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

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Validation of first chemistry mode retrieval results from the new limb-imaging FTS GLORIA with correlative MIPAS-STR observations

We report first chemistry mode retrieval results from the new airborne limb-imaging infrared FTS (Fourier transform spectrometer) GLORIA (Gimballed Limb Observer for Radiance Imaging of the Atmosphere) and comparisons with observations by the conventional airborne limb-scanning infrared FTS MIPAS-STR (Michelson Interferometer for Passive Atmospheric Sounding – STRatospheric aircraft). For GLORIA, the flights aboard the high-altitude research aircraft M55 Geophysica during the ESSenCe campaign (ESa Sounder Campaign 2011) were the very first in field deployment after several years of development. The simultaneous observations of GLORIA and MIPAS-STR during the flight on 16 December 2011 inside the polar vortex and under conditions of optically partially transparent polar stratospheric clouds (PSCs) provided us the first opportunity to compare the observations by two different infrared FTS generations directly. We validate the GLORIA results with MIPAS-STR based on the lower vertical resolution of MIPAS-STR and compare the vertical resolutions of the instruments derived from their averaging kernels. The retrieval results of temperature, HNO3, O3, H2O, CFC-11 and CFC-12 show reasonable agreement of GLORIA with MIPAS-STR and collocated in situ observations. For the horizontally binned hyperspectral limb images, the GLORIA sampling outnumbered the horizontal cross-track sampling of MIPAS-STR by up to 1 order of magnitude. Depending on the target parameter, typical vertical resolutions of 0.5 to 2.0 km were obtained for GLORIA and are typically a factor of 2 to 4 better compared to MIPAS-STR. While the improvement of the performance, characterization and data processing of GLORIA are the subject of ongoing work, the presented first results already demonstrate the considerable gain in sampling and vertical resolution achieved with GLORIA

What do aquaporin knockout studies tell us about fluid transport in epithelia?

The investigation of near-isosmotic water transport in epithelia goes back over 100 years; however, debates over mechanism and pathway remain. Aquaporin (AQP) knockouts have been used by various research groups to test the hypothesis of an osmotic mechanism as well as to explore the paracellular versus transcellular pathway debate. Nonproportional reductions in the water permeability of a water-transporting epithelial cell (e.g., a reduction of around 80–90 %) compared to the reduction in overall water transport rate in the knockout animal (e.g., a reduction of 50–60 %) are commonly found. This nonproportionality has led to controversy over whether AQP knockout studies support or contradict the osmotic mechanism. Arguments raised for and against an interpretation supporting the osmotic mechanism typically have partially specified, implicit, or incorrect assumptions. We present a simple mathematical model of the osmotic mechanism with clear assumptions and, for models based on this mechanism, establish a baseline prediction of AQP knockout studies. We allow for deviations from isotonic/isosmotic conditions and utilize dimensional analysis to reduce the number of parameters that must be considered independently. This enables a single prediction curve to be used for multiple epithelial systems. We find that a simple, transcellular-only osmotic mechanism sufficiently predicts the results of knockout studies and find criticisms of this mechanism to be overstated. We note, however, that AQP knockout studies do not give sufficient information to definitively rule out an additional paracellular pathway

Health-related quality of life in patients with primary open-angle glaucoma. An italian multicentre observational study

PurposeAs a progressive condition, glaucoma may impair health-related quality of life (HRQoL), due to vision loss and other factors. This study evaluated HRQoL in a cohort of patients treated for primary open-angle glaucoma (POAG) and assessed its association with clinical features. MethodsThis was an Italian, multicentre, cross-sectional, observational study with the subgroup of newly diagnosed patients with POAG prospectively followed up for one year. Patients with previous or new diagnosis (or strong clinical suspicion) of POAG aged >18years were considered eligible. Information was collected on demographic characteristics, medical history, clinical presentation and POAG treatments. HRQoL was measured using the 25-item National Eye Institute Visual Function Questionnaire (NEI-VFQ-25) and Glaucoma Symptom Scale (GSS). Subscale and total scores were obtained and a Pearson correlation coefficient between instruments' scores calculated. ResultsA total of 3227 patients were enrolled from 2012 to 2013 and 3169 were analysed. Mean age was 66.9years. A total of 93.8% had a previous diagnosis (median duration: 8.0years). Median values for mean deviation and pattern standard deviation were 3.9 and 3.6 dB, respectively. Mean scores on most subscales of the NEI-VFQ-25 exceeded 75.0 and mean GSS subscale scores ranged between 70.8 and 79.7 (with a total mean score of 74.8). HRQoL scores on both scales were significantly inversely associated with POAG severity. ConclusionIn this large sample of Italians treated for POAG, disease severity was limited and HRQoL scores were high. QoL decreased with advancing disease severity. These findings confirm the role of vision loss in impairing QoL in POAG, underlying the importance of timely detection and appropriate treatment

Occlusal adjustment using the bite plate-induced occlusal position as a reference position for temporomandibular disorders: a pilot study

<p>Abstract</p> <p>Background</p> <p>Many researchers have not accepted the use of occlusal treatments for temporomandibular disorders (TMDs). However, a recent report described a discrepancy between the habitual occlusal position (HOP) and the bite plate-induced occlusal position (BPOP) and discussed the relation of this discrepancy to TMD. Therefore, the treatment outcome of evidence-based occlusal adjustments using the bite plate-induced occlusal position (BPOP) as a muscular reference position should be evaluated in patients with TMD.</p> <p>Methods</p> <p>The BPOP was defined as the position at which a patient voluntarily closed his or her mouth while sitting in an upright posture after wearing an anterior flat bite plate for 5 minutes and then removing the plate. Twenty-one patients with TMDs underwent occlusal adjustment using the BPOP. The occlusal adjustments were continued until bilateral occlusal contacts were obtained in the BPOP. The treatment outcomes were evaluated using the subjective dysfunction index (SDI) and the Helkimo Clinical Dysfunction Index (CDI) before and after the occlusal adjustments; the changes in these two indices between the first examination and a one-year follow-up examination were then analyzed. In addition, the difference between the HOP and the BPOP was three-dimensionally measured before and after the treatment.</p> <p>Results</p> <p>The percentage of symptom-free patients after treatment was 86% according to the SDI and 76% according to the CDI. The changes in the two indices after treatment were significant (p < 0.001). The changes in the mean HOP-BPOP differences on the x-axis (mediolateral) and the y-axis (anteroposterior) were significant (p < 0.05), whereas the change on the z-axis (superoinferior) was not significant (p > 0.1).</p> <p>Conclusion</p> <p>Although the results of the present study should be confirmed in other studies, a randomized clinical trial examining occlusal adjustments using the BPOP as a reference position appears to be warranted.</p

Prevalence of PALB2 Mutations in Breast Cancer Patients in Multi-Ethnic Asian Population in Malaysia and Singapore

10.1371/journal.pone.0073638PLoS ONE88-POLN

Validation of MIPAS ClONO2 measurements

Altitude profiles of ClONO2 retrieved with the IMK (Institut fur Meteorologie und Klimaforschung) science-oriented data processor from MIPAS/Envisat (Michelson Interferometer for Passive Atmospheric Sounding on Envisat) mid-infrared limb emission measurements between July 2002 and March 2004 have been validated by comparison with balloon-borne (Mark IV, FIRS2, MIPAS-B), airborne (MIPAS-STR), ground-based (Spitsbergen, Thule, Kiruna, Harestua, Jungfraujoch, Izana, Wollongong, Lauder), and spaceborne (ACE-FTS) observations. With few exceptions we found very good agreement between these instruments and MIPAS with no evidence for any bias in most cases and altitude regions. For balloon-borne measurements typical absolute mean differences are below 0.05 ppbv over the whole altitude range from 10 to 39 km. In case of ACE-FTS observations mean differences are below 0.03 ppbv for observations below 26 km. Above this altitude the comparison with ACE-FTS is affected by the photochemically induced diurnal variation of ClONO2. Correction for this by use of a chemical transport model led to an overcompensation of the photochemical effect by up to 0.1 ppbv at altitudes of 30-35 km in case of MIPAS-ACE-FTS comparisons while for the balloon-borne observations no such inconsistency has been detected. The comparison of MIPAS derived total column amounts with ground-based observations revealed no significant bias in the MIPAS data. Mean differences between MIPAS and FTIR column abundances are 0.11 +/- 0.12 x 10(14) cm(-2) (1.0 +/- 1.1%) and -0.09 +/- 0.19 x 10(14) cm(-2) (-0.8 +/- 1.7%), depending on the coincidence criterion applied. chi(2) tests have been performed to assess the combined precision estimates of MIPAS and the related instruments. When no exact coincidences were available as in case of MIPAS-FTIR or MIPAS-ACE-FTS comparisons it has been necessary to take into consideration a coincidence error term to account for chi(2) deviations. From the resulting chi(2) profiles there is no evidence for a systematic over/underestimation of the MIPAS random error analysis.Peer reviewe

Visual field loss and vision-related quality of life in the Italian Primary Open Angle Glaucoma Study

The aim of this study was to examine the relationship between visual field (VF) loss, vision-related quality of life (QoL) and glaucoma-related symptoms in a large cohort of primary open angle glaucoma (POAG) patients. POAG patients with or without VF defects or "glaucoma suspect" patients were considered eligible. QoL was assessed using the validated versions of the 25-item National Eye Institute Visual Function Questionnaire (NEI-VFQ-25) and glaucoma-related symptoms were assessed using the Glaucoma Symptom Scale (GSS). Patients were classified as having VF damage in one eye (VFD-1), both eyes (VFD-2), or neither eye (VFD-0). 3227 patients were enrolled and 2940 were eligible for the analysis. 13.4% of patients were classified in the VFD-0, 23.7% in the VFD-1, and 62.9% in the VFD-2 group. GSS visual symptoms domain (Func-4) and GSS non-visual symptoms domain (Symp-6) scores were similar for the VFD-0 and VFD-1 groups (p = 0.133 and p = 0.834 for Func-4 and Symp-6, respectively). VFD-0 group had higher scores than VFD-2 both in Func-4 (p < 0.001) and Symp-6 domains (p = 0.035). Regarding the NEI-VFQ-25, our data demonstrated that bilateral VF defects are associated with vision-related QoL deterioration, irrespective of visual acuity