A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31

Although both the alpha-amylase super-family, i.e. the glycoside hydrolase (GH) clan GH-H (the GH families 13, 70 and 77), and family GH31 share some characteristics, their different catalytic machinery prevents classification of GH31 in clan GH-H. A significant but remote evolutionary relatedness is, however, proposed for clan GH-H with GH31. A sequence alignment, based on the idea that residues equivalent in the primordial catalytic GH-H/GH31 (beta/alpha)(8)-barrel may not be found in the present-day GH-H and GH31 structures at strictly equivalent positions, shows remote sequence homologies covering beta3, beta4, beta7 and beta8 of the GH-H and GH31 (beta/alpha)(8)-barrels. Structure comparison of GH13 alpha-amylase and GH31 alpha-xylosidase guided alignment of GH-H and GH31 members for construction of evolutionary trees. The closest sequence relationship displayed by GH31 is to GH77 of clan GH-H.     

Anaerobic digestion of alfalfa silage with recirculation of process liquid

Process liquid recirculation initially stimulated one-phase anaerobic digestion of alfalfa silage in two semi-continuously fed and stirred tank reactors. Thus, with increased pH, alkalinity and stability it was possible to increase the organic loading rate to 3 g VS L(-1) d(-1), as compared to 2.25 g VS L(-1) d(-1) in a control reactor without recirculation. However, the recirculation of liquid eventually caused an accumulation of organic and inorganic substances, leading to an inhibition of hydrolysis and methanogenesis. This inhibition of microbial activity was prevented in one of the processes by replacing 50% of the recirculated process liquid with water during the second half of the operation period. A multiple linear regression model of principal components using seven input variables explained the variance in output variables nearly as well as the original model using all 23 measured input variables. The results show that it is necessary to adjust the degree of liquid recirculation to reach an optimal process.     

Revisiting the peripheral sink hypothesis: inhibiting BACE1 activity in the periphery does not alter β‐amyloid levels in the CNS

Aggregation of amyloid beta (Aβ) peptides and the subsequent neural plaque formation is a central aspect of Alzheimer's disease. Various strategies to reduce Aβ load in the brain are therefore intensely pursued. It has been hypothesized that reducing Aβ peptides in the periphery, that is in organs outside the brain, would be a way to diminish Aβ levels and plaque load in the brain. In this report, we put this peripheral sink hypothesis to test by investigating how selective inhibition of Aβ production in the periphery using a β‐secretase (BACE)1 inhibitor or reduced BACE1 gene dosage affects Aβ load in the brain. Selective inhibition of peripheral BACE1 activity in wild‐type mice or mice over‐expressing amyloid precursor protein (APPswe transgenic mice; Tg2576) reduced Aβ levels in the periphery but not in the brain, not even after chronic treatment over several months. In contrast, a BACE1 inhibitor with improved brain disposition reduced Aβ levels in both brain and periphery already after acute dosing. Mice heterozygous for BACE1, displayed a 62% reduction in plasma Aβ40, whereas brain Aβ40 was only lowered by 11%. These data suggest that reduction of Aβ in the periphery is not sufficient to reduce brain Aβ levels and that BACE1 is not the rate‐limiting enzyme for Aβ processing in the brain. This provides evidence against the peripheral sink hypothesis and suggests that a decrease in Aβ via BACE1 inhibition would need to be carried out in the brain.

     

Dominant Genetic Variation and Missing Heritability for Human Complex Traits: Insights from Twin versus Genome-wide Common SNP Models

In order to further illuminate the potential role of dominant genetic variation in the “missing heritability” debate, we investigated the additive (narrow-sense heritability, h²) and dominant (δ²) genetic variance for 18 human complex traits. Within the same study base (10,682 Swedish twins), we calculated and compared the estimates from classic twin-based structural equation model with SNP-based genomic-relatedness-matrix restricted maximum likelihood [GREML(d)] method. Contributions of δ² were evident for 14 traits in twin models (average δ²_twin = 0.25, range 0.14–0.49), two of which also displayed significant δ² in the GREMLd analyses (triglycerides δ²_SNP = 0.28 and waist circumference δ²_SNP = 0.19). On average, the proportion of h²_SNP/h²_twin was 70% for ADE-fitted traits (for which the best-fitting model included additive and dominant genetic and unique environmental components) and 31% for AE-fitted traits (for which the best-fitting model included additive genetic and unique environmental components). Independent evidence for contribution from shared environment, also in ADE-fitted traits, was obtained from self-reported within-pair contact frequency and age at separation. We conclude that despite the fact that additive genetics appear to constitute the bulk of genetic influences for most complex traits, dominant genetic variation might often be masked by shared environment in twin and family studies and might therefore have a more prominent role than what family-based estimates often suggest. The risk of erroneously attributing all inherited genetic influences (additive and dominant) to the h² in too-small twin studies might also lead to exaggerated “missing heritability” (the proportion of h² that remains unexplained by SNPs).     

