The elucidation of gene expression patterns leads to a better understanding of biological processes. Real-time quantitative RT-PCR has become the standard method for in-depth studies of gene ...expression. A biologically meaningful reporting of target mRNA quantities requires accurate and reliable normalization in order to identify real gene-specific variation. The purpose of normalization is to control several variables such as different amounts and quality of starting material, variable enzymatic efficiencies of retrotranscription from RNA to cDNA, or differences between tissues or cells in overall transcriptional activity. The validity of a housekeeping gene as endogenous control relies on the stability of its expression level across the sample panel being analysed. In the present report we describe the first systematic evaluation of potential internal controls during tomato development process to identify which are the most reliable for transcript quantification by real-time RT-PCR.
In this study, we assess the expression stability of 7 traditional and 4 novel housekeeping genes in a set of 27 samples representing different tissues and organs of tomato plants at different developmental stages. First, we designed, tested and optimized amplification primers for real-time RT-PCR. Then, expression data from each candidate gene were evaluated with three complementary approaches based on different statistical procedures. Our analysis suggests that SGN-U314153 (CAC), SGN-U321250 (TIP41), SGN-U346908 ("Expressed") and SGN-U316474 (SAND) genes provide superior transcript normalization in tomato development studies. We recommend different combinations of these exceptionally stable housekeeping genes for suited normalization of different developmental series, including the complete tomato development process.
This work constitutes the first effort for the selection of optimal endogenous controls for quantitative real-time RT-PCR studies of gene expression during tomato development process. From our study a tool-kit of control genes emerges that outperform the traditional genes in terms of expression stability.
The successful development of modern gas sensing technologies requires high sensitivity and selectivity coupled to cost effectiveness, which implies the necessity to miniaturize devices while ...reducing the amount of sensing material. The appealing alternative of integrating nanoparticles of a porous metal–organic framework (MOF) onto capacitive sensors based on interdigitated electrode (IDE) chips is presented. We report the deposition of MIL-96(Al) MOF thin films via the Langmuir–Blodgett (LB) method on the IDE chips, which allowed the study of their gas/vapor sensing properties. First, sorption studies of several organic vapors like methanol, toluene, chloroform, etc. were conducted on bulk MOF. The sorption data revealed that MIL-96(Al) presents high affinity toward water and methanol. Later on, ordered LB monolayer films of MIL-96(Al) particles of ∼200 nm were successfully deposited onto IDE chips with homogeneous coverage of the surface in comparison to conventional thin film fabrication techniques such as drop-casting. The sensing tests showed that MOF LB films were selective for water and methanol, and short response/recovery times were achieved. Finally, chemical vapor deposition (CVD) of a porous thin film of Parylene C (thickness ∼250–300 nm) was performed on top of the MOF LB films to fabricate a thin selective layer. The sensing results showed an increase in the water selectivity and sensitivity, while those of methanol showed a huge decrease. These results prove the feasibility of the LB technique for the fabrication of ordered MOF thin films onto IDE chips using very small MOF quantities.
Single electron reduction is more challenging for sulfamoyl chlorides than sulfonyl chlorides. However, sulfamoyl and sulfonyl chlorides can be easily activated by Cl-atom abstraction by a silyl ...radical with similar rates. This latter mode of activation was therefore selected to access aliphatic sulfonamides, applying a single-step hydrosulfamoylation using inexpensive olefins, tris(trimethylsilyl)silane, and photocatalyst Eosin Y. This late-stage functionalization protocol generates molecules as complex as sulfonamide-containing cyclobutyl-spirooxindoles for direct use in medicinal chemistry.
Molecular editing such as insertion, deletion, and single atom exchange in highly functionalized compounds is an aspirational goal for all chemists. Here, we disclose a photoredox protocol for the ...replacement of a single fluorine atom with hydrogen in electron-deficient trifluoromethylarenes including complex drug molecules. A robustness screening experiment shows that this reductive defluorination tolerates a range of functional groups and heterocycles commonly found in bioactive molecules. Preliminary studies allude to a catalytic cycle whereby the excited state of the organophotocatalyst is reductively quenched by the hydrogen atom donor, and returned in its original oxidation state by the trifluoromethylarene.
A facile method for the regioselective hydrodifluoromethylation of alkenes is reported using difluoroacetic acid and phenyliodine(III) diacetate in tetrahydrofuran under visible‐light activation. ...This metal‐free approach stands out as it uses inexpensive reagents, does not require a photocatalyst, and displays broad functional group tolerance. The procedure is also operationally simple and scalable, and provides access in one step to high‐value building blocks for application in medicinal chemistry.
Terminal alkenes undergo net hydrodifluoromethylation in the presence of an excess of difluoroacetic acid and phenyliodine(III) diacetate in tetrahydrofuran under visible‐light irradiation (λ=450 nm). This highly practical procedure telescopes access to biorelevant building blocks that would require multiple synthetic steps applying deoxyfluorination chemistry.
Novel spiroaminodihydropyrroles probing for optimized interactions at the P3 pocket of β-secretase 1 (BACE1) were designed with the use of free energy perturbation (FEP) calculations. The resulting ...molecules showed pIC50 potencies in enzymatic BACE1 inhibition assays ranging from approximately 5 to 7. Good correlation was observed between the predicted activity from the FEP calculations and experimental activity. Simulations run with a default 5 ns approach delivered a mean unsigned error (MUE) between prediction and experiment of 0.58 and 0.91 kcal/mol for retrospective and prospective applications, respectively. With longer simulations of 10 and 20 ns, the MUE was in both cases 0.57 kcal/mol for the retrospective application, and 0.69 and 0.59 kcal/mol for the prospective application. Other considerations that impact the quality of the calculations are discussed. This work provides an example of the value of FEP as a computational tool for drug discovery.
Herein, we report a photoredox nucleophilic (radio)fluorination using TEMPO-derived alkoxyamines, a class of substrates accessible in a single step from a diversity of readily available carboxylic ...acids, halides, alkenes, alcohols, aldehydes, boron reagents, and C–H bonds. This mild and versatile one-electron pathway affords radiolabeled aliphatic fluorides that are typically inaccessible applying conventional nucleophilic substitution technologies due to insufficient reactivity and competitive elimination. Automation of this photoredox process is also demonstrated with a user-friendly and commercially available photoredox flow reactor and radiosynthetic platform, therefore expediting access to labeled aliphatic fluorides in high molar activity (A m ) for (pre)clinical evaluation.
Sulfonyl chlorides are inexpensive reactants extensively explored for functionalization, but never considered for radical hydrosulfonylation of alkenes. Herein, we report that ...tris(trimethylsilyl)silane is an ideal hydrogen atom donor enabling highly effective photoredox‐catalyzed hydrosulfonylation of electron‐deficient alkenes with sulfonyl chlorides. To increase the generality of this transformation, polarity‐reversal catalysis (PRC) was successfully implemented for alkenes bearing alkyl substituents. This late‐stage functionalization method tolerates a remarkably wide range of functional groups, is operationally simple, scalable, and allows access to building blocks which are important for medicinal chemistry and drug discovery.
Radical new approach: Sulfonyl chlorides have been applied in the radical hydrosulfonylation of alkenes. Tris(trimethylsilyl)silane is an ideal hydrogen atom donor enabling highly effective photoredox‐catalyzed hydrosulfonylation of electron‐deficient alkenes with sulfonyl chlorides. To increase the generality of this transformation, polarity‐reversal catalysis was successfully implemented for alkenes bearing alkyl substituents.
Gradient damage models used in phase-field approaches to brittle fracture are characterised by material softening and instabilities. We present novel numerical techniques for the bifurcation and ...stability analysis along quasi-static evolution paths as well as practical tools to select stable evolutions. Our approach stems from the variational approach to fracture and the theory of rate-independent irreversible processes whereby a quasi-static evolution is formulated in terms of incremental energy minimisation under unilateral constraints. Focusing on the discrete setting obtained with finite elements techniques, we discuss the links between bifurcation criteria for an evolution and stability of equilibrium states. Key concepts are presented through the analytical solution of a two-degrees-of-freedom model featuring a continuum family of bifurcation branches. We introduce numerical methods to (i) assess (second-order) stability conditions for time-discrete evolutions subject to damage irreversibility, and (ii) to select possible stable evolutions based on an energetic criterion. Our approach is based on the solution of a coupled eigenvalue problem which accounts for the time-discrete irreversibility constraint on damage. Several numerical examples illustrate that this approach allows us to filter out unstable solutions provided by standard (first-order) minimisation algorithms as well as to effectively compute stable evolution paths. We demonstrate our purpose on a multifissuration problem featuring complex fracture patterns, to show how the eigenvalue analysis enables to compute and retrieve morphological properties of emerging cracks.
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