Availability of phosphate for phytoplankton and bacteria and of labile organic carbon for bacteria at different pCO2 levels in a mesocosm study

Availability of phosphate for phytoplankton and bacteria and of glucose for bacteria at different pCO2 levels were studied in a mesocosm experiment (PeECE III). Using nutrient-depleted SW Norwegian fjord waters, three different levels of pCO2 (350 μatm: 1×CO2; 700 μatm: 2×CO2; 1050 μatm: 3×CO2) were set up, and nitrate and phosphate were added at the start of the experiment in order to induce a phytoplankton bloom. Despite similar responses of total particulate P concentration and phosphate turnover time at the three different pCO2 levels, the size distribution of particulate P and 33PO4 uptake suggested that phosphate transferred to the >10 μm fraction was greater in the 3×CO2 mesocosm during the first 6–10 days when phosphate concentration was high. During the period of phosphate depletion (after Day 12), specific phosphate affinity and specific alkaline phosphatase activity (APA) suggested a P-deficiency (i.e. suboptimal phosphate supply) rather than a P-limitation for the phytoplankton and bacterial community at the three different pCO2 levels. Specific phosphate affinity and specific APA tended to be higher in the 3×CO2 than in the 2×CO2 and 1×CO2 mesocosms during the phosphate depletion period, although no statistical differences were found. Glucose turnover time was correlated significantly and negatively with bacterial abundance and production but not with the bulk DOC concentration. This suggests that even though constituting a small fraction of the bulk DOC, glucose was an important component of labile DOC for bacteria. Specific glucose affinity of bacteria behaved similarly at the three different pCO2 levels with measured specific glucose affinities being consistently much lower than the theoretical maximum predicted from the diffusion-limited model. This suggests that bacterial growth was not severely limited by the glucose availability. Hence, it seems that the lower availability of inorganic nutrients after the phytoplankton bloom reduced the bacterial capacity to consume labile DOC in the upper mixed layer of the stratified mesocosms

Scaling and root planing with and without periodontal flap surgery

. Complete removal of calculus is a primary part of achieving a “biologically acceptable” tooth surface in the treatment of periodontitis. Rabbani et al. reported that a single episode of scaling did not completely remove subgingival calculus and that the deeper the periodontal pocket, the less complete the calculus removal. The purpose of the present study was to evaluate the effectiveness of scaling relative to calculus removal following reflection of a periodontal flap. Each of 21 patients who required multiple extractions had 2 teeth scaled, 2 teeth scaled following the reflection of a periodontal flap, and 2 teeth serve as controls. Local anesthesia was used. Following extraction, the % of subgingival tooth surfaces free of calculus was determined using the method described by Rabbani with a stereomicroscope. Results showed that while scaling only (SO) and scaling with a flap (SF) increased the % of root surface without calculus, scaling following the reflection of a flap aided calculus removal in pockets 4 mm and deeper. Comparison of SO versus SF at various pocket depths for % of tooth surfaces completely free of calculus showed 1 to 3 mm pockets to be 86% versus 86%, 4 to 6 mm pockets to be 43% versus 76% and >6 mm pockets to be 32% versus 50%. The extent of residual calculus was directly related to pocket depth, was greater following scaling only, and was greatest at the CEJ or in association with grooves, fossae or furcations. No differences were noted between anterior and posterior teeth or between different tooth surfaces.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73823/1/j.1600-051X.1986.tb01461.x.pd

Age-related changes in relative expression stability of commonly used housekeeping genes in selected porcine tissues

<p>Abstract</p> <p>Background</p> <p>Gene expression analysis using real-time RT-PCR (qRT-PCR) is increasingly important in biological research due to the high-throughput and accuracy of qRT-PCR. For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes or internal control genes is required. The stability of reference genes has a tremendous effect on the results of relative quantification of gene expression by qRT-PCR. The expression stability of reference genes could vary according to tissues, age of individuals and experimental conditions. In the pig however, very little information is available on the expression stability of reference genes. The aim of this research was therefore to develop a new set of reference genes which can be used for normalization of mRNA expression data of genes expressed in varieties of porcine tissues at different ages.</p> <p>Results</p> <p>The mRNA expression stability of nine commonly used reference genes (<it>B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP </it>and <it>YWHAZ</it>) was determined in varieties of tissues collected from newborn, young and adult pigs. geNorm, NormFinder and BestKeeper software were used to rank the genes according to their stability. geNorm software revealed that <it>RPL4, PPIA </it>and <it>YWHAZ </it>showed high stability in newborn and adult pigs, while <it>B2M, YWHAZ </it>and <it>SDHA </it>showed high stability in young pigs. In all cases, <it>GAPDH </it>showed the least stability in geNorm. NormFinder revealed that <it>TBP </it>was the most stable gene in newborn and young pigs, while <it>PPIA </it>was most stable in adult pigs. Moreover, geNorm software suggested that the geometric mean of three most stable gene would be the suitable combination for accurate normalization of gene expression study.</p> <p>Conclusions</p> <p>Although, there was discrepancy in the ranking order of reference genes obtained by different analysing software methods, the geometric mean of the <it>RPL4, PPIA </it>and <it>YWHAZ </it>seems to be the most appropriate combination of housekeeping genes for accurate normalization of gene expression data in different porcine tissues at different ages.</p

Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses (Rosa hybrida)

<p>Abstract</p> <p>Background</p> <p>Gene expression studies are a prerequisite for understanding the biological function of genes. Because of its high sensitivity and easy use, quantitative PCR (qPCR) has become the gold standard for gene expression quantification. To normalise qPCR measurements between samples, the most prominent technique is the use of stably expressed endogenous control genes, the so called reference genes. However, recent studies show there is no universal reference gene for all biological questions. Roses are important ornamental plants for which there has been no evaluation of useful reference genes for gene expression studies.</p> <p>Results</p> <p>We used three different algorithms (BestKeeper, geNorm and NormFinder) to validate the expression stability of nine candidate reference genes in different rose tissues from three different genotypes of <it>Rosa hybrida </it>and in leaves treated with various stress factors. The candidate genes comprised the classical "housekeeping genes" (<it>Actin, EF-1α, GAPDH</it>, <it>Tubulin </it>and <it>Ubiquitin</it>), and genes showing stable expression in studies in <it>Arabidopsis </it>(<it>PP2A, SAND, TIP </it>and <it>UBC</it>). The programs identified no single gene that showed stable expression under all of the conditions tested, and the individual rankings of the genes differed between the algorithms. Nevertheless the new candidate genes, specifically, <it>PP2A </it>and <it>UBC</it>, were ranked higher as compared to the other traditional reference genes. In general, <it>Tubulin </it>showed the most variable expression and should be avoided as a reference gene.</p> <p>Conclusions</p> <p>Reference genes evaluated as suitable in experiments with <it>Arabidopsis thaliana </it>were stably expressed in roses under various experimental conditions. In most cases, these genes outperformed conventional reference genes, such as <it>EF1-α </it>and <it>Tubulin</it>. We identified <it>PP2A</it>, <it>SAND </it>and <it>UBC </it>as suitable reference genes, which in different combinations may be used for normalisation in expression analyses via qPCR for different rose tissues and stress treatments. However, the vast genetic variation found within the genus <it>Rosa</it>, including differences in ploidy levels, might also influence expression stability of reference genes, so that future research should also consider different genotypes and ploidy levels.</p

Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera

Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gene expression analysis plays a fundamental role. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is currently amongst the most powerful techniques to perform gene expression studies. Nevertheless, accurate gene expression quantification strongly relies on appropriate reference gene selection for sample normalization. Concerning V. vinifera, limited information still exists as for which genes are the most suitable to be used as reference under particular experimental conditions. In this work, seven candidate genes were investigated for their stability in grapevine samples referring to four distinct stresses (Erysiphe necator, wounding and UV-C irradiation in leaves and Phaeomoniella chlamydospora colonization in wood). The expression stability was evaluated using geNorm, NormFinder and BestKeeper. In all cases, full agreement was not observed for the three methods. To provide comprehensive rankings integrating the three different programs, for each treatment, a consensus ranking was created using a non-weighted unsupervised rank aggregation method. According to the last, the three most suitable reference genes to be used in grapevine leaves, regardless of the stress, are UBC, VAG and PEP. For the P. chlamydospora treatment, EF1, CYP and UBC were the best scoring genes. Acquaintance of the most suitable reference genes to be used in grapevine samples can contribute for accurate gene expression quantification in forthcoming studiesinfo:eu-repo/semantics/publishedVersio