Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2

<p>Abstract</p> <p>Background</p> <p>The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and <it>ab initio </it>gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of <it>Chlamydomonas </it>genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve <it>ab initio </it>gene finding in <it>Chlamydomonas</it>, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 <it>Chlamydomonas </it>EST entries in GenBank using the EST assembly tool PASA.</p> <p>Results</p> <p>The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2, attains 83% sensitivity and 83% specificity for exons on short-sequence predictions. We predict about 12,000 genes in the version <it>v3 Chlamydomonas </it>genome assembly, most of which (78%) are either identical to or significantly overlap the published catalog of <it>Chlamydomonas </it>genes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 22% of the published catalog is absent from the GreenGenie2 predictions; there is also a fraction (23%) of GreenGenie2 predictions that are absent from the published gene catalog. Randomly chosen gene models were tested by RT-PCR and most support the GreenGenie2 predictions.</p> <p>Conclusion</p> <p>These data suggest that training with EST assemblies is highly effective and that GreenGenie2 is a valuable, complementary tool for predicting genes in <it>Chlamydomonas reinhardtii</it>.</p

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&lt;0.05The down-regulation of β1 AR and AT1 receptors was significantly related (r=0.62, n=12, p&lt;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

Emissions from Ethanol-Gasoline Blends: A Single Particle Perspective

Due to its agricultural origin and function as a fuel oxygenate, ethanol is being promoted as an alternative biomass-based fuel for use in spark ignition engines, with mandates for its use at state and regional levels. While it has been established that the addition of ethanol to a fuel reduces the particulate mass concentration in the exhaust, little attention has been paid to changes in the physicochemical properties of the emitted particles. In this work, a dynamometer-mounted GM Quad-4 spark ignition engine run without aftertreatment at 1,500 RPM and 100% load was used with four different fuel blends, containing 0, 20, 40 and 85 percent ethanol in gasoline. This allowed the effects of the fuel composition to be isolated from other effects. Instrumentation employed included two Aerosol Time-of-Flight Mass Spectrometers covering different size ranges for analysis of single particle composition, an Aethalometer for black carbon, a Scanning Mobility Particle Sizer for particle size distributions, a Photoelectric Aerosol Sensor for particle-bound polycyclic aromatic hydrocarbon (PAH) species and gravimetric filter measurements for particulate mass concentrations. It was found that, under the conditions investigated here, additional ethanol content in the fuel changes the particle size distribution, especially in the accumulation mode, and decreases the black carbon and total particulate mass concentrations. The molecular weight distribution of the PAHs was found to decrease with added ethanol. However, PAHs produced from higher ethanol-content fuels are associated with NO2 − (m/z—46) in the single-particle mass spectra, indicating the presence of nitro-PAHs. Compounds associated with the gasoline (e.g., sulfur-containing species) are diminished due to dilution as ethanol is added to the fuel relative to those associated with the lubricating oil (e.g., calcium, zinc, phosphate) in the single particle spectra. These changes have potential implications for the health effect impacts of particulate emissions from biofuel blends

Efficacy of temsirolimus in metastatic chromophobe renal cell carcinoma

&lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/p&gt; &lt;p&gt;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.&lt;/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