División ganglionar posquirúrgica y su efecto en el recuento ganglionar y la estadificación en pacientes con cáncer gástrico / Postoperative lymph node division and its effect on lymph node count and staging in patients with gastric cancer

Introducción. La gastrectomía y disección ganglionar es el estándar de manejo para los pacientes con cáncer gástrico. Factores como la identificación de ganglios por el patólogo, pueden tener un impacto negativo en la estadificación y el tratamiento. El objetivo de este estudio fue comparar el recuento ganglionar de un espécimen quirúrgico después de una gastrectomía completa (grupo A) y de un espécimen con un fraccionamiento por grupos ganglionares (grupo B). Métodos. Estudio de una base de datos retrospectiva de pacientes sometidos a gastrectomía D2 en el Servicio de Cirugía gastrointestinal de la Liga Contra el Cáncer seccional Risaralda, Pereira, Colombia. Se comparó el recuento ganglionar en especímenes quirúrgicos con y sin división ganglionar por regiones anatómicas previo a su envío a patología. Resultados. De los 94 pacientes intervenidos, 65 pertenecían al grupo A y 29 pacientes al grupo B. El promedio de ganglios fue de 24,4±8,6 y 32,4±14,4 respectivamente (p=0,004). El porcentaje de pacientes con más de 15 y de 25 ganglios fue menor en el grupo A que en el grupo B (27 vs 57, p=0,432 y 19 vs 24, p=0,014). El promedio de pacientes con una relación ganglionar menor 0,2 fue mayor en el grupo B (72,4 % vs 55,4 %, p=0,119). Conclusiones. Los resultados de nuestro estudio mostraron que una división por grupos ganglionares previo a la valoración del espécimen por el servicio de patología incrementa el recuento ganglionar y permite establecer de manera certera el pronóstico de los pacientes, teniendo un impacto positivo en su estadificación, para evitar el sobretratamiento

Introduction. A gastrectomy and lymph node dissection is the standard of management for patients with gastric cancer. Factors such as the identification of nodes by the pathologist can have a negative impact on staging and treatment. The objective of this study was to compare the lymph node count of a surgical specimen after a complete gastrectomy (group A) and of a specimen with lymph node by groups (group B). Methods. Study of a retrospective database of patients undergoing D2 gastrectomy in the Risaralda section of the Liga Contra el Cancer Gastrointestinal surgical service, Pereira, Colombia. The lymph node count was compared in surgical specimens with and without lymph node division by anatomical regions, prior to sending them to pathology. Results. Of the 94 patients who underwent surgery, 65 were from group A and 29 patients were from group B. The average number of nodes was 24.4±8.6 and 32.4±14.4, respectively (p=0.004). The percentage of patients with more than 15 and 25 nodes was lower in group A than in group B (27 vs 57, p=0.432 and 19 vs 24, p=0.014). The average number of patients with a nodal ratio less than 0.2 was higher in group B (72.4% vs 55.4%, p=0.119). Conclusions. The results of our study showed that a division by lymph node groups prior to the evaluation of the specimen by the pathology service increases the lymph node count and allows the prognosis of patients to be accurately established, having a positive impact on their staging, to avoid overtreatment.

Artificially Sweetened Beverages Beyond the Metabolic Risks: A Systematic Review of the Literature.

