3,040,883 research outputs found
Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield
No full textBananas (Musa spp.) are an essential fruit worldwide and rank as the fourth most significant food crop for addressing malnutrition due to their rich nutrients and starch content. The potential of their genetic diversity remains untapped due to limited molecular breeding tools. Our study examined a phenotypically diverse group of 124 accessions from the Colombian Musaceae Collection conserved in AGROSAVIA. We assessed 12 traits categorized into morphology, fruit quality, and yield, alongside sequence data. Our sequencing efforts provided valuable insights, with an average depth of about 7× per accession, resulting in 187,133 single-nucleotide polymorphisms (SNPs) against Musa acuminata (A genome) and 220,451 against Musa balbisiana (B genome). Population structure analysis grouped samples into four and five clusters based on the reference genome. By using different association models, we identified marker¿trait associations (MTAs). The mixed linear model revealed four MTAs, while the Bayesian-information and linkage-disequilibrium iteratively nested keyway and fixed and random model for circulating probability unification models identified 82 and 70 MTAs, respectively. We identified 38 and 40 candidate genes in linkage proximity to significant MTAs for the A genome and B genome, respectively. Our findings provide insights into the genetic underpinnings of morphology, fruit quality, and yield. Once validated, the SNP markers and candidate genes can potentially drive advancements in genomic-guided breeding strategies to enhance banana crop improvement. © The Author(s) 2024
Expression of Plasmodium falciparum genes involved in erythrocyte invasion varies among isolates cultured directly from patients.
No full textPlasmodium falciparum merozoites invade erythrocytes using a range of alternative ligands that includes erythrocyte binding antigenic proteins (EBAs) and reticulocyte binding protein homologues (Rh). Variation in the expression of some of these genes among culture-adapted parasite lines correlates with the use of different erythrocyte receptors. Here, expression profiles of four Rh genes and eba175 are analysed in a sample of 42 isolates cultured from malaria patients in Kenya. The profiles cluster into distinct groups, largely because of very strong negative correlations between the levels of expression of particular gene pairs (Rh1 versus Rh2b, eba175 versus Rh2b, and eba175 versus Rh4), previously associated with alternative invasion pathways in culture-adapted parasite lines. High levels of eba175 are seen in isolates in expression profile group I, and may be associated with sialic acid-dependent invasion. Groups II and III are, respectively, characterized by high levels of Rh2b and Rh4, and are more likely to be associated with sialic acid-independent invasion
Deficiencia congénita de leptina y mutación sin sentido del gen de la leptina encontrada en dos hermanas colombianas con obesidad severa
No full text11 páginasBackground: Congenital leptin deficiency is a recessive genetic disorder associated with severe early-onset obesity. It is caused by mutations in the leptin (LEP) gene, which encodes the protein product leptin. These mutations may cause nonsense-mediated mRNA decay, defective secretion or the phenomenon of biologically inactive leptin, but typically lead to an absence of circulating leptin, resulting in a rare type of monogenic extreme obesity with intense hyperphagia, and serious metabolic abnormalities. Methods: We present two severely obese sisters from Colombia, members of the same lineal consanguinity. Their serum leptin was measured by MicroELISA. DNA sequencing was performed on MiSeq equipment (Illumina) of a next-generation sequencing (NGS) panel involving genes related to severe obesity, including LEP. Results: Direct sequencing of the coding region of LEP gene in the sisters revealed a novel homozygous missense mutation in exon 3 [NM_002303.3], C350G>T [p.C117F]. Detailed information and clinical measurements of these sisters were also collected. Their serum leptin levels were undetectable despite their markedly elevated fat mass. Conclusions: The mutation of LEP, absence of detectable leptin, and the severe obesity found in these sisters provide the first evidence of monogenic leptin deficiency reported in the continents of North and South America. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.Antecedentes: la deficiencia congénita de leptina es un trastorno genético recesivo asociado con obesidad grave de aparición temprana. Es causada por mutaciones en el gen de la leptina (LEP), que codifica el producto proteico leptina. Estas mutaciones pueden causar una descomposición del ARNm mediada sin sentido, una secreción defectuosa o el fenómeno de la leptina biológicamente inactiva, pero generalmente conducen a una ausencia de leptina circulante, lo que resulta en un tipo raro de obesidad extrema monogénica con hiperfagia intensa y anomalías metabólicas graves. Métodos: Presentamos dos hermanas colombianas con obesidad severa, miembros de la misma consanguinidad lineal. Su leptina sérica se midió mediante MicroELISA. La secuenciación de ADN se realizó en un equipo MiSeq (Illumina) de un panel de secuenciación de próxima generación (NGS) que involucra genes relacionados con la obesidad severa, incluida la LEP. Resultados: La secuenciación directa de la región codificante del gen LEP en las hermanas reveló una nueva mutación homocigótica sin sentido en el exón 3 [NM_002303.3], C350G>T [p.C117F]. También se recopiló información detallada y mediciones clínicas de estas hermanas. Sus niveles séricos de leptina eran indetectables a pesar de su masa grasa notablemente elevada. Conclusiones: La mutación de LEP, la ausencia de leptina detectable y la obesidad severa encontrada en estas hermanas proporcionan la primera evidencia de deficiencia de leptina monogénica reportada en los continentes de América del Norte y del Sur. © 2019 por los autores. Licenciatario MDPI, Basilea, Suiza
DNA Genes and Chromosomes
No full textThis OER consists of an instructional sheet produced by GENIE CETL in the Department of Genetics.
By the end of this learning material you would have learnt about the components of a DNA and the process of DNA replication, gene types and sequencing and the structural properties of a chromosome.
FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila
Full text linkabstract: Gene expression patterns assayed across development can offer key clues about a gene’s function and regulatory role. Drosophila melanogaster is ideal for such investigations as multiple individual and high-throughput efforts have captured the spatiotemporal patterns of thousands of embryonic expressed genes in the form of in situ images. FlyExpress (www.flyexpress.net), a knowledgebase based on a massive and unique digital library of standardized images and a simple search engine to find coexpressed genes, was created to facilitate the analytical and visual mining of these patterns. Here, we introduce the next generation of FlyExpress resources to facilitate the integrative analysis of sequence data and spatiotemporal patterns of expression from images. FlyExpress 7 now includes over 100,000 standardized in situ images and implements a more efficient, user-defined search algorithm to identify coexpressed genes via Genomewide Expression Maps (GEMs). Shared motifs found in the upstream 5′ regions of any pair of coexpressed genes can be visualized in an interactive dotplot. Additional webtools and link-outs to assist in the downstream validation of candidate motifs are also provided. Together, FlyExpress 7 represents our largest effort yet to accelerate discovery via the development and dispersal of new webtools that allow researchers to perform data-driven analyses of coexpression (image) and genomic (sequence) data.The final version of this article, as published in G3: Genes|Genomes|Genetics, can be viewed online at: http://www.g3journal.org/content/7/8/279
Mining housekeeping genes with a Naive Bayes classifier
Full text linkThe first author was supported by the Student Awards Agency for Scotland. The second author is supported by BBSRC grant BBS RC BB/D006473/1, and under the Advanced Knowledge Technologies (AKT) Interdisciplinary Research Collaboration (IRC), which is sponsored by the UK Engineering and Physical Sciences Research Council under grant number GR/N15764/01.Background: Traditionally, housekeeping and tissue specific genes have been classified using direct assay of mRNA presence across different tissues, but these experiments are costly and the results not easy to compare and reproduce. Results: In this work, a Naive Bayes classifier based only on physical and functional characteristics of genes already available in databases, like exon length and measures of chromatin compactness, has achieved a 97% success rate in classification of human housekeeping genes ( 93% for mouse and 90% for fruit fly). Conclusion: The newly obtained lists of housekeeping and tissue specific genes adhere to the expected functions and tissue expression patterns for the two classes. Overall, the classifier shows promise, and in the future additional attributes might be included to improve its discriminating power.Peer reviewe
Acknowledgment to Reviewers of Genes in 2020
No full textPeer review is the driving force of journal development, and reviewers are gatekeepers who ensure that Genes maintains its standards for the high quality of its published papers [...
The role of Plasmodium falciparum var genes in malaria in pregnancy
No full textSequestration of Plasmodium falciparum-infected erythrocytes in the placenta is responsible for many of the harmful effects of malaria during pregnancy. Sequestration occurs as a result of parasite adhesion molecules expressed on the surface of infected erythrocytes binding to host receptors in the placenta such as chondroitin sulphate A (CSA). Identification of the parasite ligand(s) responsible for placental adhesion could lead to the development of a vaccine to induce antibodies to prevent placental sequestration. Such a vaccine would reduce the maternal anaemia and infant deaths that are associated with malaria in pregnancy. Current research indicates that the parasite ligands mediating placental adhesion may be members of the P. falciparum variant surface antigen family PfEMP1, encoded by var genes. Two relatively well-conserved subfamilies of var genes have been implicated in placental adhesion, however, their role remains controversial. This review examines the evidence for and against the involvement of var genes in placental adhesion, and considers whether the most appropriate vaccine candidates have yet been identified
Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa
No full textUnderstanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in 'responses to stress', 'ubiquitin-dependent protein catabolic processes', and 'biological regulation'. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats.Peer reviewe
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