Benchmarking in a beef cattle breeding program: Lessons from the best breeders.

Beef cattle breeding programs offer genetic evaluations and consulting services on animal breeding practices to help breeders improve the genetic merit of their herds. Some breeders are more willing to apply best practices and technologies than others. Consequently, the average genetic merit and genetic trends differ across herds. We benchmarked some parameters of an average herd (AVE) and the corresponding parameters of herds with higher genetic merit (TOP), both participating in a commercial Nellore breeding program. Expected progeny differences (EPD) for growth, reproductive and carcass traits and a selection index (SI) of animals born from 2005 to 2019 on 128 farms located in Brazil, Bolivia and Paraguay were used to compute the AVE parameters. The 20 herds with higher mean SI of animals born in the last five birth seasons were classified as TOP herds. The mean SI and EPD of animals born in the last five seasons in the TOP herds were, respectively, 89% and 79% to 206% higher (p ≤ 0.001) than those of animals from the AVE herd. Genetic trends over the entire period were also higher (50% for SI and 31% to 88% separately for each trait, p ≤ 0.006) in the TOP herds compared to the AVE herd. Although the difference in the numbers of cows, bulls and calves between the TOP and AVE herds did not reach statistical significance (p = 0.175, p = 0.273 and p = 0.061, respectively), the numbers of progeny per cow and per bull were 21% (p = 0.012) and 26% (p = 0.047) higher in the TOP herds, respectively. Multiple ovulation and embryo transfer and in vitro fertilization and embryo transfer (MOET/IVF) accounted for a higher percentage of births in the TOP herds compared to AVE (24.6% vs. 12.5%, p = 0.002). The generation interval was 17% shorter (p < 0.001) in the TOP herds compared to AVE. The average inbreeding coefficient of animals from the TOP herds (1.08 ± 0.52%) did not differ (p = 0.78) from that of AVE animals (1.26 ± 0.96%). In general, AVE herds are evolving in the desirable direction but differences in genetic merit between AVE and TOP herds are increasing over time. The more frequent use of MOET/IVF, a lower cow-to-bull ratio, and a larger family size (progeny per cow or per bull) can help achieve larger selection differentials and increase genetic trends and average genetic merits of TOP herds compared to AVE herds.

Offseason Medfly Trapping Using Makeshift Fruit-Based and Wine Vinegar Baits.

Development of cost-effective traps and attractants is important for sustainable pest management. In the case of the Medfly, Ceratitis capitata Wiedemann, a worldwide pest of fruit production, recent interest in development of mass trapping strategies and low-cost easy-to-get artisanal traps for resource poor grower use has prompted renewed interest in research on attractants and traps. Additionally, such interest is also rooted on the need for effective female attractants to monitor wild population dynamics under male-only sterile fly releases. Response of wild flies and sterile males to makeshift traps (modified polyethylene terephthalate (pet) bottles) baited with fruit juice and wine vinegar dilutions with and without the addition of sugar revealed that a 50% dilution of wine vinegar or sweetened orange juice were more attractive than the standard Torula baits during the offseason (after harvest) in a peach orchard in arid irrigated valleys of San Juan Argentina. Such results suggest that volatiles from orange peel and juice are good candidates for development of Medfly attractants, and that pet bottles baited with sweetened orange juice and wine vinegar may be used by small growers and homeowners as low-cost-effective traps for Medfly control. Our results also suggest that Medfly response to food-based and fruit-based volatiles may be seasonally dynamic, a finding with important pest management implications.

Culex quinquefasciatus carrying Wolbachia is less susceptible to entomopathogenic bacteria.

In an attempt to evaluate the susceptibility of the mosquito Culex quinquefasciatus to bacterial agents, a population naturally infected with a Wolbachia pipientis wPipSJ native strain was tested against the action of three bacterial mosquitocides, Bacillus thuringiensis subsp. israelensis, Bacillus wiedmannii biovar thuringiensis and Lysinibacillus sphaericus. Tests were carried out on mosquito larvae with and without Wolbachia (controls). Cx. quinquefasciatus naturally infected with the native wPipSJ strain proved to be more resistant to the pathogenic action of the three mosquitocidal bacterial strains. Additionally, wPipSJ was fully characterised using metagenome-assembled genomics, PCR-RFLP (PCR-Restriction Fragment Length Polymorphism) and MLST (MultiLocus Sequence Typing) analyses. This Wolbachia strain wPipSJ belongs to haplotype I, group wPip-III and supergroup B, clustering with other mosquito wPip strains, such as wPip PEL, wPip JHB, wPip Mol, and wAlbB; showing the southernmost distribution in America. The cytoplasmic incompatibility phenotype of this strain was revealed via crosses between wildtype (Wolbachia+) and antibiotic treated mosquito populations. The results of the tests with the bacterial agents suggest that Cx. quinquefasciatus naturally infected with wPipSJ is less susceptible to the pathogenic action of mosquitocidal bacterial strains when compared with the antibiotic-treated mosquito isoline, and is more susceptible to B. thuringiensis subsp. israelensis than to the other two mosquitocidal agents.

Molecular tool for monitoring the safety of Aedes (Stegomyia) aegypti Rockefeller rearing in arthropod containment facilities

Abstract The interest in and use of Aedes (Stegomyia) aegypti (Linnaeus) (Diptera: Culicidae) insectary lines increased in most laboratories around the world since the recognition of the transmission of human and animal pathogens by this mosquito species, resulting in further scientific research on tropical diseases and vectors, and the development of chemical and biological products for mosquito populations control. In recent years, approaches to mosquito populations reduction have focused on new technologies that include the release of Wolbachia-infected lines, genetically modified vector and insects subjected to radiation in the Sterile Insect Technique. In order to evaluate some of these techniques, it is essential to count with wild A. aegypti populations and the reference strain, accurately identified, maintained under laboratory conditions. This work proposes a new tool to monitor possible exchanges between reference mosquito strain and wild native populations of A. aegypti in neighboring areas, or between different lines in the same insectary. We aligned and compared ND5 gene fragments of A. aegypti from diverse sources, finding a region with putative Single Nucleotide Polymorphisms between individuals of Rockefeller (Rock) strain and different wild A. aegypti populations. These polymorphic sites in the molecular marker, allowed us to discriminate Rock reference strain from the wild A. aegypti haplotypes found in the southeast of Argentina and bordering areas with Brazil, Uruguay and Paraguay, and it can be useful as a tool for regulatory entities of mosquito insectaries at different Arthropod Containment Levels.

GEHEP 010 study: Prevalence and distribution of hepatitis B virus genotypes in Spain (2000-2016).

OBJECTIVE: To study the prevalence and distribution of HBV genotypes in Spain for the period 2000-2016. METHODS: Retrospective study recruiting 2559 patients from 17 hospitals. Distribution of HBV genotypes, as well as sex, age, geographical origin, mode of transmission, HDV-, HIV- and/or HCV-coinfection, and treatment were recorded. RESULTS: 1924 chronically HBV native Spanish patients have been recruited. Median age was 54 years (IQR: 41-62), 69.6% male, 6.3% HIV-coinfected, 3.1% were HCV-coinfected, 1.7% HDV-co/superinfected. Genotype distribution was: 55.9% D, 33.5% A, 5.6% F, 0.8% G, and 1.9% other genotypes (E, B, H and C). HBV genotype A was closely associated with male sex, sexual transmission, and HIV-coinfection. In contrast, HBV genotype D was associated with female sex and vertical transmission. Different patterns of genotype distribution and diversity were found between different geographical regions. In addition, HBV epidemiological patterns are evolving in Spain, mainly because of immigration. Finally, similar overall rates of treatment success across all HBV genotypes were found. CONCLUSIONS: We present here the most recent data on molecular epidemiology of HBV in Spain (GEHEP010 Study). This study confirms that the HBV genotype distribution in Spain varies based on age, sex, origin, HIV-coinfection, geographical regions and epidemiological groups.

New real-time-PCR method to identify single point mutations in hepatitis C virus.

AIM: To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV). METHODS: In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. LightCycler methods, based on real-time PCR with sequence-specific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest. RESULTS: Using nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10% (mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80K was detected in 14.6% of G1a patients and 0% of G1b in our setting. CONCLUSION: A fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This technique can be adapted to detect any single point mutation in highly variable genomes.

New findings in HCV genotype distribution in selected West European, Russian and Israeli regions.

BACKGROUND: HCV affects 185 million people worldwide and leads to death and morbidities. HCV has a high genetic diversity and is classified into seven genotypes and 67 subtypes. Novel anti-HCV drugs (Direct-Acting-Antivirals) eligibility, resistance and cure rates depend on HCV geno/subtype (GT). OBJECTIVES: Analysis of epidemiological information and viral GT from patients undergoing viral genotyping in 2011-2015. STUDY DESIGN: Anonymized information from 52 centers was analyzed retrospectively. RESULTS: 37,839 samples were included in the study. We show that the GT distribution is similar throughout Western European countries, with some local differences. Here GTs 1 and 2 prevalences are lower and of GT4 higher than in all previous reports. Israel has a unique GT pattern and in South Russia the GT proportions are more similar to Asia. GTs 5 and 6 were detected in very low proportions. Three cases of the recombinant genotype P were reported in Munich (Germany). In addition, we observed that GT proportion was dependant on patients gender, age and transmission route: GTs 1b and 2 were significantly more common in female, older, nosocomially-infected patients, while GTs 1a, 3 and 4 were more frequent in male, younger patients infected by tattooing, drug consume, and/or sexual practices. In infections acquired by drug consume, GTs 1a (35.0%) and 3 (28.1%) prevailed. In infections related to sexual practices lower proportion of GT3 (14.0%) and higher of GT4 (20.2%) were detected. GT4 was mostly abundant in MSM (29.6%). HIV coinfection was significantly associated with higher proportions GTs 1a and 4 (42.5% and 19.3%, respectively). CONCLUSION: Genotype prevalence evolves and correlates to epidemiological factors. Continuous surveillance is necessary to better assess hepatitis C infection in Europe and to take appropriate actions.

