Electrophoretical stretching of DNA in a hybrid microchannel

The electrophoretical stretching of DNA in a hybrid microchannel is analyzed in this paper. The channel comprises a large insulating cylinder and a hyperbolic contraction that can cause the DNA deformation. Brownian dynamics simulation is used to characterize the dynamical stretching process of a long T4 DNA in hybrid microchannels. The computational results show us the larger average extension of DNA in cylinder-hybridized microchannels than that in the single microcontractions due to the prestretched effect of cylinder on DNA. Moreover, the location and the radius of the insulating cylinder in hybrid microchannels have great effects on the stretching behavior of DNA.     

DNA stretching on the wall surfaces in curved microchannels with different radii

DNA molecule conformation dynamics and stretching were made on semi-circular surfaces with different radii (500 to 5,000 μm) in microchannels measuring 200 μm × 200 μm in cross section. Five different buffer solutions - 1× Tris-acetate-EDTA (TAE), 1× Tris-borate-EDTA (TBE), 1× Tris-EDTA (TE), 1× Tris-phosphate-EDTA (TPE), and 1× Tris-buffered saline (TBS) solutions - were used with a variety of viscosity such as 40, 60, and 80 cP, with resultant 10⁻⁴ ≤ Re ≤ 10⁻³ and the corresponding 5 ≤ Wi ≤ 12. The test fluids were seeded with JOJO-1 tracer particles for flow visualization and driven through the test channels via a piezoelectric (PZT) micropump. Micro particle image velocimetry (μPIV) measuring technique was applied for the centered-plane velocity distribution measurements. It is found that the radius effect on the stretch ratio of DNA dependence is significant. The stretch ratio becomes larger as the radius becomes small due to the larger centrifugal force. Consequently, the maximum stretch was found at the center of the channel with a radius of 500 μm.     

DNA and RNA Quadruplex-Binding Proteins

Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5'' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)_n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III₁ region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.     

Influences of Electromagnetic Energy on Bio-Energy Transport through Protein Molecules in Living Systems and Its Experimental Evidence

The influences of electromagnetic fields (EMFs) on bio-energy transport and its mechanism of changes are investigated through analytic and numerical simulation and experimentation. Bio-energy transport along protein molecules is performed by soliton movement caused by the dipole–dipole electric interactions between neighboring amino acid residues. As such, EMFs can affect the structure of protein molecules and change the properties of the bio-energy transported in living systems. This mechanism of biological effect from EMFs involves the amino acid residues in protein molecules. To study and reveal this mechanism, we simulated numerically the features of the movement of solitons along protein molecules with both a single chain and with three channels by using the Runge–Kutta method and Pang’s soliton model under the action of EMFs with the strengths of 25,500, 51,000, 76,500, and 102,000 V/m in the single-chain protein, as well as 17,000, 25,500, and 34,000 V/m in the three-chain protein, respectively. Results indicate that electric fields (EFs) depress the binding energy of the soliton, decrease its amplitude, and change its wave form. Also, the soliton disperses at 102,000 V/m in a single-chain protein and at 25,500 and 34,000 V/m in three-chain proteins. These findings signify that the influence of EMFs on the bio-energy transport cannot be neglected; however, these variations depend on both the strength and the direction of the EF in the EMF. This direction influences the biological effects of EMF, which decrease with increases in the angle between the direction of the EF and that of the dipole moment of amino acid residues; however, randomness at the macroscopic level remains. Lastly, we experimentally confirm the existence of a soliton and the validity of our conclusion by using the infrared spectra of absorption of the collagens, which is activated by another type of EF. Thus, we can affirm that both the described mechanism and the corresponding theory are correct and that EMFs or EFs can influence the features of energy transport in living systems and thus have certain biological effects.     

Flow distribution and mass transfer in a parallel microchannel contactor integrated with constructal distributors

Flow distribution and mass transfer characteristics during CO₂‐water flow through a parallel microchannel contactor integrated with two constructal distributors have been investigated numerically and experimentally. Each distributor comprises a dichotomic tree structure that feeds 16 microchannels with hydraulic diameters of 667 μm. It was found that constructal distributors could ensure a nearly uniform gas–liquid distribution at high gas flow rates where the ideal flow pattern was slug‐annular flow. Nevertheless, at small gas flow rates where the ideal flow pattern was slug flow, a significant flow maldistribution occurred primarily due to the lack of large pressure barrier inside each distributor, indicating that dynamic pressure fluctuation in parallel microchannels greatly disturbed an otherwise good flow distribution therein. It was further shown that the present parallel microchannel contactor could realize the desired mass transfer performance previously achieved in one single microchannel under relatively wide operational ranges due to the integration of constructal distributors. © 2009 American Institute of Chemical Engineers AIChE J, 2010     

Novel Sustained-Release of Propafenone through Pellets: Preparation and in Vitro/in Vivo Evaluation

In this study, an extrusion-spheronization method was applied successfully to fabricate propafenone hydrochloride (PPF) sustained-release pellets. Using scanning electron microscopy, it was shown that the PPF pellets had a mean size of approximately 950 µm with a spherical shape. The in vitro release profiles indicated that the release of PPF from the pellets exhibited a sustained release behavior. The relatively high correlation coefficient (r) values obtained from the analysis of the amount of the drug released versus the square root of time indicated that the release followed a zero order kinetic model. A similar phenomenon was also observed in a pharmacokinetic study in dogs, in which the area under the curve (AUC) of the pellet formulation was 1.2-fold higher than that of PPF tablets. The present work demonstrated the feasibility of controlled delivery of PPF utilizing microcrystalline cellulose (MCC)-based pellets.     

Transcriptional Induction of Metallothionein by Tris(pentafluorophenyl)stibane in Cultured Bovine Aortic Endothelial Cells

Vascular endothelial cells cover the luminal surface of blood vessels and contribute to the prevention of vascular disorders such as atherosclerosis. Metallothionein (MT) is a low molecular weight, cysteine-rich, metal-binding, inducible protein, which protects cells from the toxicity of heavy metals and active oxygen species. Endothelial MT is not induced by inorganic zinc. Adequate tools are required to investigate the mechanisms underlying endothelial MT induction. In the present study, we found that an organoantimony compound, tris(pentafluorophenyl)stibane, induces gene expression of MT-1A and MT-2A, which are subisoforms of MT in bovine aortic endothelial cells. The data reveal that MT-1A is induced by activation of both the MTF-1–MRE and Nrf2–ARE pathways, whereas MT-2A expression requires only activation of the MTF-1–MRE pathway. The present data suggest that the original role of MT-1 is to protect cells from heavy metal toxicity and oxidative stress in the biological defense system, while that of MT-2 is to regulate intracellular zinc metabolism.     

Dwell-Time Distribution,Long Pausing and Arrest of Single-Ribosome Translation through the mRNA Duplex

Proteins in the cell are synthesized by a ribosome translating the genetic information encoded on the single-stranded messenger RNA (mRNA). It has been shown that the ribosome can also translate through the duplex region of the mRNA by unwinding the duplex. Here, based on our proposed model of the ribosome translation through the mRNA duplex we study theoretically the distribution of dwell times of the ribosome translation through the mRNA duplex under the effect of a pulling force externally applied to the ends of the mRNA to unzip the duplex. We provide quantitative explanations of the available single molecule experimental data on the distribution of dwell times with both short and long durations, on rescuing of the long paused ribosomes by raising the pulling force to unzip the duplex, on translational arrests induced by the mRNA duplex and Shine-Dalgarno(SD)-like sequence in the mRNA. The functional consequences of the pauses or arrests caused by the mRNA duplex and the SD sequence are discussed and compared with those obtained from other types of pausing, such as those induced by “hungry” codons or interactions of specific sequences in the nascent chain with the ribosomal exit tunnel.     

Neuroprotective properties of mildronate, a small molecule, in a rat model of Parkinson's disease

Previously, we have found that mildronate [3-(2,2,2-trimethylhydrazinium) propionate dihydrate], a small molecule with charged nitrogen and oxygen atoms, protects mitochondrial metabolism that is altered by inhibitors of complex I and has neuroprotective effects in an azidothymidine-neurotoxicity mouse model. In the present study, we investigated the effects of mildronate in a rat model of Parkinson's disease (PD) that was generated via a unilateral intrastriatal injection of the neurotoxin 6-hydroxydopamine (6-OHDA). We assessed the expression of cell biomarkers that are involved in signaling cascades and provide neural and glial integration: the neuronal marker TH (tyrosine hydroxylase); ubiquitin (a regulatory peptide involved in the ubiquitin-proteasome degradation system); Notch-3 (a marker of progenitor cells); IBA-1 (a marker of microglial cells); glial fibrillary acidic protein, GFAP (a marker of astrocytes); and inducible nitric oxide synthase, iNOS (a marker of inflammation). The data show that in the 6-OHDA-lesioned striatum, mildronate completely prevented the loss of TH, stimulated Notch-3 expression and decreased the expression of ubiquitin, GFAP and iNOS. These results provide evidence for the ability of mildronate to control the expression of an array of cellular proteins and, thus, impart multi-faceted homeostatic mechanisms in neurons and glial cells in a rat model of PD. We suggest that the use of mildronate provides a protective effect during the early stages of PD that can delay or halt the progression of this neurodegenerative disease.     

Enhancing single molecule imaging in optofluidics and microfluidics

Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.     

