Effect of inclusion or non-inclusion of short lactations and cow and/or dam genetic group on genetic evaluation of Girolando dairy cattle.

The objective of this study was to evaluate the effects of inclusion or non-inclusion of short lactations and cow (CGG) and/or dam (DGG) genetic group on the genetic evaluation of 305-day milk yield (MY305), age at first calving (AFC), and first calving interval (FCI) of Girolando cows. Covariance components were estimated by the restricted maximum likelihood method in an animal model of single trait analyses. The heritability estimates for MY305, AFC, and FCI ranged from 0.23 to 0.29, 0.40 to 0.44, and 0.13 to 0.14, respectively, when short lactations were not included, and from 0.23 to 0.28, 0.39 to 0.43, and 0.13 to 0.14, respectively, when short lactations were included. The inclusion of short lactations caused little variation in the variance components and heritability estimates of traits, but their non-inclusion resulted in the re-ranking of animals. Models with CGG or DGG fixed effects had higher heritability estimates for all traits compared with models that consider these two effects simultaneously. We recommend using the model with fixed effects of CGG and inclusion of short lactations for the genetic evaluation of Girolando cattle.

Genetic and process engineering approaches for improving lipid productivity in the non-conventional oleaginous yeast Cutaneotrichosporon oleaginosus

Gli oli microbici stanno ricevendo sempre più attenzioni come possibile alternativa agli oli vegetali, nel processo di sostituzione dei combustibili fossili. Tuttavia, diversi aspetti necessitano di essere ottimizzati al fine di ottenere oli economicamente competitivi e con caratteristiche chimico-fisiche desiderate. In questa ricerca, sono stati utilizzati due differenti approcci per poter realizzare l’obiettivo preposto. Il primo, si è basato sull’ingegnerizzazione genetica del lievito C. oleaginous, al fine di incrementare la produttività di lipidi e modificare la composizione dei trigliceridi (TAG) sintetizzati. Un protocollo basato su una trasformazione genetica mediata da Agrobacterium è stato utilizzato per sovraesprimere la diacilglicerol trasnferasi (DGA1), l’enzima responsabile dell’ultimo step della sintesi dei TAG, e la Δ9-desaturasi, l’enzima che catalizza la conversione dell’acido stearico (C18:0) in acido oleico (C18:1). La selezione di colonie positive e l’analisi dei mutanti ottenuti ha confermato la buona riuscita della trasformazione. Il secondo approccio ha mirato a studiare l’influenza sulla crescita e sul profilo di lipidi accumulati da C. oleaginous da parte di diversi acidi grassi volatili (VFAs), una materia prima ottenibile da trattamenti di scarti industriali. A questo proposito, sono state utilizzate fermentazioni fed-batch su scala da 1-L basate su glucosio e miscele sintetiche di acido acetico e di VFAs come fonte di carbonio. L’utilizzo simultaneo di acido acetico e acidi secondari ha mostrato come sia possibile stimolare il metabolismo microbico al fine di incrementare l'accumulo di oli e ottenere una composizione chimica lipidica desiderata.

Mapping new non-genetic dependencies in malignant pleural mesothelioma

Malignant Pleural Mesothelioma (MPM) is a very aggressive cancer whose incidence is growing worldwide. MPM escapes the classical models of carcinogenesis and lacks a distinctive genetic fingerprint, keeping obscure the molecular events that lead to tumorigenesis. This severely impacts on the limited therapeutic options and on the lack of specific biomarkers, concurring to make MPM one of the deadliest cancers. Here we combined a functional genome-wide loss of function CRISPR/Cas9 screening with patients’ transcriptomic and clinical data, to identify genes essential for MPM progression. Besides, we explored the role of non-coding RNAs to MPM progression by analysing gene expression profiles and clinical data from the MESO-TCGA dataset. We identified TRIM28 and the lncRNA LINC00941 as new vulnerabilities of MPM, associated with disease aggressiveness and bad outcome of patients. TRIM28 is a multi-domain protein involved in many processes, including transcription regulation. We showed that TRIM28 silencing impairs MPM cells’ growth and clonogenicity by blocking cells in mitosis. RNA-seq profiling showed that TRIM28 loss abolished the expression of major mitotic players. Our data suggest that TRIM28 is part of the B-MYB/FOXM1-MuvB complex that specifically drives the activation of mitotic genes, keeping the time of mitosis. In parallel, we found LINC00941 as strongly associated with reduced survival probability in MPM patients. LINC00941 KD profoundly reduced MPM cells’ growth, migration and invasion. This is accompanied by changes in morphology, cytoskeleton organization and cell-cell adhesion properties. RNA-seq profiling showed that LINC00941 KD impacts crucial functions of MPM, including HIF1α signalling. Collectively these data provided new insights into MPM biology and demonstrated that the integration of functional screening with patients’ clinical data is a powerful tool to highlight new non-genetic cancer dependencies that associate to a bad outcome in vivo, paving the way to new MPM-oriented targeted strategies and prognostic tools to improve patients risk-based stratification.

Evaluation Of Fe Uptake And Translocation In Transgenic And Non-transgenic Soybean Plants Using Enriched Stable (57)fe As A Tracer.

A tracer experiment is carried out with transgenic T (variety M 7211 RR) and non-transgenic NT (variety MSOY 8200) soybean plants to evaluate if genetic modification can influence the uptake and translocation of Fe. A chelate of EDTA with enriched stable (57)Fe is applied to the plants cultivated in vermiculite plus substrate and the (57)Fe acts as a tracer. The exposure of plants to enriched (57)Fe causes the dilution of the natural previously existing Fe in the plant compartments and then the changed Fe isotopic ratio ((57)Fe/(56)Fe) is measured using a quadrupole-based inductively coupled plasma mass spectrometer equipped with a dynamic reaction cell (DRC). Mathematical calculations based on the isotope dilution methodology allow distinguishing the natural abundance Fe from the enriched Fe (incorporated during the experiment). The NT soybean plants acquire higher amounts of Fe from natural abundance (originally present in the soil) and from enriched Fe (coming from the (57)Fe-EDTA during the experiment) than T soybean ones, demonstrating that the NT soybean plants probably absorb higher amounts of Fe, independently of the source. The percentage of newly incorporated Fe (coming from the treatment) was approximately 2.0 and 1.1% for NT and T soybean plants, respectively. A higher fraction (90.1%) of enriched Fe is translocated to upper parts, and a slightly lower fraction (3.8%) is accumulated in the stems by NT plants than by T ones (85.1%; 5.1%). Moreover, in both plants, the Fe-EDTA facilitates the transport and translocation of Fe to the leaves. The genetic modification is probably responsible for differences observed between T and NT soybean plants.

Ssr-based Genetic Diversity And Structure Of Garlic Accessions From Brazil.

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

Comparative Study Of Transgenic And Non-transgenic Maize (zea Mays) Flours Commercialized In Brazil, Focussing On Proteomic Analyses.

Genetically modified foods are a major concern around the world due to the lack of information concerning their safety and health effects. This work evaluates differences, at the proteomic level, between two types of crop samples: transgenic (MON810 event with the Cry1Ab gene, which confers resistance to insects) and non-transgenic maize flour commercialized in Brazil. The 2-D DIGE technique revealed 99 differentially expressed spots, which were collected in 2-D PAGE gels and identified via mass spectrometry (nESI-QTOF MS/MS). The abundance of protein differences between the transgenic and non-transgenic samples could arise from genetic modification or as a result of an environmental influence pertaining to the commercial sample. The major functional category of proteins identified was related to disease/defense and, although differences were observed between samples, no toxins or allergenic proteins were found.

Morphometric and genetic changes in a population of Apis mellifera after 34 years of Africanization

Though the replacement of European bees by Africanized honey bees in tropical America has attracted considerable attention, little is known about the temporal changes in morphological and genetic characteristics in these bee populations. We examined the changes in the morphometric and genetic profiles of an Africanized honey bee population collected near where the original African swarms escaped, after 34 years of Africanization. Workers from colonies sampled in 1968 and in 2002 were morphometrically analyzed using relative warps analysis and an Automatic Bee Identification System (ABIS). All the colonies had their mitochondrial DNA identified. The subspecies that mixed to form the Africanized honey bees were used as a comparison for the morphometric analysis. The two morphometric approaches showed great similarity of Africanized bees with the African subspecies, Apis mellifera scutellata, corroborating with other markers. We also found the population of 1968 to have the pattern of wing venation to be more similar to A. m. scutellata than the current population. The mitochondrial DNA of European origin, which was very common in the 1968 population, was not found in the current population, indicating selective pressure replacing the European with the African genome in this tropical region. Both morphometric methodologies were very effective in discriminating the A. mellifera groups; the non-linear analysis of ABIS was the most successful in identifying the bees, with more than 94% correct classifications.

