DNA methylation-regulated microRNA pathways in ovarian serous cystadenocarcinoma: A meta-analysis

Epigenetic regulation has been linked to the initiation and progression of cancer. Aberrant expression of microRNAs (miRNAs) is one such mechanism that can activate or silence oncogenes (OCGs) and tumor suppressor genes (TSGs) in cells. A growing number of studies suggest that miRNA expression can be regulated by methylation modification, thus triggering cancer development. However, there is no comprehensive in silico study concerning miRNA regulation by direct DNA methylation in cancer. Ovarian serous cystadenocarcinoma (OSC) was therefore chosen as a tumor model for the present work.Twelve batches of OSC data, with at least 35 patient samples in each batch, were obtained from The Cancer Genome Atlas (TCGA) database. The Spearman rank correlation coefficient (SRCC) was used to quantify the correlation between the CpG DNA methylation level and miRNA expression level. Meta-analysis was performed to reduce the effects of biological heterogeneity among different batches. MiRNA-target interactions were also inferred by computing SRCC and meta-analysis to assess the correlation between miRNA expression and cancer-associated gene expression and the interactions were further validated by a query against the miRTarBase database.A total of 26 potential epigenetic-regulated miRNA genes that can target OCGs or TSGs in OSC were found to show biological relevance between DNA methylation and miRNA gene expression. Furthermore, some of the identified DNA-methylated miRNA genes; for instance, the miR-200 family, were previously identified as epigenetic-regulated miRNAs and correlated with poor survival of ovarian cancer. We also found that several miRNA target genes, BTG3, NDN, HTRA3, CDC25A, and HMGA2 were also related to the poor outcomes in ovarian cancer.The present study proposed a systematic strategy to construct highly confident epigenetic-regulated miRNA pathways for OSC. The findings are validated and are in line with the literature. The inclusion of direct DNA methylated miRNA events may offer another layer of explanation that along with genetics can give a better understanding of the carcinogenesis process.     

Enzyme-free and multiplexed microRNA detection using microRNA-initiated DNA molecular motor

In this work, we have developed a sensitive, simple, and enzyme-free assay for detection of microRNAs (miRNAs) by means of a DNA molecular motor consisting of two stem-loop DNAs with identical stems and complementary loop domains. In the presence of miRNA target, it can hybridize with one of the stem-loop DNA to open the stem and to produce a miRNA/DNA hybrid and a single strand (ss) DNA, the ssDNA will in turn hybridize with another stem-loop DNA and finally form a double strand (ds) DNA to release the miRNA. One of the stem-loop DNA is double-labeled by a fluorophore/quencher pair with efficiently quenched fluorescence. The formation of dsDNA can produced specific fluorescence signal for miRNA detection. The released miRNA will continuously initiate the next hybridization of the two stem-loop DNAs to form a cycle-running DNA molecular motor, which results in great fluorescence amplification. With the efficient signal amplification, as low as 1 pmol/L miRNA target can be detected and a wide dynamic range from 1 pmol/L to 2 nmol/L is also obtained. Moreover, by designing different stem-loop DNAs specific to different miRNA targets and labeling them with different fluorophores, multiplexed miRNAs can be simultaneously detected in one-tube reaction with the synchronous fluorescence spectrum (SFS) technique.     

Sensitive and Multiplexed On‐chip microRNA Profiling in Oil‐Isolated Hydrogel Chambers

Although microRNAs (miRNAs) have been shown to be excellent indicators of disease state, current profiling platforms are insufficient for clinical translation. Here, we demonstrate a versatile hydrogel‐based microfluidic approach and novel amplification scheme for entirely on‐chip, sensitive, and highly specific miRNA detection without the risk of sequence bias. A simulation‐driven approach is used to engineer the hydrogel geometry and the gel‐reaction environment is chemically optimized for robust detection performance. The assay provides 22.6 fM sensitivity over a three log range, demonstrates multiplexing across at least four targets, and requires just 10.3 ng of total RNA input in a 2 hour and 15 minutes assay.     

Separability of tight and roaming pathways to molecular decomposition

Recent studies have questioned the separability of the tight and roaming mechanisms to molecular decomposition. We explore this issue for a variety of reactions including MgH(2) → Mg + H(2), NCN → CNN, H(2)CO → H(2) + CO, CH(3)CHO → CH(4) + CO, and HNNOH → N(2) + H(2)O. Our analysis focuses on the role of second-order saddle points in defining global dividing surfaces that encompass both tight and roaming first-order saddle points. The second-order saddle points define an energetic criterion for separability of the two mechanisms. Furthermore, plots of the differential contribution to the reactive flux along paths connecting the first- and second-order saddle points provide a dynamic criterion for separability. The minimum in the differential reactive flux in the neighborhood of the second-order saddle point plays the role of a mechanism divider, with the presence of a strong minimum indicating that the roaming and tight mechanisms are dynamically distinct. We show that the mechanism divider is often, but not always, associated with a second-order saddle point. For the formaldehyde and acetaldehyde reactions, we find that the minimum energy geometry on a conical intersection is associated with the mechanism divider for the tight and roaming processes. For HNNOH, we again find that the roaming and tight processes are dynamically separable but we find no intrinsic feature of the potential energy surface associated with the mechanism divider. Overall, our calculations suggest that roaming and tight mechanisms are generally separable over broad ranges of energy covering most kinetically relevant regimes.     

细胞蛋白质组学和代谢组学整合策略表征散斑型BTB/POZ蛋白质突变调控的关键代谢通路

散斑型BTB/POZ蛋白（SPOP）是前列腺癌中突变率最高的蛋白质之一。该研究通过整合细胞蛋白质组学和代谢组学的方法，揭示SPOP突变引起的代谢紊乱及其调控的代谢通路。首先，系统地研究了LNCaP SPOP野生型及突变型高表达细胞中的代谢变化。代谢组学结果显示，SPOP野生型和突变型（SPOP_Y87N和SPOP_F133L）导入的LNCaP细胞在偏最小二乘法判别分析（PLS-DA）得分图上得到了很好的区分。进一步通过单因素方差分析发现，SPOP突变引起富马酸、苹果酸、柠檬酸、天冬氨酸和天冬酰胺等代谢物含量的增加。蛋白质组学共发现909种蛋白质在两种LNCaP SPOP突变体细胞中发生变化。分别对差异代谢物和差异蛋白质进行通路富集分析，发现三羧酸循环、氨酰基-转运核糖核酸生物合成在代谢组学和蛋白质组学分析中都发生了明显改变。最后，在SPOP敲除的Du145细胞中验证了上述研究结果。该研究证明SPOP突变可促进三羧酸循环。     

Multiparametric diagnostics of cardiomyopathies by microRNA signatures

The diagnosis of cardiomyopathies by endomyocardial biopsy analysis is the gold standard for confirmation of causative reasons but is failing if a sample does not contain the area of interest due to focal pathology. Biopsies are revealing an extract of the current situation of the heart muscle only, and the need for global organ-specific or systemic markers is obvious in order to minimize sampling errors. Global markers like specific gene expression signatures in myocardial tissue may therefore reflect the focal situation or condition of the whole myocardium. Besides gene expression profiles, microRNAs (miRNAs) represent a new group of stable biomarkers that are detectable both in tissue and body fluids. Such miRNAs may serve as cardiological biomarkers to characterize inflammatory processes, to confirm viral infections, and to differentiate various forms of infection. The predictive power of single miRNAs for diagnosis of complex diseases may be further increased if several distinctly deregulated candidates are combined to form a specific miRNA signature. Diagnostic systems that generate disease-related miRNA profiles are based on microarrays, bead-based oligo sorbent assays, or on assays based on real-time polymerase chain reactions and placed on microfluidic cards or nanowell plates. Multiparametric diagnostic systems that can measure differentially expressed miRNAs may become the diagnostic tool of the future due to their predictive value with respect to clinical course, therapeutic decisions, and therapy monitoring. We discuss here specific merits, limitations and the potential of currently available analytical platforms for diagnostics of heart muscle diseases based on miRNA profiling. Contains 34 references. Figure

Modern diagnostics of cardiomyopathies will include multiparametric analysis of microRNA profiles in endomyocardial biopsies by real-time PCR or bead-based OLISA techniques. In contrast to high-throughput screening technologies diagnostic systems are realized by down-scaling sample volumes and simultaneous measurement of a limited number of stable disease related parameters.     

Profiling of cocaine by micellar electrokinetic chromatography

The potential of micellar electrokinetic chromatography (MEKC) for the profiling of cocaine samples is described. An MEKC system containing sodium dodecyl sulfate (SDS) and methanol was optimized using a test mixture of cocaine, its common impurities (benzoylecgonine, norcocaine, tropacocaine, and trans-cinnamoylcocaine), and several degradation products. The effect of pH, percentage modifier, and concentration surfactant on the separation has been investigated. The optimal separation buffer for cocaine samples consisted of 75 mM SDS, 17.5% methanol, and 25 mM borate (pH 8.3) and was well suited to separate components of diverse polarity in one run. Various cocaine seizures have been analyzed with the MEKC system and their signatures were compared. The electrokinetic chromatograms obtained were characteristic, and differences and similarities among the samples could easily be observed. Several impurities were identified in the samples by means of migration times and comparison of recorded and library UV spectra. The composition of the samples was determined semiquantitatively using relative corrected peak areas.     

A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices

Here, an efficient method that predicts natural transition pathways between two endpoint states of an allosteric protein has been proposed. This method helps create structures that bridge these endpoints through multiple iterative and unbiased molecular dynamics simulations with explicit water. Difference distance matrices provide an approach for identifying states involving concerted slow motion. A series of structures are readily generated along the transition pathways of adenylate kinase. Predicted structures may be useful for an initial pathway to evaluate free energy landscapes via umbrella sampling and chain‐of‐states methods. © 2016 Wiley Periodicals, Inc.     

DNA-based molecular wires: multiple emission pathways of individual constructs

The extent of photon energy transfer through individual DNA-based molecular wires composed of five dyes is investigated at the single molecular level. Combining single-molecule spectroscopy and pulse interleaved excitation imaging, we have directly resolved the time evolution spectral response of individual constructs, while simultaneously probing DNA integrity. Our data clearly show that intact wires exhibit photon-transfer efficiencies close to 100% across five dyes. Dynamical and multiple pathways for the photon emission resulting from conformational freedom of the wire are readily uncovered. These results provide the basis for guiding the synthesis of DNA-based supramolecular arrays with improved photon transport at the nanometer scale.     

质谱分析福尔马林固定组织的多肽谱

福尔马林固定组织时,甲醛与蛋白质多肽链的氨基酸侧链上的功能基团,特别是氨基、亚氨基、酰氨基、羟基和巯基等相结合,使蛋白分子间形成大分子网络,蛋白不再发生迁移达到固定目的[1].     

Microtubule dynamics regulated by stathmin

Microtubules perform a variety of functions which lead to the complex regulation of intracellular transport and cell division. However, the regulation of microtubule growth is not clearly known. Based on a recent experimental finding, we explore the possibility of spatial regulation of microtubule growth by stathmin–tubulin interaction gradients. Computer simulation of the model with stathmin–tubulin interaction gradients gave regulated growth as seen in experiments. In future, the stathmin–tubulin interaction gradients can be made dynamic and its impact on the microtubule growth can be explored.     

Visual scanometric detection of DNA through silver enhancement regulated by gold-nanoparticle aggregation with a molecular beacon as the trigger

A convenient and label-free scanometric approach for DNA assay was designed by integrating a metal-ion-mediated conformational molecular beacon (MB) and silver-signal amplification regulated by gold-nanoparticle (AuNP) aggregation. The strategy was based on displacing the interaction between the target DNA sequence and a competitor Hg(2+) ion with a link DNA sequence. In the absence of the target DNA sequence, a link DNA sequence interacted with the Hg(2+) ions, thus forming an inactive cyclic conformation of the MB. This result led to the poor aggregation of polyadenosine-functionalized AuNPs (A-AuNP). In the presence of a target DNA sequence with a stronger affinity than that of the competitor, hybridization between the link DNA and target DNA sequences turned on the trigger. The polythymidine end of the resulting linear duplex structure could react with A-AuNP, thus leading to a cross-linking aggregation. This aggregation weakened AuNP-catalyzed silver enhancement on a spot substrate. Further, by using scanometric detection, the concentration of the target DNA sequence could be conveniently read out within a linear range from 1.0 to 30 nM. Interestingly, in the same amount of Hg(2+) ions, one-base mismatched DNA showed only 22% of the relative gray-scale intensity for the target DNA sequence at the same concentration, thus indicating good specificity. The designed approach, with the help of the ion-mediated conformational MB, was simple, cost effective, adaptable, and convenient and provided significant potential applications in clinical analysis.     

Contribution of molecular pathways in the micellar solubilization of monodisperse emulsion droplets

It is often proposed that oil solubilization in anionic and nonionic micelles proceeds by different mechanisms, with diffusion of the oil molecule thought to control the former, and the latter interfacially controlled. In order to investigate this hypothesis, the effect of aqueous phase viscosity, salt, and surfactant concentration during the solubilization process was studied. The progressive decrease in average droplet size of nearly monodisperse emulsions during solubilization in SDS or Tween 20 micellar solutions was monitored by light scattering, and the change in turbidity was measured by UV-vis spectrophotometer. The solubilization rates were analyzed using a population balance approach to calculate the mass transfer coefficients. Increasing the aqueous viscosity by adding sucrose reduced the mass transfer coefficients of n-tetradecane and n-dodecane but had a smaller effect on n-hexadecane. The strong dependence of the solubilization rate for the shorter chain length alkanes on aqueous viscosity supported a mechanism in which the oil undergoes molecular diffusion before being taken up by micelles. The dependence of the solubilization kinetics on surfactant concentration appeared consistent with this mechanism but yielded a slower micellar uptake rate than previously predicted theoretically. As the solute chain length increased in nonionic surfactant solutions, an interfacial mechanism mediated by micelles appeared to contribute substantially to the overall rate. Addition of salt only slightly increased the solubilization rate of n-hexadecane in SDS solutions and, thus, indicated a weak role of electrostatic interactions for ionic surfactants on the overall mechanism.     

Profiling of mouse synaptosome proteome and phosphoproteome by IEF

Synapses play important roles in neurotransmission and neuroplasticity. For an in‐depth analysis of the synaptic proteome and phosphoproteome, synaptosomal proteins from whole mouse brain were analyzed by IEF and MS resulting in the largest synaptosome proteome described to date, with 2980 unique proteins identified with two or more peptides. At the same time, 118 synaptosomal phosphoproteins were identified, eight of which are reported for the first time as phosphorylated. Expression of selected proteins in synaptosomes was investigated by Western blot. We demonstrate that IEF is a powerful method to interrogate complex samples such as brain tissue both at the proteome and the phosphoproteome level without the need of additional enrichment for phosphoproteins. The detailed synaptoproteome data set reported here will help to elucidate the molecular complexity of the synapse and contribute to our understanding of synaptic systems biology in health and disease.     

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations

Protein structure is highly diverse when considering a wide range of protein types, helping to give rise to the multitude of functions that proteins perform. In particular, certain proteins are known to adopt a knotted or slipknotted fold. How such proteins undergo mechanical unfolding was investigated utilizing a combination of single molecule atomic force microscopy (AFM), protein engineering, and steered molecular dynamics (SMD) simulations to show the mechanical unfolding mechanism of the slipknotted protein AFV3-109. Our results reveal that the mechanical unfolding of AFV3-109 can proceed via multiple parallel unfolding pathways that all cause the protein slipknot to untie and the polypeptide chain to completely extend. These distinct unfolding pathways proceed via either a two- or three-state unfolding process involving the formation of a well-defined, stable intermediate state. SMD simulations predict the same contour length increments for different unfolding pathways as single molecule AFM results, thus providing a plausible molecular mechanism for the mechanical unfolding of AFV3-109. These SMD simulations also reveal that two-state unfolding is initiated from both the N- and C-termini, while three-state unfolding is initiated only from the C-terminus. In both pathways, the protein slipknot was untied during unfolding, and no tightened slipknot conformation was observed. Detailed analysis revealed that interactions between key structural elements lock the knotting loop in place, preventing it from shrinking and the formation of a tightened slipknot conformation. Our results demonstrate the bifurcation of the mechanical unfolding pathway of AFV3-109 and point to the generality of a kinetic partitioning mechanism for protein folding/unfolding.     

Inelastic insights for molecular tunneling pathways: bypassing the terminal groups

As an example of the use of inelastic transport to deduce structure in molecular transport junctions, we compute the orientation dependence of the Inelastic Electron Tunneling (IET) spectrum of the 1-pentane monothiolate. We find that upon increasing the tilting angle of the molecule with respect to the normal to the electrode the spectrum changes as the intensity of some vibrations is enhanced. These differences occur because for higher tilting angles the tunneling path that bypasses the terminal group grows in importance. IETS can therefore be used to establish the molecular orientation in junctions terminating with alkyl chains and to investigate experimentally the relative importance of the available tunneling paths.     

Multiplexed microRNA detection by capillary electrophoresis with laser-induced fluorescence

In this study, we developed a novel assay that simultaneously detects multiple miRNAs (microRNAs) within a single capillary by combining a tandem adenosine-tailed DNA bridge-assisted splinted ligation with denaturing capillary gel electrophoresis with laser-induced fluorescence. This proposed method not only represents a significant improvement in resolution but also allows for the detection of multiple miRNAs within a single capillary based on the length differences of specified target bridge DNA. The assay's linear range covers three orders of magnitude (1.0 nM to 1.0 pM) with a limit of detection (S/N=3) as low as 190 fM (2.5 zmol). Five miRNAs of Epstein-Barr virus (EBV) were also detected in EBV-infected nasopharyngeal carcinoma cells, while they did not appear in non-virus infected cells. Moreover, the electropherogram indicated that the screening of isomiRs (isomer of miRNA) of BART2 by CE-LIF is feasible by our proposed method. The developed electrophoresis-based method for miRNA detection is fast, amplification-free, multiplexed and cost-effective, making it potentially applicable to large-scale screening of isomiRs.     

Ranking of microRNA target prediction scores by Pareto front analysis

Over the past ten years, a variety of microRNA target prediction methods has been developed, and many of the methods are constantly improved and adapted to recent insights into miRNA-mRNA interactions. In a typical scenario, different methods return different rankings of putative targets, even if the ranking is reduced to selected mRNAs that are related to a specific disease or cell type. For the experimental validation it is then difficult to decide in which order to process the predicted miRNA-mRNA bindings, since each validation is a laborious task and therefore only a limited number of mRNAs can be analysed. We propose a new ranking scheme that combines ranked predictions from several methods and - unlike standard thresholding methods - utilises the concept of Pareto fronts as defined in multi-objective optimisation. In the present study, we attempt a proof of concept by applying the new ranking scheme to hsa-miR-21, hsa-miR-125b, and hsa-miR-373 and prediction scores supplied by PITA and RNAhybrid. The scores are interpreted as a two-objective optimisation problem, and the elements of the Pareto front are ranked by the STarMir score with a subsequent re-calculation of the Pareto front after removal of the top-ranked mRNA from the basic set of prediction scores. The method is evaluated on validated targets of the three miRNA, and the ranking is compared to scores from DIANA-microT and TargetScan. We observed that the new ranking method performs well and consistent, and the first validated targets are elements of Pareto fronts at a relatively early stage of the recurrent procedure, which encourages further research towards a higher-dimensional analysis of Pareto fronts.