Comprehensive Analysis of Neonatal versus Adult Unilateral Decortication in a Mouse Model Using Behavioral,Neuroanatomical, and DNA Microarray Approaches

Previously, studying the development, especially of corticospinal neurons, it was concluded that the main compensatory mechanism after unilateral brain injury in rat at the neonatal stage was due in part to non-lesioned ipsilateral corticospinal neurons that escaped selection by axonal elimination or neuronal apoptosis. However, previous results suggesting compensatory mechanism in neonate brain were not correlated with high functional recovery. Therefore, what is the difference among neonate and adult in the context of functional recovery and potential mechanism(s) therein? Here, we utilized a brain unilateral decortication mouse model and compared motor functional recovery mechanism post-neonatal brain hemisuction (NBH) with adult brain hemisuction (ABH). Three analyses were performed: (1) Quantitative behavioral analysis of forelimb movements using ladder walking test; (2) neuroanatomical retrograde tracing analysis of unlesioned side corticospinal neurons; and (3) differential global gene expressions profiling in unlesioned-side neocortex (rostral from bregma) in NBH and ABH on a 8 × 60 K mouse whole genome Agilent DNA chip. Behavioral data confirmed higher recovery ability in NBH over ABH is related to non-lesional frontal neocortex including rostral caudal forelimb area. A first inventory of differentially expressed genes genome-wide in the NBH and ABH mouse model is provided as a resource for the scientific community.     

The Interaction of Sheep Genomic DNA with a Cobalt(II) Complex Containing p-Nitrobenzoate and N,N′-Diethylnicotinamide Ligands

The synthesized cobalt(II) complex, CoPNBDENA and the binding of this complex with sheep genomic DNA were investigated by UV–Visible absorption and viscosity techniques. Also the interaction of sheep genomic DNA with the complex was studied using the agarose gel electrophoresis method. The results indicated that the complex interacted with DNA. The nature of the binding seemed to be mainly an electrostatic interaction between DNA and the cobalt(II) complex. Other binding modes such as hydrogen bonds may also exist in this system. In this study, after the interaction of DNA–CoPNBDENA, it was observed that the migration of the DNA band became slow as the amount of cobalt(II) complex was increased. This clearly demonstrates that the CoPNBDENA complex neutralizes the negative charges of DNA.     

Ultradense and planarized antireflective vertical silicon nanowire array using a bottom-up technique

The production and characterization of ultradense, planarized, and organized silicon nanowire arrays with good crystalline and optical properties are reported. First, alumina templates are used to grow silicon nanowires whose height, diameter, and density are easily controlled by adjusting the structural parameters of the template. Then, post-processing using standard microelectronic techniques enables the production of high-density silicon nanowire matrices featuring a remarkably flat overall surface. Different geometries are then possible for various applications. Structural analysis using synchrotron X-ray diffraction reveals the good crystallinity of the nanowires and their long-range periodicity resulting from their high-density organization. Transmission electron microscopy also shows that the nanowires can grow on nonpreferential substrate, enabling the use of this technique with universal substrates. The good geometry control of the array also results in a strong optical absorption which is interesting for their use in nanowire-based optical sensors or similar devices.     

植物DNA甲基化与逆境响应

在逆境胁迫下,植物会根据自身需要调节信号传导途径,从而上调(启动)或下调(关闭)基因表达以确保自身的适应性生长及发育。近年研究显示,植物DNA甲基化变异在响应逆境胁迫过程中发挥着重要作用,生物逆境和非生物逆境都可使植物的甲基化状态发生调控性改变,从而使植物在一定程度上适应和抵抗逆境伤害。本文对植物DNA甲基化及逆境胁迫下甲基化变异方面的研究进展作一综述。     

Association of CDKN2BAS Polymorphism rs4977574 with Coronary Heart Disease: A Case-Control Study and a Meta-Analysis

The goal of our study was to explore the significant association between a non-protein coding single nucleotide polymorphism (SNP) rs4977574 of CDKN2BAS gene and coronary heart disease (CHD). A total of 590 CHD cases and 482 non-CHD controls were involved in the present association study. A strong association of rs4977574 with CHD was observed in females (genotype: p = 0.002; allele: p = 0.002, odd ratio (OR) = 1.57, 95% confidential interval (CI) = 1.18–2.08). Moreover, rs4977574 was more likely to be a risk variant of CHD under the recessive model in females (χ² = 10.29, p = 0.003, OR = 2.14, 95% CI = 1.31–2.77). A breakdown analysis by age had shown that there was an 87% increased risk of CHD for females younger than 65 years (genotype: χ² = 14.64, degrees of freedom (df) = 2, p = 0.0002; allele: χ² = 11.31, df = 1, p = 0.0008, OR = 1.87, 95% CI = 1.30–2.70). Similar observation was also found in males younger than 65 years (genotype: χ² = 8.63, df = 2, p = 0.04; allele: χ² = 7.55, df = 1, p = 0.006, OR = 1.45, 95% CI = 1.11–1.90). p values were adjusted by age, sex, smoking, high density lipoprotein cholesterol (HDL-C) and low density lipoprotein cholesterol (LDL-C). Meta-analysis of 23 studies among 36,452 cases and 39,781 controls showed a strong association between rs4977574 and the risk of CHD (p < 0.0001, OR = 1.27, 95% CI = 1.22–1.31).