Genetic Variants of Diabetes Risk and Incident Cardiovascular Events in Chronic Coronary Artery Disease

Objective: To determine whether information from genetic risk variants for diabetes is associated with cardiovascular events incidence. Methods: From the about 30 known genes associated with diabetes, we genotyped single-nucleotide polymorphisms at the 10 loci most associated with type-2 diabetes in 425 subjects from the MASS-II Study, a randomized study in patients with multi-vessel coronary artery disease. The combined genetic information was evaluated by number of risk alleles for diabetes. Performance of genetic models relative to major cardiovascular events incidence was analyzed through Kaplan-Meier curve comparison and Cox Hazard Models and the discriminatory ability of models was assessed for cardiovascular events by calculating the area under the ROC curve. Results: Genetic information was able to predict 5-year incidence of major cardiovascular events and overall-mortality in non-diabetic individuals, even after adjustment for potential confounders including fasting glycemia. Non-diabetic individuals with high genetic risk had a similar incidence of events then diabetic individuals (cumulative hazard of 33.0 versus 35.1% of diabetic subjects). The addition of combined genetic information to clinical predictors significantly improved the AUC for cardiovascular events incidence (AUC = 0.641 versus 0.610). Conclusions: Combined information of genetic variants for diabetes risk is associated to major cardiovascular events incidence, including overall mortality, in non-diabetic individuals with coronary artery disease.

Genetic analysis of average annual productivity of Nellore breeding cows (COWPROD)

With the aim of estimating the coefficient of heritability of average annual productivity of Nellore cows (COWPROD), a data set from 24,855 animals with known pedigree was analyzed. COWPROD is defined as the amount (in kilograms) of weaned calves produced yearly by one cow during her remaining time in herd ignoring a fixed period of 365 days. COWPROD was calculated regarding three standards: a) based on the post-weaning weight from the calves ignoring any kind of adjustment (COWPROD_NAJ), b) adjusted weight for the fixed effects (COWPROD_AJFIX) and c) adjusted weight for the fixed effects and for the genetic merit of the sire (COWPROD_AJFIN). The obtained heritabilities were 0.15, 0.15 and 0.16 for COWPROD_NAJ, COWPROD_AJFIX and COWPROD_AJFIN, respectively. A complete set composed of 105,158 COWPROD records on 130,740 animals in pedigree was also analyzed for predicting the genetic merit of all animals in the data set and for the calculation of the genetic, phenotypic and residual trends. Ranking correlation was high for the adjusted and non-adjusted data, yet, for some of the animals, the difference among the genetic values was large. This would be an indication that it would be better to work always with the adjusted weaning weights. The genetic trend was positive, but was of small magnitude (0.26% of the trait average) and the residual trend was negative as a consequence of the large intensification of the production system, which has been occurring in the last years in the farms studied. The phenotypic trend was also negative and intermediate between the genetic and the residual ones.

Comparison of different models to estimate genetic parameters for carcass traits in a commercial broiler line

The effect of genetic and non-genetic factors for carcass, breast meat and leg weights, and yields of a commercial broiler line were investigated using the restricted maximum likelihood method, considering four different animal models, including or excluding maternal genetic effect with covariance between direct and maternal genetic effects, and maternal permanent environmental effect. The likelihood ratio test was used to determine the most adequate model for each trait. For carcass, breast, and leg weight, and for carcass and breast yield, maternal genetic and permanent environmental effects as well as the covariance between direct and maternal genetic effects were significant. The estimates of direct and maternal heritability were 0.17 and 0.04 for carcass weight, 0.26 and 0.06 for breast weight, 0.22 and 0.02 for leg weight, 0.32 and 0.02 for carcass yield, and 0.52 and 0.04 for breast yield, respectively. For leg yield, maternal permanent environmental effect was important, in addition to direct genetic effects. For that trait, direct heritability and maternal permanent environmental variance as a proportion of the phenotypic variance were 0.43 and 0.02, respectively. The results indicate that ignoring maternal effects in the models, even though they were of small magnitude (0.02 to 0.06), tended to overestimate direct genetic variance and heritability for all traits.

Genetic Variation among Major Human Geographic Groups Supports a Peculiar Evolutionary Trend in PAX9

A total of 172 persons from nine South Amerindian, three African and one Eskimo populations were studied in relation to the Paired box gene 9 (PAX9) exon 3 (138 base pairs) as well as its 5' and 3' flanking intronic segments (232 bp and 220 bp, respectively) and integrated with the information available for the same genetic region from individuals of different geographical origins. Nine mutations were scored in exon 3 and six in its flanking regions; four of them are new South American tribe-specific singletons. Exon3 nucleotide diversity is several orders of magnitude higher than its intronic regions. Additionally, a set of variants in the PAX9 and 101 other genes related with dentition can define at least some dental morphological differences between Sub-Saharan Africans and non-Africans, probably associated with adaptations after the modern human exodus from Africa. Exon 3 of PAX9 could be a good molecular example of how evolvability works.

