Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits

Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.

Genomic breed composition of pure registered Brazilian Gir

INTRODUCTION

Gir is a Bos indicus breed originally from India, first imported to Brazil in 1850. High-performance Dairy Gir has been systematically selected in Brazil from its arrival. Since the major phenotypic difference between Gir in India and Brazil is a higher milk production in the former, it is speculated that Brazilian Gir was strategically crossed with Holstein or another Bos taurus to improve milk yield. This study evaluated the purity of Brazilian Gir breed stocks from BASA Farms in Brazil, trying to identify possible admixture events with other cattle breeds based on DNA analysis.

MATERIALS AND METHODS

The population included 1061 pure registered individuals genotyped using two commercial platforms with 37 k and 25 k SNPs. Admixture analysis was performed individually to estimate levels of genomic composition derived from six different reference populations, three indicine and three taurine breeds.

RESULTS

A Gir ancestry of 99% or higher was found for 94.2% of the population, while the remaining showed levels of non-Gir ancestry up to 6.8%. Only five individuals were identified with possible taurine ancestry, all of them exhibiting levels lower than 2%. The remaining non-Gir ancestry identified was derived from indicine breeds. The levels of admixture observed in the population were from low to non-detectable. No consistent patterns of admixture were observed indicating sustained introgression of taurine lines as means of genetic improvement.

CONCLUSION

According to these results, genetic improvement achieved by Brazilian Gir breeders is the result of within-breed selection methods applied intensively over the past five decades, rather than the result from sustained introgression.

Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle

Brazil is the largest exporter of beef in the world, and most of that beef derives from Nellore cattle. Although considered a zebu breed (Bos indicus), the history of Nellore cattle in Brazil is marked by the importation of bulls from India, the use of a Creole taurine (Bos taurus) maternal lineage to quickly expand the herds and backcrossing to Nellore bulls to recover zebu ancestry. As a consequence, the current Brazilian Nellore population carries an average taurine ancestry of approximately 1%. Although that percentage seems small, some taurine variants deviate substantially from that average, with the better-known cases being the PLAG1-Q haplotype involved with body size variation and the Guarani (P_G ) polled variant producing hornless animals. Here, we report taurine haplotypes in 9074 Nellore animals genotyped for 539 657 imputed SNP markers. Apart from PLAG1-Q and P_G , our analysis further revealed common taurine haplotypes (>3%) spanning genes related to immunity, growth, reproduction and hair and skin phenotypes. Using data from 22 economically important traits, we showed that many of the major QTL previously reported in the breed are at least partially driven by taurine haplotypes. As B. taurus and B. indicus haplotypes are highly divergent, presenting widely different sets of functional variants, our results provide promising targets for future scrutiny in Nellore cattle.

Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle

Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs

In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single-step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (-0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six-residue deletion that is fixed in the canine species but absent in non-canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six-residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids.

Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls

Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.

Genomic clues of the evolutionary history of Bos indicus cattle

Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.

Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed

The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus-specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.

Dietary fat modulation of hepatic lipase variant -514 C/T for lipids: a crossover randomized dietary intervention trial in Caribbean Hispanics

The hepatic lipase (LIPC) locus is a well-established determinant of high-density lipoprotein cholesterol (HDL-C) concentrations, an association that is modified by dietary fat in observational studies. Dietary interventions are lacking. We investigated dietary modulation of LIPC rs1800588 (-514 C/T) for lipids and glucose using a randomized crossover design comparing a high-fat Western diet and a low-fat traditional Hispanic diet in individuals of Caribbean Hispanic descent (n = 42, 4 wk/phase). No significant gene-diet interactions were observed for HDL-C. However, differences in dietary response according to LIPC genotype were observed. In major allele carriers (CC/CT), HDL-C (mmol/l) was higher following the Western diet compared with the Hispanic diet: phase 1 (Western: 1.3 ± 0.03; Hispanic: 1.1 ± 0.04; P = 0.0004); phase 2 (Western: 1.4 ± 0.03; Hispanic: 1.2 ± 0.03; P = 0.0003). In contrast, HDL-C in TT individuals did not differ by diet. Only major allele carriers benefited from the higher-fat diet for HDL-C. Secondarily, we explored dietary fat quality and rs1800588 for HDL-C and triglycerides (TG) in a Boston Puerto Rican Health Study (BPRHS) subset matched for diabetes and obesity status (subset n = 384). In the BPRHS, saturated fat was unfavorably associated with HDL-C and TG in rs1800588 TT carriers. LIPC rs1800588 appears to modify plasma lipids in the context of dietary fat. This new evidence of genetic modulation of dietary responses may inform optimal and personalized dietary fat advice and reinforces the importance of studying genetic markers in diet and cardiometabolic health.

Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle

Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (F_st ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and F_st was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.

Genome wide association study on early puberty in Bos indicus

The aim of this study was to evaluate a genome wide association study (GWAS) approach to identify single nucleotide polymorphisms (SNPs) associated with fertility traits (early puberty) in Nellore cattle (Bos indicus). Fifty-five Nellore cows were selected from a herd monitored for early puberty onset (positive pregnancy at 18 months of age). Extremes of this phenotype were selected; 30 and 25 individuals were pregnant and non-pregnant, respectively, at that age. DNA samples were genotyped using a high-density SNP chip (>777.000 SNP). GWAS using a case-control strategy highlighted a number of significant markers based on their proximity with the Bonferroni correction line. Results indicated that chromosomes 5, 6, 9, 10, and 22 were associated with the traits of interest. The most significant SNPs on these chromosomes were rs133039577, rs110013280, rs134702839, rs109551605, and rs41639155. Candidate genes, as well as quantitative trait loci (QTL) previously reported in the Ensembl and Cattle QTLdb databases, were further investigated. Analysis of the regions close to the SNP on chromosomes 9 and 10 revealed that four QTL had been previously classified under the reproduction category. In conclusion, we have identified SNPs in close proximity to genes associated with reproductive traits. Moreover, U6 spliceosomal RNA was present on three different chromosomes, which is possibly associated with age at first calving, suggesting that it might be a strong candidate for future studies.

A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle

The aim of this study was to identify candidate genes and genomic regions associated with ultrasound-derived measurements of the rib-eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for REA; OSBPL3 and SUDS3 for BFT; and RARRES1 and VEPH1 for RFT. The physiological pathway related to lipid metabolism (CLSTN2, OSBPL3, RARRES1 and VEPH1) was identified. The significant markers within previously reported QTLs reinforce the importance of the genomic regions, and the other loci offer candidate genes that have not been related to carcass traits in previous investigations.

Genome-wide association with residual body weight gain in Bos indicus cattle

Weight gain is a key performance trait for beef cat-tle; however, attention should be given to the production costs for better profitability. Therefore, a feed efficiency trait based on per-formance can be an interesting approach to improve performance without increasing food costs. To identify candidate genes and ge-nomic regions associated with residual body weight gain (RWG), we conducted a genome-wide association study (GWAS) with 720 Nellore cattle using the GRAMMAR-Gamma association test. We identified 30 significant single nucleotide polymorphisms (SNPs), especially on chromosomes 2, 8, 12, and 17. Several genes and quantitative train loci (QTLs) present in the regions identified were appointed; we highlight DMRT2 (doublesex and mab-3 related tran-scription factor 2), IFFO2 (intermediate filament family orphan 2), LNX2 (ligand of numb-protein X 2), MTIF3 (mitochondrial transla-tional initiation factor 3), and TRNAG-CCC (transfer RNA glycine anticodon CCC). The metabolic pathways that can explain part of the phenotypic variation in RWG are related to oxidative stress and muscle control.

Synthesis of plastic scintillation microspheres: alpha/beta discrimination

Plastic scintillation microspheres (PSm) have been developed as an alternative for liquid scintillation cocktails due to their ability to avoid the mixed waste, besides other strengths in which the possibility for alpha/beta discrimination is included. The aim of this work was to evaluate the capability of PSm containing two combinations of fluorescence solutes (PPO/POPOP and pT/Bis-MSB) and variable amounts of a second organic solvent (naphthalene) to enhance the alpha/beta discrimination. Two commercial detectors with different Pulse Shape Discrimination performances (Quantulus and Triathler) were used to evaluate the alpha/beta discrimination. An optimal discrimination of alpha/beta particles was reached, with very low misclassification values (2% for beta particles and 0.5% for alpha particles), when PSm containing PPO/POPOP and between 0.6 and 2.0 g of naphthalene were evaluated using Triathler and the appropriate programme for data processing.

Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

The genome-wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354,147 single-nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777,962 SNPs) and Illumina BovineSNP50 (54,609) by imputation were used. After quality control and imputation, 290,620 SNPs remained in the association analysis, using R package Genome-wide Rapid Association using Mixed Model and Regression method GRAMMAR-Gamma. A genomic region with six significant SNPs, at Bonferroni-corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10(-8)) explained 5.62% of the phenotypic variance and had the allele substitution effect of -0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.

Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep

A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F(1) rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume - PCV and faecal egg count - FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm) were scored and corrected by Genoprob prior to qxpak analysis that included Box-Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box-Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL.

Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources

In livestock genetic resource conservation, decision making about conservation priorities is based on the simultaneous analysis of several different criteria that may contribute to long-term sustainable breeding conditions, such as genetic and demographic characteristics, environmental conditions, and role of the breed in the local or regional economy. Here we address methods to integrate different data sets and highlight problems related to interdisciplinary comparisons. Data integration is based on the use of geographic coordinates and Geographic Information Systems (GIS). In addition to technical problems related to projection systems, GIS have to face the challenging issue of the non homogeneous scale of their data sets. We give examples of the successful use of GIS for data integration and examine the risk of obtaining biased results when integrating datasets that have been captured at different scales.

Myostatin (GDF8) single nucleotide polymorphisms in Nellore cattle

The myostatin gene, also known as GDF8 (growth differentiation factor 8), is located on bovine chromosome 2 (BTA2); it has three exons and two introns. Myostatin is specifically expressed during embryonic development and in adult skeletal muscle, functioning as a negative regulatory protein. Several cattle breeds (Piedmontese, Belgian Blue and Blond'Aquitaine, and others) show polymorphisms in this gene; these polymorphisms are directly related to the double muscling phenotype. We looked for polymorphisms in the Nellore cattle myostatin gene and compared them with those known for taurine breeds. Seven regions, covering the three exons of this gene, were amplified by polymerase chain reaction and sequenced, including the untranslated region. DNA from 30 adult Nellore animals was collected; DNA sequencing revealed three, seven and four polymorphisms in exons 1, 2 and 3, respectively. We found previously reported polymorphisms, as well as several new ones; for instance, 37 polymorphisms were found in the untranslated region segment, and in introns 1 and 2 there were one and three polymorphisms, respectively. The high degree of allelic heterogeneity in the myostatin gene could be related to its high mutation rate; it also could be the result of a long history of artificial selection for meat production, which has probably favored such modifications and maintained them in cattle populations. These polymorphisms identified in Nellore cattle could be useful for breeding programs.

258 FACTORS AFFECTING COMMERCIAL SEXING PROGRAM AND MULTIPLE GENETIC ANALYSIS PERSPECTIVES OF IN VITRO-PRODUCED BOVINE EMBRYOS

The present study aimed to evaluate the interactions among different factors on the viability and sex ratio of in vitro-produced (IVP) bovine embryos, submitted to a large scale sexing program. Additionally, whole genome amplification (WGA) technology was used to amplify genomic DNA from IVP bovine embryo biopsies, in order to perform multiple genetic analyses. The survey was performed in a 4650 IVP bovine sexed embryo database. Embryos were biopsied by a microaspiration technique and sex was determined by PCR of DNA from the biopsy. Only female embryos were transferred to synchronized recipients. Pregnancy diagnosis and fetal sex determination were carried out by ultrasound. The variables were classified in accordance with embryo sex (male, female, and indeterminate), five laboratories (A, B, C, D, and E), six bovine breeds (Nellore, Brahman, Girolando, Simmental, Holstein, and Jersey), embryo stage (MO, EB, BL, XB, and HB), embryo quality (1, 2, and 3) and biopsy quality (“standard” and “nonstandard”). The statistical analysis was carried out by association chi-square test, chi-square for a 1:1 ratio, and logistic regression analysis (PROC LOGISTIC) of SAS. PCR showed 93.3% efficiency, 93.2% accuracy, and male and female rates of 52.9% and 47.1%, respectively. Mortality rate of biopsied embryos was 10.3% and pregnancy rate was 31.7%. Significant differences were not observed between male and female viability, although indeterminate embryos resulted in more death after micromanipulation. For quality 2 and 3 embryos, the mortality rate after biopsy was 3.19 and 11.37 fold higher, respectively, than for quality 1 embryos. For embryos whose biopsies were classified as nonstandard, the embryonic mortality rate was 3.6-fold higher than standard ones. Mortality rate was not affected by embryo stage at biopsy (P > 0.05). Although sex ratio was significantly skewed to male embryos, differences were not observed among laboratories (P > 0.05) and breeds (P > 0.05) on the sex ratio of IVP bovine embryos. To test the feasibility of using WGA method for multiple genetic analysis, biopsies from 28 IVP embryos were submitted to the GenomePlex Single Cell System (Sigma-Aldrich, St. Louis, MO, USA). Aliquots from each DNA sample were purified using column chromatography and submitted to PCR using sexing primers BRY4a, SRY, UMN0920, and S4B. PCR was successful and in agreement among tested DNA aliquots from each single biopsy. The WGA strategy used herein was a useful tool for applications involving restricted amounts of starting genetic material (DNA), such as in preimplantation genetic diagnosis using IVP bovine embryos. To FAPESP and UNESP.

Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758)

The Pampas deer (Ozotoceros bezoarticus) is one of the most endangered Neotropical cervid with populations that have been drastically reduced to small and isolated ones, mainly because of its habitat destruction. Random amplified polymorphic DNA (RAPD) markers were used to analyze population divergence and genetic variation within and between two populations corresponding to distinct subspecies. The RAPD markers displayed substantial genetic variation with all animals possessing unique RAPD phenotypes over 105 polymorphic bands produced by 15 primers. An analysis of molecular variance (AMOVA) and a neighbor-joining cluster analysis were performed to assess levels of differentiation between populations. No differentiation was recorded and about 96.0% (P<0.00001) of the total variance was attributable to variation within populations. This result is quite distinct from data obtained by the analysis of the mtDNA control region, and is discussed on the basis of genetic differences between the different markers and the male-biased dispersal patterns generally observed in the mammal species. The data presented herein are potentially useful for future taxonomic and genetic studies in this species, for the monitoring of the genetic variation observed within these populations, and for the development of management guidelines for its conservation.

Genetic diversity of microsatellite loci in Leopardus pardalis, Leopardus wiedii and Leopardus tigrinus

The microsatellite loci FCA045, FCA077, FCA008, and FCA096 are highly variable molecular markers which were used to determine the genetic diversity in 148 captive Leopardus sp. The PCR-amplified products of microsatellite loci were characterized in ABI Prism 310 Genetic Analyzer. Allele numbers, heterozygosity, polymorphism information content, exclusive allele number, and shared alleles were calculated. Sixty-five alleles were found and their sizes ranged from 116 to 216 bp in four microsatellite loci. The heterozygosity ranged from 0.36 to 0.81 in Leopardus pardalis, 0.57 to 0.67 in L. tigrinus and 0.80 to 0.92 in L. wiedii. The polymorphism information content was from 0.80 to 0.88 in L. pardalis, 0.76 to 0.88 in L. tigrinus and 0.77 to 0.90 in L. wiedii. The margay (L. wiedii) showed the highest index of polymorphism among the three species in this study. These results imply that microsatellite DNA markers can help in the study of the genetic diversity of Leopardus specimens.

Comparison of parasitological, immunological and molecular methods for the diagnosis of leishmaniasis in dogs with different clinical signs

Aiming to improve the diagnosis of canine leishmaniasis (CanL) in an endemic area of the Northwest region of São Paulo State, Brazil, the efficacy of parasitological, immunological and molecular diagnostic methods were studied. Dogs with and without clinical signs of the disease and positive for Leishmania, by direct parasite identification on lymph node smears and/or specific antibody detection by ELISA, were selected for the study. According to the clinical signs, 89 dogs attending the Veterinary Hospital of UNESP in Araçatuba (SP, Brazil) were divided into three groups: symptomatic (36%), oligosymptomatic (22%) and asymptomatic (22%). Twenty-six dogs from an area non-endemic for CanL were used as negative controls (20%). Fine-needle aspiration biopsies (FNA) of popliteal lymph nodes were collected and Diff-Quick-stained for optical microscopy. Direct immunofluorescence, immunocytochemistry and parasite DNA amplification by PCR were also performed. After euthanasia, fragments of popliteal lymph nodes, spleen, bone marrow and liver were collected and processed for HE and immunohistochemistry. Parasite detection by both HE and immunohistochemistry was specifically more effective in lymph nodes, when compared with the other organs. Immunolabeling provided higher sensitivity for parasite detection in the tissues. In the symptomatic group, assay sensitivity was 75.61% for direct parasite search on Diff-Quick-stained FNAs, 92.68% for direct immunofluorescence, 92.68% for immunocytochemistry and 100% for PCR; the corresponding values in the other clinical groups were: 32, 60, 76 and 96% (oligosymptomatic), and 39.13, 73.91, 100 and 95.65% (asymptomatic). Results of the control animals from the CanL non-endemic area were all negative, indicating that the methods used were 100% specific.

Significantly improved PCR-based clonality testing in B-cell malignancies by use of multiple immunoglobulin gene targets. Report of the BIOMED-2 Concerted Action BHM4-CT98-3936

Polymerase chain reaction (PCR) assessment of clonal immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements is an important diagnostic tool in mature B-cell neoplasms. However, lack of standardized PCR protocols resulting in a high level of false negativity has hampered comparability of data in previous clonality studies. In order to address these problems, 22 European laboratories investigated the Ig/TCR rearrangement patterns as well as t(14;18) and t(11;14) translocations of 369 B-cell malignancies belonging to five WHO-defined entities using the standardized BIOMED-2 multiplex PCR tubes accompanied by international pathology panel review. B-cell clonality was detected by combined use of the IGH and IGK multiplex PCR assays in all 260 definitive cases of B-cell chronic lymphocytic leukemia (n=56), mantle cell lymphoma (n=54), marginal zone lymphoma (n=41) and follicular lymphoma (n=109). Two of 109 cases of diffuse large B-cell lymphoma showed no detectable clonal marker. The use of these techniques to assign cell lineage should be treated with caution as additional clonal TCR gene rearrangements were frequently detected in all disease categories. Our study indicates that the BIOMED-2 multiplex PCR assays provide a powerful strategy for clonality assessment in B-cell malignancies resulting in high Ig clonality detection rates particularly when IGH and IGK strategies are combined.

Improved reliability of lymphoma diagnostics via PCR-based clonality testing: — Report of the BIOMED-2 Concerted Action BHM4-CT98-3936

The diagnosis of malignant lymphoma is a recognized difficult area in histopathology. Therefore, detection of clonality in a suspected lymphoproliferation is a valuable diagnostic criterion. We have developed primer sets for the detection of rearrangements in the B- and T-cell receptor genes as reliable tools for clonality assessment in lymphoproliferations suspected for lymphoma. In this issue of Leukemia, the participants of the BIOMED-2 Concerted Action CT98-3936 report on the validation of the newly developed clonality assays in various disease entities. Clonality was detected in 99% of all B-cell malignancies and in 94% of all T-cell malignancies, whereas the great majority of reactive lesions showed polyclonality. The combined BIOMED-2 results are summarized in a guideline, which can now be implemented in routine lymphoma diagnostics. The use of this standardized approach in patients with a suspect lymphoproliferation will result in improved diagnosis of malignant lymphoma.

Caspase-3 and caspase-6 in ductal breast carcinoma: a descriptive study

Caspases are the main point in the apoptotic process. We have collected some information from 210 cases of Ductal breast cancer (pT1 - pT2) such as tumour size, histological differentiation degree, lymph node status and tumor necrosis in the infiltrating component and we have evaluated the number of apoptotic cells or bodies by TUNEL technique as well as immunohistochemical studies to evaluate the expression of caspase 3 and caspase 6, and proliferation index. Our results show that lymph node status and cell atypism are independent prognostic factors for recurrence and mortality and only tumour size is an independent prognostic factor for recurrence. However, the apoptotic index and the immunohistochemical expression of caspases and cell proliferation index have not turned out to be independent prognostic factors neither for recurrence nor mortality. These results show that classic prognostic factors known until now are the most important factors to predict the evolution of the illness.

[Asymptomatic forms of the Severe Acute Respiratory Syndrome (SARS)]

Introduction

Une épidémie de pneumopathies atypiques est apparue en novembre 2002 dans la région Chinoise de Guangdong. Elle a ensuite été décrite sous le nom de syndrome respiratoire aigu sévère (SRAS) à partir de nouveaux foyers survenus à Hanoi et à Hong Kong en février 2003. En France, 5 cas reliés au même patient source ont été rapportés.

Observation

Nous rapportons l’observation d’un patient de 52 ans contact direct avec un cas probable de SRAS. À l’admission, le patient présente une hyperthermie isolée sans symptomatologie respiratoire associée à une lymphopénie et une cytolyse hépatique. La radiographie thoracique est normale. La tomodensitométrie thoracique objective l’existence d’un aspect en verre dépoli sous pleural. L’étude par PCR des prélèvements naso-pharyngés précoces (36^e heure) à la recherche du coronavirus associé au SARS sera négative. La confirmation du cas sera obtenue par l’étude sérologique.

Conclusions

Cette observation illustre l’existence de présentations cliniques frustres du syndrome respiratoire aigu sévère. La contagiosité des formes pauci symptomatiques n’est pas connue. Des analyses sérologiques permettront de mieux les préciser. Le danger actuel d’une recrudescence saisonnière particulièrement hivernale ne peut être écarté. Dans ce contexte, l’existence et la reconnaissance des formes pauci symptomatiques pour lesquelles la contagiosité ne peut être écartée est primordiale.

FOXP3, a selective marker for a subset of adult T-cell leukaemia/lymphoma

FOXP3 is a forkhead transcription factor family member, implicated in T-cell regulation, activation and differentiation. FOXP3 has been shown to be a master control gene for the development and function of CD4+/CD25+ regulatory T-cells (T(reg)). In this study, FOXP3 protein expression has been analysed using a new anti-FOXP3 monoclonal antibody in 172 paraffin-embedded lymphoma samples. FOXP3 expression in tumour cells was confined to adult T-cell leukaemia/lymphoma (ATLL) cases (17/25, 68%), with some variability in the intensity of the staining and the proportion of positive cells. No other lymphoma types studied exhibited FOXP3 expression in the malignant population. The selective expression of FOXP3 by tumour cells in ATLL makes this antibody a potentially useful diagnostic tool.

[Diverticula of the appendix and their complications: value of sonography (review of 21 cases)]

PURPOSE

Diverticulosis is defined by the presence of diverticula along any segment of the GI tract. Diverticulosis and its associated complications may involve the appendix. The imaging and histological findings of 21 cases of diverticulitis of the appendix are reviewed.

MATERIALS AND METHODS

Sonography, because of its high spatial resolution, is an ideal imaging technique to diagnose diverticulitis of the appendix.

RESULTS

Similar to diverticulosis of the large bowel, diverticula of the appendix correspond to pseudo-diverticula composed of mucosa and sub mucosa herniating through the muscular layer. Chronic inflammatory changes affect the surrounding appendicular wall, as confirmed by histological examination. Clinical symptoms range from chronic right lower quadrant abdominal pain to acute appendicitis and even peritonitis.

CONCLUSION

Based on this retrospective analysis of 21 cases, it is possible to describe the specific and sensitive imaging findings for diagnosis of simple and complicated forms of diverticulitis of the appendix. Surgery is the treatment of choice because of the high risk of perforation.

Improvement in embryo recovery using double uterine flushing

The objective of the present study was to evaluate the effects of double uterine flushing on the recovery of embryos/ova in cattle. Two hundred and ten embryo recovery procedures were conducted using a double uterine flushing method, and the results were compared with 432 conventional single-flushing procedures. Cyclic Limousin (n = 403) and Guzera (n = 239) donor cows received an intravaginal progesterone releasing device and 2 mg of estradiol benzoate on Day 0. Between Days 5 and 9, donors received decreasing doses of FSH, which ranged from 200 to 300 IU (Bos indicus) and 300 to 500 IU (Bos taurus). On the afternoon of Day 7, donors received an injection of 500 microg cloprostenol and progesterone implants were removed 12 h later (morning of Day 8). Artificial insemination was performed between 14 and 26 h after first detection of behavioral estrus. Cows were randomly assigned to have embryos recovered by a double-flushing method (n = 210) or the conventional single-flushing procedure (n = 432). For the double-flushing procedure, after first flushing the whole uterus with 1L of Dubelco's Phosphate Buffered Saline (DPBS), a Foley catheter was positioned in the uterine body to permit refilling of the uterus with fresh DPBS (80-150 mL). The catheter was closed with the plunger of a disposable 5 mL syringe, and the donors were allowed to rest in a holding area for 30 min. Thereafter, a second flush was performed to recover the solution remaining in the uterus. Animals from the control group were subjected to a single uterine flush. From 210 double-flushing procedures, 1409 viable embryos were recovered. In comparison, from 432 cows receiving the single-flushing procedure, 1993 embryos were recovered. Double flushing increased (P < 0.05) the number of embryos recovered per procedure compared to single flushing (6.7 +/- 0.4 versus 4.6 +/- 0.2, respectively; mean +/- S.E.M.). When double flushing was performed, average recovered embryos/ova increased (P < 0.05) from 8.3 +/- 0.4 to 12.7 +/- 0.7 in Limousin and from 7.9 to 11.5 in Guzera. Also, utilization of double flushing increased (P < 0.05) the number of viable embryos from 4.7 +/- 0.3 to 6.9 +/- 0.5 in Limousin and from 4.5 +/- 0.4 to 6.4 +/- 0.7 in Guzera. Mean total embryos/ova was similar (P > 0.05) between the control group and after the first uterine flushing in the double-flushing group; therefore, both flushings were conducted efficiently. In conclusion, double uterine flushing increased embryo recovery in cattle.

Production of a cloned calf from a fetal fibroblast cell line

The present study examined the in vitro and in vivo development of bovine nuclear-transferred embryos. A bovine fetal fibroblast culture was established and used as nucleus donor. Slaughterhouse oocytes were matured in vitro for 18 h before enucleation. Enucleated oocytes were fused with fetal fibroblasts with an electric stimulus and treated with cytochalasin D and cycloheximide for 1 h followed by cycloheximide alone for 4 h. Reconstructed embryos were cultured for 7-9 days and those which developed to blastocysts were transferred to recipient cows. Of 191 enucleated oocytes, 83 (43.5%) were successfully fused and 24 (28.9%) developed to blastocysts. Eighteen freshly cloned blastocysts were transferred to 14 recipients, 5 (27.8%) of which were pregnant on day 35 and 3 (16.7%) on day 90. Of the three cows that reached the third trimester, one recipient died of hydrallantois 2 months before term, one aborted fetus was recovered at 8 months of gestation, and one delivered by cesarian section a healthy cloned calf. Today, the cloned calf is 15 months old and presents normal body development (378 kg) and sexual behavior (libido and semen characteristics).

Practical considerations of embryo manipulation: preimplantation genetic typing

In the past years, research in embryo technologies is moving to the establishment of preimplantation genetic typing or also denominated preimplantation genetic diagnosis (PGD). The objectives of these tests are the prevention of genetic diseases transmission and the prediction of phenotypic characteristics, as well as sex determination, genetic disorders and productive and reproductive profiles, prior to the embryo transfer or freezing, during early stages of development. This paper points out the state-of-the-art of PGD, mainly in cattle and discuss the perspectives of multiloci genetic analysis of embryos.

Diagnostic accuracy of compression ultrasonography for the detection of asymptomatic deep venous thrombosis in medical patients--the TADEUS project

We assessed the accuracy of venous compression ultrasonography (CUS) for the detection of asymptomatic deep vein thrombosis in 122 consecutive patients, with a mean age of 69 years, who were hospitalised in an internal medicine unit. All included patients had CUS within 48 h of admission. Twelve out of 17 patients with a positive CUS underwent phlebography, as the others withdrew their consent, whereas the remaining 105 patients with a negative serial CUS testing were clinically followed-up at 3 months. We found that CUS had a sensitivity and a specificity of respectively 1 (95% CI, 0.73 to 1) and 1 (95% CI, 0.96 to 1) for the detection of asymptomatic deep vein thrombosis. Kappa-coefficients for intra-observer and inter-observer agreements were respectively 0.88 and 0.56. We concluded that venous compression ultrasonography, performed as described, fulfils requirements of a screening test that could be available for prophylactic clinical trials or epidemiological researches.

[Unusual course of a pulmonary artery catheter through a persistent superior vena cava]

We report the unusual course of a pulmonary artery catheter through a persistent left-sided superior vena cava. After left subclavian vein cannulation and downward left-sided paramediastinum course, the Swan-Ganz catheter enters the right pulmonary artery. Haemodynamic monitoring was consistent with the diagnosis of septic shock developed by this 56-year-old woman, after cephalic duodenopancreatectomy. Persistent left-sided superior vena cava occurs in 0.5% of the population and 5-10% of patients with congenital heart diseases. It drains into the right atrium through the coronary sinus in 92% of cases and is associated with an absent right superior vena cava in 20% of cases. The left-sided superior vena cava persists when the caudal part of the left anterior cardinal vein does not degenerate. A persistent left superior vena cava may be medically relevant during implantation of pacemaker leads or radiofrequency ablation, during cardiac surgery for placement of a retrograde coronary sinus cardioplegia catheter and during transjugular intrahepatic portosystemic shunt placement.

