Rapid weed adaptation and range expansion in response to agriculture over the past two centuries

North America has experienced a massive increase in cropland use since 1800, accompanied more recently by the intensification of agricultural practices. Through genome analysis of present-day and historical samples spanning environments over the past two centuries, we studied the effect of these changes in farming on the extent and tempo of evolution across the native range of the common waterhemp (Amaranthus tuberculatus), a now pervasive agricultural weed. Modern agriculture has imposed strengths of selection rarely observed in the wild, with notable shifts in allele frequency trajectories since agricultural intensification in the 1960s. An evolutionary response to this extreme selection was facilitated by a concurrent human-mediated range shift. By reshaping genome-wide diversity across the landscape, agriculture has driven the success of this weed in the 21st century

Diagnóstico tecnológico Magdalena Medio Antioqueño

El diagnóstico tecnológico para la parte de la subregión del Magdalena Medio Antioqueño tiene como propósito presentar la realidad agropecuaria de esta área y así tener fundamentos muy aproximados para la definición y formulación de proyectos de investigación, transferencia de tecnología y apoyo a la producción. El presente documento apunta hacia este objetivo y contempla información social como población estratificada de acuerdo a su ubicación y actividad productiva; información socioeconómica como tenencia de tierra, usos del suelo; información sobre áreas agroecológicas homogéneas, aspectos económicos diversos y tecnología local de producción sobre las distintas especies agrícolas y pecuarias prioritarias en la subregión

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa. Moreover, we show that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Our results also reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral A. thaliana population began to split by 120-90 kya, during the last interglacial and Abbassia pluvial, and Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for diverse species, including humans, implying a key role for climatic events during interglacial and pluvial periods in shaping the histories and current distributions of a wide range of species.Peer Reviewe

Bovine SLC11A1 3´ UTR SSCP genotype evaluated by a macrophage in vitro killing assay employing a Brucella abortus strain

The 3¢ untranslated region (3¢ UTR) of the bovine natural resistanceassociated macrophage gene (NRAMP1 or SLC11A1) was genotyped in Colombian Creole Blanco Orejinegro (BON) (Bos taurus) (n = 140) and Zebu Brahman (Bos indicus) (Z) (n = 20) cattle and their crosses (BON · Zebu Brahman [B · Z] [n = 10]; Zebu Brahman · BON [Z · B] [n = 10]), and in animals from a Holstein · BON (H · B) (n = 10) cross. Direct sequencing and single-strand conformation polymorphism analysis (SSCP) helped in detecting the polymorphic behaviour. The association between resistance to brucellosis infection and SSCP genotype was evaluated using a macrophage in vitro killing assay employing a virulent Brucella abortus strain. The 3¢ UTR (GT) repeated polymorphism was gentoyped and its association with resistance to brucellosis was evaluated. When all breeds were grouped, a high frequency in the homozygote GT12 (AA genotype) (0.823) and a very low frequency in the homozygote GT10 (BB genotype) (0.047) were detected. The BON (0.963), Z · B (0.60) and H · B (1.00) cattle showed high GT12 allele frequencies, unlike that seen for the B · Z and Zebu cattle (0.3002 and 0.218, respectively). The GT10 allele was only found in the Zebu cattle (0.391). A significant association (p < 0.001) was found between the B. abortus macrophage in vitro killing assay phenotypes and the bovine SLC11A1 3¢ UTR genotypes, which suggests that the A allele may be associated with resistance. Because only nine animals had the BB genotype, the results require some confirmation in more extensive populations.Ganadería bovin

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA

Discovery of Phytophthora infestans Genes Expressed in Planta through Mining of cDNA Libraries

BACKGROUND: Phytophthora infestans (Mont.) de Bary causes late blight of potato and tomato, and has a broad host range within the Solanaceae family. Most studies of the Phytophthora--Solanum pathosystem have focused on gene expression in the host and have not analyzed pathogen gene expression in planta. METHODOLOGY/PRINCIPAL FINDINGS: We describe in detail an in silico approach to mine ESTs from inoculated host plants deposited in a database in order to identify particular pathogen sequences associated with disease. We identified candidate effector genes through mining of 22,795 ESTs corresponding to P. infestans cDNA libraries in compatible and incompatible interactions with hosts from the Solanaceae family. CONCLUSIONS/SIGNIFICANCE: We annotated genes of P. infestans expressed in planta associated with late blight using different approaches and assigned putative functions to 373 out of the 501 sequences found in the P. infestans genome draft, including putative secreted proteins, domains associated with pathogenicity and poorly characterized proteins ideal for further experimental studies. Our study provides a methodology for analyzing cDNA libraries and provides an understanding of the plant--oomycete pathosystems that is independent of the host, condition, or type of sample by identifying genes of the pathogen expressed in planta

Performance of different biofilters in a recirculating system for rainbow trout farming

Objective. To evaluate the performance of different biofilters in a recirculating aquaculture system (RAS) for trout farming. Materials and methods. It was used a 1m3 plastic tank for fries farming; fabric bags to solids retention; a submersible pump; a constant water level and flow distribution box; six up flow biofilters in 3” PVC tube; sand of D10=0.45mm as carrier. The reactors were operated at local temperature and with hydraulic retention time (HRT) of 11 min, the biofilters were inoculated in the next way: R1-Control: RAS water; R2-Fish culture farm sludges; R3- Water from aerated lagoon of Antanas landfill (AL); R4-Aquarium sediments; R5- Aerated lagoon of AL sludges; R6-Sludges from sulfidogenic reactor of AL. The weight gain (WG) and the food conversion (FC) were evaluated, some physic-chemical parameters were monitored and the nitrogen and suspended solids removal efficiency were evaluated. Results. The WG of the cultured animals was 1.58 g/d and the FC was 1.41. There were no differences for ammonium and nitrite removal between the reactors; the average removal efficiencies were: ammonium 4.78%, nitrite 27.2%, nitrate 32.3%, suspended solids 37.5%; R4 and R5 reactors presented the best performance on nitrate removal, with average efficiencies of 47.4% and 42.8%. R3 presented the best SS removal with an average of 58.2%. Conclusions. The RAS water treatment system guaranteed appropriated liquid quality conditions for trout farming; the most efficient reactor for removal of the different forms of nitrogen was the inoculated with the aerated lagoon of AL sludges. RESUMEN Objetivo. Evaluar el desempeño de diferentes biofiltros en un sistema de recirculación (SRA) para cultivo de trucha arcoiris. Materiales y métodos. Se utilizó: un tanque de 1m3 para cultivo de alevines, bolsas de lienzo para retención de sólidos, bomba sumergible, caja de nivel constante y distribución de flujo, seis biofiltros en tubo de PVC de 3”, arena con D10=0.45mm como medio soporte. Los biofiltros se operaron a temperatura ambiente y con tiempo de retención hidráulica (TRH) de 11 min, se inocularon así: R1-Control: Aguas del SRA; R2-Lodos estación piscícola; R3-Agua Laguna aireada relleno sanitario Antanas (RSA); R4-Sedimentos acuarios; R5-Lodos laguna aireada RSA; R6-Lodos reactor sulfidogénico RSA. Se evaluó la ganancia de peso (GP) y la conversión alimenticia (CA), se monitorearon parámetros físico-químicos y se evaluó la eficiencia de remoción de nitrógeno y sólidos suspendidos. Resultados. La GP de los animales fue de 1.58 g/d y la CA de 1.41. No hubo diferencias para remoción de amonio ni nitritos entre reactores; las eficiencias medias de remoción fueron: amonio 4.78%, nitrito 27.2%, nitrato 32.3%, sólidos suspendidos 37.5%. Los reactores R4 y R5 presentaron mejor remoción de nitratos, con eficiencias medias de 47.4% y 42.8%. El R3 reportó la mejor remoción de SS con promedio del 58.2%. Conclusiones. El sistema de tratamiento del agua en el SRA garantizó condiciones de calidad del líquido, apropiadas para el cultivo de la trucha; el reactor más eficiente para la remoción de las formas de nitrógeno evaluadas fue el inoculado con lodos de la laguna aireada del RSA

Interrelationship between TP53 gene deletion, protein expression and chromosome 17 aneusomy in gastric adenocarcinoma

Background: This study evaluates the existence of numerical alterations of chromosome 17 and TP53 gene deletion in gastric adenocarcinoma. the p53 protein expression was also evaluated, as well as, possible associations with clinicopathological characteristics.Methods: Dual-color fluorescence in situ hybridization and immunostaining were performed in twenty gastric cancer samples of individuals from Northern Brazil.Results: Deletion of TP53 was found in all samples. TP53 was inactivated mainly by single allelic deletion, varying to 7-39% of cells/case. Aneusomy of chromosome 17 was observed in 85% of cases. Chromosome 17 monosomy and gain were both observed in about half of cases. Cells with gain of chromosome 17 frequently presented TP53 deletion. the frequency of cells with two chr17 and one TP53 signals observed was higher in diffuse than in intestinal-type GC. Immunoreactivity of p53 was found only in intestinal-type samples. the frequency of cells with two chr17 and two TP53 signals found was higher in samples with positive p53 expression than in negative cases in intestinal-type GC.Conclusion: We suggest that TP53 deletion and chromosome 17 aneusomy is a common event in GC and other TP53 alterations, as mutation, may be implicated in the distinct carcinogenesis process of diffuse and intestinal types.Financiadora de Estudos e Projetos (FINEP CT-INFRA/FADESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fed Univ Para, Inst Biol Sci, Humans Cytogenet Lab, BR-66075900 Belem, Para, BrazilUniv Fed Piaui, Dept Biol, Campus Minist Reis Velloso Parnaiba, Teresina, PI, BrazilUniversidade Federal de São Paulo, Dept Morphol, Div Genet, São Paulo, BrazilUniv Fed Ceara, Sch Med, Dept Pathol, Mol Genet Lab, Fortaleza, Ceara, BrazilFed Univ Para, Joao de Barros Barreto Univ Hosp, BR-66075900 Belem, Para, BrazilUniversidade Federal de São Paulo, Dept Morphol, Div Genet, São Paulo, BrazilFinanciadora de Estudos e Projetos (FINEP CT-INFRA/FADESP): 0927-03. RRBWeb of Scienc