Asymmetric isolating barriers between different microclimatic environments caused by low immigrant survival

Spatially variable selection has the potential to result in local adaptation unless counteracted by gene flow. Therefore, barriers to gene flow will help facilitate divergence between populations that differ in local selection pressures. We performed spatially and temporally replicated reciprocal field transplant experiments between inland and coastal habitats using males of the common blue damselfly (Enallagma cyathigerum) as our study organism. Males from coastal populations had lower local survival rates than resident males at inland sites, whereas we detected no differences between immigrant and resident males at coastal sites, suggesting asymmetric local adaptation in a source–sink system. There were no intrinsic differences in longevity between males from the different environments suggesting that the observed differences in male survival are environment-dependent and probably caused by local adaptation. Furthermore, the coastal environment was found to be warmer and drier than the inland environment, further suggesting local adaptation to microclimatic factors has lead to differential survival of resident and immigrant males. Our results suggest that low survival of immigrant males mediates isolation between closely located populations inhabiting different microclimatic environments.     

Sequencing of 15 622 gene‐bearing BACs clarifies the gene‐dense regions of the barley genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole‐genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene‐containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical‐mapped gene‐bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene‐enriched BACs and are characterized by high recombination rates, there are also gene‐dense regions with suppressed recombination. We made use of published map‐anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D‐genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map‐based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene‐dense but low recombination is particularly relevant.     

Parasitic spawning in sand gobies: an experimental assessment of nest-opening size, sneaker male cues, paternity, and filial cannibalism

Sneaking is common in nest-building fish with paternal care,but the role of nest-opening size in protecting against entryby sneaker males has never been tested before. Using the sandgoby (Pomatoschistus minutus), a fish with exclusive paternalcare, experimental manipulations of nest openings provided nosupport for the hypothesis that nest openings serve as physicalor visual defense or that sneaker males prefer to parasitizenests with wide openings. Female mating preference was alsonot influenced by nest-opening size. However, female courtshipbehavior and visibility were important cues for sneaker males.Most sneak entries occurred when the nest holder was occupiedwith courtship, chasing another sneaker male or nest building.In half the cases of observed sneak entry, the sneaker malefertilized eggs, also when sneaking only occurred before spawning.Sneak entry and its duration were good estimates of stolen paternity,but neither sneak entries nor degree of fertilizations werecorrelated with filial cannibalistic behavior. Testes size didnot explain parasitic spawning success in replicates with geneticallydetermined sneaking. However, all sneaker males without breedingcoloration had huge testes and small sperm duct glands, whereasnest-holding males had small testes and large sperm duct glands,and sneaker males with breeding coloration were intermediate.     

Infection with genotoxin‐producing Salmonella enterica synergises with loss of the tumour suppressor APC in promoting genomic instability via the PI3K pathway in colonic epithelial cells

Several commensal and pathogenic Gram‐negative bacteria produce DNA‐damaging toxins that are considered bona fide carcinogenic agents. The microbiota of colorectal cancer (CRC) patients is enriched in genotoxin‐producing bacteria, but their role in the pathogenesis of CRC is poorly understood. The adenomatous polyposis coli (APC) gene is mutated in familial adenomatous polyposis and in the majority of sporadic CRCs. We investigated whether the loss of APC alters the response of colonic epithelial cells to infection by Salmonella enterica, the only genotoxin‐producing bacterium associated with cancer in humans. Using 2D and organotypic 3D cultures, we found that APC deficiency was associated with sustained activation of the DNA damage response, reduced capacity to repair different types of damage, including DNA breaks and oxidative damage, and failure to induce cell cycle arrest. The reduced DNA repair capacity and inability to activate adequate checkpoint responses was associated with increased genomic instability in APC‐deficient cells exposed to the genotoxic bacterium. Inhibition of the checkpoint response was dependent on activation of the phosphatidylinositol 3‐kinase pathway. These findings highlight the synergistic effect of the loss of APC and infection with genotoxin‐producing bacteria in promoting a microenvironment conducive to malignant transformation.     

Body size evolution in an old insect order: No evidence for Cope's Rule in spite of fitness benefits of large size

We integrate field data and phylogenetic comparative analyses to investigate causes of body size evolution and stasis in an old insect order: odonates (“dragonflies and damselflies”). Fossil evidence for “Cope's Rule” in odonates is weak or nonexistent since the last major extinction event 65 million years ago, yet selection studies show consistent positive selection for increased body size among adults. In particular, we find that large males in natural populations of the banded demoiselle (Calopteryx splendens) over several generations have consistent fitness benefits both in terms of survival and mating success. Additionally, there was no evidence for stabilizing or conflicting selection between fitness components within the adult life‐stage. This lack of stabilizing selection during the adult life‐stage was independently supported by a literature survey on different male and female fitness components from several odonate species. We did detect several significant body size shifts among extant taxa using comparative methods and a large new molecular phylogeny for odonates. We suggest that the lack of Cope's rule in odonates results from conflicting selection between fitness advantages of large adult size and costs of long larval development. We also discuss competing explanations for body size stasis in this insect group.