A Constructive Genetic Algorithm for permutation flowshop scheduling

The general flowshop scheduling problem is a production problem where a set of n jobs have to be processed with identical flow pattern on in machines. In permutation flowshops the sequence of jobs is the same on all machines. A significant research effort has been devoted for sequencing jobs in a flowshop minimizing the makespan. This paper describes the application of a Constructive Genetic Algorithm (CGA) to makespan minimization on flowshop scheduling. The CGA was proposed recently as an alternative to traditional GA approaches, particularly, for evaluating schemata directly. The population initially formed only by schemata, evolves controlled by recombination to a population of well-adapted structures (schemata instantiation). The CGA implemented is based on the NEH classic heuristic and a local search heuristic used to define the fitness functions. The parameters of the CGA are calibrated using a Design of Experiments (DOE) approach. The computational results are compared against some other successful algorithms from the literature on Taillard`s well-known standard benchmark. The computational experience shows that this innovative CGA approach provides competitive results for flowshop scheduling; problems. (C) 2007 Elsevier Ltd. All rights reserved.

Evaluation of Adaptive Genetic Algorithm to Environmental Modeling of Peponapis and Cucurbita

This paper presents a free software tool that supports the next-generation Mobile Communications, through the automatic generation of models of components and electronic devices based on neural networks. This tool enables the creation, training, validation and simulation of the model directly from measurements made on devices of interest, using an interface totally oriented to non-experts in neural models. The resulting model can be exported automatically to a traditional circuit simulator to test different scenarios.

Jointly multi-user detection and channel estimation with genetic algorithm

This work aims at proposing the use of the evolutionary computation methodology in order to jointly solve the multiuser channel estimation (MuChE) and detection problems at its maximum-likelihood, both related to the direct sequence code division multiple access (DS/CDMA). The effectiveness of the proposed heuristic approach is proven by comparing performance and complexity merit figures with that obtained by traditional methods found in literature. Simulation results considering genetic algorithm (GA) applied to multipath, DS/CDMA and MuChE and multi-user detection (MuD) show that the proposed genetic algorithm multi-user channel estimation (GAMuChE) yields a normalized mean square error estimation (nMSE) inferior to 11%, under slowly varying multipath fading channels, large range of Doppler frequencies and medium system load, it exhibits lower complexity when compared to both maximum likelihood multi-user channel estimation (MLMuChE) and gradient descent method (GrdDsc). A near-optimum multi-user detector (MuD) based on the genetic algorithm (GAMuD), also proposed in this work, provides a significant reduction in the computational complexity when compared to the optimum multi-user detector (OMuD). In addition, the complexity of the GAMuChE and GAMuD algorithms were (jointly) analyzed in terms of number of operations necessary to reach the convergence, and compared to other jointly MuChE and MuD strategies. The joint GAMuChE-GAMuD scheme can be regarded as a promising alternative for implementing third-generation (3G) and fourth-generation (4G) wireless systems in the near future. Copyright (C) 2010 John Wiley & Sons, Ltd.

Genetic variability in S(1) families from different maize populations.

Genetic variability in S(1) families from different maize populations. The objectives of the present work were directed towards the study of genetic: variablilty In seven maize populations with a broad genetic base, as a guide for population improvement. The field evaluation was conducted in completely randomized blocks, at one location (Anhembi, Sao Paulo state) with different groups, of S(1) families Obtained from seven populations (GO-D: dent type, GO-F: flint type, GO-L: long car, GO-G: thick Car; and composites G3, G4 and GO-S). Estimates were obtained for genetic variance (progeny mean basis), phenotypic variance of families means, and coefficient of heritability (broad sense) for progeny means. Estimates of heritability were high for Car weight (0,89 to 0.94), car length (0.77 to 0.88) and car diameter (0.77 to 0.92); and lower for plant height (0.58 to 0.80) and Car height (0.54 to 0.84), thus showing the high Potential of the populations for recurrent selection based oil S, families. Ear yield in the base populations used as controls varied front 11,200 kg ha(-1) (GO-D) to 12,800 kg ha(-1) (G3). The means of S(1) families varied from 6,070 kg ha(-1) (GO-F) to 7,380 kg ha(-1) (G4); the Inbreeding depression in S(1) Families varied front 37.5% (G4) to 48.0% (G3) relative to the non-inbred population.