Validation of commercial DNA tests for quantitative beef quality traits

Associations between 3 commercially available genetic marker panels (GeneSTAR Quality Grade, GeneSTAR Tenderness, and Igenity Tender-GENE) and quantitative beef traits were validated by the US National Beef Cattle Evaluation Consortium. Validation was interpreted to be the independent confirmation of the associations between genetic tests and phenotypes, as claimed by the commercial genotyping companies. Validation of the quality grade test (GeneSTAR Quality Grade) was carried out on 400 Charolais x Angus crossbred cattle, and validation of the tenderness tests (GeneSTAR Tenderness and Igenity Tender-GENE) was carried out on over 1,000 Bos taurus and Bos indicus cattle. The GeneSTAR Quality Grade marker panel is composed of 2 markers (TG5, a SNP upstream from the start of the first exon of thyroglobulin, and QG2, an anonymous SNP) and is being marketed as a test associated with marbling and quality grade. In this validation study, the genotype results from this test were not associated with marbling score; however, the association of substituting favorable alleles of the marker panel with increased quality grade (percentage of cattle grading Choice or Prime) approached significance (P < or = 0.06), mainly due to the effect of 1 of the 2 markers. The GeneSTAR Tenderness and Igenity TenderGENE marker panels are being marketed as tests associated with meat tenderness, as assessed by Warner-Bratzler shear force. These marker panels share 2 common mu-calpain SNP, but each has a different calpastatin SNP. In both panels, there were highly significant (P < 0.001) associations of the calpastatin marker and the mu-calpain haplotype with tenderness. The genotypic effects of the 2 tenderness panels were similar to each other, with a 1 kg difference in Warner-Bratzler shear force being observed between the most and least tender genotypes. Unbiased and independent validation studies are important to help build confidence in marker technology and also as a potential source of data required to enable the integration of marker data into genetic evaluations. As DNA tests associated with more beef production traits enter the marketplace, it will become increasingly important, and likely more difficult, to find independent populations with suitable phenotypes for validation studies.     

Point mutations including a novel Pro-197-Phe mutation confer cross-resistance to acetolactate synthase (ALS) inhibiting herbicides in Lactuca serriola in Australia

BACKGROUND

Control of prickly lettuce has become increasingly difficult for lentil growers in southern Australia because of widespread resistance to common herbicides, a lack of alternative herbicide options and the prolific production of highly mobile seed. This study aimed to quantify acetolactate synthase (ALS)-inhibiting herbicide resistance in the Mid North (MN) and Yorke Peninsula (YP) of South Australia, characterize the resistance mutations present and investigate population structure and gene flow in this species.

RESULTS

Resistance was identified in all populations tested, with average survival of 92% to chlorsulfuron and 95% to imazamox + imazapyr. Five different amino acid substitutions were identified at proline 197 of the ALS gene. There was no significant difference in the median lethal dose (LD₅₀) between plants with these five different substitutions when treated with metsulfuron-methyl; however, the imidazolinone resistance level was higher in plants with a phenylalanine substitution and lower in plants with a serine. Population structure based on 701 single nucleotide polymorphisms and 271 individuals provided evidence for both independent evolution of the same mutation in different populations, as well as frequent short- to medium-distance dispersal accompanied by occasional long-distance dispersal events. The overall inbreeding coefficient (F_IS) was calculated at 0.5174, indicating an intermediate level of outcrossing despite the cross-pollination experiment showing only low outcrossing. In the structure analyses, most individuals from YP were assigned to a single cluster, whereas most individuals from MN were assigned 50% to each of two clusters, indicating some genetic differences between these two regions, but also evidence for dispersal between them.

CONCLUSIONS

Use of imidazolinone herbicides has selected for mutations conferring higher levels of resistance, such as the Pro-197-Phe mutation, and resulted in further spread of resistance in this species. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

Hertz-level measurement of the optical clock frequency in a single 88Sr+ ion

The frequency of the 5s 2S(1/2)-4d 2D(5/2) electric quadrupole clock transition in a single, trapped, laser-cooled 88Sr+ ion has been measured by using an optical frequency comb referenced to a cesium fountain primary frequency standard. The frequency of the transition is measured as 444,779,044,095,484.6 (1.5) hertz, with a fractional uncertainty within a factor of 3 of that of the cesium standard. Improvements required to obtain a cesium-limited frequency measurement are described and are expected to lead to a 88Sr+ optical clock with stability and reproducibility exceeding that of the primary cesium standard.     

Polarization of the C. elegans embryo by RhoGAP-mediated exclusion of PAR-6 from cell contacts

Early embryos of some metazoans polarize radially to facilitate critical patterning events such as gastrulation and asymmetric cell division; however, little is known about how radial polarity is established. Early embryos of Caenorhabditis elegans polarize radially when cell contacts restrict the polarity protein PAR-6 to contact-free cell surfaces, where PAR-6 regulates gastrulation movements. We have identified a Rho guanosine triphosphatase activating protein (RhoGAP), PAC-1, which mediates C. elegans radial polarity and gastrulation by excluding PAR-6 from contacted cell surfaces. We show that PAC-1 is recruited to cell contacts, and we suggest that PAC-1 controls radial polarity by restricting active CDC-42 to contact-free surfaces, where CDC-42 binds and recruits PAR-6. Thus, PAC-1 provides a dynamic molecular link between cell contacts and PAR proteins that polarizes embryos radially.     

