Mechanical properties of Xenopus egg cytoplasmic extracts

Cytoplasmic extracts prepared from Xenopus laevis eggs are used for the reconstitution of a wide range of processes in cell biology, and offer a unique environment in which to investigate the role of cytoplasmic mechanics without the complication of preorganized cellular structures. As a step toward understanding the mechanical properties of this system, we have characterized the rheology of crude interphase extracts. At macroscopic length scales, the extract forms a soft viscoelastic solid. Using a conventional mechanical rheometer, we measure the elastic modulus to be in the range of 2-10 Pa, and loss modulus in the range of 0.5-5 Pa. Using pharmacological and immunological disruption methods, we establish that actin filaments and microtubules cooperate to give mechanical strength, whereas the intermediate filament cytokeratin does not contribute to viscoelasticity. At microscopic length scales smaller than the average network mesh size, the response is predominantly viscous. We use multiple particle tracking methods to measure the thermal fluctuations of 1 microm embedded tracer particles, and measure the viscosity to be approximately 20 mPa-s. We explore the impact of rheology on actin-dependent cytoplasmic contraction, and find that although microtubules modulate contractile forces in vitro, their interactions are not purely mechanical.     

Developing liquid chromatography ion mobility mass spectometry techniques

When a packet of ions in a buffer gas is exposed to a weak electric field, the ions will separate according to differences in their mobilities through the gas. This separation forms the basis of the analytical method known as ion mobility spectroscopy and is highly efficient, in that it can be carried out in a very short time frame (micro- to milliseconds). Recently, efforts have been made to couple the approach with liquid-phase separations and mass spectrometry in order to create a high-throughput and high-coverage approach for analyzing complex mixtures. This article reviews recent work to develop this approach for proteomics analyses. The instrumentation is described briefly. Several multidimensional data sets obtained upon analyzing complex mixtures are shown in order to illustrate the approach as well as provide a view of the limitations and required future work.     

Microsecond-to-millisecond conformational dynamics demarcate the GluR2 glutamate receptor bound to agonists glutamate, quisqualate, and AMPA

Chemical shift changes and internal motions on microsecond-to-millisecond time scales of the S1S2 ligand-binding domain of the GluR2 ionotropic glutamate receptor have been studied by NMR spectroscopy in the presence of the agonists glutamic acid (glutamate), quisqualic acid (quisqualate), and alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA). Although the crystal structures of the three agonist-bound forms of GluR2 S1S2 ligand-binding domain are very similar, chemical shift changes imply that AMPA-bound GluR2 S1S2 is conformationally distinct from glutamate- and quisqualate-bound forms of GluR2 S1S2. NMR spin relaxation measurements for backbone amide (15)N nuclei reveal that GluR2 S1S2 exhibits reduced chemical exchange line broadening, resulting from microsecond-to-millisecond conformational dynamics, in AMPA-bound compared to glutamate- and quisqualate-bound states. The largest changes in line broadening are observed for two regions of GluR2 S1S2: Val683 and the segment around Lys716-Cys718. The differences in binding affinity of these agonists do not explain the differences in microsecond-to-millisecond conformational dynamics because quisqualate and AMPA bind with similar affinities that are 10-fold greater than the affinity of glutamate. Differences in conformational mobility may reflect differences in the binding mode of AMPA in the GluR2 S1S2 active site compared to the other two ligands. The sites of conformational mobility in GluR2 S1S2 imply that subtle differences exist between the agonists glutamate, quisqualate, and AMPA in modulating glutamate receptor function.     

Affinity purification of streptavidin using tobacco mosaic virus particles as purification tags

A new protein affinity purification system has been developed. Recombinant tobacco mosaic virus (TMV) was used as an affinity matrix for isolation and purification of the given protein of interest. In model experiments, streptavidin-specific heptapeptide sequence TLIAHPQ was inserted into TMV coat protein near the C end. This oligopeptide did not interfere significantly with viral replication, assembly, and movement. Recombinant TMV functioned as an epitope tag recognizing streptavidin in plant protein extracts. Plant protein extracts containing streptavidin were incubated with recombinant TMV virions. Affinity complexes of viral particles with the protein of interest were collected by centrifugation. Recombinant TMV-streptavidin complex was dissociated with 0.2M acetic acid, pH 4.6, and was passed through membrane filter Nanosep 300K by centrifugation. The filtrate contained pure streptavidin. Recombinant TMV was left on the filter. TMV particles collected from the filter could be used for at least two more purification cycles. The streptavidin-specific recombinant TMV system was applied successfully for purification of streptavidin from Streptomyces avidinii. The authors believe that the TMV-based affinity system can also be used for the purification of other proteins.     

Sequencing of the reannotated LMNB2 gene reveals novel mutations in patients with acquired partial lipodystrophy

The etiology of acquired partial lipodystrophy (APL, also called "Barraquer-Simons syndrome") is unknown. Genomic DNA mutations affecting the nuclear lamina protein lamin A cause inherited partial lipodystrophy but are not found in patients with APL. Because it also encodes a nuclear lamina protein (lamin B2) and its genomic structure was recently reannotated, we sequenced LMNB2 as a candidate gene in nine white patients with APL. In four patients, we found three new rare mutations in LMNB2: intron 1 -6G-->T, exon 5 c.643G-->A (p.R215Q; in two patients), and exon 8 c.1218G-->A (p.A407T). The combined frequency of these mutations was 0.222 in the patients with APL, compared with 0.0018 in a multiethnic control sample of 1,100 subjects (P = 2.1 x 10-7) and 0.0045 in a sample of 330 white controls (P = 1.2 x 10-5). These novel heterozygous mutations are the first reported for LMNB2, are the first reported among patients with APL, and indicate how sequencing of a reannotated candidate gene can reveal new disease-associated mutations.     

Effect of the soil yeast <Emphasis Type="Italic">Cryptococcus laurentii</Emphasis> on the photosynthetic water and nutrient-use efficiency and respiratory carbon costs of a Mediterranean sclerophyll, <Emphasis Type="Italic">Agathosma betulina</Emphasis> (Berg.) Pillans

Nothing is known about the effect of soil yeasts on the photosynthetic resource-use and carbon dynamics of plants. Here, we determined the effect of a plant growth-promoting isolate of Cryptococcus laurentii on the photosynthetic water and nutrient-use efficiencies, as well as the carbon economy of a Mediterranean sclerophyll, Agathosma betulina, grown under axenic conditions. The data showed that the higher photosynthetic water-use efficiency in yeast-inoculated plants was a consequence of higher maximum rates of CO₂ assimilation, which was not related to foliar N and P content. We propose that photosynthetic stimulation in yeast-inoculated plants was a result of the increased demand for photosynthates of the yeast-root symbiosis.     

Impacts of a population outbreak of the urchin Tripneustes gratilla amongst Lord Howe Island coral communities

Subtidal reef surveys within the Lord Howe Island Marine Park revealed that populations of the sea urchin Tripneustes gratilla underwent an explosive outbreak in some regions of the park over a 2-year period. This urchin was rare or absent during 2006 surveys at 33 sites studied, but at sites off northern Lord Howe Island in 2008, densities averaged >1.3 m⁻². Dramatic increases in T. gratilla density (exceeding 4 m⁻²) were observed at some sites. We quantify community-level impacts of T. gratilla using ‘before-after’ and ‘control-impact’ data. Zones closed to fishing exhibited similar increases in T. gratilla density to zones open to fishing. Although not previously reported as a keystone species affecting coral habitat, T. gratilla was found to possess an ‘ecosystem engineer’ function. Outbreak sites were characterised by significant declines in cover of foliose algae, including red algae, which decreased from 11.2% in 2006 compared to 2.5% in 2008. Brown foliose algae also declined at sites where T. gratilla outbreaks occurred, averaging 20.4% in 2006 compared to 1.8% in 2008. By contrast, crustose coralline algal cover increased at sites where high T. gratilla densities were observed, from 2.7% in 2006 to an average of 42.6% in 2008. We found no clear indication of impacts on sessile invertebrates or flow-on effects to other levels of the food web, with no significant change in coral cover or densities of mobile invertebrates or fish populations associated with the T. gratilla outbreak.     

Synthesis and biodistribution of [11C]A-836339, a new potential radioligand for PET imaging of cannabinoid type 2 receptors (CB2)

Recently, A-836339 [2,2,3,3-tetramethylcyclopropanecarboxylic acid [3-(2-methoxyethyl)-4,5-dimethyl-3H-thiazol-(2Z)-ylidene]amide] (1) was reported to be a selective CB₂ agonist with high binding affinity. Here we describe the radiosynthesis of [¹¹C]A-836339 ([¹¹C]1) via its desmethyl precursor as a candidate radioligand for imaging CB₂ receptors with positron-emission tomography (PET). Whole body and the regional brain distribution of [¹¹C]1 in control CD1 mice demonstrated that this radioligand exhibits specific uptake in the CB₂-rich spleen and little specific in vivo binding in the control mouse brain. However, [¹¹C]1 shows specific cerebral uptake in the lipopolysaccharide (LPS)-induced mouse model of neuroinflammation and in the brain areas with Aβ amyloid plaque deposition in a mouse model of Alzheimer’s disease (APPswe/PS1dE9 mice). These data establish a proof of principle that CB₂ receptors binding in the neuroinflammation and related disorders can be measured in vivo.     

Genus age,provincial area and the taxonomic structure of marine faunas

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.