A simplified courtship conditioning protocol to test learning and memory in Drosophila

In Drosophila, a male that has previously been sexually rejected reduces its courtship behavior when confronted again with an unreceptive female. This reduced courting time reflects a memory formation process. Here, we describe a simplified protocol to perform the courtship conditioning assay for assessing the reduced courting time, using regular lab equipment and handmade tools. Every step of the procedure, from raising flies and training to testing and quantification of this memory-related behavior, can be implemented in any practice laboratory.We would like to thank Javier Gil Castillo for its invaluable help and advices in 3D printing. We also thank the flies from Bloomington Stock Center. We would like to thank BioRender (www.biorender.com) for the open-access platform used to create the graphical abstract. This work was supported by the Spanish Research Agency (Ministerio de Innovacion y Ciencia [MICINN]) under the grant PGC2018-094630-B-100 to F.A.M., cofinanced by the European Regional Development Fund (ERDF) to F.A.M. F.A.M. is a recipient of a RyC-2014-14961 contract. B.G.-M. is a recipient of a FPI-UAM predoctoral fellowship, grant number SFPI/2020/00878. C.G.B. is a recipient of a FPU predoctoral fellowship, grant number FPU19/04449 (MEFP). S.P.-F. is a recipient of a JAE intro fellowship, grant number JAEINT_21_02520 (CSIC)

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses

Regeneración de campus para la creación de un laboratorio vivo de sostenibilidad ("living lab") en el Campus de Excelencia Internacional de Moncloa

La Universidad Politécnica de Madrid (UPM) a través de su Centro de Innovación en Tecnología para el Desarrollo Humano (itdUPM) está propiciando la generación de conciencia, conocimiento y soluciones innovadoras que contribuyen al cumplimiento de los Objetivos de Desarrollo Sostenible a través de un edificio que sirve como laboratorio de prueba para nuevas tecnologías verdes y como plataforma de ideación colaborativa y activación social

Use of the HPRT gene to study nuclease-induced DNA double-strand break repair

© The Authors 2015. Published by Oxford University Press. Understanding the mechanisms of chromosomal double-strand break repair (DSBR) provides insight into genome instability, oncogenesis and genome engineering, including disease gene correction. Research into DSBR exploits rare-cutting endonucleases to cleave exogenous reporter constructs integrated into the genome. Multiple reporter constructs have been developed to detect various DSBR pathways. Here, using a single endogenous reporter gene, the X-chromosomal disease gene encoding hypoxanthine phosphoribosyltransferase (HPRT), we monitor the relative utilization of three DSBR pathways following cleavage by I-SceI or CRISPR/Cas9 nucleases. For I-SceI, our estimated frequencies of accurate or mutagenic nonhomologous end-joining and gene correction by homologous recombination are 4.1, 1.5 and 0.16%, respectively. Unexpectedly, I-SceI and Cas9 induced markedly different DSBR profiles. Also, using an I-SceI-sensitive HPRT minigene, we show that gene correction is more efficient when using long double-stranded DNA than single- or double-stranded oligonucleotides. Finally, using both endogenous HPRT and exogenous reporters, we validate novel cell cycle phase-specific I-SceI derivatives for investigating cell cycle variations in DSBR. The results obtained using these novel approaches provide new insights into template design for gene correction and the relationships between multiple DSBR pathways at a single endogenous disease gene.This work was supported in part by the Biotechnology and Biological Research Council (BB/H003371/1 to A.C.G.P.), the Medical Research Council (MC_PC_12003 to T.C.H.), Cancer Research UK (C5255/A15935 to S.A.) and University of Oxford (Clarendon Scholarship to S.A.). Funding to pay the Open Access publication charges for this article was provided by the Research Councils UK open access fund

Avanços recentes em nutrição de larvas de peixes

Os requisitos nutricionais de larvas de peixes são ainda mal compreendidos, o que leva a altas mortalidades e problemas de qualidade no seu cultivo. Este trabalho pretende fazer uma revisão de novas metodologias de investigação, tais como estudos com marcadores, genómica populacional, programação nutricional, génomica e proteómica funcionais, e fornecer ainda alguns exemplos das utilizações presentes e perspectivas futuras em estudos de nutrição de larvas de peixes

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Sistemas produtivos de caprinocultura leiteira no semiárido paraibano: caracterização, principais limitantes e avaliação de estratégias de intervenção

Oito propriedades de leite caprino do semiárido paraibano foram acompanhadas, multidisciplinarmente, durante dois anos, com os objetivos de identificar os principais fatores limitantes da produção, assim como propor e avaliar estratégias de intervenção. Utilizou-se um questionário para obtenção de informações sobre as propriedades e práticas de manejo. Avaliou-se o balanço forrageiro de cada propriedade e foram feitas propostas para correção. Os animais foram identificados para que se viabilizasse a escrituração zootécnica e o controle da produção individual de leite. O diagnóstico das principais enfermidades foi estabelecido. Para análise dos dados, utilizou-se análise de variância, regressão linear múltipla e o teste t. O número médio de animais nos rebanhos era 53 cabeças (início do estudo), 62 (final do primeiro ano) e 49 (último ano). Nenhum rebanho tinha padrão racial definido. Na análise do balanço anual de forragem do primeiro ano, sete propriedades tiveram déficit forrageiro na seca, enquanto apenas duas apresentaram déficit durante o período chuvoso. No segundo ano, após as intervenções, seis das oito propriedades apresentaram déficit durante a seca e duas durante a chuva. Entretanto, em seis propriedades, se fossem armazenadas forragens no período da chuva, a quantidade de alimento produzida durante a chuva seria suficiente para manter os animais durante a estação seca. A média da produção de leite diária nas propriedades foi 1,19 litros por cabra. Os problemas mais graves de instalações foram identificados nos cabriteiros. No início do estudo, nenhum produtor realizava escrituração zootécnica, a qual foi gradativa e parcialmente implantada. As principais enfermidades diagnosticadas foram parasitoses gastrintestinais, linfadenite caseosa, mastite subclínica, ectima contagioso e ceratoconjuntivite. A prevalência de linfadenite, mastite e parasitoses gastrintestinais foram reduzidas, após a adoção de práticas adequadas. Problemas reprodutivos foram relatados por 75% dos proprietários. Em quatro propriedades, as taxas de mortalidade de animais jovens foram maiores do que as aceitáveis (8%). Após análise dos dados, observou-se que a assistência técnica permanente e multidisciplinar pode minimizar os fatores limitantes à caprinocultura leiteira. O estudo demonstrou que os produtores aceitam a implantação de novas tecnologias, desde que estas sejam gradativamente implantadas e adequadas aos sistemas de produção

Skewed X-inactivation is common in the general female population

X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants

Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events42Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases