A marker weighting approach for enhancing within-family accuracy in genomic prediction.

Genomic selection is revolutionizing plant breeding. However, its practical implementation is still very challenging, since predicted values do not necessarily have high correspondence to the observed phenotypic values. When the goal is to predict within-family, it is not always possible to obtain reasonable accuracies, which is of paramount importance to improve the selection process. For this reason, in this research, we propose the Adversaria-Boruta (AB) method, which combines the virtues of the adversarial validation (AV) method and the Boruta feature selection method. The AB method operates primarily by minimizing the disparity between training and testing distributions. This is accomplished by reducing the weight assigned to markers that display the most significant differences between the training and testing sets. Therefore, the AB method built a weighted genomic relationship matrix that is implemented with the genomic best linear unbiased predictor (GBLUP) model. The proposed AB method is compared using 12 real data sets with the GBLUP model that uses a nonweighted genomic relationship matrix. Our results show that the proposed AB method outperforms the GBLUP by 8.6, 19.7, and 9.8% in terms of Pearson's correlation, mean square error, and normalized root mean square error, respectively. Our results support that the proposed AB method is a useful tool to improve the prediction accuracy of a complete family, however, we encourage other investigators to evaluate the AB method to increase the empirical evidence of its potential.

Do feature selection methods for selecting environmental covariables enhance genomic prediction accuracy?

Genomic selection (GS) is transforming plant and animal breeding, but its practical implementation for complex traits and multi-environmental trials remains challenging. To address this issue, this study investigates the integration of environmental information with genotypic information in GS. The study proposes the use of two feature selection methods (Pearson's correlation and Boruta) for the integration of environmental information. Results indicate that the simple incorporation of environmental covariates may increase or decrease prediction accuracy depending on the case. However, optimal incorporation of environmental covariates using feature selection significantly improves prediction accuracy in four out of six datasets between 14.25% and 218.71% under a leave one environment out cross validation scenario in terms of Normalized Root Mean Squared Error, but not relevant gain was observed in terms of Pearson´s correlation. In two datasets where environmental covariates are unrelated to the response variable, feature selection is unable to enhance prediction accuracy. Therefore, the study provides empirical evidence supporting the use of feature selection to improve the prediction power of GS.

Tick Densities and Infection Prevalence on Coastal Islands in Massachusetts, USA: Establishing a Baseline.

Tick-borne diseases and a tick-induced red meat allergy have become increasingly common in the northeastern USA and elsewhere. At the scale of local communities, few studies have documented tick densities or infection levels to characterize current conditions and provide a baseline for further monitoring. Using the town of Nantucket, MA, as a case study, we recorded tick densities by drag sampling along hiking trails in nature preserves on two islands. Nymphal blacklegged ticks (Ixodes scapularis Say) were most abundant at shadier sites and least common in grasslands and scrub oak thickets (Quercus ilicifolia). Lone star ticks (Amblyomma americanum L.) were common on Tuckernuck Island and rare on Nantucket Island, while both tick species were more numerous in 2021 compared to 2020 and 2022. We tested for pathogens in blacklegged nymphs at five sites over two years. In 2020 and 2021, infection levels among the four Nantucket Island sites averaged 10% vs. 19% for Borrelia burgdorferi, 11% vs. 15% for Babesia microti, and 17% (both years) for Anaplasma phagocytophilum, while corresponding levels were significantly greater on Tuckernuck in 2021. Our site-specific, quantitative approach represents a practical example of how potential exposure to tick-borne diseases can be monitored on a local scale.

[Choledocholithiasis and pregnancy. Hybrid laparo-endoscopic treatment in one step]. / Coledocolitiasis y embarazo. Tratamiento hibrido laparo-endoscópico en una etapa.

BACKGROUND: Complications associated with choledocholithiasis are uncommon during pregnancy. However, when it occurs, the morbidity and mortality related for the product and the mother increases, so a proper treatment is imperative in these patients. CLINICAL CASE: A 25-year-old pregnant woman on her second trimester. The current condition was started four days prior to the hospital admission with abdominal pain in the right upper quadrant with nausea and vomit.Twenty-four hours later jaundice and dark urine is observed. Physical examination shows scleral jaundice, right upper quadrant abdominal pain without peritoneal irritation. Uterus at umbilicus level without uterine activity. Uterus at umbilicus level without uterine activity. Laboratory tests showed elevated bilirubin and transaminases without leukocytosis; ultrasound reported live intrauterine unique product, with a heart rate of 128 beats per minute, gallbladder with multiple images inside that cast acoustic shadowing, and a 10 mm common bile duct dilated bile duct with dilatation of intrahepatic bile ducts. It was perform laparoscopic cholecystectomy with intraoperative cholangiography and placement of a transcystic jaguar guide for selective cannulation of the common bile duct. Intraoperative endoscopic retrograde cholangiopancreatography was performed with endoscopic stone extraction. The outcome was satisfactory with a hospital discharge at 48 hours. CONCLUSION: Current evidence has shown that the combined use of laparoscopy and therapeutic endoscopic cholangiography in one step is effective for the treatment of choledocholithiasis, decreasing the risk of complications associated with cannulation of the bile duct.

Antecedentes: las complicaciones asociadas con la coledocolitiasis son poco comunes durante el embarazo. Sin embargo, cuando aparecen incrementan la morbilidad y mortalidad para el feto y la madre. Caso clínico: paciente femenina de 25 años de edad, en el segundo trimestre de embarazo. El padecimiento actual lo inició cuatro días previos a su ingreso al hospital, con dolor abdominal en el hipocondrio derecho acompañado de náuseas y vómito. A las 24 horas se agregó ictericia y coluria. A la exploración física se encontró tinte ictérico, dolor en el hipocondrio derecho, sin irritación peritoneal. Útero a nivel de la cicatriz umbilical, sin actividad uterina. Los exámenes de laboratorio mostraron: elevación de bilirrubinas y transaminasas, sin leucocitosis; el ultrasonido reportó producto único vivo intrauterino, con frecuencia cardiaca de 128 latidos por minuto, vesícula biliar con múltiples litos en su interior, colédoco 10 mm y dilatación de vía biliar. Se realizó colecistectomía laparoscópica y colangiografía transoperatoria con colocación de guía transcística para canulación selectiva de la vía biliar. Durante la colangiografía endoscópica transoperatoria se extrajeron algunos litos. La evolución fue satisfactoria, toleró la dieta y fue fue dada de alta del hospital a las 48 horas. Conclusión: en el tratamiento de la coledocolitiasis y embarazo la combinación de laparoscopia y colangiografía endoscópica terapéutica en un solo tiempo es eficaz porque disminuye el riesgo de complicaciones asociadas con la canulación de la vía biliar.

MSH1-induced non-genetic variation provides a source of phenotypic diversity in Sorghum bicolor.

MutS Homolog 1 (MSH1) encodes a plant-specific protein that functions in mitochondria and chloroplasts. We showed previously that disruption or suppression of the MSH1 gene results in a process of developmental reprogramming that is heritable and non-genetic in subsequent generations. In Arabidopsis, this developmental reprogramming process is accompanied by striking changes in gene expression of organellar and stress response genes. This developmentally reprogrammed state, when used in crossing, results in a range of variation for plant growth potential. Here we investigate the implications of MSH1 modulation in a crop species. We found that MSH1-mediated phenotypic variation in Sorghum bicolor is heritable and potentially valuable for crop breeding. We observed phenotypic variation for grain yield, plant height, flowering time, panicle architecture, and above-ground biomass. Focusing on grain yield and plant height, we found some lines that appeared to respond to selection. Based on amenability of this system to implementation in a range of crops, and the scope of phenotypic variation that is derived, our results suggest that MSH1 suppression provides a novel approach for breeding in crops.

The chloroplast triggers developmental reprogramming when mutS HOMOLOG1 is suppressed in plants.

Multicellular eukaryotes demonstrate nongenetic, heritable phenotypic versatility in their adaptation to environmental changes. This inclusive inheritance is composed of interacting epigenetic, maternal, and environmental factors. Yet-unidentified maternal effects can have a pronounced influence on plant phenotypic adaptation to changing environmental conditions. To explore the control of phenotypy in higher plants, we examined the effect of a single plant nuclear gene on the expression and transmission of phenotypic variability in Arabidopsis (Arabidopsis thaliana). MutS HOMOLOG1 (MSH1) is a plant-specific nuclear gene product that functions in both mitochondria and plastids to maintain genome stability. RNA interference suppression of the gene elicits strikingly similar programmed changes in plant growth pattern in six different plant species, changes subsequently heritable independent of the RNA interference transgene. The altered phenotypes reflect multiple pathways that are known to participate in adaptation, including altered phytohormone effects for dwarfed growth and reduced internode elongation, enhanced branching, reduced stomatal density, altered leaf morphology, delayed flowering, and extended juvenility, with conversion to perennial growth pattern in short days. Some of these effects are partially reversed with the application of gibberellic acid. Genetic hemicomplementation experiments show that this phenotypic plasticity derives from changes in chloroplast state. Our results suggest that suppression of MSH1, which occurs under several forms of abiotic stress, triggers a plastidial response process that involves nongenetic inheritance.