OSCA: a comprehensive open-access system of analysis of posterior capsular opacification

BACKGROUND: This paper presents and tests a comprehensive computerised system of analysis of digital images of posterior capsule opacification (PCO). It updates and expands significantly on a previous presentation to include facilities for selecting user defined central areas and for registering and subsequent merging of images for artefact removal. Also, the program is compiled and thus eliminates the need for specialised additional software. The system is referred to in this paper as the open-access systematic capsule assessment (OSCA). The system is designed to be evidence based, objective and openly available, improving on current systems of analysis. METHODS: Principal features of the OSCA system of analysis are discussed. Flash artefacts are automatically located in two PCO images and the images merged to produce a composite free from these artefacts. For this to be possible the second image has to be manipulated with a registration technique to bring it into alignment with the first. Further image processing and analysis steps use a location-sensitive entropy based texture analysis of PCO. Validity of measuring PCO progression of the whole new system is assessed along with visual significance of scores. Reliability of the system is assessed. RESULTS: Analysis of PCO by the system shows ability to detect early progression of PCO, as well as detection of more visually significant PCO. Images with no clinical PCO produce very low scores in the analysis. Reliability of the system of analysis is demonstrated. CONCLUSION: This system of PCO analysis is evidence-based, objective and clinically useful. It incorporates flash detection and removal as well as location sensitive texture analysis. It provides features and benefits not previously available to most researchers or clinicians. Substantial evidence is provided for this system's validity and reliability

Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga \u3ci\u3eNannochloropsis oceanica\u3c/i\u3e CCMP1779

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogendepleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus

Catalytically inactive DNA ligase IV promotes DNA repair in living cells.

Funder: French National Cancer InstituteDNA double strand breaks (DSBs) are induced by external genotoxic agents (ionizing radiation or genotoxins) or by internal processes (recombination intermediates in lymphocytes or by replication errors). The DNA ends induced by these genotoxic processes are often not ligatable, requiring potentially mutagenic end-processing to render ends compatible for ligation by non-homologous end-joining (NHEJ). Using single molecule approaches, Loparo et al. propose that NHEJ fidelity can be maintained by restricting end-processing to a ligation competent short-range NHEJ complex that 'maximizes the fidelity of DNA repair'. These in vitro studies show that although this short-range NHEJ complex requires DNA ligase IV (Lig4), its catalytic activity is dispensable. Here using cellular models, we show that inactive Lig4 robustly promotes DNA repair in living cells. Compared to repair products from wild-type cells, those isolated from cells with inactive Lig4 show a somewhat increased fraction that utilize micro-homology (MH) at the joining site consistent with alternative end-joining (a-EJ). But unlike a-EJ in the absence of NHEJ, a large percentage of joints isolated from cells with inactive Lig4 occur with no MH - thus, clearly distinct from a-EJ. Finally, biochemical assays demonstrate that the inactive Lig4 complex promotes the activity of DNA ligase III (Lig3)

Thermoelectric properties of epitaxial TbAs:InGaAs nanocomposites

International audienceInGaAs lattice-matched to InP was grown by molecular beam epitaxy with randomly distributed TbAs nanoparticles for thermoelectric power generation applications. TbAs:InGaAs is expected to have a large thermoelectric figure of merit, ZT, particularly at high temperatures, owing to energy band alignment between the nanoparticles and their surrounding matrix. Here, the room temperature thermoelectric properties were measured as a function of TbAs concentration, revealing a maximum thermoelectric power factor of 2.38 W/mK2 and ZT of 0.19 with 0.2% TbAs. Trends in the thermoelectric properties closely resemble those found in comparable ErAs:InGaAs nanocomposite materials. However, nanoparticles were not observed by scanning transmission electron microscopy in the highest ZT TbAs:InGaAs sample, unlike the highest ZT ErAs:InGaAs sample (0.2% ErAs) and two higher concentration TbAs:InGaAs samples examined. Consistent with expectations concerning the positioning of the Fermi level in these materials, ZT was enhanced by TbAs incorporation largely due to a high Seebeck coefficient, whereas ErAs provided InGaAs with higher conductivity but a lower Seebeck coefficient than that of TbAs:InGaAs. Thermal conductivity was reduced significantly from that of intrinsic thin-film InGaAs only with TbAs concentrations greater than ∼1.7%

Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.

Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair.Wellcome Trust for a Programme Grant (O93167/Z/10/Z; 2011–2016) and Investigator Award (200814/Z/16/Z

Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga <em>Nannochloropsis oceanica</em> CCMP1779

<div><p>Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes <em>Nannochloropsis oceanica</em> an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of <em>N. oceanica</em> CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the <em>N. oceanica</em> CCMP1779 gene repertoire with the recently published <em>N. gaditana</em> genome identified 2,649 genes likely specific to <em>N. oceanica</em> CCMP1779. Many of these <em>N. oceanica</em>–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of <em>N. oceanica</em> CCMP1779 are provided. The availability of genomic and transcriptomic data for <em>Nannochloropsis oceanica</em> CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus.</p> </div

Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga <i>Nannochloropsis oceanica</i> CCMP1779

Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga <i>Nannochloropsis oceanica</i> CCMP177