Showing papers in "Genetics and Molecular Research in 2005"

Genetics of efficient feed utilization and national cattle evaluation: a review.

Abstract: Selection for the wide range of traits for which most beef breed associations calculate expected progeny differences focus on increasing the outputs of the production system, thereby increasing the genetic potential of cattle for reproductive rates, weights, growth rates, and end-product yield. Feed costs, however, represent a large proportion of the variable cost of beef production and genetic improvement programs for reducing input costs should include traits related to feed utilization. Feed conversion ratio, defined as feed inputs per unit output, is a traditional measure of efficiency that has significant phenotypic and genetic correlations with feed intake, growth rate, and mature size. One limitation is that favorable decreases in feed to gain either directly or due to correlated response to increasing growth rate do not necessarily relate to improvement in efficiency of feed utilization. Residual feed intake is defined as the difference between actual feed intake and that predicted on the basis of requirements for maintenance of body weight and production. Phenotypic independence of residual feed intake with growth rate, body weight, and other energy depots can be forced. However, genetic associations may remain when a phenotypic prediction approach is used. Heritability estimates for phenotypic residual feed intake have been moderate, ranging from 0.26 to 0.43. Genetic correlations of phenotypic residual feed intake with feed intake have been large and positive, suggesting that improvement would produce a correlated response of decreased feed intake. Residual feed intake estimated by genetic regression results in a zero genetic correlation with its predictors, which reduces concerns over long-term antagonistic responses such as increased mature size and maintenance requirements. The genetic regression approach requires knowledge of genetic covariances of feed intake with weight and production traits. Cost of individual feed intake measurements on potential replacements must be considered in implementation of national cattle evaluations for efficiency of feed utilization. These costs need to be compared to expected, and, if possible, realized rates of genetic change and the associated reduction in feed input requirements.

Cytogenetic and genotoxic effects of the insecticides, imidacloprid and methamidophos.

Abstract: We examined the cytogenetic and genotoxic effects of the neonicotinoid insecticide imidacloprid and the organophosphate in- secticide methamidophos, when administered alone or in combination These insecticides were tested with the bone marrow chromosome ab- erration assay and micronucleus test in rats and by the bacterial muta- tion assay (Salmonella/microsome mutagenicity assay) Wistar albino rats were orally fed daily with laboratory chow treated with various concentrations of insecticides, 50 and 100 mg/kg imidacloprid, 25 and 5 mg/kg methamidophos, and 25 and 5 mg/kg imidacloprid plus methami- dophos, respectively, for 90 days Numerical and structural chromoso- mal aberrations were evaluated Significant differences were detected between all the insecticide-administered groups versus the control group and between the two concentrations of the pesticide-treated groups Both concentrations of the insecticides induced a dose-related increase

DNA repair gene polymorphisms and susceptibility to familial breast cancer in a group of patients from Campinas, Brazil.

Abstract: Several studies have reported that the genes involved in DNA repair and in the maintenance of genome integrity play a crucial role in protecting against mutations that lead to cancer. Epidemiologic evidence has shown that the inheritance of genetic variants at one or more loci results in a reduced DNA repair capacity and in an increased risk of cancer. Polymorphisms have been identified in several DNA repair genes, such as XRCC1, XPD, XRCC3, and RAD51, but the influence of specific genetic variants on repair phenotype and cancer risk has not yet been clarified. This was a case-control study design with three case groups: 53 women with breast cancer and family history; 33 women with sporadic breast cancer; 175 women with no breast cancer but with family history. The control group included 120 women with no breast cancer and no family history. The PCR-RFLP method was used to analyze the XRCC1-Arg399Gln, XPD-Lys751Gln, XRCC3-Thr241Met, and RAD51-G135C polymorphisms. No statistically significant differences were found between the case groups and the control group for any of the polymorphisms analyzed, and also between the breast cancer and family history group and the sporadic breast cancer group. Sample sizes of women with breast cancer, whether familial or sporadic, were insufficient to show any small true differences between the groups, but we have to consider that currently there is no clear consensus with respect to the association of these polymorphisms with breast cancer risk. Considering the data available, it can be conjectured that if there is any risk association between these single-nucleotide polymorphisms and breast cancer, this risk will probably be minimal. The greater the risk associated with cancer, the smaller the sample size required to demonstrate this association, and the data of different studies are usually, therefore, more concordant.

Antigenotoxic and antimutagenic potential of an annatto pigment (norbixin) against oxidative stress.

Abstract: Carotenoids are 40-carbon molecules with conjugated double bonds, making them particularly effective for quenching free radicals. They have always been believed to possess anticancer properties, which could be due to their antioxidant potential. Norbixin is an unusual dicarboxylic water-soluble carotenoid present as a component in the pericarp of the seeds of Bixa orellana L. (from the Bixaceae family), a tropical shrub commonly found in Brazil. The main carotenoids present in these seeds, bixin and norbixin, form a coloring material, known as annatto, which is mainly used in the food industry. As annatto is only used as a coloring material, most studies of annatto pigments have focused on the determination of annatto levels in food. However, little attention has been given to the biological properties of bixin and norbixin. We evaluated the effect of norbixin on the response of Escherichia coli cells to DNA damage induced by UV radiation, hydrogen peroxide (H2O2) and superoxide anions (O2*-)) and found that norbixin protects the cells against these agents. Norbixin enhanced survival at least 10 times. The SOS induction by UVC was inhibited 2.3 times more when cells were grown in the presence of norbixin. We also found that norbixin has antimutagenic properties, with a maximum inhibition of H2O2-induced mutagenic activity of 87%, based on the Salmonella mutagenicity test.

Oxidative stress response in Paracoccidioides brasiliensis.

Abstract: Survival of pathogenic fungi inside human hosts depends on evasion from the host immune system and adaptation to the host environment. Among different insults that Paracoccidioides brasilien- sis has to handle are reactive oxygen and nitrogen species produced by the human host cells, and by its own metabolism. Knowing how the parasite deals with reactive species is important to understand how it establishes infection and survives within humans. The initiative to de- scribe the P. brasiliensis transcriptome fostered new approaches to study oxidative stress response in this organism. By examining genes related to oxidative stress response, one can evaluate the parasite's abil- ity to face this condition and infer about possible ways to overcome this ability. We report the results of a search of the P. brasiliensis assembled expressed sequence tag database for homologous sequences involved in oxidative stress response. We described several genes coding proteins involved in antioxidant defense, for example, catalase and superoxide dismutase isoenzymes, peroxiredoxin, cytochrome c peroxidase, gluta- thione synthesis enzymes, thioredoxin, and the transcription factors Yap1

Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers.

Abstract: Penaeid shrimps are an important resource in crustacean fisheries, representing more than the half of the gross production of shrimp worldwide. In the present study, we used a sample of wide-ranging diversity (41 shrimp species) and two mitochondrial markers (758 bp) to clarify the evolutionary relationships among Penaeidae genera. Three different methodologies of tree reconstruction were employed in the study: maximum likelihood, neighbor joining and Bayesian analysis. Our results suggest that the old Penaeus genus is monophyletic and that the inclusion of the Solenocera genus within the Penaeidae family remains uncertain. With respect to Metapenaeopsis monophyly, species of this genus appeared clustered, but with a nonsignificant bootstrap value. These results elucidate some features of the unclear evolution of Penaeidae and may contribute to the taxonomic characterization of this family.

Genetic characterization of European-Zebu composite bovine using RFLP markers.

Abstract: A population of 370 European-Zebu composite beef heif- ers, consisting of six different breed compositions (A-F), were charac- terized genetically, using RFLP markers of luteinizing hormone receptor (LHR) and follicle-stimulating hormone receptor (FSHR) genes. Our objectives were to genetically characterize this population and to deter- mine the structure and the genetic variability of this hybrid herd. The genotypes were determined through PCR, followed by digestion with restriction endonucleases. The PCR-RFLP analysis made it possible to identify the LHR and FSHR genotypes, as well as to characterize the degree of heterozygosis, which was high for all of the breed composi- tions, for both loci, except for two combinations for LHR (B and C). The observed heterozygosity (H o ) was lower than the expected heterozy- gosity (H e ) for compositions C (for LHR) and A and D (for FSHR); however, for the population as a whole, H o was above H e (with a mean of 57 versus 46%, respectively), reflecting the elevated genetic variabil- ity in this population and also the informative value of the RFLP mark-

Association among oxidized LDL levels, MnSOD, apolipoprotein E polymorphisms, and cardiovascular risk factors in a south Brazilian region population.

Abstract: Oxidized LDL (ox-LDL) is involved in the initiation and progression of atherosclerosis. Many factors can affect the LDL oxidation such as oxidative stress. The present study tested whether ox-LDL levels would be associated with apolipoprotein E (APOE), manganese superoxide dismutase (MnSOD) Ala16Val polymorphisms, and classic cardiovascular risk factors. ox-LDL levels were measured by thiobarbituric acid-reactive substances and both polymorphisms were determined by polymerase chain reaction/restriction fragment length polymorphism in a sample of 252 subjects (70 men, 182 women, mean age, 54-85 years). Subjects with ox-LDL >or=0.5 nmol/mg apoprotein were considered the high level group (HLG, N = 82) and subjects with ox-LDL <0.5 nmol/mg apoprotein were considered the expected level group (ELG, N = 170). Classic risk factors were also evaluated. The results showed that diabetes mellitus was more prevalent in HLG, whereas other cardiovascular risk factors were similar between groups. The APOE genotype frequencies did not differ between HLG and ELG subjects. However, AA genotype from MnSOD polymorphism was more frequent in ELG (chi(2) = 8.48; P = 0.014). AV and VV subjects from ELG present highest ox-LDL levels (OR = 3.61; CI95% = 1.42-9.17) than AA. Additional analysis did not find gene-gene interactions associated with ox-LDL levels. Multivariate analysis showed that diabetes and the MnSOD polymorphism were independent factors associated with higher ox-LDL levels in HLG. The results suggest that an important framework on modulation of the redox status influenced by genetic polymorphisms could affect the cardiovascular homeostasis.

Differential molecular response of the transcripts B2A2 and B3A2 to imatinib mesylate in chronic myeloid leukemia.

Abstract: Chronic myeloid leukemia (CML) originates from the hematopoietic stem cell and is characterized by the reciprocal transloca- tion t(9;22)(q34;q11), which results in the BCR-ABL fusion gene on chro- mosome 22q-, also known as the Philadelphia chromosome. This chi- meric gene codes for a cytoplasmic protein with constitutive tyrosine- kinase activity, responsible for cellular transformation and leukemogen- esis in CML. The aim of this observational cohort study was to discrimi- nate and quantify BCR-ABL transcripts in the peripheral blood of pa- tients with CML who were treated with imatinib mesylate (Glivec ® , Novartis). Twenty-two patients were followed for six months during treatment. Quantitative real time polymerase chain reaction was per- formed before treatment and after 3 and 6 months from treatment initia- tion. As compared with the third month, there was a significant decrease in BCR-ABL expression in the sixth month of treatment (P = 0.0002). At the sixth month, there was a significant difference in the levels of the

Multiple Mantel tests and isolation-by-distance, taking into account long-term historical divergence.

Abstract: Mantel tests of matrix correspondence have been widely used in population genetics to examine microevolutionary processes, such as isolation-by-distance (IBD). We used partial and multiple Mantel tests to simultaneously test long-term historical effects and current divergence and equilibrium processes, such as IBD. We used these procedures to calculate genetic divergence among Eugenia dysenterica (Myrtaceae) populations in Central Brazil. The Nei's genetic distances between pairs of local populations were strongly correlated with geographic distances, suggesting an IBD process, but field observations and the geographic distribution of the samples suggest that populations may have been subjected to more complex evolutionary processes of genetic divergence. Partial Mantel regression was used to partition the effects of geographic structure and long-term divergence associated with a possible historical barrier. The R(2) of the model with both effects was 73.3%, and after the partition 21.9% of the variation in the genetic distances could be attributed to long-term historical divergence alone, whereas only 1.5% of the variation in genetic distances could be attributed to IBD. As expected, there was a large overlap between these processes when explaining genetic divergence, so it was not possible to entirely partition divergence between historical and contemporary processes.

Support vector machines for novel class detection in Bioinformatics.

Abstract: Novelty detection techniques might be a promising way of dealing with high-dimensional classification problems in Bioinformatics. We present preliminary results of the use of a one-class support vector machine approach to detect novel classes in two Bioinformatics data- bases. The results are compatible with theory and inspire further inves- tigation.

Inheritance of parthenocarpy in summer squash (Cucurbita pepo L)

Abstract: The inheritance of the tendency to set parthenocarpic fruit in the summer squash (Cucurbita pepo L.) line Whitaker was studied. Two parental lines, Whitaker (parthenocarpic) and Caserta (non- parthenocarpic), and the F 1 and F 2 generations and backcrosses to both parents were tested. The parthenocarpic tendency of individual plants was scored on a scale from 1 (non-parthenocarpic fruit) to 5 (partheno- carpic fruit). The Whitaker line produced parthenocarpic fruit and had a mean score of 4.2, whereas Caserta did not set parthenocarpic fruit and had a score of 1.55. The heritability estimates indicated that genetic gains from selection were feasible. The additive-dominant model showed a good fit, with epistasis being negligible or nonexistent. The hypothesis of monogenic inheritance with incomplete dominance was not rejected within the degree of dominance range from 0.2 to 0.5. These results indicate that parthenocarpy is controlled by a single locus, with incom- plete dominance in the direction of parthenocarpic expression.

Development of bovine embryos reconstructed by nuclear transfer of transfected and non-transfected adult fibroblast cells.

Abstract: An association of two techniques, nuclear transfer (NT), and transfection of somatic animal cells, has numerous potential applica- tions and considerable impact, mainly in agriculture, medicine, pharmacy, and fundamental biology. In addition, somatic cell nuclear transfer is the most efficient alternative to produce large transgenic animals. We com- pared in vitro and in vivo developmental capacities of NT using fibro- blast cells isolated from a 14-month-old cloned Simmental heifer (FCE) vs the same line transfected with a plasmid containing neomycin-resis- tant genes (TFCE). There were no significant differences (P > 0.5) in either fusion (116/149 = 78% vs 216/301 = 72%), cleavage (78/116 = 67% vs 141/216 = 65%) and blastocyst (35/116 = 30% vs 52/216 =

Cell signaling pathways in Paracoccidioides brasiliensis--inferred from comparisons with other fungi.

Abstract: The human fungal pathogen Paracoccidioides brasiliensis is an ascomycete that displays a temperature-dependent dimorphic transition, appearing as a mycelium at 22 degrees C and as a yeast at 37 degrees C, this latter being the virulent form We report on the in silico search made of the P brasiliensis transcriptome-expressed sequence tag database for components of signaling pathways previously known to be involved in morphogenesis and virulence in other species of fungi, including Saccharomyces cerevisiae, Cryptococcus neoformans, Candida albicans, and Aspergillus fumigatus Using this approach, it was possible to identify several protein cascades in P brasiliensis, such as i) mitogen-activated protein kinase signaling for cell integrity, cell wall construction, pheromone/mating, and osmo-regulation, ii) the cAMP/PKA system, which regulates fungal development and virulence, iii) the Ras protein, which allows cross-talking between cascades, iv) calcium-calmodulin-calcineurin, which controls cell survival under oxidative stress, high temperature, and membrane/cell wall perturbation, and v) the target of rapamycin pathway, controlling cell growth and proliferation The ways in which P brasiliensis responds to the environment and modulates the expression of genes required for its survival and virulence can be inferred through comparison with other fungi for which this type of data is already available

The use of RAPD to characterize Bipolaris sorokiniana isolates.

