Guidelines for Negotiating Scientific Collaboration

Whether it's sharing reagents with a laboratory on the other side of the world or working with the postdoc at the neighboring bench, some simple rules of collaboration might help

Inhibition of cPLA2-Mediated Arachidonic Acid Release by Cyclic AMP Defines a Negative Feedback Loop for P2Y-Receptor Activation in Mdck-D1 Cells

In Madin-Darby canine kidney D1cells extracellular nucleotides activate P2Y receptors that couple to several signal transduction pathways, including stimulation of multiple phospholipases and adenylyl cyclase. For one class of P2Y receptors, P2Y2 receptors, this stimulation of adenylyl cyclase and increase in cAMP occurs via the conversion of phospholipase A2 (PLA2)-generated arachidonic acid (AA) to prostaglandins (e.g. PGE2). These prostaglandins then stimulate adenylyl cyclase activity, presumably via activation of prostanoid receptors. In the current study we show that agents that increase cellular cAMP levels (including PGE2, forskolin, and the β-adrenergic agonist isoproterenol) can inhibit P2Y receptor-promoted AA release. The protein kinase A (PKA) inhibitor H89 blocks this effect, suggesting that this feedback inhibition occurs via activation of PKA. Studies with PGE2indicate that inhibition of AA release is attributable to inhibition of mitogen-activated protein kinase activity and in turn of P2Y receptor stimulated PLA2 activity. Although cAMP/PKA-mediated inhibition occurs for P2Yreceptor-promoted AA release, we did not find such inhibition for epinephrine (α1-adrenergic) or bradykinin-mediated AA release. Taken together, these results indicate that negative feedback regulation via cAMP/PKA-mediated inhibition of mitogen-activated protein kinase occurs for some, but not all, classes of receptors that promote PLA2 activation and AA release. We speculate that receptor-selective feedback inhibition occurs because PLA2activation by different receptors in Madin-Darby canine kidney D1 cells involves the utilization of different signaling components that are differentially sensitive to increases in cAMP or, alternatively, because of compartmentation of signaling components

Receptor Number and Caveolar Co-Localization Determine Receptor Coupling Efficiency to Adenylyl Cyclase

Recent evidence suggests that many signaling molecules localize in microdomains of the plasma membrane, particularly caveolae. In this study, overexpression of adenylyl cyclase was used as a functional probe of G protein-coupled receptor (GPCR) compartmentation. We found that three endogenous receptors in neonatal rat cardiomyocytes couple with different levels of efficiency to the activation of adenylyl cyclase type 6 (AC6), which localizes to caveolin-rich membrane fractions. Overexpression of AC6 enhanced the maximal cAMP response to β1-adrenergic receptor (β1AR)-selective activation 3.7-fold, to β2AR-selective activation only 1.6-fold and to prostaglandin E2 (PGE2) not at all. Therefore, the rank order of efficacy in coupling to AC6 is β1AR \u3e β2AR \u3e prostaglandin E2 receptor (EP2R). β2AR coupling efficiency was greater when we overexpressed the receptor or blocked its desensitization by expressing βARKct, an inhibitor of G protein-coupled receptor kinase activation, but was not significantly greater when cells were treated with pertussis toxin. Assessment of receptor and AC expression indicated co-localization of AC5/6, β1AR, and β2AR, but not EP2R, in caveolin-rich membranes and caveolin-3 immunoprecipitates, likely explaining the observed activation of AC6 by βAR subtypes but lack thereof by PGE2. When cardiomyocytes were stimulated with a βAR agonist, β2AR were no longer found in caveolin-3 immunoprecipitates; an effect that was blocked by expression of βARKct. Thus, agonist-induced translocation of β2AR out of caveolae causes a sequestration of receptor from effector and likely contributes to the lower efficacy of β2AR coupling to AC6 as compared with β1AR, which do not similarly translocate. Therefore, spatial co-localization is a key determinant of efficiency of coupling by particular extracellular signals to activation of GPCR-linked effectors