Bioprospecting from Marine Sediments of New Brunswick,Canada: Exploring the Relationship between Total Bacterial Diversity and Actinobacteria Diversity

Actinomycetes are an important resource for the discovery of natural products with therapeutic properties. Bioprospecting for actinomycetes typically proceeds without a priori knowledge of the bacterial diversity present in sampled habitats. In this study, we endeavored to determine if overall bacterial diversity in marine sediments, as determined by 16S rDNA amplicon pyrosequencing, could be correlated with culturable actinomycete diversity, and thus serve as a powerful tool in guiding future bioprospecting efforts. Overall bacterial diversity was investigated in eight marine sediments from four sites in New Brunswick, Canada, resulting in over 44,000 high quality sequences (x = 5610 per sample). Analysis revealed all sites exhibited significant diversity (H’ = 5.4 to 6.7). Furthermore, statistical analysis of species level bacterial communities (D = 0.03) indicated community composition varied according to site and was strongly influenced by sediment physiochemical composition. In contrast, cultured actinomycetes (n = 466, 98.3% Streptomyces) were ubiquitously distributed among all sites and distribution was not influenced by sediment composition, suggesting that the biogeography of culturable actinomycetes does not correlate with overall bacterial diversity in the samples examined. These actinomycetes provide a resource for future secondary metabolite discovery, as exemplified by the antimicrobial activity observed from preliminary investigation.     

Mercury-induced blood anomalies in the freshwater teleost

Experimental Hg poisoning in the fish, Barbus conchonius led to marked hematological anomalies. Acute exposure to 181 μg L^?1 mercuric chloride (96 h LC50) led to erythrocytic anomalies including vacuolation, nuclear deterioration, microcytosis and collapsed cytoplasmic membranes. In addition, there was significant thrombocytosis and neutropenia together with a slight reduction in lymphocyte count. Chronic exposure to 36 and 60 μg L^?1 mercuric chloride led to poikilocytosis, hypochromia, fragmentation and nuclear displacement in erythrocytes. The large lymphocytes revealed vacuolation, cellular and nuclear hypertrophy and cytoplasmic outgrowths. Thrombocytosis, lymphocytosis, neutropenia and mild basophilia were manifested in fish subjected to chronic poisoning.     

Listeria monocytogenes gastroenteritis in sheep

Extract

Listeria monocytogenes is widely distributed in the environment of farm animals. It is found in soil, faeces and nasal secretions of healthy animals, water troughs and animal feeds. Under certain conditions it becomes pathogenic, causing serious disease in cattle and sheep. Most commonly it causes meningoencephalitis but, on occasion, septicaemic listeriosis results in abortion, and more recently it has been associated with gastroenteritis.     

Comparative pathogenicity of Theileria annulata strains

Summary

Twenty three susceptible crossbred calves were inoculated with five Indian strains of Theileria annulata, collected from natural cases of tropical theileriosis at Ludhiana, Hissar, Jaipur, Uruli‐Kanchan and Bangalore. All the strains produced clinical disease with typical symptoms and lesions of acute theileriosis. The strains were considered highly virulent and equally pathogenic.     

Microbial Contamination of the Abdominal Cavity in Commercial Carcasses Subject to Delays Before Evisceration

Abstract

Sir: Hygiene regulations require that carcasses be eviscerated soon after slaughter, and in recent years there have been moves in some countries to impose a relatively short time limit between death and evisceration. Although a number of reasons can be advanced for the utility of such a requirement,(3) Gill, C. O. 1979. Intrinsic bacteria in meat. J. Appl. Bacterial., 47: 367–378. [Crossref] , [Google Scholar] there is little doubt that a major original and continuing consideration is the belief that delays in evisceration can lead to contamination of carcasses by bacterial invasion from the intestine. It has been demonstrated that no such invasion actually occurs and that muscle tissue is usually sterile until exposed surfaces are contaminated by extraneous organisms.(1) Koneman, E. W. 1970. Post-mortem bacteriology. CRC Crit. Rev. Clin. Lab. Sci., 1: 5–23. [Taylor &; Francis Online] , [Google Scholar]     

Biological nitrogen fixation in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) by <Superscript>15</Superscript>N isotope-dilution and identification of associated culturable diazotrophs

The nitrogen-fixing capacity of a range of commercial cultivars of maize (Zea mays L.) was evaluated by the ¹⁵N isotope-dilution method. Biological nitrogen fixation (BNF) expressed as percent nitrogen derived from air (Ndfa) ranged from 12 to 33 regardless of nitrogen fertilization. BNF was not affected by mineral nitrogen fertilization except on cultivar Topacio and PAU-871 cultivars. Subsequently, culturable bacterial diazotrophs were isolated from endophytic tissue of maize: seed, root, stem, and leaf. All isolates were able to grow on N-free semisolid medium. Eleven bacteria isolates showed nitrogen-fixing capacity by the reduction of acetylene to ethylene and confirmed by PCR the presence of nifH gene in their genome. Identification of the 11 isolates was performed by bacteriological methods, 16S rRNA gene sequences, and phylogenetic analysis, which indicated that the bacteria isolated were closely related to Pantoea, Pseudomonas, Rhanella, Herbaspirillum, Azospirillum, Rhizobium (Agrobacterium), and Brevundimonas. This study demonstrated that maize cultivars obtain significant nitrogen from BNF, varying by maize cultivar and nitrogen fertilization level. The endophytic diazotrophic bacteria isolated from root, stem, and leaf tissues of maize cultivars may contribute to BNF in these plants.