MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.     

Oncoprotein CIP2A promotes the disassembly of primary cilia and inhibits glycolytic metabolism

In most mammalian cells, the primary cilium is a microtubule‐enriched protrusion of the plasma membrane and acts as a key coordinator of signaling pathways during development and tissue homeostasis. The primary cilium is generated from the basal body, and cancerous inhibitor of protein phosphatase 2A (CIP2A), the overexpression of which stabilizes c‐MYC to support the malignant growth of tumor cells, is localized in the centrosome. Here, we show that CIP2A overexpression induces primary cilia disassembly through the activation of Aurora A kinase, and CIP2A depletion increases ciliated cells and cilia length in retinal pigment epithelium (RPE1) cells. CIP2A depletion also shifts metabolism toward the glycolytic pathway by altering the expression of metabolic genes related to glycolysis. However, glycolytic activation in CIP2A‐depleted cells does not depend on cilia assembly, even though enhanced cilia assembly alone activates glycolytic metabolism. Collectively, these data suggest that CIP2A promotes primary cilia disassembly and that CIP2A depletion induces metabolic reprogramming independent of primary cilia.     

Early feed restriction of lambs modifies ileal epimural microbiota and affects immunity parameters during the fattening period

Bacteria firmly attached to the gastrointestinal epithelium during the pre-weaning phase may show a significant impact on nutrient processing, immunity parameters, health and feed efficiency of lambs during post-weaning phases. Thus, the aim of this study was to describe the differences in the ileal epimural microbiota (e.g. total bacteria, Prevotella spp., Bifidobacterium spp. and Lactobacillus spp.) of fattening lambs promoted by early feed restriction during the suckling phase trying to elucidate some of the underlying mechanisms behind changes in feed efficiency during the fattening period. A total of 24 Merino lambs (average BW 4.81±0.256 kg) were used, 12 of them (ad libitum, ADL) kept permanently in individual pens with their mothers, whereas the other 12 lambs were separated from their dams for 9 h each day to be exposed to milk restriction (RES). After weaning (BW=15 kg) all the animals were penned individually, offered the same complete pelleted diet (35 g/kg BW per day) and slaughtered at a BW of 27 kg. During the fattening period, reduced gain : feed ratio (0.320 v. 0.261, P<0.001) was observed for the RES group. Moreover, increments of Prevotella spp. were detected in the ileal epimural microbiota of RES lambs (P<0.05). There were also higher numbers of infiltrated lymphocytes (T and B cells) in the ileal lamina propria (P<0.05), a higher M-cell labelling intensity in ileal Peyer’s patches domes (P<0.05) and a trend towards a thickening of the submucosa layer when compared with the ADL group (P=0.057). Some other immunological parameters, such as an increased immunoglobulin A (IgA) production (pg IgA/µg total protein) and increments in CD45+ cells were also observed in the ileum of RES group (P<0.05), whereas transforming growth factor β and toll-like receptor gene expression was reduced (P<0.05). In conclusion, early feed restriction during the suckling phase promoted changes in ileal epimural microbiota and several immunity parameters that could be related to differences in feed efficiency traits during the fattening period of Merino lambs.     

Shoal size as a key determinant of vulnerability to capture under a simulated fishery scenario

Group living is widespread among animals and has a range of positive effects on individual foraging and predator avoidance. For fishes, capture by humans constitutes a major source of mortality, and the ecological effects of group living could carry‐over to harvest scenarios if fish are more likely to interact with fishing gears when in social groups. Furthermore, individual metabolic rate can affect both foraging requirements and social behaviors, and could, therefore, have an additional influence on which fish are most vulnerable to capture by fishing. Here, we studied whether social environment (i.e., social group size) and metabolic rate exert independent or interactive effects on the vulnerability of wild zebrafish (Danio rerio) to capture by a baited passive trap gear. Using video analysis, we observed the tendency for individual fish to enter a deployed trap when in different shoal sizes. Fish in larger groups were more vulnerable to capture than fish tested individually or at smaller group sizes. Specifically, focal fish in larger groups entered traps sooner, spent more total time within the trap, and were more likely to re‐enter the trap after an escape. Contrary to expectations, there was evidence that fish with a higher SMR took longer to enter traps, possibly due to a reduced tendency to follow groupmates or attraction to conspecifics already within the trap. Overall, however, social influences appeared to largely overwhelm any link between vulnerability and metabolic rate. The results suggest that group behavior, which in a natural predation setting is beneficial for avoiding predators, could be maladaptive under a trap harvest scenario and be an important mediator of which traits are under harvest associated selection.     

Sugars act as signal molecules and osmotica to regulate the expression of α-amylase genes and metabolic activities in germinating cereal grains

The molecular mechanisms that initiate and control the metabolic activities of seed germination are largely unknown. Sugars may play important roles in regulating such metabolic activities in addition to providing an essential carbon source for the growth of young seedlings and maintaining turgor pressure for the expansion of tissues during germination. To test this hypothesis, we investigated the physiological role of sugars in the regulation of -amylase gene expression and carbohydrate metabolism in embryo and endosperm of germinating rice seeds. RNA gel blot analysis revealed that in the embryo and aleurone cells, expression of four -amylase genes was differentially regulated by sugars via mechanisms beyond the well-known hormonal control mechanism. In the aleurone cells, expression of these -amylase genes was regulated by gibberellins produced in the embryo and by osmotically active sugars. In the embryo, expression of two -amylase genes and production of gibberellins were transient, and were probably induced by depletion of sugars in the embryo upon imbibition, and suppressed by sugars influx from the endosperm as germination proceeded. The differential expression of the four -amylase genes in the embryo and aleurone cells was probably due to their markedly different sensitivities to changes in tissue sugar levels. Our study supports a model in which sugars regulate the expression of -amylase genes in a tissue-specific manner: via a feedback control mechanism in the embryo and via an osmotic control mechanism in the aleurone cells. An interactive loop among sugars, gibberellins, and -amylase genes in the germinating cereal grain is proposed.     

Physiological energetics of the zebra musselDreissena polymorpha in lakes III. Metabolism and net growth efficiency

Oxygen consumption and ammonia excretion of the zebra musselDreissena polymorpha from 3 sites in lakes were estimated regularly over the course of 1 1/2 years at ambient temperature. They showed a pronounced annual cycle, when expressed in absolute terms (at standard shell length) and in weight specific terms (at standard tissue weight). The atomic ratio of oxygen consumed to ammonia-N released (O/N ratio) was lowest in late summer at all sites (10 to 20) and highest during winter and spring (50 to > 100). The mean body weight exponent pooled from these sites was 0.78 (95% confidence interval±0.07) for the oxygen consumption rate and 0.80 (confidence interval±0.10) for the ammonia excretion rate. Both oxygen consumption and ammonia excretion were significantly correlated with the water temperature at the 2 shallow water sites, where temperature variation was most pronounced. Correlation with seston content or gonad volume were insignificant at these sites. The quotient of filtration capacity to oxygen consumption rate was about 3 times higher at the site with the poorest food conditions compared to the other sites. Net growth efficiency was highly variable; its annual average was 35 to 40 per cent and independent of locality and animal size.     

The influence of photon flux density (PFD) on short term 14C incorporation into proteins,carbohydrates and lipids in freshwater algae

The effect of photon flux density (PFD) on the partitioning of photosynthetically fixed ¹⁴CO₂-C into major intracellular end products was investigated for three species of freshwater planktonic algae (Nitzschia palea, Monoraphidium minutum and Synechococcus elongatus belonging to three different classes. This study was designed to investigate the phenomenon of polysaccharide synthesis associated with the saturation of protein synthesis and to test if this process is common to all three phytoplankton species. Protein synthesis was saturated at low PFD in all three species of algae studied. However, fixed carbon was differentially stored, namely in lipids in Nitzschia palea (Bacillariophyceae), in polysaccharides in Monoraphidium minutum (Chlorophyceae), and in low molecular weight metabolites (LMW) in Synechococcus elongatus (Cyanophyceae). The results of this transient state study indicate that the metabolic pathways of algae can easily be controlled by different irradiance. Furthermore, it appears that the difference in the patterns of synthesis is taxonomy dependent.