Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

Indexación: Web of Science.Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e(-5). None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).http://journal.frontiersin.org/article/10.3389/fmicb.2016.02035/ful

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Roll-to-roll manufacturing of micro components based on advanced printing, structuring and lamination of ceramic tapes is rapidly progressing. This large-scale and cost-effective manufacturing process of ceramic micro devices is however prone to hide defects within the visually opaque tape stacks. To achieve a sustainable manufacturing with zero defects in the future, there is an urgent need for reliable inspection systems. The systems to be developed have to perform high-resolution in-process quality control at high speed. Optical coherence tomography (OCT) is a promising technology for detailed in-depth inspection and metrology. Combined with infrared screening of larger areas it can solve the inspection demands in the roll-to-roll ceramic tape processes. In this thesis state-of-art commercial and laboratory OCT systems, operating at the central wavelength of 1.3 µm and 1.7 µm respectively, are evaluated for detecting microchannels, metal prints, defects and delaminations embedded in alumina and zirconia ceramic layers at hundreds of micrometers beneath surfaces. The effect of surface roughness induced scattering and scattering by pores on the probing radiation, is analyzed by experimentally captured and theoretically simulated OCT images of the ceramic samples, while varying surface roughnesses and operating wavelengths. By extending the Monte Carlo simulations of the OCT response to the mid-infrared the optimal operating wavelength is found to be 4 µm for alumina and 2 µm for zirconia. At these wavelengths we predict a sufficient probing depth of about 1 mm and we demonstrate and discuss the effect of rough surfaces on the detectability of embedded boundaries. For high-precision measurement a new and automated 3D image processing algorithm for analysis of volumetric OCT data is developed. We show its capability by measuring the geometric dimensions of embedded structures in ceramic layers, extracting features with irregular shapes and detecting geometric deformations. The method demonstrates its suitability for industrial applications by rapid inspection of manufactured samples with high accuracy and robustness. The new inspection methods we demonstrate are finally analyzed in the context of measurement uncertainty, both in the axial and lateral cases, and reveal that scattering in the sample indeed affects the lateral measurement uncertainty. Two types of image artefacts are found to be present in OCT images due to multiple reflections between neighboring boundaries and inhomogeneity of refractive index. A wavefront aberration is found in the OCT system with a scanning scheme of two galvo mirrors, and it can be corrected using our image processing algorithm.QC 20140428Multilayer (FP7-NMP4-2007-214122

Virtual Immersions in Science: the outreach program of the Scuola Normale Superiore

With the project “Virtual Immersions in Science: a path of excellence from Research to Outreach” (VIS), we set ourselves the ambitious goal to divulge and disseminate the latest scientific research results produced by the Scuola Normale Superiore (SNS) and by top level Italian scientists working in our country and in the rest of the world, providing an idea as to the type of activity carried out by researchers as well as how research is actually carried out, and showing the most dynamic and creative side of contemporary scientific activity. VIS has met with extraordinary public success, coverage by the major media including local and national television and newspapers, and enthusiastic feedback from all the participants, already in their hundreds of thousands

Why does low intensity, long-day lighting promote growth in Petunia, Impatiens, and tomato?

Numerous reports demonstrate that low intensity, long-day (LD) lighting treatments can promote growth. However, there are conflicting suggestions as to the mechanisms involved. This study examines the responses of Petunia, Impatiens, and tomato to LD lighting treatments and concludes that no single mechanism can explain the growth promotion observed in each case. Petunia showed the most dramatic response to photoperiod; up to a doubling in dry weight (DW) as a result of increasing daylength from 8 h d–1 to 16 h d–1.This could be explained by an increase in specific leaf area (SLA) comparable to that seen with shading. At low photosynthetic photon flux densities (PPFD), the increased leaf area more than compensated for any loss in photosynthetic capacity per unit leaf area. In Petunia, the response may, in part, have also been due to changes in growth habit. Impatiens and tomato showed less dramatic increases in DW as a result of LD lighting, but no consistent effects on SLA or growth habit were observed. In tomato, increased growth was accompanied by increased chlorophyll content, but this had no significant effect on photosynthesis. In both species, increased growth may have been due to a direct effect of LD lighting on photosynthesis. This is contrary to the generally held view that light of approx. 3 – 4 μmol m–2 s–1 is unlikely to have any significant impact on net photosynthesis. Nevertheless, we show that the relationship between PPFD and net photosynthesis is non-linear at low light levels, and therefore low intensity LD lighting can offset respiration very efficiently. Furthermore, a small increase in photosynthesis will have a greater impact when ambient light levels are low

The effects of day and night temperature on Chrysanthemum morifolium: investigating the safe limits for temperature integration

The impact of day and night temperatures on pot chrysanthemum (cultivars ‘Covington’ and ‘Irvine’) was assessed by exposing cuttings, stuck in weeks 39, 44, and 49, to different temperature regimes in short-days. Glasshouse heating setpoints of 12°, 15°, 18°, and 21°C, were used during the day, with venting at 2°C above these set-points. Night temperatures were then automatically manipulated to ensure that all of the treatments achieved similar mean diurnal temperatures. Plants were grown according to commercial practice and the experiment was repeated over 2 years. Increasing the day temperature from approx. 19°C to 21°C, and compensating by reducing the night temperature, did not have a significant impact on flowering time, although plant height was increased.This suggests that a temperature integration strategy which involves higher vent temperatures, and exploiting solar gain to give higher than normal day temperatures, should have minimal impact on crop scheduling. However, lowering the day-time temperature to approx. 16°C, and compensating with a warmer night, delayed flowering by up to 2 weeks. Therefore, a strategy whereby, in Winter, more heat is added at night under a thermally-efficient blackout screen may result in flowering delays.Transfers between the temperature regimes showed that the flowering delays were proportional to the amount of time spent in a low day-time temperature regime. Plants flowered at the same time, irrespective of whether they were transferred on a 1-, 2-, or 4-week cycle

The effects of long-day lighting and removal of young leaves on tomato yield

While low intensity long-day (LD) lighting has been shown to enhance the growth of young plants under low light levels, its effect on the yield of a long-season glasshouse tomato crop has not been previously examined. LD were provided by the use of tungsten lamps (2.8 μmol m-2 s-1 at approx. 0.5 m from the ground) between 04.00 h to sunrise and from sunset until 20.00 h (GMT). LD lighting increased leaf chlorophyll contents, and the numbers of flowers and fruits set per truss when the plants were young. However, this treatment did not affect the total yield of tomatoes. Different leaf removal treatments were applied within each glasshouse compartment. A previous experiment had shown that reducing the leaf area index (LAI) from 5.2 to 2.6, by removing old leaves, did not affect yield. It was also thought that removal of young leaves reduced the total vegetative sink-strength and favoured assimilate partitioning into the fruit. Therefore, removal of young leaves could increase fruit yield. In the present experiments, one-third of the leaves were removed in March (those immediately below each truss) and, subsequently, every third leaf was removed at an early stage of its development. This reduced the LAI from 4.1 to 2.9 and resulted in a loss of yield from 3 – 4 weeks after leaf removal until the end of the experiment, at which point there was an 8% loss of cumulative yield due to a reduction in the average number of fruits set per truss and in mean fruit weight. We postulate that the light which would have been intercepted by young photosynthetically-efficient leaves at the top of the canopy was intercepted instead by older leaves which were less efficient, reducing overall net canopy photosynthesis

Measuring Progress on the Control of Porcine Reproductive and Respiratory Syndrome (PRRS) at a Regional Level: The Minnesota N212 Regional Control Project (Rcp) as a Working Example.

Due to the highly transmissible nature of porcine reproductive and respiratory syndrome (PRRS), implementation of regional programs to control the disease may be critical. Because PRRS is not reported in the US, numerous voluntary regional control projects (RCPs) have been established. However, the effect of RCPs on PRRS control has not been assessed yet. This study aims to quantify the extent to which RCPs contribute to PRRS control by proposing a methodological framework to evaluate the progress of RCPs. Information collected between July 2012 and June 2015 from the Minnesota Voluntary Regional PRRS Elimination Project (RCP-N212) was used. Demography of premises (e.g. composition of farms with sows = SS and without sows = NSS) was assessed by a repeated analysis of variance. By using general linear mixed-effects models, active participation of farms enrolled in the RCP-N212, defined as the decision to share (or not to share) PRRS status, was evaluated and used as a predictor, along with other variables, to assess the PRRS trend over time. Additionally, spatial and temporal patterns of farmers' participation and the disease dynamics were investigated. The number of farms enrolled in RCP-N212 and its geographical coverage increased, but the proportion of SS and NSS did not vary significantly over time. A significant increasing (p<0.001) trend in farmers' decision to share PRRS status was observed, but with NSS producers less willing to report and a large variability between counties. The incidence of PRRS significantly (p<0.001) decreased, showing a negative correlation between degree of participation and occurrence of PRRS (p<0.001) and a positive correlation with farm density at the county level (p = 0.02). Despite a noted decrease in PRRS, significant spatio-temporal patterns of incidence of the disease over 3-weeks and 3-kms during the entire study period were identified. This study established a systematic approach to quantify the effect of RCPs on PRRS control. Despite an increase in number of farms enrolled in the RCP-N212, active participation is not ensured. By evaluating the effect of participation on the occurrence of PRRS, the value of sharing information among producers may be demonstrated, in turn justifying the existence of RCPs