Optimal clone identifier for genomic shotgun libraries: OC Identifier tool

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray. ©FUNPEC-RP.

Heuristics and meta-heuristics for lot sizing and scheduling in the soft drinks industry: A comparison study

This chapter studies a two-level production planning problem where, on each level, a lot sizing and scheduling problem with parallel machines, capacity constraints and sequence-dependent setup costs and times must be solved. The problem can be found in soft drink companies where the production process involves two interdependent levels with decisions concerning raw material storage and soft drink bottling. Models and solution approaches proposed so far are surveyed and conceptually compared. Two different approaches have been selected to perform a series of computational comparisons: an evolutionary technique comprising a genetic algorithm and its memetic version, and a decomposition and relaxation approach. © 2008 Springer-Verlag Berlin Heidelberg.

Transmission network expansion planning considering uncertainty in generation and demand

This paper presents a mathematical model and a methodology to solve a transmission network expansion planning problem considering uncertainty in demand and generation. The methodology used to solve the problem, finds the optimal transmission network expansion plan that allows the power system to operate adequately in an environment with uncertainty. The model presented results in an optimization problem that is solved using a specialized genetic algorithm. The results obtained for known systems from the literature show that cheaper plans can be found satisfying the uncertainty in demand and generation. ©2008 IEEE.

Transmission network expansion planning considering multiple generation scenarios

This paper presents a mathematical model and a methodology to solve a transmission network expansion planning problem considering open access. The methodology finds the optimal transmission network expansion plan that allows the power system to operate adequately in an environment with multiples generation scenarios. The model presented is solved using a specialized genetic algorithm. The methodology is tested in a system from the literature. ©2008 IEEE.

Planeamiento de la expansión de sistemas de transmisión considerando contingencias y demanda incierta

This paper presents a methodology and a mathematical model to solve the expansion planning problem that takes into account the effect of contingencies in the planning stage, and considers the demand as a stochastic variable within a specified range. In this way, it is possible to find a solution that minimizes the investment costs guarantying reliability and minimizing future load shedding. The mathematical model of the expansion planning can be represented by a mixed integer nonlinear programming problem. To solve this problem a specialized Genetic Algorithm combined with Linear Programming was implemented.

Locus no cromossomo 19 influencia positivamente o número de oócitos recuperados em ciclos estimulados

Objective: To evaluate if identified loci associated with normal age of menopause variation and early menopause can account for the poor response to controlled ovarian stimulation. Methods: A total of 71 patients, with age ≤ 35 years old, undergoing intracytoplasmic sperm injection were tested for three of the four newly identified genetic variants associated with normal variation in menopausal age and early menopause. Patients were divided into two groups: poor responder group (PR group, n=21) and normoresponder group (NR group, n=50). The influence of risk allele frequency on the response to controlled ovarian stimulation (COS) was evaluated. Logistic regression models were used. Results: There was no significant difference in the incidence of the genetic variants between NR and PR group. The risk allele for chromosome 19 variant (rs4806660) demonstrated a protective effect. The presence of a risk allele, either in homozygosis or in heterozygosis, was associated with an increased response to COS, resulting in an elevated number of follicles (Coef: 2.54, P= 0.041) and retrieved oocytes (Coef: 1.41, P= 0.041). Conclusions: Genetic variants rs244715, rs9379896 and rs4806660 are not risk factors for poor ovarian response. Instead, rs4806660 is associated with higher number of follicles and retrieved oocytes. It could be hypothesized that rs4806660 is associated with an increased response to gonadotrophin stimulus. © Todos os direitos reservados a SBRA - Sociedade Brasileira de Reprodução Assistida.

A combinatorial approach for transmission expansion & reactive power planning

A metaheuristic technique for solving the short-term transmission network expansion and reactive power planning problems, at the same time, in regulated power systems using the AC model is presented. The problem is solved using a real genetic algorithm (RGA). For each topology proposed by RGA an indicator is employed to identify the weak buses for new reactive power sources allocation. The fitness function is calculated using the cost of each configuration as well as constraints deviation of an AC optimal power flow (OPF) in which the minimum reactive generation of new reactive sources and the active power losses are objectives. With allocation of reactive power sources at load buses, the circuit capacity increases and the cost of installation could be decreased. The method is tested in a well known test system, presenting good results when compared with other approaches. © 2011 IEEE.

Tabu search to solve the Synchronized and Integrated Two-Level Lot Sizing and Scheduling Problem

This paper proposes a tabu search approach to solve the Synchronized and Integrated Two-Level Lot Sizing and Scheduling Problem (SITLSP). It is a real-world problem, often found in soft drink companies, where the production process has two integrated levels with decisions concerning raw material storage and soft drink bottling. Lot sizing and scheduling of raw materials in tanks and products in bottling lines must be simultaneously determined. Real data provided by a soft drink company is used to make comparisons with a previous genetic algorithm. Computational results have demonstrated that tabu search outperformed genetic algorithm in all instances. Copyright 2011 ACM.

Influence of δβ-thalassemia or regulatory elements in individuals with increased fetal Hb levels in the São Paulo northwest population

Fetal hemoglobin (Hb F), formed by two alpha globin chains (α) and two gamma chains (γ) (α2 γ2), has reduced expression in adults, ranging from 0 to 1% of total hemoglobin. Increased levels of Hb F are due to mutations in the β-globin family, which cause hereditary persistence of fetal hemoglobin (HPFH) and delta-beta thalassemia (δβ-thalassemia).The control of the production takes place by the regulatory region and regions outside the β-globin family, among them 2q16, 6q23, 8q, and Xp22.2.The aims of this study were to determine the presence and frequency of two mutations for δβ-thalassemia, the XmnI polymorphism and β-globin haplotypes in healthy individuals with increased Hb F in the State of São Paulo. We analyzed 60 samples of peripheral blood of healthy adults, without complaints of anemia. The samples were separated into two groups according to Hb F level: group I - 34 samples with Hb F ranging from 2 to 15% and group II - 26 samples with Hb F over 15%. In relation to the polymorphisms examined, we found three heterozygous individuals (5%) for Spanish δβ-thalassemia, belonging to group I, whose Hb F levels were within the normal range.The Sicilian δβ-thalassemia mutation was not found, indicating the need to study other polymorphisms related to the increase of Hb F in adult life.The frequency of XmnI polymorphism was 33.3% and the mean Hb F levels were 15.48 ± 11.69%.The frequency observed in our study for this polymorphic site is higher than that found in the literature for healthy subjects.This polymorphism was more prevalent in individuals with Hb F levels below 15%. For four samples positive for this polymorphism, the Hb F levels were explained by the presence of HPFH and Spanish δβ-thalassemia mutations, so that the presence of the XmnI polymorphic site was not a determinant in the overexpression of γ-globin genes. Regarding β-globin haplotypes, 18 alleles and 27 distinct genotypic patterns were found.The pattern Atp1/Atp2 was the mostfrequent genotype (13.72%).Of the 18 alleles, 13 showed atypical patterns.The results show that the haplotype V was the most frequent (27.45%), followed by atypical Atp2 (13.72%) and Atp1 (11.76%), and that there was a higher correlation with the presence of HPFH and XmnI polymorphism.The high frequency of haplotype V in our samples and high frequency of atypical haplotypes may reflect a high rate of miscegenation in this population, suggesting an ethnic characteristic for the Brazilian population, requiring the evaluation of population genetic markers to corroborate this hypothesis. © FUNPEC-RP.

Optimal trajectory and solution of the inverse kinematics of a robotic manipulator by genetic algorithms

This paper presents the generation of optimal trajectories by genetic algorithms (GA) for a planar robotic manipulator. The implemented GA considers a multi-objective function that minimizes the end-effector positioning error together with the joints angular displacement and it solves the inverse kinematics problem for the trajectory. Computer simulations results are presented to illustrate this implementation and show the efficiency of the used methodology producing soft trajectories with low computing cost. © 2011 Springer-Verlag Berlin Heidelberg.

Transmission network expansion planning considering phase-shifter transformers

This paper presents a novel mathematical model for the transmission network expansion planning problem. Main idea is to consider phase-shifter (PS) transformers as a new element of the transmission system expansion together with other traditional components such as transmission lines and conventional transformers. In this way, PS are added in order to redistribute active power flows in the system and, consequently, to diminish the total investment costs due to new transmission lines. Proposed mathematical model presents the structure of a mixed-integer nonlinear programming (MINLP) problem and is based on the standard DC model. In this paper, there is also applied a specialized genetic algorithm aimed at optimizing the allocation of candidate components in the network. Results obtained from computational simulations carried out with IEEE-24 bus system show an outstanding performance of the proposed methodology and model, indicating the technical viability of using these nonconventional devices during the planning process. Copyright © 2012 Celso T. Miasaki et al.

Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens

In the past, the focus of broiler breeding programs on yield and carcass traits improvement led to problems related to meat quality. Awareness of public concern for quality resulted in inclusion of meat quality traits in the evaluation process. Nevertheless, few genes associated with meat quality attributes are known. Previous studies mapped quantitative trait loci for weight at 35 and 42 days in a region of GGA4 flanked by the microsatellite markers, MCW0240 and LEI0063. In this region, there are 2 fibroblast growth factor binding protein (FGFBP) genes that play an important role in embryogenesis, cellulardifferentiation, and proliferation in chickens. The objective of this study was to identify and associate single nucleotide polymorphisms (SNPs) in FGFBP1 and FGFBP2 with performance, carcass, and meat quality in experimental and commercial chicken populations. In the commercial population, SNP g.2014G>A in FGFBP1 was associated with decreased carcass weight (P < 0.05), and SNP g.651G>A in FGFBP2 was associated with thawing loss and meat redness content (P < 0.05). Four haplotypes were constructed based on 2 SNPs and were associated with breast weight, thawing loss, and meat redness content. The diplotypes were associated with thawing loss, lightness, and redness content. The SNPs evaluated in the present study may be used as markers in poultry breeding programs to aid in improving growth and meat quality traits. © FUNPEC-RP.

Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens

Two functional and positional candidate genes were selected in a region of chicken chromosome 1 (GGA1), based on their biological roles, and also where several quantitative trait loci (QTL) have been mapped and associated with performance, fatness and carcass traits in chickens. The insulin-like growth factor 1 (IGF1) gene has been associated with several physiological functions related to growth. The lysine (K)-specific demethylase 5A (KDM5A) gene participates in the epigenetic regulation of genes involved with the cell cycle. Our objective was to find associations of selected single-nucleotide polymorphisms (SNPs) in these genes with performance, fatness and carcass traits in 165 F2 chickens from a resource population. In the IGF1 gene, 17 SNPs were detected, and in the KDM5A gene, nine SNPs were detected. IGF1 SNP c. 47673G > A was associated with body weight and haematocrit percentage, and also with feed intake and percentages of abdominal fat and gizzard genotype × sex interactions. KDM5A SNP c. 34208C > T genotype × sex interaction affected body weight, feed intake, percentages of abdominal fat (p = 0. 0001), carcass, gizzard and haematocrit. A strong association of the diplotype × sex interaction (p < 0. 0001) with abdominal fat was observed, and also associations with body weight, feed intake, percentages of carcass, drums and thighs, gizzard and haematocrit. Our findings suggest that the KDM5A gene might play an important role in the abdominal fat deposition in chickens. The IGF1 and KDM5A genes are strong candidates to explain the QTL mapped in this region of GGA1. © 2012 Institute of Plant Genetics, Polish Academy of Sciences, Poznan.

An Integrative Genomic and Transcriptomic Analysis Reveals Potential Targets Associated with Cell Proliferation in Uterine Leiomyomas

Background: Uterine Leiomyomas (ULs) are the most common benign tumours affecting women of reproductive age. ULs represent a major problem in public health, as they are the main indication for hysterectomy. Approximately 40-50% of ULs have non-random cytogenetic abnormalities, and half of ULs may have copy number alterations (CNAs). Gene expression microarrays studies have demonstrated that cell proliferation genes act in response to growth factors and steroids. However, only a few genes mapping to CNAs regions were found to be associated with ULs. Methodology: We applied an integrative analysis using genomic and transcriptomic data to identify the pathways and molecular markers associated with ULs. Fifty-one fresh frozen specimens were evaluated by array CGH (JISTIC) and gene expression microarrays (SAM). The CONEXIC algorithm was applied to integrate the data. Principal Findings: The integrated analysis identified the top 30 significant genes (P<0.01), which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell proliferation, including FGFR1 and IGFBP5. Transcriptional and protein analyses showed that FGFR1 (P = 0.006 and P<0.01, respectively) and IGFBP5 (P = 0.0002 and P = 0.006, respectively) were up-regulated in the tumours when compared with the adjacent normal myometrium. Conclusions: The integrative genomic and transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs. © 2013 Cirilo et al.

Multiobjective short-term planning of electric power distribution systems using NSGA-II

This paper presents a mixed integer nonlinear programming multiobjective model for short-term planning of distribution networks that considers in an integrated manner the following planning activities: allocation of capacitor banks; voltage regulators; the cable replacement of branches and feeders. The objective functions considered in the proposed model are: to minimize operational and investment costs and minimize the voltage deviations in the the network buses, subject to a set of technical and operational constraints. A multiobjective genetic algorithm based on a Non-Dominated Sorting Genetic Algorithm (NSGA-II) is proposed to solve this model. The proposed mathematical model and solution methodology is validated testing a medium voltage distribution system with 135 buses. © 2013 Brazilian Society for Automatics - SBA.