, A.G., Moynagh, P.N., O'Neill, L.A.J., Lipid peroxidation is involved in the activation of NF-κB by tumor necrosis factor but interleukin-1 in the human endothelial cell line ECV304 (1997) The Journal of Biological Chemistry, 272, pp. 25941-25950Bradford, M.M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding (1976) Analytical Biochemistry, 72, pp. 248-254Chang, C.T., Huang, S.S., Lin, S.S., Amagaya, S., Ho, H.Y., Hou, W.C., Shie, P.H., Huang, G.J., Antiinflammatory activities of tormentic acid from suspension cells of Eriobotrya Japonica ex vivo and in vivo (2011) Food Chemistry, 127, pp. 1131-1137Cheung, K.L., Kong, A.N., Molecular targets of dietary phenethyl isothiocyanate and sulforaphane for cancer chemoprevention (2010) AAPS Journals, 12, pp. 87-97Ciz, M., Pavelková, M., Gallová, L., Králová, J., Kubala, L., Lojek, A., The influence of wine polyphenols on reactive oxygen and nitrogen species production by murine macrophages RAW 264.7 (2008) Physiological Research, 57, pp. 393-402Coskun, M., Olsen, J., Seidelin, J.B., Nielsen, O.H., MAP kinases in inflammatory bowel disease (2011) Clinica Chimica Acta, 412, pp. 513-520Dias, A.S., Lima, A.C., Santos, A.L., Rabelo, T.K., Serafini, M.R., Andrade, C.R., Fernandes, X.A., Araujo, B.S., Redox properties of A. cochliacarpos (Gomes) Barneby and Sime (Fabaceae) stem bark ethanol extract and fractions (2012) Natural Product Research, , 10.1080/14786419.2012.722083Fraga, C.G., Oteiza, P.I., Dietary flavonoids: Role of (-)-epicatechin and related procyanidins in cell signaling (2011) Free Radical Biology and Medicine, 51, pp. 813-823Gloire, G., Legrand-Poels, S., Piette, J., NF-kappaB activation by reactive oxygen species, fifteen years later (2006) Biochemical Pharmacology, 72, pp. 1493-1505Gordon, S., Taylor, P.R., Monocyte and macrophage heterogeneity (2005) Nature Reviews Immunology, 5, pp. 953-964Guha, M., Mackman, N., LPS induction of gene expression in human monocytes (2001) Cell Signaling, 13, pp. 85-94Hatada, E.N., Krappmann, D., Scheidereit, C., NF-kappaB and the innate immune response (2000) Current Opinion in Immunology, 12, pp. 52-58Havsteen, B., The biochemistry and medical significance of the flavonoids (2002) Pharmacology and Therapeutics, 96, pp. 67-202Huang, S.M., Wu, C.H., Yen, G.C., Effects of flavonoids on the expression of the pro-inflammatory response in human monocytes induced by ligation of the receptor for AGEs (2006) Molecular Nutrition and Food Research, 50, pp. 1129-1139Itzkowitz, S.H., Molecular biology of dysplasia and cancer in inflammatory bowel disease (2006) Gastroenterology Clinics of North America, 35, pp. 553-571Joo, S.Y., Song, Y.A., Park, Y.L., Myung, E., Chung, C.Y., Park, K.J., Cho, S.B., Joo, Y.E., Epigallocatechin-3-gallate inhibits LPS-induced NF-κB and MAPK signaling pathways in bone marrow-derived macrophages (2012) Gut and Liver, 6, pp. 188-196Kaminska, B., MAPK signalling pathways as molecular targets for anti-inflammatory therapy - 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Abarema cochliacarpos reduces LPS-induced inflammatory response in murine peritoneal macrophages regulating ROS-MAPK signal pathway

Ethnopharmacological relevance: Abarema cochliacarpos (Gomes) Barneby and Grimes (Fabaceae), known by the vulgar name of Babatena, has been traditionally used in Northeast Brazil, as an anti-inflammatory remedy. Previous studies have demonstrated its anti-inflammatory and antiulcer effects in skin lesion, alcohol gastric ulcer and acute and chronic colitis. Aims: The present study was designed to evaluate the antioxidant and anti-inflammatory effects of the butanolic fraction from A. cochliacarpos (BFAC) and its major flavonoid, (+)-catechin, in LPS-stimulated murine peritoneal macrophages. Moreover, we studied the role of mitogen-activated protein kinase (MAPK)s and NF-kB signaling pathways possibly involved in the beneficial effects. Materials and methods: The quantification of the extract was carried out by ultra-performance liquid chromatography analysis. Cell viability was determined using SRB assay. Nitric oxide (NO) production was analyzed by Griess method and intracellular reactive oxygen species (ROS) by fluorescence analysis. In addition, cyclooxygenase (COX-2) and inducible nitric oxide synthase (iNOS) expression, MAPK activation and IkappaBalpha (IKB alpha) degradation, were determined by Western blot. Results: After BFAC characterization, (+)-catechin was revealed as its major constituent. Both BFAC and (+)-catechin, exerted significant anti-oxidant and anti-inflammatory effects inhibiting LPS-induced intracellular ROS and NO production in peritoneal macrophages. Additionally, the extract but also its major component reduced pro-inflammatory proteins expression probably through c-Jun N-terminal kinase and p38 MAPK signaling pathways. Conclusion: These data suggest that the beneficial effects of BFAC might be mediated, at least in part, by the presence of (+)-catechin. Conclusively our findings confirm the potential of A. cochliacarpos as a new therapeutic strategy for the management of inflammatory and oxidative stress-related diseases. (C) 2013 Elsevier Ireland Ltd. All rights reserved.1491140147Fundacion CarolinaMinisterio de Ciencia y tecnologia [AGL2008-02475]Consejeria de Innovacion Ciencia y Empresa [AGR-6609]Junta de Andalucia (Spain)Ministerio de Ciencia y tecnologia [AGL2008-02475]Consejeria de Innovacion Ciencia y Empresa [AGR-6609

Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.

Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST) were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations