Assessment of genetic diversity and population structure in cultured Australian Pacific oysters

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (H_E) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low‐density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.     

Some plasma hormones and metabolites in the Pyrenean brown trout (Salmo trutta fario).

1. Pyrenean brown trout (Salmo trutta fario) from 200 to 1700 g were analysed in lots of 12 specimens in March, April, July and October 1988, and in January 1989. 2. Hormones (insulin, glucagon, cortisol) and metabolites (glucose, lactate, proteins, triglycerides) were determined in plasma. 3. Body parameters (length and weight) increased progressively, while plasma metabolites and hormones were more dependent on seasonal and sexual conditions. 4. Plasma insulin presented a maximum in spring (11 ng/ml) and a minimum in January (5 ng/ml). A clear relationship between insulin and annual growth rates was established. Plasma glucagon showed annual values between 700 and 1500 pg/ml, with significant seasonal variations. The molar ratio glucagon/insulin oscillated from 0.21 in January to 0.38 in July. 5. Plasma glucose variations agreed with those of pancreatic hormones, especially evident with glucagon levels. Proteins were more uniform throughout year, and plasma lipids were especially associated to the reproductive state in females.     

Temporal properties of some biological systems and their fractal attractors

In this paper we analyse time series data as the growth of organisms using markers such as treerings and otolith deposits (fish). The series studied belong to two tree species (Pinus uncinata, Fagus sylvatica) and one fish species (Dicentrarchus labrax). Spectral analyses of the time series growth show that the main frequencies of fluctuation may be due to variations of the energy input. However, any causal explanation must consider the internal continuous readjustment in the system as reported by the corresponding chaotic properties of the asymptotic decay of the spectra time structure. Since the output of noisy and chaotic systems tend to show similar spectral densities, an attempt to differentiate them has been carried out. The chaotic behaviour has been characterized by the study of the attractors. The dimmensions of these multiple topologies were 3.2 and 3.4 for the tree species and 2.3 for the fish species. Therefore, we are dealing with fractal attractors and the minimum number of variables that can be used to describe the systems are 4 and 3 respectively. It is suggested that some of the variables that most influence growth are those obtained by the response functions in the case of trees.     

Moonlighting activity of the epigenetic machinery restrains infection

Intracellular bacterial pathogens have evolved a range of mechanisms, including manipulation of the host cell epigenetic machinery and host cell gene expression rewiring, to parasitize and thrive inside host phagocytes. A new study in The EMBO Journal (Yaseen et al, 2018 ) reports that, conversely, host macrophages can use epigenetic modulators to modify the cell surface of invading pathogens and counteract infection. This study opens new avenues to better understand host–pathogen interactions and to develop novel, more effective antimicrobial strategies.     

Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet

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TGFB1 polymorphisms and TGF-β1 plasma levels identify gastric adenocarcinoma patients with lower survival rate and disseminated disease

TGF-β1 is involved in tumour growth. Four TGFB1 SNPs and TGF-β1 production by stimulated PBMC were determined in seventy-eight gastric adenocarcinoma patients. In addition, TGF-β1 levels were measured in the plasma of further thirty patients. rs1800471-G/C genotype was prevalent in patients (20.7%) compared to controls (8.4%), as it also was the rs1800468 SNP-G/A genotype in stage IV patients (20.7%) compared to stage I, II and III patients, combined (10.3%). Conversely, the T/T rs1800469 SNP-T/T genotype was absent in the former group and present in 19.0% in the latter. Furthermore, the rs1800469-C/rs1800470-T (CT) haplotype was found in 15.0% of stage IV patients as compared to 3.0% of the remaining patients (3.0%) and also identifies patients with worse five-year life expectancy (P = .03). TGF-β1 synthesis by stimulated PBMCs was significantly lower in patients with the risk SNPs or haplotype, compared to the alternative genotype. Finally, TGF-β1 plasma levels were lower in patients with worse life expectancy. Analysis of TGFB1 SNPs and measurement of plasma TGF-β1 levels serves to identify patients at risk of developing a more aggressive disease.     

Closure to efficient causation, computability and artificial life

The major insight in Robert Rosen's view of a living organism as an (M,R)-system was the realization that an organism must be “closed to efficient causation”, which means that the catalysts needed for its operation must be generated internally. This aspect is not controversial, but there has been confusion and misunderstanding about the logic Rosen used to achieve this closure. In addition, his corollary that an organism is not a mechanism and cannot have simulable models has led to much argument, most of it mathematical in nature and difficult to appreciate. Here we examine some of the mathematical arguments and clarify the conditions for closure.