Identification and modelling of aerobic hydrolysis in activated sludge systems, application of optimal experimental

Atıksularda Kimyasal Oksijen İhtiyacı (KOİ) fraksiyonlarının ve bunlara ait giderim  kinetiğinin belirlenebilmesi aktif çamur tasarımı ve işletilmesi açısından büyük önem taşımaktadır. Özellikle, yavaş ayrışan organik maddenin atıksularda yüksek miktarlarda olduğu bilinmektedir. Genelde, ayrışabilen KOİ fraksiyonlarını hızlı ve yavaş ayrışan KOİ olarak sınıflandırmak mümkündür. Ancak, atıksuyun tipi ve özelliğine bağlı olarak bu fraksiyonlar değişkenlik gösterdiği gibi çözünmüş, partiküler veya çökelebilir formlarda bulunabilmektedir. Hidroliz prosesi aktif çamur tesislerinin işletilmesinde çıkış suyu kalitesinin, fazla çamur oluşumu, oksijen ihtiyacı ve nutrient giderimi açısından büyük rol oynamaktadır. Özellikle deri, tekstil vb. endüstriyel atıksularında olduğu gibi çok yüksek miktarda yavaş ayrışan çözünmüş formdaki organik maddeye ait biyolojik giderim atıksu arıtma tesisi çıkış suyu kalitesi açısından önem taşımaktadır. Bu çalışma kapsamında, kesikli yürütülen respirometrik   deneylerin kullanılması ile çoğalma ve hidroliz kinetiğine ait sistem tanımlanması yapılmıştır. Seçilen aktif çamur modeli çoğalma, hidroliz ve ölüm olmak üzere 3 proses ve 7 parametreden oluşmaktadır. Sistemin tanımlanması, teorik ve pratik sistem tanımlama adımlarını kapsamaktadır. Teorik sistem tanımlamada, Taylor Serileri ile lineerize edilen modelden respirometrik verileri kullanarak hangi parametre gruplarının elde edilebileceği bulunmuştur. Pratik sistem tanımlamada ise gerçek veriler kullanılarak, parametre tahminleri yapılmış ve güvenilirlik aralıkları belirlenmiştir. Optimal Deney Tasarımı simülasyonlarından, deneyin başlangıç F/M (Substrat/Mikroorganizma) oranının azaltılmasının deneyin güvenilirliğini arttıracağı ancak bunun yanında parametreler arasındaki korelasyonu  da arttıracağı kanıtlanmıştır. Anahtar Kelimeler: Modelleme, hidroliz, sistem tanımlama, oksijen tüketim hızı, Optimal Deney Tasarımı.Appropriate determination of accurate COD fractionation together with degradation kinetics of organic matter has a prime importance on the design and operation of activated sludge systems. In general, regarding the total biodegradable COD, raw domestic wastewaters approximately contain readily biodegradable and slowly biodegradable substrates at fractions around 30% and 70%, respectively. On the other hand, compared to domestic wastewaters, industrial wastewaters contain much higher fraction of slowly biodegradable substrate which directly influence the effluent quality of treatment plants. In this respect, the determination  of slowly biodegradable matter as well as its degradation characteristics are crucial in terms of wastewater treatment plant design and operation. Hydrolysis process has already been known as the rate limiting step in organic carbon removal from industrial and domestic wastewaters. Considering the effluent quality, hydrolysis mechanism also plays a dominant role in delicate balance of electron donor/electron acceptor ratios in biological nutrient removal type activated sludge systems as an important carbon source. In addition to that, sludge production from activated sludge plant is also affected by the nature of slowly biodegradable matter. In parallel to the vast developments in activated sludge modeling, respirometry has always been effectively utilized as a convenient tool for influent wastewater characterization which can be regarded as a corner stone of activated sludge modeling. To date, numerious respirometric tests have been applied for gathering information on the stoichiometry and kinetics of biodegradable substrates in raw wastewaters. However, the proposed methodologies were mostly devoted to the estimation of growth associated parameters such as maximum growth rate, active fraction of biomass, heterotrophic yield and half saturation growth constant for heterotrophs etc. In this study, surface-saturation type hydrolysis kinetics was investigated based on short-term oxygen uptake rate measurements. An identifiability study were performed in order to find out best identifiable parameter groups from respirometric data with the aid of non-linear degradation model. Basically, the model has been constitued using the reactions of (i) aerobic heterotrophic growth (ii) hydrolysis of particulate matter and (iii) endogenous decay processes. Basically, the model has 7 parameters to be estimated from a single respirogram. The model identification procedure comprises the theoretical and practical identifiability studies. In theoretical identifiability study, identifiable combinations of model parameter that can be extracted from available data is studied for a certain model. Non-linear model under study was linearized with the aid of Taylor Series Expansion method. By neglecting the growth of heterotrophs under low initial F/M ratio, 6 parameter combinations were found to be theoretically identifiable from batch respirogram. On the other hand, the maximum rates governing the growth (mH) and hydrolysis (kh) were found to be individually identifiable if considerable growth of heterotrophs are taking place during the course of the experiment. From the identifiability study, it was also found that all parameters combinations include the heterotrophic yield coefficient, YH. In addition, the parameter combinations containing hydrolysis parameters always include the initial active heterotrophic biomass, XH0 as a state variable. In practical identifiability, the identifiable parameter combinations of a selected model were estimated. In this study, the information of the experiments were simulated for different initial F/M (Food/Microorganism) ratio by comparing the amount of information as well as the correlation degree among the estimated parameters. The information contents of the experiments were evaluated on the basis of Optimal Experimental Design (OED) methodology. In this regard, the effects of initial conditions on information content of experiments was evaluated via comparing the scalar functions of Fisher Information Matrix (FIM). These scalar functions were selected as the D-Criterion and E- Criterion which summarize the information volume and the correlation degree among parameters, respectively. Finally, it was found that applying lower initial F/M ratio increases the information content of the experiment, on the other hand it also increases the correlation among the estimated parameters. Keywords: Modelling, hydrolysis, identifiability, oxygen uptake rate, optimal experimental design

Shortened surveillance intervals following suboptimal bowel preparation for colonoscopy: Results of a national survey

Purpose: Suboptimal bowel preparation can result in decreased neoplasia detection, shortened surveillance intervals, and increased costs. We assessed bowel preparation recommendations and the relationship to self-reported proportion of suboptimal bowel preparations in practice; and evaluated the impact of suboptimal bowel preparation on colonoscopy surveillance practices. A random sample of a national organization of gastroenterologists in the U.S. was surveyed. Methods: Demographic and practice characteristics, bowel preparation regimens, and proportion of suboptimal bowel preparations in practice were ascertained. Recommended follow-up colonoscopy intervals were evaluated for optimal and suboptimal bowel preparation and select clinical scenarios. Results: We identified 6,777 physicians, of which 1,354 were randomly selected; 999 were eligible, and 288 completed the survey. Higher proportion of suboptimal bowel preparations/week (≥10 %) was associated with hospital/university practice, teaching hospital affiliation, greater than 25 % Medicaid insured patients, recommendation of PEG alone and sulfate-free. Those reporting greater than 25 % Medicare and privately insured patients, split dose recommendation, and use of MoviPrep® were associated with a less than 10 % suboptimal bowel preparations/week. Shorter surveillance intervals for three clinical scenarios were reported for suboptimal preparations and were shortest among participants in the Northeast who more often recommended early follow-up for normal findings and small adenomas. Those who recommended 4-l PEG alone more often advised less than 1 year surveillance interval for a large adenoma. Conclusions: Our study demonstrates significantly shortened surveillance interval recommendations for suboptimal bowel preparation and that these interval recommendations vary regionally in the United States. Findings suggest an interrelationship between dietary restriction, purgative type, and practice and patient characteristics that warrant additional research