Nonlinear dynamo action in rotating convection and shear

Copyright © 2005 Cambridge University Press. Published version reproduced with the permission of the publisherMagnetic field amplification by the motion of an electrically conducting fluid is studied, using a rotating plane-layer geometry. The fluid flow is driven by convection, and by a moving bottom boundary, which leads to an Ekman layer localized at the base of the system. The system thus has the structure of an interface dynamo, with convection lying over a thin layer of shear. The combination of shear in the Ekman layer and convection above leads to amplification of seed magnetic fields. In kinematic regimes the magnetic field is mostly localized in sheets in the shear layer, but thin tongues are pulled out by the convection above and folded. The nonlinear saturation of these growing fields is studied at moderately high values of magnetic Reynolds number and Taylor number. It is found that the sheets of field tend to gain fine-scale structure when the dynamo saturates, breaking up into tubes, and the fluid flow shows complex time-dependence. Although the magnetic field lies predominantly within the highly sheared Ekman layer, this flow remains remarkably unchanged despite the action of Lorentz forces. Instead, the effect of the field is to suppress or modify the convection above. A simple alpha-omega dynamo model is set up, and gives some insights into the dynamo processes occurring in the full magnetohydrodynamic simulation

Fretting Corrosion Behavior of Additive Manufactured and Cryogenic-Machined Ti6Al4V for Biomedical Applications

Metal ion release, caused by synergistic effect of wear and corrosion, is one of the major concerns related to the prostheses lifetime. In this work, samples of additive manufactured Ti6Al4V are machined under dry cutting and cryogenic cooling conditions and their performances in terms of corrosion and fretting corrosion response are investigated. A wet and temperature-controlled apparatus equipped with an electro-chemical cell is designed and set-up in order to evaluate the fretting corrosion effect acting at the interfaces. The obtained results show that the cryogenic machining improves the corrosion and fretting corrosion behavior of the investigated additive manufactured Ti6Al4V

Population Size, Genetic Diversity and Molecular Evidence of a Recent Population Bottleneck in Hynobius chinensis, an Endangered Salamander Species

Severe population declines can reduce species to small populations, offering permissive conditions for deleterious processes. For example, following such events, species can become prone to inbreeding and genetic drift which can lead to a loss of genetic diversity and evolutionary potentials. Hynobius chinensis is a poorly studied very rare and declining endangered amphibian species endemic to China in Changyang County. We investigated adult census population size by monitoring breeding populations from 2015 to 2018, developed microsatellite markers from the transcriptome and used them to investigate genetic diversity, and a population bottleneck in this species. We found H. chinensis in 4 different localities in a total area of 2.18 km2 and estimated the overall adult census population size at 386–404 individuals. The adult census size (mean ± SE) per breeding pond ranged from 44 ± 6 to 141 ± 8 individuals and appeared smaller than that reported in closely related species in undisturbed habitats. We developed and characterized 13 microsatellite markers in total. Analysis of data at 7 loci (N = 118) in Hardy-Weinberg equilibrium gathered from the largest population showed that genetic diversity level was low. The average number of alleles per locus was 2.14. The observed and expected heterozygosities averaged 0.38 and 0.40, respectively. The inbreeding coefficient was –0.06. All tests performed to investigate a population bottleneck, i.e. The Garza-Williamson test, Heterozygosity excess test, Mode shift test of allele frequency, and effective population size estimates detected a population bottleneck. The contemporary and the historical effective population sizes were estimated at 36 and 234 individuals, respectively. We argue that as bottleneck effects, the studied population may have become prone to genetic drift and inbreeding, losing microsatellite alleles and heterozygosity. Our results suggest that populations of H. chinensis may have been extirpated in the study area

Ice-sheet collapse and sea-level rise at the Bølling warming 14,600 years ago

Past sea-level records provide invaluable information about the response of ice sheets to climate forcing. Some such records suggest that the last deglaciation was punctuated by a dramatic period of sea-level rise, of about 20 metres, in less than 500 years. Controversy about the amplitude and timing of this meltwater pulse (MWP-1A) has, however, led to uncertainty about the source of the melt water and its temporal and causal relationships with the abrupt climate changes of the deglaciation. Here we show that MWP-1A started no earlier than 14,650 years ago and ended before 14,310 years ago, making it coeval with the Bolling warming. Our results, based on corals drilled offshore from Tahiti during Integrated Ocean Drilling Project Expedition 310, reveal that the increase in sea level at Tahiti was between 12 and 22 metres, with a most probable value between 14 and 18 metres, establishing a significant meltwater contribution from the Southern Hemisphere. This implies that the rate of eustatic sea-level rise exceeded 40 millimetres per year during MWP-1A

Environmental and diagenetic controls on the morphology and calcification of the Ediacaran metazoan Cloudina

Abstract Cloudina is a globally distributed Ediacaran metazoan, with a tubular, funnel-in-funnel form built of thin laminae (ca. 1–10 μm). To what degree local environmental controlled morphology, and whether early diagenesis controlled the degree of calcification of Cloudina, is debated. Here we test these hypotheses by considering assemblages from four, coeval localities from the Upper Omkyk Member, Nama Group, Namibia, from inner ramp to mid-ramp reef across the Zaris Subbasin. We show that sinuosity of the Cloudina tube is variable between sites, as is the relative thickness of the tube wall, suggesting these features were environmentally controlled. Walls are thickest in high-energy reef settings, and thinnest in the low-energy, inner ramp. While local diagenesis controls preservation, all diagenetic expressions are consistent with the presence of weakly calcified, organic-rich laminae, and lamina thicknesses are broadly constant. Finally, internal ‘cements’ within Cloudina are found in all sites, and pre-date skeletal breakage, transport, as well as syn-sedimentary botryoidal cement precipitation. Best preservation shows these to be formed by fine, pseudomorphed aragonitic acicular crystals. Sr concentrations and Mg/Ca show no statistically significant differences between internal Cloudina cements and botryoidal cements, but we infer all internal cements to have precipitated when Cloudina was still in-situ and added considerable mechanical strength, but may have formed post-mortem or in abandoned parts of the skeleton

Listeriolysin O Is Strongly Immunogenic Independently of Its Cytotoxic Activity

The presentation of microbial protein antigens by Major Histocompatibility Complex (MHC) molecules is essential for the development of acquired immunity to infections. However, most biochemical studies of antigen processing and presentation deal with a few relatively inert non-microbial model antigens. The bacterial pore-forming toxin listeriolysin O (LLO) is paradoxical in that it is cytotoxic at nanomolar concentrations as well as being the source of dominant CD4 and CD8 T cell epitopes following infection with Listeria monocytogenes. Here, we examined the relationship of LLO toxicity to its antigenicity and immunogenicity. LLO offered to antigen presenting cells (APC) as a soluble protein, was presented to CD4 T cells at picomolar to femtomolar concentrations- doses 3000–7000-fold lower than free peptide. This presentation required a dose of LLO below the cytotoxic level. Mutations of two key tryptophan residues reduced LLO toxicity by 10–100-fold but had no effect on its presentation to CD4 T cells. Thus there was a clear dissociation between the cytotoxic properties of LLO and its very high antigenicity. Presentation of LLO to CD8 T cells was not as robust as that seen in CD4 T cells, but still occurred in the nanomolar range. APC rapidly bound and internalized LLO, then disrupted endosomal compartments within 4 hours of treatment, allowing endosomal contents to access the cytosol. LLO was also immunogenic after in vivo administration into mice. Our results demonstrate the strength of LLO as an immunogen to both CD4 and CD8 T cells

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases