Numerical approximation for algorithmic tangent moduli for nonlinear viscoelastic model with CSDA method.

This work revisits the notion of complex step derivative approximation (CSDA) and presents its use in constitutive model of a class of nonlinear viscoelastic materials. The effectiveness of a CSDA is evaluated by putting it through a series of straightforward examples. After that, the idea of the CSDA is put to use in order to carry out a numerical evaluation of the algorithmic tangent moduli of a viscoelastic constitutive model. The performance of the constitutive models is evaluated through the use of three different numerical tests, and the results are compared to those that were achieved by the application of an analytical method. In comparison to other numerical differentiation techniques, It has been found that the CSDA scheme is the most computationally efficient and robust method of numerical differentiation, regardless of the size of the finite difference interval.

Cold-shock Domain Protein A (CSDA) Influences Hepatocyte Growth Factor-medicated Cell Proliferation and Metastasis in Gastric Cancer Cells.

BACKGROUND/AIM: A role for cold-shock domain (CSD) proteins in abnormal cell proliferation has been suggested in the literature. The aim of this study was to investigate the effect of hepatocyte growth factor (HGF)-induced up-regulation of CSD protein A (CSDA) expression on vascular endothelial growth factor (VEGF) expression and its role in gastric cancer cell invasion and proliferation. MATERIALS AND METHODS: We assessed effects on two gastric cancer cell lines using reverse transcription-polymerase chain reaction, western blotting, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays, and CSDA knockdown with short hairpin RNA. RESULTS: Hepatocyte growth factor (HGF) elevates CSDA levels in gastric cancer cell lines. To elucidate the mechanism by which HGF prompts CSDA expression and its impact on vascular endothelial growth factor (VEGF), we applied the Mitogen Activated Protein Kinase (MAPK) inhibitor PD098059 and conducted analyses using western blot. Following the administration of PD098059, a reduction in the protein levels of HGF-stimulated VEGF was observed. Additionally, silencing of CSDA resulted in diminished levels of both VEGF and phosphorylated extracellular signal-regulated kinase (ERK). The suppression of CSDA also led to reduced HGF-induced cell proliferation and diminished invasive capabilities in vitro. Furthermore, our research pinpointed a potential activator protein-1 (AP-1) binding site within the VEGF promoter zone, validating its activity via chromatin immunoprecipitation assays. Electrophoretic mobility shift assays further disclosed that HGF-induced CSDA augmentation correlates with an increase in AP-1 binding to VEGF. CONCLUSION: CSDA is crucial for the proliferation of gastric cancer cells, and the inhibition of this protein could impede the advancement of gastric cancer.

The absence of CsdA in Escherichia coli increases DNA replication and cell size but decreases growth rate at low temperature.

The CsdA protein is a highly conserved, DEAD-box RNA helicase and assists RNA structural remodeling at low temperature. We show that the fast-growing wild-type (WT) cells contain higher number of replication origins per cell with bigger cell size and the slowly growing cells possess less number of replication origins per cell with smaller cell size. The absence of CsdA leads to production of larger cells with higher number of origins per cell but slower growth at low temperature in an independent-manner of growth media. The phenotypes in ΔcsdA mutant are reversed by ectopic expression of CsdA or RNase R. A global transcription analysis shows that the absence of CsdA leads to significant decreases in transcription of about 200 genes at low temperature. These genes are associated with essential metabolic pathways, flagger assembly and cell division (minDE). It is likely that the slow growth of ΔcsdA cell results from the decreased transcription of essential metabolic genes, and the larger ΔcsdA cell could be a result of decreased transcription of minDE. The increased transcription of the nrdHIEF genes in ΔcsdA mutant is a likely reason that promotes DNA replication. We conclude that CsdA coordinates the cell cycle to growth by stabilizing mRNA of essential metabolic and cell division genes and degrading mRNA for nucleotide metabolic genes at low temperature.

Stopping power and CSDA range calculations of electrons and positrons over the 20 eV-1 GeV energy range in some water equivalent polymer gel dosimeters.

In this study, the stopping power, CSDA range and radiation yield calculations of electrons and positrons over the 20 eV-1 GeV energy range in some water equivalent polymer gel dosimeters were performed. For collision stopping power calculations of electrons and positrons the effective charge concept proposed by Sugiyama were considered. Here, both the effective charge of incident electrons and positrons (z*) and the effective charge (Z*) and the effective mean excitation energy (I*) of the target material were calculated. For the density effect correction the Fano model was selected. For the radiative stopping power analytical model based on the ratio between the collision and the radiative stopping power discribed by Attix was considered. For CSDA range and radition yield the continuous slowing down approximation (CSDA) was considered and the calculations were performed using numerical integral methods. Because of their water equivalent and 3D dose distribution properties, MAGIC and MAGAS polymer gels were selected as a target materials. The calculations were performed by programming all the equations discribed in this study as a computational code. The results of the stopping power, range and radiation yield were compared with those of ESTAR program and PENELOPE Monte Carlo modelling. Some deviations in low and high energy region between the calculated and reference data were observed. However, the similarity between calculated and reference data is remarkable. For the collision stopping power and CSDA range a good agreement between the calculated and reference data was observed for energies >1 keV. Whereas, for the radiative stopping power a good agreement was observed for energies >100 keV.

Continuous slowing-down approximation ranges of biological materials for 0.05-10 MeV alpha particles by using different approach methods.

The goal of this study was to calculate the range values of alpha particles in bone, MS20 tissue substitute, and muscle targets using different approach methods. The range values were calculated using Gauss quadrature, Simpson 1/3, and trapezoidal numerical integration methods in continuous slowing-down approximation (CSDA). Overall, the Gauss quadrature method gave the best CSDA range values for the target materials. These results will be conducive to studies involving the interaction of radiation with biological materials.

Relationship between dose and stopping power values for electrons in skin and muscle tissues.

Absorbed dose and stopping power of the target material are two important parameters for determining the radiation effects. In this work, the relationship between these two parameters has been investigated for electron beams incident on skin and muscle tissue. Absorbed dose was obtained by using the EGSnrc code and the stopping power values were calculated by considering the velocity-depended effective charge and mean excitation values. To obtain the relationship between absorbed dose and stopping power values, these parameters were graphed together and simple fitting functions have been obtained. The results obtained show that these parameters are linearly correlated with each other.

On pathlength and energy straggling of megavoltage electrons slowing down.

PURPOSE: to elucidate the effects of multiple scattering and energy-loss straggling on electron beams slowing down in materials. METHODS: EGSnrc Monte Carlo simulations are done using a purpose-written user-code. RESULTS: Plots are presented of the primary electron's energy as a function of pathlength for 20 MeV electrons incident on water and tantalum as are plots of the overall distribution of pathlengths as the 20 MeV electrons slow down under various Monte Carlo scenarios in water and tantalum. The distributions range from 1 % to 135 % of the CSDA range in water and from 1 % to 186 % in tantalum. The effects of energy-loss straggling on energy spectra at depth and electron fluence at depth are also presented. CONCLUSIONS: The role of energy-loss straggling and multiple scattering are shown to play a significant role in the range straggling which determines the dose fall-off region in electron beam dose vs depth curves and a significant role in the energy distributions as a function of depth.

Development of a new code for stopping power and CSDA range calculation of incident charged particles, part A: Electron and positron.

The stopping power of targets against incident charged particles and their range through matter are commonly considered as two important parameters in radiation and health physics studies. The exact calculation of these parameters is very crucial in many applications of radiation. The main objective of this study is the development of a new code for stopping power and range calculation of incident electron and positron projectiles. In this case, the interactions with matter are mainly due to the collision process and the Bremsstrahlung radiation emission. For collision stopping power, the Moller and Bhabha relations were considered for electron and positron, respectively. Some sophisticated correlations based on the Fano model have been selected for density correction term. For the radiative stopping power, a multifunction analytical model was developed based on an extensive literature review. All the equations were consolidated and programmed via the development of a new computational code using the C# programming language. Some simple and compound generic materials were considered for the verification process. Graphite, Silicon and Copper were selected as simple materials; whilst compound materials include air, water and the A-150- Tissue-Equivalent Plastic (A150TEP). The results of the stopping power and the range of incident particles were compared with well-known ICRU reports as well as Monte Carlo simulation. The results are consistent and in agreement with reference data. The maximum relative error of the collision stopping power was about 5% in comparison with ICRU reports for both electron and positron. However, for the positron projectile at low energies, some minor discrepancies were observed between the calculated collision stopping power and the MCNPX data. For the radiative stopping power, some deviations were observed in the low energy region and the model borders. The maximum relative error in the total stopping power was about 5-6% in comparison with ICRU reports and 15-20% in comparison with the MCNPX.

Cancer-Specific MicroRNA Analysis with a Nonenzymatic Nucleic Acid Circuit.

Sensitive detection of gastric cancer-related biomarkers in human serum provides a promising means for early cancer diagnosis. Herein, we report the design of a nucleic acid circuit for gastric cancer-related microRNA-27a (miRNA-27a) detection based on dual toehold-mediated circular strand displacement amplification (CSDA). In the presence of miRNA-27a, the hybridization between miRNA-27a and probe DNA on magnetic beads through toehold 1 leads to the release of fluorescent DNA and the exposure of a new toehold 2 on linker DNA. After hybridization with catalytic DNA, CSDA is initiated and target miRNA-27a is released to participate in the next cyclic reaction; therefore, a greatly enhanced fluorescence signal is produced. The efficient magnetic separation makes the sensitive detection of miRNA-27a be accomplished within 45 min. With the efficient CSDA, the detection limit of the system (0.8 pM) is ∼100 folds lower than that of the system based on strand displacement without CSDA (79.3 pM). Furthermore, the system also showed good stability and sensitivity to discriminate single-base mismatch, which allows the detection of miRNA-27a in human serum samples. This study provides a novel platform and approach for the rapid quantitative determination of miRNA, which has great potential in clinical diagnosis and disease treatment.

Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.

CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first time that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex.

Akt-mediated phosphorylation controls the activity of the Y-box protein MSY3 in skeletal muscle.

BACKGROUND: The Y-box protein MSY3/Csda represses myogenin transcription in skeletal muscle by binding a highly conserved cis-acting DNA element located just upstream of the myogenin minimal promoter (myogHCE). It is not known how this MSY3 activity is controlled in skeletal muscle. In this study, we provide multiple lines of evidence showing that the post-translational phosphorylation of MSY3 by Akt kinase modulates the MSY3 repression of myogenin. METHODS: Skeletal muscle and myogenic C2C12 cells were used to study the effects of MSY3 phosphorylation in vivo and in vitro on its sub-cellular localization and activity, by blocking the IGF1/PI3K/Akt pathway, by Akt depletion and over-expression, and by mutating potential MSY3 phosphorylation sites. RESULTS: We observed that, as skeletal muscle progressed from perinatal to postnatal and adult developmental stages, MSY3 protein became gradually dephosphorylated and accumulated in the nucleus. This correlated well with the reduction of phosphorylated active Akt. In C2C12 myogenic cells, blocking the IGF1/PI3K/Akt pathway using LY294002 inhibitor reduced MSY3 phosphorylation levels resulting in its accumulation in the nuclei. Knocking down Akt expression increased the amount of dephosphorylated MSY3 and reduced myogenin expression and muscle differentiation. MSY3 phosphorylation by Akt in vitro impaired its binding at the MyogHCE element, while blocking Akt increased MSY3 binding activity. While Akt over-expression rescued myogenin expression in MSY3 overexpressing myogenic cells, ablation of the Akt substrate, (Ser126 located in the MSY3 cold shock domain) promoted MSY3 accumulation in the nucleus and abolished this rescue. Furthermore, forced expression of Akt in adult skeletal muscle induced MSY3 phosphorylation and myogenin derepression. CONCLUSIONS: These results support the hypothesis that MSY3 phosphorylation by Akt interferes with MSY3 repression of myogenin circuit activity during muscle development. This study highlights a previously undescribed Akt-mediated signaling pathway involved in the repression of myogenin expression in myogenic cells and in mature muscle. Given the significance of myogenin regulation in adult muscle, the Akt/MSY3/myogenin regulatory circuit is a potential therapeutic target to counteract muscle degenerative disease.

Spectroscopic localization by simultaneous acquisition of the double-spin and stimulated echoes.

PURPOSE: To design a proton MR spectroscopy ((1) H-MRS) localization sequence that combines the signal-to-noise-ratio (SNR) benefits of point resolved spectroscopy (PRESS) with the high pulse bandwidths, low chemical shift displacements (CSD), low specific absorption rates (SAR), short echo times (TE), and superior radiofrequency transmit field (B1+) immunity of stimulated echo acquisition mode (STEAM), by simultaneously refocusing and acquiring both the double-spin and stimulated echo coherence pathways from the volume of interest. THEORY AND METHODS: We propose a family of (1)H-MRS sequences comprising three orthogonal spatially selective pulses with flip angles 90° < α, ß, γ < 128°. The stimulated and double-spin echo are refocused in-phase simultaneously by altering the pulses' phases, flip angles and timing, as well as the interpulse gradient spoiling moments. The ≈ 90° nutations of α, ß, γ provide STEAM-like advantages (lower SAR, in-plane CSD and TE; greater B1+ immunity), but with SNRs comparable with PRESS. RESULTS: Phantom and in vivo brain experiments show that 83-100% of the PRESS SNR (metabolite-dependent) is achieved at under 75% of the SAR and 66% lower in-plane CSD. CONCLUSION: The advantages of STEAM can be augmented with the higher SNR of PRESS by combining the spin and stimulated echoes. Quantification, especially of J-coupled resonances and intermediate and long TEs, must be carefully considered.

Structural changes during cysteine desulfurase CsdA and sulfur acceptor CsdE interactions provide insight into the trans-persulfuration.

In Escherichia coli, three cysteine desulfurases (IscS, SufS, and CsdA) initiate the delivery of sulfur for various biological processes such as the biogenesis of Fe-S clusters. The sulfur generated as persulfide on a cysteine residue of cysteine desulfurases is further transferred to Fe-S scaffolds (e.g. IscU) or to intermediate cysteine-containing sulfur acceptors (e.g. TusA, SufE, and CsdE) prior to its utilization. Here, we report the structures of CsdA and the CsdA-CsdE complex, which provide insight into the sulfur transfer mediated by the trans-persulfuration reaction. Analysis of the structures indicates that the conformational flexibility of the active cysteine loop in CsdE is essential for accepting the persulfide from the cysteine of CsdA. Additionally, CsdA and CsdE invoke a different binding mode than those of previously reported cysteine desulfurase (IscS) and sulfur acceptors (TusA and IscU). Moreover, the conservation of interaction-mediating residues between CsdA/SufS and CsdE/SufE further suggests that the SufS-SufE interface likely resembles that of CsdA and CsdE.

Differential proteomic analysis of abnormal intramyoplasmic aggregates in desminopathy.

Desminopathy is a subtype of myofibrillar myopathy caused by desmin mutations and characterized by protein aggregates accumulating in muscle fibers. The aim of this study was to assess the protein composition of these aggregates. Aggregates and intact myofiber sections were obtained from skeletal muscle biopsies of five desminopathy patients by laser microdissection and analyzed by a label-free spectral count-based proteomic approach. We identified 397 proteins with 22 showing significantly higher spectral indices in aggregates (ratio >1.8, p<0.05). Fifteen of these proteins not previously reported as specific aggregate components provide new insights regarding pathomechanisms of desminopathy. Results of proteomic analysis were supported by immunolocalization studies and parallel reaction monitoring. Three mutant desmin variants were detected directly on the protein level as components of the aggregates, suggesting their direct involvement in aggregate-formation and demonstrating for the first time that proteomic analysis can be used for direct identification of a disease-causing mutation in myofibrillar myopathy. Comparison of the proteomic results in desminopathy with our previous analysis of aggregate composition in filaminopathy, another myofibrillar myopathy subtype, allows to determine subtype-specific proteomic profile that facilitates identification of the specific disorder. BIOLOGICAL SIGNIFICANCE: Our proteomic analysis provides essential new insights in the composition of pathological protein aggregates in skeletal muscle fibers of desminopathy patients. The results contribute to a better understanding of pathomechanisms in myofibrillar myopathies and provide the basis for hypothesis-driven studies. The detection of specific proteomic profiles in different myofibrillar myopathy subtypes indicates that proteomic analysis may become a useful tool in differential diagnosis of protein aggregate myopathies.

Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA.

CsdA is one of five E. coli DEAD-box helicases and as a cold-shock protein assists RNA structural remodeling at low temperatures. The helicase has been shown to catalyze duplex unwinding in an ATP-dependent way and accelerate annealing of complementary RNAs, but detailed kinetic analyses are missing. Therefore, we performed kinetic measurements using a coupled annealing and strand displacement assay with high temporal resolution to analyze how CsdA balances the two converse activities. We furthermore tested the hypothesis that the unwinding activity of DEAD-box helicases is largely determined by the substrate's thermodynamic stability using full-length CsdA and a set of RNAs with constant length, but increasing GC content. The rate constants for strand displacement did indeed decrease with increasing duplex stability, with a calculated free energy between -31.3 and -40 kcal/mol being the limit for helix unwinding. Thus, our data generally support the above hypothesis, showing that for CsdA substrate thermal stability is an important rate limiting factor.