The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

Identification of cilia genes that affect cell-cycle progression using whole-genome transcriptome analysis in Chlamydomonas reinhardtti

Cilia are microtubule based organelles that project from cells. Cilia are found on almost every cell type of the human body and numerous diseases, collectively termed ciliopathies, are associated with defects in cilia, including respiratory infections, male infertility, situs inversus, polycystic kidney disease, retinal degeneration, and Bardet-Biedl Syndrome. Here we show that Illumina-based whole-genome transcriptome analysis in the biflagellate green alga Chlamydomonas reinhardtii identifies 1850 genes up-regulated during ciliogenesis, 4392 genes down-regulated, and 4548 genes with no change in expression during ciliogenesis. We examined four genes up-regulated and not previously known to be involved with cilia (ZMYND10, NXN, GLOD4, SPATA4) by knockdown of the human orthologs in human retinal pigment epithelial cells (hTERT-RPE1) cells to ask whether they are involved in cilia-related processes that include cilia assembly, cilia length control, basal body/centriole numbers, and the distance between basal bodies/centrioles. All of the genes have cilia-related phenotypes and, surprisingly, our data show that knockdown of GLOD4 and SPATA4 also affects the cell cycle. These results demonstrate that whole-genome transcriptome analysis during ciliogenesis is a powerful tool to gain insight into the molecular mechanism by which centrosomes and cilia are assembled

776-1 Selective Down-regulation of Angiotensin II AT1 Receptors in Failing Human Heart: Relationship to β1-Receptor Down-regulation

The renin-angiotensin and adrenergic nervous systems exhibit multiple levels of cross-regulation in heart failure. These systems are bidirectionally activated in concert; i.e. activation of one system activates the other. We compared the behavior of angiotensin II AT1 and AT2 receptors with β1, -and, β2-adrenergic receptors in a high-yield crude membrane fraction prepared from nonfailing and failing human ventricular myocardium. Ang II receptors were measured by 125I saralasin binding, with Bmax determined by saturation binding displaceable by 1μM cold saralasin. AT1 and AT2 receptor fractions were determined by the amount of specific binding displaceable by 1μM losartan. β1-adrenergic receptor density was determined by saturation binding of 125I ICYP, with the, β1 fraction determined by binding displaceable by 0.2μM CGP 20712A. Results in end-stage human left ventricular myocardium failing as a result of idiopathic dilated cardiomyopathy were compared to nonfailing controls taken from age- and gender-matched organ donors not used for transplant because of blood type or body size mismatch: (Receptor density is in fmol/mg±SEM)β1-ARβ2-ARAT1AT2Nonfailing (n=6)59.0±9.420.7±4.04.14±0.621.52±0.43Failing (n = 6)28.3±2.8*17.2±2.61.53±0.57*2.68±0.51*p<0.05The down-regulation of β1 AR and AT1 receptors was significantly related (r=0.62, n=12, p<0.05)Conclusions(1) Compared to β adrenergic receptors ang II receptors are very low density in the human heart. (2) The AT1 receptor sUbtype predominates in the nonfailing human heart. (3) ATl but not AT2 receptors are downregulated in failing heart. (4) Down-regulation of Ang-II AT1 receptor is similar in degree to down-regulation of β1-adrenergic receptors. These data suggest that the AT1 and β1 receptors are respectively exposed to increased concentrations of mutually activatedlinduced norepinephrine and Ang-II in the failing human heart

Efficacy of temsirolimus in metastatic chromophobe renal cell carcinoma

<p>Background: Renal cell carcinoma (RCC) is a histopathologically and molecularly heterogeneous disease with the chromophobe subtype (chRCC) accounting for approximately 5% of all cases. The median overall survival of advanced RCC has improved significantly since the advent of tyrosine kinase inhibitors and mammalian target of rapamycin (mTOR) inhibitors. However, high-quality evidence for the use of new generation tyrosine kinase inhibitors in patients with advanced chRCC is lacking. Few published case reports have highlighted the use of temsirolimus in chRCC.</p> <p>Case presentation: Here, we report the case of a 36-year-old Caucasian woman with metastatic chRCC with predominantly skeletal metastases who was refractory to sunitinib who demonstrated a durable clinical response to temsirolimus lasting 20 months. We review the available evidence pertaining to the use of new generation molecularly targeted agents, in particular mTOR inhibitors in chRCC and discuss their emerging role in the management of this disease which would aid the oncologists faced with the challenge of treating this rare type of RCC.</p> <p>Conclusion: Conducting randomised clinical trials in this rarer sub-group of patients would be challenging and our case report and the evidence reviewed would guide the physicians to make informed decision regarding the management of these patients.</p&gt

Light-Scattering Observation Of Surface Acoustic Modes In High-Order Brillouin Zones Of A Si(001) Grating

In Brillouin light-scattering (BLS) measurements of an ion-milled Si(001) surface grating with grating wavelength Lambda(G) =0.35 mu m, we have observed numerous high-order zone-folded surface acoustic modes between the second and third zone boundaries associated with the grating. A surprisingly intense signal from a zone-folded longitudinal resonance was observed in the absence of direct hybridization with the Rayleigh modes. The relative intensities of all of the modes have been calculated by allowing for coupling between modes related by up to two grating reciprocal-lattice vectors, and for a grating profile with nonzero first and second Fourier amplitudes. The Fourier amplitudes inferred from the BLS measurements and calculations agree very well with those obtained from a direct measurement of the grating profile using atomic-force microscopy

In-beam internal conversion electron spectroscopy with the SPICE detector

The SPectrometer for Internal Conversion Electrons (SPICE) has been commissioned for use in conjunction with the TIGRESS $\gamma$-ray spectrometer at TRIUMF's ISAC-II facility. SPICE features a permanent rare-earth magnetic lens to collect and direct internal conversion electrons emitted from nuclear reactions to a thick, highly segmented, lithium-drifted silicon detector. This arrangement, combined with TIGRESS, enables in-beam $\gamma$-ray and internal conversion electron spectroscopy to be performed with stable and radioactive ion beams. Technical aspects of the device, capabilities, and initial performance are presented

Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton

Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as “bacterial microtubules” (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening

Mapping the Operation of the Miniature Combustion Aerosol Standard (Mini-CAST) Soot Generator

The Jing Ltd. miniature combustion aerosol standard (Mini- CAST) soot generator is a portable, commercially available burner that is widely used for laboratory measurements of soot processes. While many studies have used the Mini-CAST to generate soot with known size, concentration, and organic carbon fraction under a single or few conditions, there has been no systematic study of the burner operation over a wide range of operating conditions. Here, we present a comprehensive characterization of the microphysical, chemical, morphological, and hygroscopic properties of Mini- CAST soot over the full range of oxidation air and mixing N2 flow rates. Very fuel-rich and fuel-lean flame conditions are found to produce organic-dominated soot with mode diameters of 10–60 nm, and the highest particle number concentrations are produced under fuel-rich conditions. The lowest organic fraction and largest diameter soot (70–130 nm) occur under slightly fuel-lean conditions. Moving from fuel-rich to fuel-lean conditions also increases the O:C ratio of the soot coatings from ~0.05 to ~0.25, which causes a small fraction of the particles to act as cloud condensation nuclei near the Kelvin limit (κ ~ 0–10−3). Comparison of these property ranges to those reported in the literature for aircraft and diesel engine soots indicates that the Mini-CAST soot is similar to real-world primary soot particles, which lends itself to a variety of process-based soot studies. The trends in soot properties uncovered here will guide selection of burner operating conditions to achieve optimum soot properties that are most relevant to such studies

SPT-3G: A Next-Generation Cosmic Microwave Background Polarization Experiment on the South Pole Telescope

We describe the design of a new polarization sensitive receiver, SPT-3G, for the 10-meter South Pole Telescope (SPT). The SPT-3G receiver will deliver a factor of ~20 improvement in mapping speed over the current receiver, SPTpol. The sensitivity of the SPT-3G receiver will enable the advance from statistical detection of B-mode polarization anisotropy power to high signal-to-noise measurements of the individual modes, i.e., maps. This will lead to precise (~0.06 eV) constraints on the sum of neutrino masses with the potential to directly address the neutrino mass hierarchy. It will allow a separation of the lensing and inflationary B-mode power spectra, improving constraints on the amplitude and shape of the primordial signal, either through SPT-3G data alone or in combination with BICEP-2/KECK, which is observing the same area of sky. The measurement of small-scale temperature anisotropy will provide new constraints on the epoch of reionization. Additional science from the SPT-3G survey will be significantly enhanced by the synergy with the ongoing optical Dark Energy Survey (DES), including: a 1% constraint on the bias of optical tracers of large-scale structure, a measurement of the differential Doppler signal from pairs of galaxy clusters that will test General Relativity on ~200 Mpc scales, and improved cosmological constraints from the abundance of clusters of galaxies.Comment: 21 pages, 9 figures. To be published in Proceedings of SPIE Volume 9153. Presented at SPIE Astronomical Telescopes + Instrumentation 2014, conference 915