We carried out a review of the available literature on the effects that artificially sweetened beverages (ASBs) such as diet soda (DS) have on health, particularly those not related to incident diabetes mellitus, obesity, and metabolic syndrome. A search of scientific articles was carried out using 11 different databases: PubMed, Cochrane, LILACS, MEDLINE Ovid, JAMA Network, IBECS, Cumed, Scopus, SciELO, MEDLINE-EBSCO, and Taylor & Francis Online. Articles published in the last 10 years were considered, considering cross-sectional studies, retrospective or prospective cohort studies, case-control studies, and randomized controlled clinical trials. Only articles in Spanish or English were considered using the MeSH (Medical Subject Heading) and DeCS (Descriptores en Ciencias de la Salud) terms, including "Diet soda," "Health," "Artificial sweetener," "Gaseosa sin azúcar," "Refresco sin azúcar," and "Salud." Additionally, Boolean operators "AND" and "Y" were used. A total of 1,323 articles were obtained in the initial search, of which 21 main ones were selected for review, which included the topic of DS consumption and explored the health consequences that it poses on different organs. The question of whether ASBs such as DS are a preferred substitute is becoming more and more important in terms of public policy due to mounting evidence of the potential negative health effects of their excessive consumption. This systematic review, the first of its kind to our knowledge, sheds light on how excessive DS consumption can affect multiple organ systems, and associations have been made to mental health burden, delays in child neurodevelopment, cardiac remodeling, worsening retinopathy in diabetics, incidental end-stage renal disease, non-Hodgkin's lymphoma and multiple myeloma in men, rheumatoid arthritis in women, hip fractures, dental erosion, increases in breath alcohol concentration when used in alcoholic beverages, and accelerated cell aging. Further studies should delve further to understand the pathophysiologic mechanisms of these associations.

New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.

Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.

Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments.

TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful reverse genetics method in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. Pooled high throughput sequencing (HTS) of the targeted genes allows efficient identification and sample assignment of variants within genes of interest in hundreds of individuals. Although TILLING has been used successfully in different crops and even applied to natural populations, one of the main issues for a successful TILLING experiment is that most currently available bioinformatics tools for variant detection are not designed to identify mutations with low frequencies in pooled samples or to perform sample identification from variants identified in overlapping pools. Our research group maintains the Next Generation Sequencing Experience Platform (NGSEP), an open source solution for analysis of HTS data. In this manuscript, we present three novel components within NGSEP to facilitate the design and analysis of TILLING experiments: a pooled variants detector, a sample identifier from variants detected in overlapping pools and a simulator of TILLING experiments. A new implementation of the NGSEP calling model for variant detection allows accurate detection of low frequency mutations within pools. The samples identifier implements the process to triangulate the mutations called within overlapping pools in order to assign mutations to single individuals whenever possible. Finally, we developed a complete simulator of TILLING experiments to enable benchmarking of different tools and to facilitate the design of experimental alternatives varying the number of pools and individuals per pool. Simulation experiments based on genes from the common bean genome indicate that NGSEP provides similar accuracy and better efficiency than other tools to perform pooled variants detection. To the best of our knowledge, NGSEP is currently the only tool that generates individual assignments of the mutations discovered from the pooled data. We expect that this development will be of great use for different groups implementing TILLING as an alternative for plant breeding and even to research groups performing pooled sequencing for other applications.

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean.

Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.

Genomic Variability of Phytophthora palmivora Isolates from Different Oil Palm Cultivation Regions in Colombia.

Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete Phytophthora palmivora, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for P. palmivora, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of P. palmivora with oil palm and could be further exploited as tools for the development of effective strategies for disease control.

NGSEP3: accurate variant calling across species and sequencing protocols.

MOTIVATION: Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features. RESULTS: Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats. We performed extensive benchmark experiments comparing NGSEP to state-of-the-art software using real data from three sequencing protocols and four species with different distributions of repetitive elements. NGSEP consistently shows comparative accuracy and better efficiency compared to the existing solutions. We expect that this work will contribute to the continuous improvement of quality in variant calling needed for modern applications in medicine and agriculture. AVAILABILITY AND IMPLEMENTATION: NGSEP is available as open source software at http://ngsep.sf.net. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fine-mapping of angular leaf spot resistance gene Phg-2 in common bean and development of molecular breeding tools.

KEY MESSAGE: The Common Bean Angular Leaf Spot Resistance Gene Phg-2 was fine-mapped to a 409-Kbp region, and molecular markers for breeders were developed and validated in field experiments. Common bean (Phaseolus vulgaris L.) is an important food legume in Latin America, Asia and Africa. It is an important source of protein, carbohydrates and micro-minerals, particularly for smallholder farmers. Common bean productivity is affected by angular leaf spot (ALS) disease caused by the pathogenic fungus Pseudocercospora griseola, resulting in significant yield losses, particularly in low-input smallholder farming systems in the tropics. The ALS resistance gene Phg-2, which was found in several highly resistant common bean genotypes, was investigated in crosses between Mesoamerican pre-breeding lines and elite Andean breeding lines. Next-generation sequencing (NGS) data sets were used to design new SNP-based molecular markers. The Phg-2 locus was confirmed to be the major locus providing ALS resistance in these crosses. The locus was fine-mapped to a 409-Kbp region on chromosome 8. Two clusters of highly related LRR genes were identified in this region, which are the best candidate genes for Phg-2. Molecular markers were identified that are closely linked to the Phg-2 resistance gene and also highly specific to the donor germplasm. Marker-assisted selection (MAS) was used to introgress the Phg-2 resistance locus into Andean breeding germplasm using MAB lines. The usefulness of molecular markers in MAS was confirmed in several field evaluations in complex breeding crosses, under inoculation with different ALS pathotypes. This project demonstrates that NGS data are a powerful tool for the characterization of genetic loci and can be applied in the development of breeding tools.

Genomic Analysis of Colombian Leishmania panamensis strains with different level of virulence.

The establishment of Leishmania infection in mammalian hosts and the subsequent manifestation of clinical symptoms require internalization into macrophages, immune evasion and parasite survival and replication. Although many of the genes involved in these processes have been described, the genetic and genomic variability associated to differences in virulence is largely unknown. Here we present the genomic variation of four Leishmania (Viannia) panamensis strains exhibiting different levels of virulence in BALB/c mice and its application to predict novel genes related to virulence. De novo DNA sequencing and assembly of the most virulent strain allowed comparative genomics analysis with sequenced L. (Viannia) panamensis and L. (Viannia) braziliensis strains, and showed important variations at intra and interspecific levels. Moreover, the mutation detection and a CNV search revealed both base and structural genomic variation within the species. Interestingly, we found differences in the copy number and protein diversity of some genes previously related to virulence. Several machine-learning approaches were applied to combine previous knowledge with features derived from genomic variation and predict a curated set of 66 novel genes related to virulence. These genes can be prioritized for validation experiments and could potentially become promising drug and immune targets for the development of novel prophylactic and therapeutic interventions.

Resequencing of Common Bean Identifies Regions of Inter-Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding.

Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A. Gray), and L. were sequenced by whole-genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between and the two other domesticated species, but also within , affecting hundreds of protein-coding genomic regions. A large number of inter-gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.

Non-destructive Phenotyping to Identify Brachiaria Hybrids Tolerant to Waterlogging Stress under Field Conditions.

Brachiaria grasses are sown in tropical regions around the world, especially in the Neotropics, to improve livestock production. Waterlogging is a major constraint to the productivity and persistence of Brachiaria grasses during the rainy season. While some Brachiaria cultivars are moderately tolerant to seasonal waterlogging, none of the commercial cultivars combines superior yield potential and nutritional quality with a high level of waterlogging tolerance. The Brachiaria breeding program at the International Center for Tropical Agriculture, has been using recurrent selection for the past two decades to combine forage yield with resistance to biotic and abiotic stress factors. The main objective of this study was to test the suitability of normalized difference vegetation index (NDVI) and image-based phenotyping as non-destructive approaches to identify Brachiaria hybrids tolerant to waterlogging stress under field conditions. Nineteen promising hybrid selections from the breeding program and three commercial checks were evaluated for their tolerance to waterlogging under field conditions. The waterlogging treatment was imposed by applying and maintaining water to 3 cm above soil surface. Plant performance was determined non-destructively using proximal sensing and image-based phenotyping and also destructively via harvesting for comparison. Image analysis of projected green and dead areas, NDVI and shoot biomass were positively correlated (r ≥ 0.8). Our results indicate that image analysis and NDVI can serve as non-destructive screening approaches for the identification of Brachiaria hybrids tolerant to waterlogging stress.