Egomotion estimation with optic flow and air velocity sensors

We develop a method that allows a flyer to estimate its own motion (egomotion), the wind velocity, ground slope, and flight height using only inputs from onboard optic flow and air velocity sensors. Our artificial algorithm demonstrates how it could be possible for flying insects to determine their absolute egomotion using their available sensors, namely their eyes and wind sensitive hairs and antennae. Although many behaviors can be performed by only knowing the direction of travel, behavioral experiments indicate that odor tracking insects are able to estimate the wind direction and control their absolute egomotion (i.e., groundspeed). The egomotion estimation method that we have developed, which we call the opto-aeronautic algorithm, is tested in a variety of wind and ground slope conditions using a video recorded flight of a moth tracking a pheromone plume. Over all test cases that we examined, the algorithm achieved a mean absolute error in height of 7% or less. Furthermore, our algorithm is suitable for the navigation of aerial vehicles in environments where signals from the Global Positioning System are unavailable.     

Glucose homeostasis in rainbow trout fed a high-carbohydrate diet: metformin and insulin interact in a tissue-dependent manner

Carnivorous fish species such as the rainbow trout (Oncorhynchus mykiss) are considered to be "glucose intolerant" because of the prolonged hyperglycemia experienced after intake of a carbohydrate-enriched meal. In the present study, we use this species to study glucose homeostasis in fish chronically infused with the hypoglycemic agents, insulin, and metformin, and fed with a high proportion of carbohydrates (30%). We analyzed liver, skeletal muscle, and white adipose tissue (WAT), which are insulin- and metformin-specific targets at both the biochemical and molecular levels. Trout infused with the combination of insulin and metformin can effectively utilize dietary glucose at the liver, resulting in lowered glycemia, increased insulin sensitivity, and glucose storage capacity, combined with reduced glucose output. However, in both WAT and skeletal muscle, we observed decreased insulin sensitivity with the combined insulin + metformin treatment, resulting in the absence of changes at the metabolic level in the skeletal muscle and an increased potential for glucose uptake and storage in the WAT. Thus, the poor utilization by rainbow trout of a diet with a high proportion of carbohydrate can at least be partially improved by a combined treatment with insulin and metformin, and the glucose intolerance observed in this species could be, in part, due to some of the downstream components of the insulin and metformin signaling pathways. However, the predominant effects of metformin treatment on the action of insulin in these three tissues thought to be involved in glucose homeostasis remain exclusive in this species.     

Seed germination of Agave species as influenced by substrate water potential

Background

Plants of Agave spp. perform Crassulacean acid metabolism (CAM) and are highly drought-tolerant, but little is known concerning seed germination under low water availability. The aim of this study was to assess the effect of substrate water potential (Ψ_W) on seed germination and contrast hydrotime parameters of seven valuable and commercially-important Agave species from different geographical distributions and climatic regions of Mexico. Our hypothesis was that seed germination of Agave species is not affected by low water availability independently of seed biomass and the climate of their distribution area.

Results

Seed germination (at 25°C and in the dark) between 85 and 100% for all species occurred within 80–180 h at -0.03 MPa and 250–430 h at -1.0 MPa. Seed germination at -1.5 MPa declined to less than 50% (p < 0.05) for A. asperrima and A. cupreata but did not change significantly for A. americana var. marginata, A. lechuguilla and A. striata, although they showed the lowest mean base water potential (-2.01 to -2.64 MPa). Seed germination of 40% Agave species, from arid and semi-arid climates in this study, was not affected by the lower Ψ_W.

Conclusion

Germination of seeds of Agave species is moderately affected by low water availability, is partially dependent of their ecological distribution, and is independent of seed mass.     

Evaluation of viral genome assembly and diversity estimation in deep metagenomes

Background

Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes.

Results

We created in silico metagenomes mimicking various platforms at different sequencing depths. The CLC assembler revealed subpar compared to IDBA_UD and CAMERA , which are metagenomic-specific. Up to a saturation point, Illumina platforms proved more capable of reconstructing large portions of viral genomes compared to 454. Read length was an important factor for limiting chimericity, while scaffolding marginally improved contig length and accuracy. The genome length of the various viruses in the metagenomes did not significantly affect genome reconstruction, but the co-existence of highly similar genomes was detrimental. When evaluating diversity estimation tools, we found that PHACCS results were more accurate than those from CatchAll and clustering, which were both orders of magnitude above expected.

Conclusions

Assemblers designed specifically for the analysis of metagenomes should be used to facilitate the creation of high-quality long contigs. Despite the high coverage possible, scientists should not expect to always obtain complete genomes, because their reconstruction may be hindered by co-existing species bearing highly similar genomic regions. Further development of metagenomics-oriented assemblers may help bypass these limitations in future studies. Meanwhile, the lack of fully reconstructed communities keeps methods to estimate viral diversity relevant. While none of the three methods tested had absolute precision, only PHACCS was deemed suitable for comparative studies.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-989) contains supplementary material, which is available to authorized users.     

Large-Scale Assessment of Mediterranean Marine Protected Areas Effects on Fish Assemblages

Marine protected areas (MPAs) were acknowledged globally as effective tools to mitigate the threats to oceans caused by fishing. Several studies assessed the effectiveness of individual MPAs in protecting fish assemblages, but regional assessments of multiple MPAs are scarce. Moreover, empirical evidence on the role of MPAs in contrasting the propagation of non-indigenous-species (NIS) and thermophilic species (ThS) is missing. We simultaneously investigated here the role of MPAs in reversing the effects of overfishing and in limiting the spread of NIS and ThS. The Mediterranean Sea was selected as study area as it is a region where 1) MPAs are numerous, 2) fishing has affected species and ecosystems, and 3) the arrival of NIS and the northward expansion of ThS took place. Fish surveys were done in well-enforced no-take MPAs (HP), partially-protected MPAs (IP) and fished areas (F) at 30 locations across the Mediterranean. Significantly higher fish biomass was found in HP compared to IP MPAs and F. Along a recovery trajectory from F to HP MPAs, IP were similar to F, showing that just well enforced MPAs triggers an effective recovery. Within HP MPAs, trophic structure of fish assemblages resembled a top-heavy biomass pyramid. Although the functional structure of fish assemblages was consistent among HP MPAs, species driving the recovery in HP MPAs differed among locations: this suggests that the recovery trajectories in HP MPAs are likely to be functionally similar (i.e., represented by predictable changes in trophic groups, especially fish predators), but the specific composition of the resulting assemblages may depend on local conditions. Our study did not show any effect of MPAs on NIS and ThS. These results may help provide more robust expectations, at proper regional scale, about the effects of new MPAs that may be established in the Mediterranean Sea and other ecoregions worldwide.     

A Regional analysis of Maize Biological Diversity in Southeastern Guanajuato, MéXico

Four environments with contrasting potential for agricultural productivity and infrastructure development were identified in Guanajuato State, México, to test hypotheses about the relaciónship of maize biological diversity to the region’s potential for agricultural productivity and infrastructure development. Samples of all types of maize grown by a random sample of farmers were collected from each environment. Landraces were the dominant maize class in all four environments; the use of improved varieties was negligible. Several diversity indices were calculated, and no statistically significant differences were apparent between the environments with the most contrasting agroecological and infrastructural conditions. Statistical differences in diversity are apparent when the development of infrastructure interacts with agroecological factors in an environment. Qualitative data suggest that the richness of maize populations may be associated with maize yield potential in a geographical area, whereas the evenness of maize populations may be associated with the presence of infrastructure. These findings suggest further hypotheses about regional patterns of maize diversity.     

Relationship between Tobacco,cagA and vacA i1 Virulence Factors and Bacterial Load in Patients Infected by Helicobacter pylori

MethodsBiopsies of the gastric corpus and antrum from 155 consecutive patients in whom there was clinical suspicion of infection by H. pylori were processed. In 106 patients H. pylori infection was detected. Molecular methods were used to quantify the number of microorganisms and presence of cagA and vacA i1 genes. A standardized questionnaire was used to obtain patients’ clinical data and lifestyle variables, including tobacco and alcohol consumption. Adjusted Odds Ratios (OR_adjusted) were estimated by unconditional logistic regression.ResultscagA was significantly associated with active-smoking at endoscope: OR_adjusted 4.52. Evidence of association was found for vacA i1 (OR_adjusted 3.15). Bacterial load was higher in active-smokers, although these differences did not yield statistical significance (median of 262.2 versus 79.4 copies of H. pylori per cell).ConclusionsThe association between smoking and a higher risk of being infected by a virulent bacterial population and with higher bacterial load, support a complex interaction between H. pylori infection and environmental factors.