Cloning and functional expression of a Boophilus microplus cathepsin L-like enzyme

A cysteine proteinase gene homologous to cathepsins L genes was isolated from a B. microplus cDNA library. The precursor protein deduced from the nucleotide sequence contains 332 amino acid residues consisting of a signal sequence (pre-region), a pro-region and a mature proteinase. The DNA fragment coding for the proenzyme was cloned and expressed using the E. coli expression vector pMAL-p. The recombinant protein (MBP+PROCP) once activated is able to hydrolyze synthetic substrates as well as protein substrates like hemoglobin, vitellin and gelatin. Its optimal enzymatic activity on both fluorogenic and protein substrates was found to occur at an acidic pH. Expression of the proteinase gene was tested by RT-PCR with tick larvae RNA. Detection of amplified sequences indicates that the gene is expressed at this stage of the tick life cycle and the molecule is therefore potentially a target for chemotherapy or an immunogen in a vaccine.

Sonographic evaluation of digital annular pulley tears

OBJECTIVE

To evaluate the sonographic (US) appearance of digital annular pulley (DAP) tears in high-level rock climbers.

DESIGN AND PATIENTS

We performed a retrospective analysis of the US examinations of 16 high-level rock climbers with clinical signs of DAP lesions. MRI and surgical evaluation were performed in five and three patients respectively. The normal US and MRI appearances of DAP were evaluated in 40 and three normal fingers respectively.

RESULTS

Nine of 16 patients presented a DAP tear. In eight subjects (seven with complete tears involving the fourth finger and one the fifth finger), US diagnosis was based on the indirect sign of volar bowstringing of the flexor tendons. Injured pulleys were not appreciated by US. Tears concerned the A2 and A3 in six patients and the A3 and A4 in two patients. A2 pulley thickening and hypoechogenicity compatible with a partial tear was demonstrated in one patient. MRI and surgical data correlated well with the US findings. Four patients had tenosynovitis of the flexor tendons but no evidence of pulley disruption. US examinations of three patients were normal. In the healthy subjects US demonstrated DAP in 16 of 40 digits.

CONCLUSION

US can diagnose DAP tears and correlates with the MRI and surgical data. Because of its low cost and non-invasiveness we suggest US as the first imaging modality in the evaluation of injuries of the digital pulley.

Predictors of atopy in HIV-infected patients

BACKGROUND

Some studies have reported an increase of atopy in HIV-infected (HIV+) patients, but the cause still remains unclear.

OBJECTIVE

To determine the prevalence of atopy in HIV+ patients and to investigate its predictors.

METHODS

Seventy-four HIV+ hospitalized patients (46 of them with AIDS) were studied prospectively for the presence of atopy, based on immediate hypersensitivity to common allergens by prick test. Serum immunoglobulins, specific IgE, lymphocyte subsets, and the expression of low affinity IgE receptor (CD23) on B cells were determined.

RESULTS

Thirty-one percent of patients presented IgE values greater than 150 ku/L (39% of patients without AIDS and 26% of AIDS patients; P = .23) and 47% showed an increase (> or = 2%) in the percentage of CD23+ B cells. Non-AIDS patients had higher IgE values than AIDS patients (346 +/- 605 versus 175 +/- 276; P = .16). Atopy prevalence was higher in non-AIDS than in AIDS patients (28% versus 11%; P = .06). Specific IgE agreed with positive prick test in 58% of cases. Multivariate analysis showed that a personal history suggestive of allergic disease and IgE > 150 ku/L were predictors of atopy, while gender, risk group, CD4+ T cells, CD23 expression on B cells, and AIDS were not associated.

CONCLUSIONS

HIV+ patients present a higher prevalence of atopy in early stages of HIV infection than general population. Since allergic reactions could accelerate HIV-infection by increasing type 2 cytokines, it is important to evaluate the atopic state in HIV+ patients with IgE > 150 ku/L or with suggestive allergic history in order to prevent it.

Detection and differentiation of Leptospira spp. serovars in bovine semen by polymerase chain reaction and restriction fragment length polymorphism

In view of the importance of venereal transmission of bovine leptospirosis, the objective of the present study was to apply the polymerase chain reaction (PCR) to 26 serovars of Leptospira interrogans, L. borgpetersenii, L. santarosai, L. noguchii and L. biflexa, to determine the detection threshold in semen samples and to evaluate the possibility of differentiation among serovars using 19 restriction endonucleases. The results showed that all serovars were amplified and the detection threshold in semen samples of a bull was 100 bacteria/ml. Using endonucleases we could classify the 26 serovars into eight groups. The present results show that PCR is a method of great potential for the detection of Leptospira spp. at bovine artificial insemination centers.