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast.

Culex pipiens is the most cosmopolitan mosquito of the Pipiens Assemblage. By studying the nature of interactions between this species and microorganisms common to its breeding environment we can unravel important pitfalls encountered during development. We tested the survival rate of larval stages, pupae and adults of a Cx. pipiens colony exposed to a variety of microorganisms in laboratory conditions and assessed the transmission to offspring (F1) by those organisms that secured development up to adulthood. Three complementary experiments were designed to: 1) explore the nutritional value of yeasts and other microorganisms during Cx. pipiens development; 2) elucidate the transstadial transmission of yeast to the host offspring; and 3) to examine the relevance of all these microorganisms in female choice for oviposition-substratum. The yeast Saccharomyces cerevisiae proved to be the most nutritional diet, but despite showing the highest survival rates, vertical transmission to F1 was never confirmed. In addition, during the oviposition trials, none of the gravid females was attracted to the yeast substratum. Notably, the two native bacterial strains, Klebsiella sp. and Aeromonas sp., were the preferred oviposition media, the same two bacteria that managed to feed neonates until molting into 2nd instar larvae. Our results not only suggest that Klebsiella sp. or Aeromonas sp. serve as attractants for oviposition habitat selection, but also nurture the most fragile instar, L1, to assure molting into a more resilient stage, L2, while yeast proves to be the most supportive diet for completing development. These experiments unearthed survival traits that might be considered in the future development of strategies of Cx. pipiens control. These studies can be extended to other members of the Pipiens Assemblage.

Complex Genotype Mixtures Analyzed by Deep Sequencing in Two Different Regions of Hepatitis B Virus.

This study assesses the presence and outcome of genotype mixtures in the polymerase/surface and X/preCore regions of the HBV genome in patients with chronic hepatitis B virus (HBV) infection. Thirty samples from ten chronic hepatitis B patients were included. The polymerase/surface and X/preCore regions were analyzed by deep sequencing (UDPS) in the first available sample at diagnosis, a pre-treatment sample, and a sample while under treatment. HBV genotype was determined by phylogenesis. Quasispecies complexity was evaluated by mutation frequency and nucleotide diversity. The polymerase/surface and X/preCore regions were validated for genotyping from 113 GenBank reference sequences. UDPS yielded a median of 10,960 sequences per sample (IQR 16,645) in the polymerase/surface region and 11,595 sequences per sample (IQR 14,682) in X/preCore. Genotype mixtures were more common in X/preCore (90%) than in polymerase/surface (30%) (p<0.001). On X/preCore genotyping, all samples were genotype A, whereas polymerase/surface yielded genotypes A (80%), D (16.7%), and F (3.3%) (p = 0.036). Genotype changes in polymerase/surface were observed in four patients during natural quasispecies dynamics and in two patients during treatment. There were no genotype changes in X/preCore. Quasispecies complexity was higher in X/preCore than in polymerase/surface (p = 0.004). The results provide evidence of genotype mixtures and differential genotype proportions in the polymerase/surface and X/preCore regions. The genotype dynamics in HBV infection and the different patterns of quasispecies complexity in the HBV genome suggest a new paradigm for HBV genotype classification.

High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods.

Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.

Clinical application of estimating hepatitis B virus quasispecies complexity by massive sequencing: correlation between natural evolution and on-treatment evolution.

AIM: To evaluate HBV quasispecies (QA) complexity in the preCore/Core regions in relation to HBeAg status, and explore QA changes under natural evolution and nucleoside analogue (NUC) treatment. METHODS: Ultra-deep pyrosequencing of HBV preCore/Core regions in 30 sequential samples (baseline [diagnosis], treatment-free, and treatment-nonresponse) from 10 retrospectively selected patients grouped according to HBeAg status over time: HBeAg+ (N = 4), HBeAg- (N = 2), and fluctuating HBeAg (transient seroreversion/seroconversion pattern) (N = 4). QA complexity was defined by Shannon entropy, mutation frequency, nucleotide diversity, and mutation frequency of amino acids (MfAA) in preCore and Core. RESULTS: The QA was less complex in HBeAg+ than in HBeAg- or fluctuating HBeAg. High complexity in preCore was associated with decreased viral replication (preCore MfAA negatively correlated with HBV-DNA, p = 0.005). QA complexity in the treatment-free period negatively correlated with values seen during treatment. Specific variants were mainly selected in the Core region in HBeAg- and fluctuating HBeAg patients, suggesting higher immune pressure than in HBeAg+. CONCLUSIONS: The negative correlation between QA natural evolution and on-treatment evolution indicates the importance of pre-treatment QA study to predict QA changes in NUC nonresponders. Study of QA complexity could be useful for managing HBV infection.

Distribution of mosquitoes in the south east of Argentina and first report on the analysis based on 18S rDNA and COI sequences.

Although Mar del Plata is the most important city on the Atlantic coast of Argentina, mosquitoes inhabiting such area are almost uncharacterized. To increase our knowledge in their distribution, we sampled specimens of natural populations. After the morphological identification based on taxonomic keys, sequences of DNA from small ribosomal subunit (18S rDNA) and cytochrome c oxidase I (COI) genes were obtained from native species and the phylogenetic analysis of these sequences were done. Fourteen species from the genera Uranotaenia, Culex, Ochlerotatus and Psorophora were found and identified. Our 18S rDNA and COI-based analysis indicates the relationships among groups at the supra-species level in concordance with mosquito taxonomy. The introduction and spread of vectors and diseases carried by them are not known in Mar del Plata, but some of the species found in this study were reported as pathogen vectors.

Karyotype morphology suggests that the Nyctibius griseus (Gmelin, 1789) carries an ancestral ZW-chromosome pair to the order Caprimulgiformes (Aves).

Studies of karyotypes have been revealing important information on the taxonomic relationships and evolutionary patterns in various groups of birds. However, the order Caprimulgiformes is one of the least known in terms of its cytotaxonomy. So far, there are no cytogenetic data in the literature on birds belonging to 3 of 5 families of this order -Nyctibiidae, Steatornithidae and Aegothelidae. For this reason, the aim of our study was to describe the karyotype of Nyctibius griseus (Gmelin, 1789) (Aves, Nyctibiidae, Caprimulgiformes) and contribute with new data that could help to clarify the evolutionary relationships in this group. Bone marrow was cultured directly to obtain material for the chromosome study. C-banding was used to visualize the constitutive heterochromatin and Ag-NOR-banding to reveal nucleolus organizer regions. The diploid number observed was 2n=86±. Using sequential Giemsa/C-banding staining, we determined that the W chromosome was entirely C-band positive with the two most prominent markers in the interstitial and distal regions of the long arm. The nucleolus organizer regions showed a typical location in a pair of microchromosomes that exhibited Ag-NOR.The results obtained for Nyctibius griseus suggest that, of all the species studied in the references cited, it has the most ancestral sex chromosome composition of the order Caprimulgiformes.

Fatores genéticos que influenciam a qualidade da carne bovina - revisão / Genetic factors influencing beef cattle quality - a review

A carne bovina deve corresponder as expectativas do consumidor, no que se refere aos atributos de qualidade sanitária, nutritiva e organoléptica. Numerosas pesquisas têm demonstrado que a composição genética dos animais é o fator intrínseco que mais afeta a qualidade da carne bovina, e asua composição de ácidos graxos. As diferenças genéticas existentes entre os bovinos podem ser exploradas mediante cruzamentos seletivos para melhorar a qualidade da carne. Trabalhos desenvolvidos recentemente demonstram que o DNA mitocondrial pode ser outro importante fator que afeta a qualidade da carne. Para que, modificações na qualidade da carne somente sejam postas em prática pelos produtores, deve haver incentivos econômicos.

Características de carcaça de cordeiros terminados em confinamento, com dietas contendo diferentes níveis protéicos / Carcass characteristics of lambs finished in drylot with diets contend different protein levels

Trinta e dois cordeiros (¹/2 Texel + » Bergamácia + » Corriedale), 16 machos inteiros e 16 fêmeas, foram alimentados durante 71 dias com dietas isoenergéticas (72 por cento NDT), variando os níveis protéicos (12, 16, 20 e 24 por cento PB) em baias individuais, com avaliaçäo de carcaça após abate. O rendimento verdadeiro médio da carcaça foi 54 por cento, enquanto o rendimento comercial médio foi 48 por cento. Verificou-se que os níveis protéicos entre 12 e 24 por cento näo afetaram o peso da carcaça quente e fria; o rendimento comercial da carcaça, o índice de compacidade da carcaça e do pernil, bem como a condiçäo corporal, conformaçäo, cobertura de gordura, consistência da gordura, cor da carne, espessura de gordura e deposiçäo de gordura. Os animais terminados com dietas com 12 por cento de proteína bruta foram os que apresentaram maior rendimento verdadeiro de carcaça