The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain

Aminoacyl-tRNA synthetases catalyze the specific charging of amino acid residues on tRNAs. Accurate recognition of a tRNA by its synthetase is achieved through sequence and structural signalling. It has been shown that tRNAs undergo large conformational changes upon binding to enzymes, but little is known about the conformational rearrangements in tRNA-bound synthetases. To address this issue the crystal structure of the dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast was solved in its free form and compared to that of the protein associated to the cognate tRNA(Asp). The use of an enzyme truncated in N terminus improved the crystal quality and allowed us to solve and refine the structure of free AspRS at 2.3 A resolution. For the first time, snapshots are available for the different macromolecular states belonging to the same tRNA aminoacylation system, comprising the free forms for tRNA and enzyme, and their complex. Overall, the synthetase is less affected by the association than the tRNA, although significant local changes occur. They concern a rotation of the anticodon binding domain and a movement in the hinge region which connects the anticodon binding and active-site domains in the AspRS subunit. The most dramatic differences are observed in two evolutionary conserved loops. Both are in the neighborhood of the catalytic site and are of importance for ligand binding. The combination of this structural analysis with mutagenesis and enzymology data points to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.     

Ethylene induces epidermal cell death at the site of adventitious root emergence in rice

In deepwater rice (Oryza sativa), adventitious root primordia initiate at the nodes as part of normal development. Emergence of the roots is dependent on flooding of the plant and is mediated by ethylene action. Root growth was preceded by the induced death of epidermal cells of the node external to the tip of the root primordium. Cell death proceeded until the epidermis split open. Through this crack the root eventually emerged. Induced death was confined to nodal epidermal cells covering the tip of the primordia. Our results suggest that this process facilitates adventitious root emergence and prevents injury to the growing root. Cell death was inducible not only by submergence but also by application of 1-aminocyclopropane-1-carboxylic acid, the natural precursor of ethylene and it was suppressed in the presence of 2,5-norbornadiene (bicyclo[2.2.1]hepta-2,5-diene), an inhibitor of ethylene action. Adventitious root growth and epidermal cell death are therefore linked to the ethylene signaling pathway, which is activated in response to low oxygen stress.     

A 24β-ethyl-Δ7-steryl glucopyranoside from Cucurbita pepo seeds

In the seeds of Cucurbita pepo three closely related 24-ethyl-Δ⁷-steryl glucosides were identified by hydrolytic studies and spectral analysis as spinasteryl-β-D-glucopyranoside, the new 3-O-(β-D-glucopyranosyl)-24β-ethyl-5α-cholesta-7,25(27)-dien-3β-ol and the corresponding Δ^22E,25,(27)-trienol. Except for its occurrence in cucumber seeds the latter is so far unknown as a natural product.     

Mc2 receptor knockdown modulates differentiation and lipid composition in adipocytes

The melanocortin system is involved in central and peripheral regulation of energy homeostasis. In adipocytes, the melanocortin 2 receptor (MC2R) transmits ACTH-dependent signaling and its expression rises substantially during adipocyte differentiation. An in vitro system of retrovirally expressed shRNA directed against Mc2r mRNA in 3T3-L1 cells was established and effects of Mc2r knockdown (kd) in comparison to cells expressing non-targeting shRNA (control) were explored in differentiated adipocytes. Morphology, gene expression, lipolysis and fatty acid composition were analyzed. While gross morphology was unchanged extractable amount of lipids was reduced to 70-80% in kd cell lines (p<0.01). Moreover, expression changes of Pparγ2, aP2, and Pref1 indicated reduced differentiation in Mc2r kd cells. Intriguingly, not only ACTH, but also norepinephrine stimulated lipolysis were substantially reduced demonstrating functional significance of MC2R for general lipolysis pathway. Analysis of fatty acid composition in triglyceride and phospholipid fractions showed a lowered ratio of C16:1/C16:0 and C18:1/C18:0, but increased concentrations of arachidonic acid upon Mc2r knockdown. Reduction of mono-unsaturated fatty acids (MUFAs) was associated with lower expression of stearoyl-Coenzyme A desaturase 1 and 2 in kd cells (21±8% vs. 100±13%, p=0.01 and 32±3% vs. 100±15%, p=0.046). Conversely, high doses of ACTH resulted in gene expression changes, mirroring Mc2r knockdown (higher Pparγ2, Scd1, Hsl expression). MC2R plays an important role for regular lipolytic function and lipid composition in 3T3-L1 adipocytes. Of interest, desaturase expression was reduced and MUFA content accordingly altered in kd cells.     

Automatic Fortran to C++ conversion with FABLE

Background

In scientific computing, Fortran was the dominant implementation language throughout most of the second part of the 20th century. The many tools accumulated during this time have been difficult to integrate with modern software, which is now dominated by object-oriented languages.

Results

Driven by the requirements of a large-scale scientific software project, we have developed a Fortran to C++ source-to-source conversion tool named FABLE. This enables the continued development of new methods even while switching languages. We report the application of FABLE in three major projects and present detailed comparisons of Fortran and C++ runtime performances.

Conclusions

Our experience suggests that most Fortran 77 codes can be converted with an effort that is minor (measured in days) compared to the original development time (often measured in years). With FABLE it is possible to reuse and evolve legacy work in modern object-oriented environments, in a portable and maintainable way. FABLE is available under a nonrestrictive open source license. In FABLE the analysis of the Fortran sources is separated from the generation of the C++ sources. Therefore parts of FABLE could be reused for other target languages.     

Loss of protein expression and recurrent DNA hypermethylation of the GNG7 gene in squamous cell carcinoma of the head and neck

Although down-regulation of GNG7 in cancer was reported before, its role in carcinogenesis is poorly understood. It belongs to a family of large G-proteins that may be involved in cell-contact-induced growth arrest and function in tumor suppression. In the present study, we stained immunohistochemically 188 tumors derived from larynx or floor of the mouth for GNG7 protein and confronted it with clinicopathologic data. Moreover, we performed bisulfite pyrosequencing to analyze GNG7 promoter methylation. We identified recurrent loss of GNG7 protein expression in 68/188 (36%) cases and promoter hypermethylation in (42/98; 43%) primary tumors, predominantly in young patients (p?相似文献   

NeuroPXI: A real-time multi-electrode array system for recording,processing and stimulation of neural networks and the control of high-resolution neural implants for rehabilitation

The increasing number of channels offered by new Microelectrode Array (MEA) systems raises the problem of data handling and analysis in real time. The goal of the RETINE project is to develop a new MEA system, called NeuroPXI, offering 256 channels with online features for MEA data recording, processing and stimulation. This system is a complete redesign of the ASIC-based BioMEA system developed previously. NeuroPXI is based on a front-end device featuring integrated electronics handling signal amplification and current-mode stimulation, and a back-end device handling real-time data processing and 2D spatiotemporal stimulus generation. Initial tests of this system have been performed on mouse spinal cord networks in which waves of activity were successfully recorded. Further tests of NeuroPXI, performed on rats, will consist first, in recording activity waves in the newborn retina and second, in patterned retinal stimulation combined with optical cortical recordings of the primary visual cortex. Such experiments have recently been conducted using the BioMEA system with standard pulse stimuli, and will be repeated with the NeuroPXI system to include more complex 2D-pattern stimuli.     

In vitro proliferation of adult human beta-cells

A decrease in functional beta-cell mass is a key feature of type 2 diabetes. Glucagon-like peptide 1 (GLP-1) analogues induce proliferation of rodent beta-cells. However, the proliferative capacity of human beta-cells and its modulation by GLP-1 analogues remain to be fully investigated. We therefore sought to quantify adult human beta-cell proliferation in vitro and whether this is affected by the GLP-1 analogue liraglutide.Human islets from 7 adult cadaveric organ donors were dispersed into single cells. Beta-cells were purified by FACS. Non-sorted cells and the beta-cell enriched ("beta-cells") population were plated on extracellular matrix from rat (804G) and human bladder carcinoma cells (HTB9) or bovine corneal endothelial ECM (BCEC). Cells were maintained in culture+/-liraglutide for 4 days in the presence of BrdU.Rare human beta-cell proliferation could be observed either in the purified beta-cell population (0.051±0.020%; 22 beta-cells proliferating out of 84'283 beta-cells counted) or in the non-sorted cell population (0.055±0.011%; 104 proliferating beta-cells out of 232'826 beta-cells counted), independently of the matrix or the culture conditions. Liraglutide increased human beta-cell proliferation on BCEC in the non-sorted cell population (0.082±0.034% proliferating beta-cells vs. 0.017±0.008% in control, p<0.05).These results indicate that adult human beta-cell proliferation can occur in vitro but remains an extremely rare event with these donors and particular culture conditions. Liraglutide increases beta-cell proliferation only in the non-sorted cell population and only on BCEC. However, it cannot be excluded that human beta-cells may proliferate to a greater extent in situ in response to natural stimuli.