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Many Biological Processes (many + biological_process)
Selected AbstractsRapid Generation of Biologically Relevant Hydrogels Containing Long-Range Chemical GradientsADVANCED FUNCTIONAL MATERIALS, Issue 1 2010Jiankang He Abstract Many biological processes are regulated by gradients of bioactive chemicals. Thus, the generation of materials with embedded chemical gradients may be beneficial for understanding biological phenomena and generating tissue-mimetic constructs. Here a simple and versatile method to rapidly generate materials containing centimeter-long gradients of chemical properties in a microfluidic channel is described. The formation of a chemical gradient is initiated by a passive-pump-induced forward flow and further developed during an evaporation-induced backward flow. The gradient is spatially controlled by the backward flow time and the hydrogel material containing the gradient is synthesized via photopolymerization. Gradients of a cell-adhesion ligand, Arg-Gly-Asp-Ser (RGDS), are incorporated in poly(ethylene glycol)-diacrylate (PEG-DA) hydrogels to test the response of endothelial cells. The cells attach and spread along the hydrogel material in a manner consistent with the RGDS-gradient profile. A hydrogel containing a PEG-DA concentration gradient and constant RGDS concentration is also shown. The morphology of cells cultured on such hydrogel changes from round in the lower PEG-DA concentration regions to well-spread in the higher PEG-DA concentration regions. This approach is expected to be a valuable tool to investigate the cell,material interactions in a simple and high-throughput manner and to design graded biomimetic materials for tissue engineering applications. [source] Computer simulations of protein translocationPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 9 2006Serdal Kirmizialtin Many biological processes involve translocation of protein molecules across pores. Shown in the cover picture of this issue is a snapshot from a computer simulation of the protein ubiquitin that is forced mechanically to enter a narrow cylindrical pore. As the force f applied at one end of the molecule pulls it along the pore, the confinement within the pore causes the protein to unfold. The ensuing changes in the protein's entropy and energy lead to a free energy barrier, which has to be surmounted for the translocation to occur. The magnitude of this barrier is estimated by Kirmizialtin et al. in the article [1]. The plot was generated by using the PyMol software. This paper is a presentation from the 1st Institute for the Theory of Advanced Materials in Information Technology Workshop on Computational Materials and Electronics held 20,22 October 2005 in Austin, USA. The present issue has been guest-edited by James Chelikowsky and Alex Demkov. The background of the cover shows a photograph of the tower of the University of Texas at Austin. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Differential Equation Modeling of HIV Viral Fitness Experiments: Model Identification, Model Selection, and Multimodel InferenceBIOMETRICS, Issue 1 2009Hongyu Miao Summary Many biological processes and systems can be described by a set of differential equation (DE) models. However, literature in statistical inference for DE models is very sparse. We propose statistical estimation, model selection, and multimodel averaging methods for HIV viral fitness experiments in vitro that can be described by a set of nonlinear ordinary differential equations (ODE). The parameter identifiability of the ODE models is also addressed. We apply the proposed methods and techniques to experimental data of viral fitness for HIV-1 mutant 103N. We expect that the proposed modeling and inference approaches for the DE models can be widely used for a variety of biomedical studies. [source] Fibroblast elongation and dendritic extensions in constrained versus unconstrained microtissuesCYTOSKELETON, Issue 3 2009Dylan M. Dean Abstract Cytoskeletal tension is fundamental to many biological processes, including germ layer sorting during embryogenesis [Krieg et al., 2008]. In vitro, such tension influences cell sorting in self-assembled, 3D microtissues and can be of sufficient magnitude to cause complex-shaped microtissue failure [Dean et al., 2007]. To examine the process of failure under cell-derived tension, we subjected normal human fibroblasts (NHFs) to directed self-assembly [Dean et al., 2007] in micro-molds designed to yield self-constraining microtissues. As cells contracted in this assay, the constrained microtissues narrowed, thinned and ultimately failed at their midpoints. By adding small numbers of GFP+ cells, changes in cell movement and morphology were assessed and compared to those of unconstrained microtissues. We found that cells formed numerous dendritic extensions within an hour of self-assembly and retracted these extensions as they elongated up to 30 times their initial diameter (,600 ,m) just prior to failure. Surprisingly, significant coordination in cell motility was observed over large distances within microtissues. Pharmacologic interventions showed that failure was myosin II and Rho kinase dependent and inhibition of failure resulted in shorter cells with greater numbers of extensions. These findings further our understanding of cellular self-assembly and introduce the use of GFP+ cells with directed self-assembly as a scaffold-free analogue to fibroblast-populated collagen gels (FPCGs). Cell Motil. Cytoskeleton 2009. © 2009 Wiley-Liss, Inc. [source] Development of micropost force sensor array with culture experiments for determination of cell traction forcesCYTOSKELETON, Issue 7 2007Bin Li Abstract Cell traction forces (CTFs) are critical for cell motility and cell shape maintenance. As such, they play a fundamental role in many biological processes such as angiogenesis, embryogenesis, inflammation, and wound healing. To determine CTFs at the sub-cellular level with high sensitivity, we have developed high density micropost force sensor array (MFSA), which consists of an array of vertically standing poly(dimethylsiloxane) (PDMS) microposts, 2 ,m in diameter and 6 ,m in height, with a center-to-center distance of 4 ,m. In combination with new image analysis algorithms, the MFSA can achieve a spatial resolution of 40 nm and a force sensitivity of 0.5 nN. Culture experiments with various types of cells showed that this MFSA technology can effectively determine CTFs of cells with different sizes and traction force magnitudes. Cell Motil. Cytoskeleton 2007. © 2007 Wiley-Liss, Inc. [source] Simultaneous detection of S -adenosylmethionine and S -adenosylhomocysteine in mouse and rat tissues by capillary electrophoresisELECTROPHORESIS, Issue 7-8 2003Eric O. Uthus Abstract A capillary electrophoresis method for the determination of S -adenosylmethionine (SAM) and S -adenosylhomocysteine (SAH) in rat liver and kidney and mouse liver is described. The method can also be used to determine SAM in whole blood. The method provides rapid (approximately 16 min sample to sample) resolution of both compounds in perchloric extracts of tissues. Separation was performed by using an uncoated 50 ,m ID capillary with 60 cm total length (50 cm to the detector window). Samples were separated at 22.5 kV and the separation running buffer was 200 mM glycine pH 1.8 (with HCl). The method compares favorably to HPLC methods (r,2 = 0.994 for SAM, r,2 = 0.998 for SAH) and has a mass detection limit of about 10 fmol for both SAM and SAH at a signal-to-noise ratio of 3. The method is linear over ranges of 1,100 ,M SAM and 1,250 ,M SAH. This method can be used to determine tissue concentrations of SAM and SAH, two metabolites that can provide insight into many biological processes. [source] T-cell-specific deletion of gp130 renders the highly susceptible IL-10-deficient mouse resistant to intestinal nematode infectionEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 8 2009Nicolas Fasnacht Abstract Gp130 is the common receptor of the IL-6 family of cytokines and is involved in many biological processes, including acute phase response, inflammation and immune reactions. To investigate the role of gp130 under inflammatory conditions, T-cell-specific conditional gp130 mice were first bred to the IL-10-deficient background and were then infected with the gastrointestinal nematode Trichuris muris. While IL-10,/, mice were highly susceptible to T. muris, developed a mixed Th1/Th17 response and displayed severe inflammation of the caecum, infection of mice with an additional T-cell-specific deletion of gp130 signalling completely reversed the phenotype. These mice showed an accelerated worm expulsion that was associated with the rapid generation of a strong Th2 immune response and a significant increase in Foxp3-expressing Treg. Therefore, gp130 signalling in T cells regulates a switch between proinflammatory and pathogenic Th1/Th17 cells and regulatory Th2/Treg in vivo. Taken together, the data demonstrate that gp130 signalling in T cells is a positive regulator of inflammatory processes, favouring the Th1/Th17 axis. [source] Relevance between lipid metabolism-associated genes and rat liver regenerationHEPATOLOGY RESEARCH, Issue 8 2008Cunshuan Xu Aim:, Lipids are important in constituting cell structure and participating in many biological processes, particularly in energy supplementation to cells. The aim of the present study is to elucidate the action of lipid metabolism-associated genes on rat liver regeneration (LR). Methods:, Lipid metabolism-associated genes were obtained by collecting website data and retrieving related articles, and their expression changes in the regenerating rat liver were checked by the Rat Genome 230 2.0 array. Results:, In total, 280 genes involved in lipid metabolism were proven to be LR-associated by comparing the gene expression discrepancy between the partial-hepatectomy and sham-operation groups. The initial and total expression numbers of these genes occurring in the initial phase, G0/G1 transition, cell proliferation, cell differentiation, and structure,functional rebuilding of LR were 128, 33, 135, 6, and 267, 147, 1026, 306, respectively, illustrating that these genes were initially expressed mainly in the initiation stage and functioned in different phases. Upregulation (850 times) and downregulation (749 times), as well as 25 types of expression patterns, showed that the physiological and biochemical activities were diverse and complicated in LR. Conclusion:, According to the results of the chip detection, it was presumed that fatty acid synthesis at 24,66 h, leukotriene and androgen synthesis at 16,168 h, prostaglandin synthesis at 2,96 h, triglyceride synthesis at 18,24 h, glycosphingolipid synthesis at 0.5,66 h, metabolism of phosphatidyl inositol and sphingomyelin at 2,16 h, and cholesterol catabolism at 30,168 h were enhanced. Throughout almost the whole LR, the genes participating in estrogen, glucocorticoid, and progesterone synthesis, and triglyceride catabolism were upregulated, while phospholipid and glycosphingolipid catabolism were downregulated. [source] MicroRNA-10b is overexpressed in malignant glioma and associated with tumor invasive factors, uPAR and RhoCINTERNATIONAL JOURNAL OF CANCER, Issue 6 2009Takashi Sasayama Abstract MicroRNAs (miRNAs) are effective post-transcriptional regulators of gene expression and are important in many biological processes. Although the oncogenic and tumor suppressive functions of several miRNAs have been characterized, the role of miRNAs in mediating tumor invasion and migration remains largely unexplored. Recently, miR-10b was identified as an miRNA highly expressed in metastatic breast cancer, promoting cell migration and invasion. Here, we performed real-time reverse transcriptase polymerase chain reaction (RT-PCR) assays on 43 glioma samples (17 glioblastoma, 6 anaplastic astrocytoma, 10 low-grade astrocytoma, 6 oligodendroglioma and 4 ependymoma) and 6 glioma cell lines. We found that miR-10b expression was upregulated in all glioma samples compared to non-neoplastic brain tissues. The expression levels of miR-10b were associated with higher grade glioma. In addition, mRNA expressions of RhoC and urokinase-type plasminogen activator receptor (uPAR), which were thought to be regulated by miR-10b via HOXD10, were statistically significantly correlated with the expression of miR-10b (p < 0.001, p = 0.001, respectively). Also, protein expression levels of RhoC and uPAR were associated with expression levels of miR-10b (p = 0.009, p = 0.014, respectively). Finally, multifocal lesions on enhanced MRI of 7 malignant gliomas were associated with higher expression levels of miR-10b (p = 0.02). Our data indicated that miR-10b might play some role in the invasion of glioma cells. © 2009 UICC [source] Methionine gamma-lyase: The unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancersIUBMB LIFE, Issue 11 2009Dan Sato Abstract Sulfur-containing amino acids (SAAs) are essential components in many biological processes and ubiquitously distributed to all organisms. Both biosynthetic and catabolic pathways of SAAs are heterogeneous among organisms and between developmental stages, and regulated by the environmental changes. Limited lineage of organisms ranging from archaea to plants, but not human, possess a unique enzyme methionine gamma-lyase (MGL, EC 4.4.1.11) to directly degrade SAA to ,-keto acids, ammonia, and volatile thiols. The reaction mechanisms and the physiological roles of this enzyme are partially demonstrated by the enzymological analyzes, structure determination, isotopic labeling of the intermediate metabolites, and functional analyzes of deficient mutants. MGL has been exploited as a drug target for the infectious diseases caused by parasitic protozoa and anaerobic periodontal bacteria. In addition, MGL has been utilized to develop therapeutic interventions of various cancers, by introducing recombinant proteins to deplete methionine essential for the growth of cancer cells. In this review, we discuss the current understanding of enzymological properties, putative physiological roles, and therapeutic applications of MGL. © 2009 IUBMB IUBMB Life, 61(11): 1019,1028, 2009 [source] Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complexJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2009Zhigang Zhou Abstract Cathepsin B, a ubiquitous lysosomal cysteine protease, is involved in many biological processes related to several human diseases. Inhibitors targeting the enzyme have been investigated as possible diseases treatments. A set of 37 compounds were recently found active in a high throughput screening assay to inhibit the catalytic activity of Cathepsin B, with chemical structures and biological test results available to the public in the PubChem BioAssay Database (AID 820). In this study, we compare these experimental activities to the results of theoretical predictions from binding affinity calculation with a LR-MM-PNSA approach based on docked complexes. Strong correlations (r2 = 0.919 and q2 = 0.887 for the best) are observed between the theoretical predictions and experimental biological activity. The models are cross-validated by four independent predictive experiments with randomly split compounds into training and test sets. Our results also show that the results based on protein dimer show better correlations with experimental activity when compared to results based on monomer in the in silico calculations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Phosphopeptide fragmentation and analysis by mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2009Paul J. Boersema Abstract Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision-induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss-dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS3 and multistage activation (MSA), have been designed to generate more sequence-informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron-driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large-scale phosphoproteomics studies. Copyright © 2009 John Wiley & Sons, Ltd. [source] Synthesis, conformational analysis and biological activities of lanthionine analogs of a cell adhesion modulatorJOURNAL OF PEPTIDE SCIENCE, Issue 2 2001Haitao Li Abstract Cell adhesion is critical for many biological processes, such as hemostasis, wound healing, tumor metastasis and inflammation. Integrins are important mediators of cell adhesion. The integrin ,4,1, also known as VLA-4, is a cell surface receptor involved in inflammation. A cyclic peptide, 1-FCA-Arg-c[Cys-Asp-Thz-Cys]-OH, is a potent antagonist to VLA-4 with an IC50 of 2.4 n,,. In the current study, we synthesized the lanthionine analogs of 1-FCA-Arg-c[Cys-Asp-Thz-Cys]-OH and determined the conformations of both the parent compound and its lanthionine analog in solution by NMR and computer simulations. The lanthionine analog retains its selectivity to VLA-4 with high nanomolar potency. Both molecules adopt similar topological arrangements in their conformations, while some important differences remain in the sulfur bridge region, which may cause the difference in potency. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] Capillary gas-chromatographic determination of spermidine in hair lotionJOURNAL OF SEPARATION SCIENCE, JSS, Issue 9 2006Veniero Gambaro Abstract Biogenic polyamines, such as spermidine (SPD, NH2,(CH2)4,NH,(CH2)3,NH2), are ubiquitous polycationic molecules which play a definitive role in many biological processes such as nucleic acid metabolism, protein synthesis, and cell growth. SPD is commonly used as an ingredient in hair lotions, because it seems to promote hair growth. This work describes a capillary GC method for quantitative determination of SPD in hair lotions using 1,6-diaminohexane as internal standard, a methyl silicone capillary column, and a flame ionisation detector. Aliquots of hair lotion were treated with an alkaline aqueous solution and internal standard was added. The emulsion was extracted with diethyl ether containing ethyl chloroformate. Ether extracts, evaporated to dryness and reconstituted in ethyl acetate, were analysed by capillary GC with flame ionisation detection. Validation took into account the specificity, linearity, precision, and accuracy of the analytical method: these parameters were valid for the quantitative determination of SPD in hair lotion. [source] Merging Organic and Polymer Chemistries to Create Glycomaterials for Glycomics ApplicationsMACROMOLECULAR BIOSCIENCE, Issue 8 2006Géraldine Coullerez Abstract Summary: Oligosaccharides at cell surfaces are known to play a critical role in many biological processes such as biorecognition, interactions between cells and with artificial surfaces, immune response, infection and inflammation. In order to facilitate studies of the role of sugars, an increasing number of novel tools are becoming available. New synthetic strategies now provide much more efficient access to complex carbohydrates or glycoconjugates. Branched carbohydrates and hybrids of carbohydrates conjugated to polymers have been prepared using solution and/or solid-phase synthesis and advanced methods of polymerization. These materials are essential for the development of methodologies to study and map the molecular structure-function relationship at interfaces. This article highlights recent advances in the synthesis of carbohydrates and polymer hybrids mimicking the properties and functionalities of the natural oligosaccharides, as well as selected applications in biology, biotechnology and diagnostics. [source] Elucidation of spermidine interaction with nucleotide ATP by multiple NMR techniquesMAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2010Zhiyan Song Abstract Interaction of polyamines with nucleotides plays a key role in many biological processes. Here we use multiple NMR techniques to characterize interaction of spermidine with adenosine 5,-triphosphate (ATP). Two-dimensional 1H- 15N spectra obtained from gs-HMBC experiments at varied pH show significant shift of N-1 peak around pH 2.0,7.0 range, suggesting that spermidine binds to N-1 site of ATP base. The binding facilitates N-1 deprotonation, shifting its pKa from 4.3 to 3.4. By correlating 15N and 31P chemical shift data, it is clear that spermidine is capable of concurrently binding to ATP base and phosphate sites around pH 4.0,7.0. The self-diffusion constants derived from 1H PFG-diffusion measurements provide evidence that binding of spermidine to ATP is in 1:1 ratio, and pH variations do not induce significant nucleotide self-association in our samples. 31P spectral analysis suggests that at neutral pH, Mg2+ ion competes with spermidine and shows stronger binding to ATP phosphates. From 31P kinetic measurements of myosin-catalyzed ATP hydrolysis, it is found that binding of spermidine affects the stability and reactivity of ATP. These NMR results are important for advancing the studies on nucleotide,polyamine interaction and its impact on nucleotide structures and activities under varied conditions. Copyright © 2009 John Wiley & Sons, Ltd. [source] Autonomous plasmid-like replication of a conjugative transposonMOLECULAR MICROBIOLOGY, Issue 2 2010Catherine A. Lee Summary Integrative and conjugative elements (ICEs), a.k.a. conjugative transposons, are mobile genetic elements involved in many biological processes, including pathogenesis, symbiosis and the spread of antibiotic resistance. Unlike conjugative plasmids that are extra-chromosomal and replicate autonomously, ICEs are integrated in the chromosome and replicate passively during chromosomal replication. It is generally thought that ICEs do not replicate autonomously. We found that when induced, Bacillus subtilis ICEBs1 undergoes autonomous plasmid-like replication. Replication was unidirectional, initiated from the ICEBs1 origin of transfer, oriT, and required the ICEBs1 -encoded relaxase NicK. Replication also required several host proteins needed for chromosomal replication, but did not require the replicative helicase DnaC or the helicase loader protein DnaB. Rather, replication of ICEBs1 required the helicase PcrA that is required for rolling circle replication of many plasmids. Transfer of ICEBs1 from the donor required PcrA, but did not require replication, indicating that PcrA, and not DNA replication, facilitates unwinding of ICEBs1 DNA for horizontal transfer. Although not needed for horizontal transfer, replication of ICEBs1 was needed for stability of the element. We propose that autonomous plasmid-like replication is a common property of ICEs and contributes to the stability and maintenance of these mobile genetic elements in bacterial populations. [source] Concentration of vascular endothelial growth factor (VEGF) in the serum of patients with malignant bone tumors,PEDIATRIC BLOOD & CANCER, Issue 6 2001Gerold Holzer MD Abstract Background Vascular endothelial growth factor (VEGF) is recognized as an important stimulator of angiogenesis. Formation of new blood vessels by angiogenic factors occurs in many biological processes, both physiological and pathological, among others in growth of primary solid malignant tumors and metastasis. This implies that the inhibition of angiogenic factors like VEGF would result in a suppression of tumor growth and metastasis formation. The aim of the present study was to compare preoperative serum VEGF levels of patients having malignant bone tumors with healthy controls to identify serum VEGF levels as a tumor marker. Procedure Blood sera from patients with high-grade osteosarcoma (n,=,17), chondrosarcoma (n,=,4) and Ewing sarcoma (n,=,6) were taken at the time of diagnosis before biopsy and compared with sera from 129 healthy persons. To measure VEGF levels in serum, a commercially available ELISA was used (Quantikine Human VEGF Immunoassay; R&D Systems). Results The observed geometric mean VEGF levels and 95% confidence intervals are 232.0 pg ml,1 (168.9,318.5) for patients with high-grade osteosarcoma, 325.5 pg ml,1 (169.3,625.8) for patients with chondrosarcoma, 484.3 pg ml,1 (284.0,826.0) for patients with Ewing sarcoma, as compared to 216.2 pg ml,1 (192.8,242.5) for healthy individuals. Conclusions While the sample means for the three groups of sarcoma patients were higher than the respective mean for the healthy controls, only the mean for the group with Ewing sarcoma is statistically significantly higher than the mean for the healthy controls. Despite the significant difference, VEGF levels are not suitable as a marker for Ewing sarcoma. Med. Pediatr. Oncol. 36:601,604, 2001. © 2001 Wiley-Liss, Inc. [source] The galectin family and digestive disease,THE JOURNAL OF PATHOLOGY, Issue 1 2008P Demetter Abstract The soluble-type lectins or galectins constitute a family of proteins defined by shared consensus amino acid sequence and affinity for beta-galactose-containing oligosaccharides. These molecules are widely distributed in the animal kingdom; to date, 15 mammalian galectins have been described but more are likely to be discovered. These proteins are involved in many biological processes including cell,cell and cell,matrix adhesion, growth regulation, signaling, and cytokine secretion. Over the last decade, a vast amount of reports has shown the importance of several galectins in the development and progression of malignancies in the digestive tract, mainly colorectal cancers. More recent data indicate that some of these molecules are also involved in inflammatory bowel diseases. This review focuses on the current knowledge of galectin expression and putative functions in the oesophagus, stomach, small intestine, and colon. It also highlights that the rapid accumulation of research data promises future scenarios in which individual members of the galectin family and/or their ligands will be used as diagnostic and therapeutic modalities for neoplastic as well as inflammatory disorders. However, the concretization of these potential modalities requires substantial improvements in terms of standardization of galectin expression evaluation together with prospective validation of the present data. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Overexpression of yeast spermidine synthase impacts ripening, senescence and decay symptoms in tomatoTHE PLANT JOURNAL, Issue 5 2010Savithri Nambeesan Summary Polyamines (PAs) are ubiquitous, polycationic biogenic amines that are implicated in many biological processes, including plant growth and development, but their precise roles remain to be determined. Most of the previous studies have involved three biogenic amines: putrescine (Put), spermidine (Spd) and spermine (Spm), and their derivatives. We have expressed a yeast spermidine synthase (ySpdSyn) gene under constitutive (CaMV35S) and fruit-ripening specific (E8) promoters in Solanum lycopersicum (tomato), and determined alterations in tomato vegetative and fruit physiology in transformed lines compared with the control. Constitutive expression of ySpdSyn enhanced intracellular levels of Spd in the leaf, and transiently during fruit development, whereas E8 - ySpdSyn expression led to Spd accumulation early and transiently during fruit ripening. The ySpdSyn transgenic fruits had a longer shelf life, reduced shriveling and delayed decay symptom development in comparison with the wild-type (WT) fruits. An increase in shelf life of ySpdSyn transgenic fruits was not facilitated by changes in the rate of water loss or ethylene evolution. Additionally, the expression of several cell wall and membrane degradation-related genes in ySpdSyn transgenic fruits was not correlated with an extension of shelf life, indicating that the Spd-mediated increase in fruit shelf life is independent of the above factors. Crop maturity, indicated by the percentage of ripening fruits on the vine, was delayed in a CaMV35S - ySpdSyn genotype, with fruits accumulating higher levels of the antioxidant lycopene. Notably, whole-plant senescence in the transgenic plants was also delayed compared with WT plants. Together, these results provide evidence for a role of PAs, particularly Spd, in increasing fruit shelf life, probably by reducing post-harvest senescence and decay. [source] Engineering the catalytic domain of human protein tyrosine phosphatase , for structure-based drug discoveryACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2006Artem G. Evdokimov Protein tyrosine phosphatases (PTPs) play roles in many biological processes and are considered to be important targets for drug discovery. As inhibitor development has proven challenging, crystal structure-based design will be very helpful to advance inhibitor potency and selectivity. Successful application of protein crystallography to drug discovery heavily relies on high-quality crystal structures of the protein of interest complexed with pharmaceutically interesting ligands. It is very important to be able to produce protein,ligand crystals rapidly and reproducibly for as many ligands as necessary. This study details our efforts to engineer the catalytic domain of human protein tyrosine phosphatase , (HPTP,-CD) with properties suitable for rapid-turnaround crystallography. Structures of apo HPTP,-CD and its complexes with several novel small-molecule inhibitors are presented here for the first time. [source] Cloning, overexpression, purification, crystallization and preliminary X-ray analysis of a female-specific lipocalin (FLP) expressed in the lacrimal glands of Syrian hamstersACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Ved Prakash Dubey Proteins belonging to the lipocalin superfamily are usually secretory proteins of molecular mass ,20,kDa with a hydrophobic pocket for the binding and transport of diverse small ligands. Various lipocalins have been associated with many biological processes, e.g. immunomodulation, odorant transport, pheromonal activity, retinoid transport, cancer-cell interactions etc. However, the exact functions of many lipocalins and the ligands bound by them are unclear. Previously, the cDNA of a 20,kDa lipocalin (FLP) which is female-specifically expressed in the lacrimal glands of Syrian (golden) hamsters and secreted in the tears of females has been identified and cloned. His-tagged recombinant FLP (rFLP) has now been cloned, overexpressed in Escherichia coli as a soluble protein and purified to homogeneity using Ni-affinity followed by size-exclusion chromatography. Purified rFLP was crystallized using the sitting-drop vapour-diffusion method. The crystals tested belonged to space group P212121 and diffracted to beyond 1.86,Ĺ resolution. Solvent-content analysis indicated the presence of one monomer in the asymmetric unit. [source] Putting numbers on the network connectionsBIOESSAYS, Issue 8 2007Gary D. Stormo DNA,protein interactions are fundamental to many biological processes, including the regulation of gene expression. Determining the binding affinities of transcription factors (TFs) to different DNA sequences allows the quantitative modeling of transcriptional regulatory networks and has been a significant technical challenge in molecular biology for many years. A recent paper by Maerkl and Quake1 demonstrated the use of microfluidic technology for the analysis of DNA,protein interactions. An array of short DNA sequences was spotted onto a glass slide, which was then covered with a microfluidic device allowing each spot to be within a chamber into which the flow of materials was controlled by valves. By trapping the DNA,protein complexes on the surface and measuring their concentrations microscopically, they could determine the binding affinity to a large number of DNA sequences that were varied systematically. They studied four TFs from the basic helix,loop,helix family of proteins, all of which bind to E-box sites with the consensus CAnnTG (where "n" can be any base), and showed that variations in affinity for different sites allows each TF to regulate different genes. BioEssays 29:717,721, 2007. © 2007 Wiley Periodicals, Inc. [source] A Bayesian Approach to Modeling Associations Between Pulsatile HormonesBIOMETRICS, Issue 2 2009Nichole E. Carlson Summary Many hormones are secreted in pulses. The pulsatile relationship between hormones regulates many biological processes. To understand endocrine system regulation, time series of hormone concentrations are collected. The goal is to characterize pulsatile patterns and associations between hormones. Currently each hormone on each subject is fitted univariately. This leads to estimates of the number of pulses and estimates of the amount of hormone secreted; however, when the signal-to-noise ratio is small, pulse detection and parameter estimation remains difficult with existing approaches. In this article, we present a bivariate deconvolution model of pulsatile hormone data focusing on incorporating pulsatile associations. Through simulation, we exhibit that using the underlying pulsatile association between two hormones improves the estimation of the number of pulses and the other parameters defining each hormone. We develop the one-to-one, driver,response case and show how birth,death Markov chain Monte Carlo can be used for estimation. We exhibit these features through a simulation study and apply the method to luteinizing and follicle stimulating hormones. [source] The Structure of Glycosaminoglycans and their Interactions with ProteinsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 6 2008Neha S. Gandhi Glycosaminoglycans (GAGs) are important complex carbohydrates that participate in many biological processes through the regulation of their various protein partners. Biochemical, structural biology and molecular modelling approaches have assisted in understanding the molecular basis of such interactions, creating an opportunity to capitalize on the large structural diversity of GAGs in the discovery of new drugs. The complexity of GAG,protein interactions is in part due to the conformational flexibility and underlying sulphation patterns of GAGs, the role of metal ions and the effect of pH on the affinity of binding. Current understanding of the structure of GAGs and their interactions with proteins is here reviewed: the basic structures and functions of GAGs and their proteoglycans, their clinical significance, the three-dimensional features of GAGs, their interactions with proteins and the molecular modelling of heparin binding sites and GAG,protein interactions. This review focuses on some key aspects of GAG structure,function relationships using classical examples that illustrate the specificity of GAG,protein interactions, such as growth factors, anti-thrombin, cytokines and cell adhesion molecules. New approaches to the development of GAG mimetics as possible new glycotherapeutics are also briefly covered. [source] Deforming DNA: From Physics to BiologyCHEMPHYSCHEM, Issue 9-10 2009Chantal Prévost Dr. Abstract DNA molecules do the twist: The DNA double helix is a remarkably adaptable molecule that can undergo major conformational rearrangements without being irreversibly damaged. Indeed, DNA deformation is an intrinsic feature of many biological processes. In this Minireview, the authors summarize recent advances in the study of DNA deformation. The picture shows five different conformations of the double helix of DNA. The DNA double helix has become a modern icon which symbolizes our understanding of the molecular basis of life. It is less widely recognized that the double helix proposed by Watson and Crick more than half a century ago is a remarkably adaptable molecule that can undergo major conformational rearrangements without being irreversibly damaged. Indeed, DNA deformation is an intrinsic feature of many of the biological processes in which it is involved. Over the last two decades, single-molecule experiments coupled with molecular modeling have transformed our understanding of DNA flexibility, while the accumulation of high-resolution structures of DNA,protein complexes have demonstrated how organisms can exploit this property as a useful feature for preserving, reading, replicating, and packaging the genetic message. In this Minireview we summarize the information now available on the extreme,and the less extreme,deformations of the double helix. [source] | |||||||||||||||||||