Abstract: Bipolaris sorokiniana is a phytopathogenic fungus causing diseases of cereal crops such as common root rot, the leaf spot disease, seedling blight, and black point of the grain. Random-amplified polymorphic DNA (RAPD) assay was used to investigate the genetic diversity of 20 isolates collected from different cultivars in wheat-producing regions in Brazil. Seventy primers, with random nucleotide sequences, were tested. Reproducibility to amplify the genomic DNA of isolates was found for 30 of the 70 primers tested, generating between 1 and 17 fragments ranging from 0.35 to 2.0 kb (average size). The degree of similarity between samples was calculated through simple association and the dendrogram was assessed using the unweighted pair group method with arithmetical average. After the RAPD analyses 19 isolates were closely grouped, having a similarity coefficient of >or= 78%. Isolate I017 showed very low similarity coefficients, ranging between 38 and 46%. The RAPD analyses provided important information as to the degree of genetic variability and the relationship between the isolates investigated, revealing polymorphism and establishing electrophoretic profiles useful to characterize the phytopathogen.

Long survival in a 69,XXX triploid infant in Greece.

Abstract: The live birth of a triploidy infant is a very rare event and death usually occurs within the first hours of life. Triploid cases with a survival of more than two months are infrequent. We report on an infant with a 69,XXX chromosome constitution who survived 164 days. Chromosomal analysis demonstrated a 69,XXX karyotype with no evidence of mosaicism. This is the longest survival reported for this condition to date in Greece and the fourth longest worldwide. The infant was admitted to our clinic several times due to respiratory problems, and supplementary oxygen was required. The improved survival of our case was possibly due to better management of respiratory illness and prematurity, and these are essential factors that physicians should consider carefully with such rare cases.

Reconstruction of phylogenetic trees using the ant colony optimization paradigm.

Abstract: We developed a new approach for the reconstruction of phylogenetic trees using ant colony optimization metaheuristics. A tree is constructed using a fully connected graph and the problem is approached similarly to the well-known traveling salesman problem. This methodology was used to develop an algorithm for constructing a phylogenetic tree using a pheromone matrix. Two data sets were tested with the algorithm: complete mitochondrial genomes from mammals and DNA sequences of the p53 gene from several eutherians. This new methodology was found to be superior to other well-known softwares, at least for this data set. These results are very promising and suggest more efforts for further developments.

Characters that differ between diploid and haploid honey bee (Apis mellifera) drones

Abstract: Diploid males have long been considered a curiosity contradictory to the haplo-diploid mode of sex determination in the Hymenoptera. In Apis mellifera, 'false' diploid male larvae are eliminated by worker cannibalism immediately after hatching. A 'cannibalism substance' produced by diploid drone larvae to induce worker-assisted suicide has been hypothesized, but it has never been detected. Diploid drones are only removed some hours after hatching. Older larvae are evidently not regarded as 'false males' and instead are regularly nursed by the brood-attending worker bees. As the pheromonal cues presumably are located on the surface of newly hatched bee larvae, we extracted the cuticular secretions and analyzed their chemical composition by gas chromatograph-mass spectrometry (GC-MS) analyses. Larvae were sexed and then reared in vitro for up to three days. The GC-MS pattern that was obtained, with alkanes as the major compounds, was compared between diploid and haploid drone larvae. We also examined some physical parameters of adult drones. There was no difference between diploid and haploid males in their weight at the day of emergence. The diploid adult drones had fewer wing hooks and smaller testes. The sperm DNA content was 0.30 and 0.15 pg per nucleus, giving an exact 2:1 ratio for the gametocytes of diploid and haploid drones, respectively. Vitellogenin was found in the hemolymph of both types of imaginal drones at 5 to 6 days, with a significantly lower titer in the diploids.

