Detection and Enhancement of Ketocarotenoid Accumulation in the Newly Isolated Sarcinoid Green Microalga Chlorosarcinopsis PY02

The sarcinoid alga PY02 is a newly isolated soil alga native to western Thailand. In this study PY02 is described, the carotenoid profile of the green and red forms of the algal cells are compared, and the effect of nitrogen reduction and media volume on ketocarotenoid production are reported. Partial sequences of the genes from elongation factor Tu (tufA) and 18S rRNA reveal that the alga is from theChlorosarcinopsisgenus. Growth studies demonstrated thatChlorosarcinopsisPY02 is capable of photoautotrophic, heterotrophic and mixotrophic growth. A gradual change in colony colour from green to red was observed over a period of four weeks under mixotrophic conditions. Pigment analysis of lyophilized red cells using ultrahigh performance liquid chromatography (UPLC) with Photo Diode Array Detection (PDA), showed for the first time that an alga from the genusChlorosarcinopsisis capable of producing ketocarotenoids such as adonixanthin and 3-OH-echinenone, with canthaxanthin as the dominant pigment. Interestingly, a reduction of nitrogen in the medium exerts a positive effect on the rate of colour change from one month to less than seven days. Enhancements of the canthaxanthin content from 520 to 1504 or 1427 µg·gDW-1were detected under 50% and 10% nitrogen content, respectively. An increase of 16% in biomass production of PY02 was unexpectedly detected from a 50% nitrogen reduction under mixotrophic culture. Notably, in liquid mixotrophic media with volumes of 15, 30 and 60 mL, the lowest volume produced a significantly higher biomass and canthaxanthin content

Effect of floor type on the performance, physiological and behavioural responses of finishing beef steers

peer-reviewedBackground:The study objective was to investigate the effect of bare concrete slats (Control), two types of mats [(Easyfix mats (mat 1) and Irish Custom Extruder mats (mat 2)] fitted on top of concrete slats, and wood-chip to simulate deep bedding (wood-chip placed on top of a plastic membrane overlying the concrete slats) on performance, physiological and behavioral responses of finishing beef steers. One-hundred and forty-four finishing steers (503 kg; standard deviation 51.8 kg) were randomly assigned according to their breed (124 Continental cross and 20 Holstein–Friesian) and body weight to one of four treatments for 148 days. All steers were subjected to the same weighing, blood sampling (jugular venipuncture), dirt and hoof scoring pre study (day 0) and on days 23, 45, 65, 86, 107, 128 and 148 of the study. Cameras were fitted over each pen for 72 h recording over five periods and subsequent 10 min sampling scans were analysed. Results: Live weight gain and carcass characteristics were similar among treatments. The number of lesions on the hooves of the animals was greater (P < 0.05) on mats 1 and 2 and wood-chip treatments compared with the animals on the slats. Dirt scores were similar for the mat and slat treatments while the wood-chip treatment had greater dirt scores. Animals housed on either slats or wood-chip had similar lying times. The percent of animals lying was greater for animals housed on mat 1 and mat 2 compared with those housed on concrete slats and wood chips. Physiological variables showed no significant difference among treatments. Conclusions: In this exploratory study, the performance or welfare of steers was not adversely affected by slats, differing mat types or wood-chip as underfoot material

Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits

Carotenoids represent some of the most important secondary metabolites in the human diet, and tomato (Solanum lycopersicum) is a rich source of these health-promoting compounds. In this work, a novel and fruit-related regulator of pigment accumulation in tomato has been identified by artificial neural network inference analysis and its function validated in transgenic plants. A tomato fruit gene regulatory network was generated using artificial neural network inference analysis and transcription factor gene expression profiles derived from fruits sampled at various points during development and ripening. One of the transcription factor gene expression profiles with a sequence related to an Arabidopsis (Arabidopsis thaliana) ARABIDOPSIS PSEUDO RESPONSE REGULATOR2-LIKE gene (APRR2-Like) was up-regulated at the breaker stage in wild-type tomato fruits and, when overexpressed in transgenic lines, increased plastid number, area, and pigment content, enhancing the levels of chlorophyll in immature unripe fruits and carotenoids in red ripe fruits. Analysis of the transcriptome of transgenic lines overexpressing the tomato APPR2-Like gene revealed up-regulation of several ripening-related genes in the overexpression lines, providing a link between the expression of this tomato gene and the ripening process. A putative ortholog of the tomato APPR2-Like gene in sweet pepper (Capsicum annuum) was associated with pigment accumulation in fruit tissues. We conclude that the function of this gene is conserved across taxa and that it encodes a protein that has an important role in ripening

Distinguishing Asthma Phenotypes Using Machine Learning Approaches.

Asthma is not a single disease, but an umbrella term for a number of distinct diseases, each of which are caused by a distinct underlying pathophysiological mechanism. These discrete disease entities are often labelled as asthma endotypes. The discovery of different asthma subtypes has moved from subjective approaches in which putative phenotypes are assigned by experts to data-driven ones which incorporate machine learning. This review focuses on the methodological developments of one such machine learning technique-latent class analysis-and how it has contributed to distinguishing asthma and wheezing subtypes in childhood. It also gives a clinical perspective, presenting the findings of studies from the past 5 years that used this approach. The identification of true asthma endotypes may be a crucial step towards understanding their distinct pathophysiological mechanisms, which could ultimately lead to more precise prevention strategies, identification of novel therapeutic targets and the development of effective personalized therapies

Crystal structure of geranylgeranyl pyrophosphate synthase (CrtE) involved in cyanobacterial terpenoid biosynthesis

Cyanobacteria are photosynthetic prokaryotes that perform oxygenic photosynthesis. Due to their ability to use the photon energy of sunlight to fix carbon dioxide into biomass, cyanobacteria are promising hosts for the sustainable production of terpenoids, also known as isoprenoids, a diverse class of natural products with potential as advanced biofuels and high-value chemicals. However, the cyanobacterial enzymes involved in the biosynthesis of the terpene precursors needed to make more complicated terpenoids are poorly characterized. Here we show that the predicted type II prenyltransferase CrtE encoded by the model cyanobacterium Synechococcus sp. PCC 7002 is homodimeric and able to synthesize C20-geranylgeranyl pyrophosphate (GGPP) from C5-isopentenyl pyrophosphate (IPP) and C5-dimethylallyl pyrophosphate (DMAPP). The crystal structure of CrtE solved to a resolution of 2.7 Å revealed a strong structural similarity to the large subunit of the heterodimeric geranylgeranyl pyrophosphate synthase 1 from Arabidopsis thaliana with each subunit containing 14 helices. Using mutagenesis, we confirmed that the fourth and fifth amino acids (Met-87 and Ser-88) before the first conserved aspartate-rich motif (FARM) play important roles in controlling chain elongation. While the WT enzyme specifically produced GGPP, variants M87F and S88Y could only generate C15-farnesyl pyrophosphate (FPP), indicating that residues with large side chains obstruct product elongation. In contrast, replacement of M87 with the smaller Ala residue allowed the formation of the longer C25-geranylfarnesyl pyrophosphate (GFPP) product. Overall, our results provide new structural and functional information on the cyanobacterial CrtE enzyme that could lead to the development of improved cyanobacterial platforms for terpenoid production

Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition

Limited contribution of permafrost carbon to methane release from thawing peatlands

Models predict that thaw of permafrost soils at northern high-latitudes will release tens of billions of tonnes of carbon (C) to the atmosphere by 21001-3. The effect on the Earth's climate depends strongly on the proportion of this C which is released as the more powerful greenhouse gas methane (CH4), rather than carbon dioxide (CO2)1,4; even if CH4 emissions represent just 2% of the C release, they would contribute approximately one quarter of the climate forcing5. In northern peatlands, thaw of ice-rich permafrost causes surface subsidence (thermokarst) and water-logging6, exposing substantial stores (10s of kg C m-2, ref. 7) of previously-frozen organic matter to anaerobic conditions, and generating ideal conditions for permafrost-derived CH4 release. Here we show that, contrary to expectations, although substantial CH4 fluxes (>20 g CH4 m 2 yr-1) were recorded from thawing peatlands in northern Canada, only a small amount was derived from previously-frozen C (<2 g CH4 m-2 yr-1). Instead, fluxes were driven by anaerobic decomposition of recent C inputs. We conclude that thaw-induced changes in surface wetness and wetland area, rather than the anaerobic decomposition of previously-frozen C, may determine the effect of permafrost thaw on CH4 emissions from northern peatlands

Carotenoid accumulation during tomato fruit ripening is modulated by the auxin-ethylene balance

Background : Tomato fruit ripening is controlled by ethylene and is characterized by a shift in color from green to red, a strong accumulation of lycopene, and a decrease in β-xanthophylls and chlorophylls. The role of other hormones, such as auxin, has been less studied. Auxin is retarding the fruit ripening. In tomato, there is no study of the carotenoid content and related transcript after treatment with auxin. Results : We followed the effects of application of various hormone-like substances to “Mature-Green” fruits. Application of an ethylene precursor (ACC) or of an auxin antagonist (PCIB) to tomato fruits accelerated the color shift, the accumulation of lycopene, α-, β-, and δ-carotenes and the disappearance of β-xanthophylls and chlorophyll b. By contrast, application of auxin (IAA) delayed the color shift, the lycopene accumulation and the decrease of chlorophyll a. Combined application of IAA + ACC led to an intermediate phenotype. The levels of transcripts coding for carotenoid biosynthesis enzymes, for the ripening regulator Rin, for chlorophyllase, and the levels of ethylene and abscisic acid (ABA) were monitored in the treated fruits. Correlation network analyses suggest that ABA, may also be a key regulator of several responses to auxin and ethylene treatments. Conclusions : The results suggest that IAA retards tomato ripening by affecting a set of (i) key regulators, such as Rin, ethylene and ABA, and (ii) key effectors, such as genes for lycopene and β-xanthophyll biosynthesis and for chlorophyll degradation

Synchrotron validation of inline coherent imaging for tracking laser keyhole depth

In situ monitoring is critical to the increasing adoption of laser powder bed fusion (LPBF) and laser welding by industry for manufacture of complex metallic components. Optical coherence tomography (OCT), an interferometric imaging technique adapted from medical applications, is now widely used for operando monitoring of morphology during high-power laser material processing. However, even in stable processing regimes, some OCT depth measurements from the keyhole (vapor cavity formed at laser beam spot) appear too shallow or too deep when compared to ex situ measurements of weld depth. It has remained unclear whether these outliers are due to imaging artifacts, multiple scattering of the imaging beam within the keyhole, or real changes in keyhole depth, making it difficult to accurately extract weld depth and determine error bounds. To provide a definitive explanation, we combine inline coherent imaging (ICI), a type of OCT, with synchrotron X-ray imaging for simultaneous, operando monitoring of the full 2-dimensional keyhole profile at high-speed (280 kHz and 140 kHz, respectively). Even in a highly turbulent pore-generation mode, the depth measured with ICI closely follows the keyhole depth extracted from radiography (>80% within ± 14 µm). Ray-tracing simulations are used to confirm that the outliers in ICI depth measurements (that significantly disagree with radiography) primarily result from multiple reflections of the imaging light (57%). Synchrotron X-ray imaging also enables tracking of bubble and pore formation events. Pores are generated during laser welding when the sidewalls of the keyhole rapidly (>10 m/s) collapse inwards, pinching off a bubble from the keyhole root and resulting in a rapid decrease in keyhole depth. Evidence of bubble formation can be found in ICI depth profiles alone, as rapid depth changes exhibit moderate correlation with bubble formation events (0.26). This work moves closer to accurate, localized defect detection during laser welding and LPBF using ICI

InterPro in 2017-beyond protein family and domain annotations

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences