Homoplastic microinversions and the avian tree of life

Background: Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasyfree evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results: We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions: Microinversions can provide valuable phylogenetic information, although power analysis indicate

Chemical-genetic disruption of clathrin function spares adaptor complex 3-dependent endosome vesicle biogenesis

A role for clathrin in AP-3–dependent vesicle biogenesis has been inferred from biochemical interactions and colocalization between this adaptor and clathrin. The functionality of these molecular associations, however, is controversial. We comprehensively explore the role of clathrin in AP-3–dependent vesicle budding, using rapid chemical-genetic perturbation of clathrin function with a clathrin light chain–FKBP chimera oligomerizable by the drug AP20187. We find that AP-3 interacts and colocalizes with endogenous and recombinant FKBP chimeric clathrin polypeptides in PC12-cell endosomes. AP-3 displays, however, a divergent behavior from AP-1, AP-2, and clathrin chains. AP-3 cofractionates with clathrin-coated vesicle fractions isolated from PC12 cells even after clathrin function is acutely inhibited by AP20187. We predicted that AP20187 would inhibit AP-3 vesicle formation from endosomes after a brefeldin A block. AP-3 vesicle formation continued, however, after brefeldin A wash-out despite impairment of clathrin function by AP20187. These findings indicate that AP-3–clathrin association is dispensable for endosomal AP-3 vesicle budding and suggest that endosomal AP-3–clathrin interactions differ from those by which AP-1 and AP-2 adaptors productively engage clathrin in vesicle biogenesis

Microbial diversity in waters, sediments and microbial mats evaluated using fatty acid-based methods

The review summarises recent advances towards a greater comprehensive assessment of microbial diversity in aquatic environments using the fatty acid methyl esters and phospholipid fatty acids approaches. These methods are commonly used in microbial ecology because they do not require the culturing of micro-organisms, are quantitative and reproducible and provide valuable information regarding the structure of entire microbial communities. Because some fatty acids are associated with taxonomic and functional groups of micro-organisms, they allow particular groups of micro-organisms to be distinguished. The integration of fatty acid-based methods with stable isotopes, RNA and DNA analyses enhances our knowledge of the role of micro-organisms in global nutrient cycles, functional activity and phylogenetic lineages within microbial communities. Additionally, the analysis of fatty acid profiles enables the shifts in the microbial diversity in pristine and contaminated environments to be monitored. The main objective of this review is to present the use of lipid-based approaches for the characterisation of microbial communities in water columns, sediments and biomats

Low temperature (< 100 °c) deposited P-type cuprous oxide thin films: Importance of controlled oxygen and deposition energy

With the emergence of transparent electronics, there has been considerable advancement in n-type transparent semiconducting oxide (TSO) materials, such as ZnO, InGaZnO, and InSnO. Comparatively, the availability of p-type TSO materials is more scarce and the available materials are less mature. The development of p-type semiconductors is one of the key technologies needed to push transparent electronics and systems to the next frontier, particularly for implementing p-n junctions for solar cells and p-type transistors for complementary logic/circuits applications. Cuprous oxide (Cu2O) is one of the most promising candidates for p-type TSO materials. This paper reports the deposition of Cu2O thin films without substrate heating using a high deposition rate reactive sputtering technique, called high target utilisation sputtering (HiTUS). This technique allows independent control of the remote plasma density and the ion energy, thus providing finer control of the film properties and microstructure as well as reducing film stress. The effect of deposition parameters, including oxygen flow rate, plasma power and target power, on the properties of Cu2O films are reported. It is known from previously published work that the formation of pure Cu2O film is often difficult, due to the more ready formation or co-formation of cupric oxide (CuO). From our investigation, we established two key concurrent criteria needed for attaining Cu2O thin films (as opposed to CuO or mixed phase CuO/Cu2O films). First, the oxygen flow rate must be kept low to avoid over-oxidation of Cu2O to CuO and to ensure a non-oxidised/non-poisoned metallic copper target in the reactive sputtering environment. Secondly, the energy of the sputtered copper species must be kept low as higher reaction energy tends to favour the formation of CuO. The unique design of the HiTUS system enables the provision of a high density of low energy sputtered copper radicals/ions, and when combined with a controlled amount of oxygen, can produce good quality p-type transparent Cu2O films with electrical resistivity ranging from 102 to 104 Ω-cm, hole mobility of 1-10 cm2/V-s, and optical band-gap of 2.0-2.6 eV. These material properties make this low temperature deposited HiTUS Cu 2O film suitable for fabrication of p-type metal oxide thin film transistors. Furthermore, the capability to deposit Cu2O films with low film stress at low temperatures on plastic substrates renders this approach favourable for fabrication of flexible p-n junction solar cells. © 2011 Elsevier B.V. All rights reserved

Positive regulation of T cell activation and integrin adhesion by the adapter Fyb/Slap

The molecular adapter Fyb/Slap regulates signaling downstream of the T cell receptor (TCR), but whether it plays a positive or negative role is controversial. We demonstrate that Fyb/Slap-deficient T cells exhibit defective proliferation and cytokine production in response to TCR stimulation. Fyb/Slap is also required in vivo for T cell-dependent immune responses. Functionally, Fyb/Slap has no apparent role in the activation of known TCR signaling pathways, F-actin polymerization, or TCR clustering. Rather, Fyb/Slap regulates TCR-induced integrin clustering and adhesion. Thus, Fyb/Slap is the first molecular adapter to be identified that couples TCR stimulation to the avidity modulation of integrins governing T cell adhesion.link_to_subscribed_fulltex