Screening for glycosylphosphatidylinositol-anchored proteins in the Paracoccidioides brasiliensis transcriptome.

Abstract: Open reading frames in the transcriptome of Paracoc- cidioides brasiliensis were screened for potential glycosylphosphati- dylinositol (GPI)-anchored proteins, which are a functionally and struc- turally diverse family of post-translationally modified molecules found in a variety of eukaryotic cells. Numerous studies have demonstrated that various GPI anchor sequences can affect the localization of these pro- teins in the plasma membrane or the cell wall. The GPI anchor core is produced in the endoplasmic reticulum by sequential addition of monosac- charides and phospho-ethanolamine to phosphatidylinositol. The com- plete GPI anchor is post-translationally attached to the protein carboxyl- terminus by GPI transamidases. Removal of this GPI lipid moiety by phospholipases generates a soluble form of the protein. The identifica- tion of putative GPI-attached proteins in the P. brasiliensis transcrip- tome was based on the following criteria: the presence of an N-terminal signal peptide for secretion and a hydrophobic region in the C-terminus presenting the GPI-attachment site. The proteins that were identified were in several functional categories: i) eight proteins were predicted to be enzymes (Gel1, Gel2, Gel3, α-amylase, aspartic proteinase, Cu-Zn

Reconfigurable systems for sequence alignment and for general dynamic programming

Abstract: Reconfigurable systolic arrays can be adapted to effi- ciently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic architecture that can be applied for the efficient treatment of several dynamic program- ming methods for resolving well-known problems, such as global and local sequence alignment, approximate string matching and longest com- mon subsequence. The dynamicity of the reconfigurability was found to be useful for practical applications in the construction of sequence align- ments. A VHDL (VHSIC hardware description language) version of this new architecture was implemented on an APEX FPGA (Field pro- grammable gate array). It would be several magnitudes faster than the software algorithm alternatives.

Hydrolases in the hypopharyngeal glands of workers of Scaptotrigona postica and Apis mellifera (Hymenoptera, Apinae)

Abstract: Hydrolytic enzymes from hypopharyngeal gland extracts of newly emerged, nurse and foraging workers of two eusocial bees, Scaptotrigona postica, a native Brazilian stingless bee, and the Africanized honey bee (Apis mellifera) in Brazil, were compared. The hypopharyngeal gland is rich in enzymes in both species. Fifteen different enzymes were found in the extracts, with only a few quantitative differences between the species. Some of the enzymes present in the extracts may have intracellular functions, while others seem to be digestive enzymes. Scaptotrigona postica, had lower beta-glucosidase and higher lipase esterase activities than A. mellifera. The differences may be due to different feeding habits and behavioral peculiarities of the two species.

Optimization of a multiplex minisequencing protocol for population studies and medical genetics.

Abstract: Several technologically sophisticated high-throughput tech- niques have been recently developed for the study of human single nucleo- tide polymorphisms and the diagnosis of point mutations in human dis- eases. However, there is also a need for simple and inexpensive tech- niques suitable for clinical services and small research laboratories. Minisequencing meets the latter requirements. It is simple, non-radioac- tive and can be easily multiplexed by adding oligonucleotide tails of in- creasing size to the sequencing oligonucleotide primers. To optimize the minisequencing protocol, we designed a test multiplex system capable of typing simultaneously 12 different human autosomal single nucleotide polymorphisms. We discovered that the quality of minisequencing prim- ers and the careful selection of the tail sequences were especially criti- cal for success. This optimized protocol permits rapid genotyping at low cost and can serve as a blueprint for the creation of multiplex minisequencing systems suitable to virtually any typing application in population studies and medical genetics.

The cell wall of Paracoccidioides brasiliensis: insights from its transcriptome.

Abstract: The cell wall of a human pathogenic fungus is in contact with the host, serves as a barrier against host defense mechanisms and harbors most fungal antigens. In addition, cell wall biosynthesis path- ways have been recognized as essential to viability and as specific drug targets. Paracoccidioides brasiliensis is a dimorphic fungus that pre- sents mycelium morphology in the free environment and causes infec- tion in a yeast form. The morphogenetic conversion is correlated with changes in the cell wall composition, organization and structure. Based on transcriptome analysis, the enzymes involved in the biosynthesis and remodeling of cell wall polysaccharides, as well as several cell wall- associated molecules of P. brasiliensis, were identified and addressed in further detail.

Evidence for a natural hybrid of peacock bass (Cichla monoculus vs Cichla temensis) based on esterase electrophoretic patterns.

Abstract: Esterase (Est) and esterase-D (Est-D) electrophoretic patterns identified by starch gel electrophoresis of skeletal muscle pro- tein extracts of 184 specimens of three species of peacock bass, locally known as tucunares (Cichla monoculus, C. temensis and Cichla sp), plus four specimens of a supposed hybrid (C. monoculus vs C. temensis), collected from the Central Amazon, were examined to determine if they could aid in identifying a supposed hybrid between C. monoculus and C. temensis. Six zones of electrophoretic activity were found with these enzyme systems. The Est enzyme showed one zone of activity, formed by bands 1, 2 and 3, plus three zones of activity, presumably controlled by Est-1, 2 and 3 loci. The Est-D enzyme had two zones of activity, presumably controlled by Est-D1 and Est-D2 loci. Cichla monoculus and C. temensis shared band 2 and alleles Est-1 1 , Est-2 1 , Est-3 2 , and Est-D1 1 , and therefore these were useless for identifying hybrids be- tween the two species. However, a probable hybrid pattern of bands 1, 2, and 3, presumably generated by a combination of pattern 12 from C. monoculus with pattern 23 from C. temensis, resulting from a possible cross between these two species, was detected. Although the Est-D2 locus cannot be considered an ideal diagnostic marker for identifying the supposed hybrid (C. monoculus vs C. temensis), as it is polymorphic, it

Heritability and expected selection response for yield traits in blanched asparagus.

Abstract: Despite the continuous breeding that has been conducted with asparagus (Asparagus officinalis L.) since the beginning of the last century, there is little information on parameters for predicting direct and indirect selection response. Yield traits for blanched asparagus pro- duction were studied along a two-year period in a half-sib family popula- tion planted in Zavalla, Argentina. Half-sib family mean heritability val- ues were low for total yield and marketable spear number (0.31 and 0.35), intermediate for marketable yield and total spear number (0.55 and 0.64), and relatively high for spear diameter and spear weight (0.75 and 0.74). An average increase in marketable yield of 15.9% is ex- pected after each cycle of selection of the top 5% of the families. Total yield failed to express significant genetic correlations with any of the yield components; meanwhile marketable yield showed highly signifi- cant relations with market spear number (0.96) and spear weight (0.89). Indirect selection response over yield components (CRx) failed to be advantageous over direct selection (Rx), since the ratio CRx/Rx was always equal or below unity.

Genetic and non-genetic effects on productive and reproductive traits of cows in dual-purpose herds in southeastern Mexico.

Abstract: Data on productive and reproductive performance of cows in dual-purpose herds were analyzed to determine the effect of some environmental and genetic factors on saleable milk yield (SMY), lactation length (LL), daily saleable milk per lactation (DMYL), calving interval (CI), and daily saleable milk per calving interval (MYCI) in dual- purpose herds in Yucatan, Mexico. Repeatabilities (r e ) for these traits were also estimated. Data were obtained from monthly visits to 162 herds from 1996 to 2000. The fixed factors studied were: region (cen- tral, eastern and southern), parity number (1 to 6), calving year (1996 to 2000) and calving season (dry, rainy and windy and rainy), genetic group (low- ( 50%) grade cows with European genes). About 2700 to 7700 cows were evaluated for each trait. All factors had significant effects (P < 0.05) on the traits except for region on CI and calving season on DMYL. The overall means for SMY, LL, DMYL, CI, and MYCI were: 1322.3 ± 80.5 kg, 224.8 ± 1.3 days,

Effectiveness of liposomes to transfect livestock fibroblasts.

Abstract: The development of an efficient transfection system in livestock cells is an important step towards investigating gene transfer and the functioning and production of transgenic animals. Important factors involved in cationic liposome mediated gene transfer were evaluated through in vitro transfection of bovine, caprine and ovine fibroblast cells. Transfection of plasmid DNA complexes of different commercially available liposomes (Lipofectamine, Lipofectin, Cellfectin and DMRIE-C; Gibco-BRL, USA) was evaluated utilizing the following parameters: DNA/liposome ratio, cell density, DNA conformation, and the effect of transfection time on the efficiency of bovine fibroblasts to express a reporter gene. The effects and concentrations of liposomes were also evaluated in caprine and ovine fibroblasts. Lipofectamine alone and Lipofectamine with Plus reagent induced high-frequency expression of beta-galactosidase and neo genes in all cells evaluated (47 and 88.3%, respectively). Regarding phenotype, chromosomal stability was similar in transfected and non-transfected cells. The parameters set in this study will establish a foundation for utilizing transfected fibroblast cells to generate transgenic animals through nuclear transfer technology and gene function studies.

Gene selection based on multi-class support vector machines and genetic algorithms

Abstract: Microarrays are a new technology that allows biologists to better understand the interactions between diverse pathologic state at the gene level. However, the amount of data generated by these tools becomes problematic, even though data are supposed to be automatically analyzed (e.g., for diagnostic purposes). The issue becomes more complex when the expression data involve multiple states. We present a novel approach to the gene selection problem in multi-class gene expression-based cancer classification, which combines support vector machines and genetic algorithms. This new method is able to select small subsets and still improve the classification accuracy.

Construction of a human Fab phage display library from antibody repertoires of osteosarcoma patients.

Abstract: Osteosarcoma is the commonest type of primary malig- nant bone tumor, frequently found in adolescents at sites of rapid bone growth. Despite current management protocols, up to half of the pa- tients succumb to this disease. Moreover, there is no well-characterized molecular marker for diagnosis and prognosis. Since phage display meth- odology allows the selection of human antibody fragments with potential use in clinical applications, we applied this procedure to construct a re- combinant Fab (antigen binding fragment) library from patients with os- teosarcoma. We used peripheral blood lymphocyte total RNA from 11 osteosarcoma patients and cloned recombinant Fab representing the µ, γ and κ chain antibody repertoires of these individuals. The resulting li- brary was cloned in the pComb3X vector and attained 1.45 x 10 8 differ- ent functional forms. BstO I fingerprinting and DNA sequencing analy- sis of randomly selected clones revealed the diversity of the library, dem- onstrating that Fab harbors Vκ chains from subgroups I to V, biased

General metabolism of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis.

Abstract: Annotation of the transcriptome of the dimorphic fungus Paracoccidioides brasiliensis has set the grounds for a global understanding of its metabolism in both mycelium and yeast forms. This fungus is able to use the main carbohydrate sources, including starch, and it can store reduced carbons in the form of glycogen and trehalose; these provide energy reserves that are relevant for metabolic adaptation, protection against stress and infectivity mechanisms. The glyoxylate cycle, which is also involved in pathogenicity, is present in this fungus. Classical pathways of lipid biosynthesis and degradation, including those of ketone body and sterol production, are well represented in the database of P. brasiliensis. It is able to synthesize de novo all nucleotides and amino acids, with the sole exception of asparagine, which was confirmed by the fungus growth in minimal medium. Sulfur metabolism, as well as the accessory synthetic pathways of vitamins and co-factors, are likely to exist in this fungus.