DNA methylation profiling in nanochannels

We report the profiling of the 5-methyl cytosine distribution within single genomic-sized DNA molecules at a gene-relevant resolution. This method linearizes and stretches DNA molecules by confinement to channels with a dimension of about 250×200 nm(2). The methylation state is detected using fluorescently labeled methyl-CpG binding domain proteins (MBD), with high signal contrast and low background. DNA barcodes consisting of methylated and non-methylated segments are generated, with both short and long concatemers demonstrating spatially resolved MBD binding. The resolution of the technique is better than 10 kbp, and single-molecule read-lengths exceeding 140 kbp have been achieved.     

Entropic depletion of DNA in triangular nanochannels

Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes.     

Stretching of DNA confined in nanochannels with charged walls

There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.     

Measurements of DNA barcode label separations in nanochannels from time-series data

We analyzed time-series data for fluctuations of intramolecular segments of barcoded E. coli genomic DNA molecules confined in nanochannels with sizes near the persistence length of DNA. These dynamic data allowed us to measure the probability distribution governing the distance between labels on the DNA backbone, which is a key input into the alignment methods used for genome mapping in nanochannels. Importantly, this dynamic method does not require alignment of the barcode to the reference genome, thereby removing a source of potential systematic error in a previous study of this type. The results thus obtained support previous evidence for a left-skewed probability density for the distance between labels, albeit at a lower magnitude of skewness. We further show that the majority of large fluctuations between labels are short-lived events, which sheds further light upon the success of the linearized DNA genome mapping technique. This time-resolved data analysis will improve existing genome map alignment algorithms, and the overall idea of using dynamic data could potentially improve the accuracy of genome mapping, especially for complex heterogeneous samples such as cancer cells.     

Modeling the relaxation time of DNA confined in a nanochannel

Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 (2012)], which have been difficult to validate due to the lack of direct experimental data. Furthermore, the model calculation shows that as the channel size passes below approximately 100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping.     

The effects of different syringe volume, needle size and sample volume on blood gas analysis in syringes washed with heparin

Introductıon:

We evaluated the effect of different syringe volume, needle size and sample volume on blood gas analysis in syringes washed with heparin.

Materials and methods:

In this multi-step experimental study, percent dilution ratios (PDRs) and final heparin concentrations (FHCs) were calculated by gravimetric method for determining the effect of syringe volume (1, 2, 5 and 10 mL), needle size (20, 21, 22, 25 and 26 G) and sample volume (0.5, 1, 2, 5 and 10 mL). The effect of different PDRs and FHCs on blood gas and electrolyte parameters were determined. The erroneous results from nonstandardized sampling were evaluated according to RiliBAK’s TEa.

Results:

The increase of PDRs and FHCs was associated with the decrease of syringe volume, the increase of needle size and the decrease of sample volume: from 2.0% and 100 IU/mL in 10 mL-syringe to 7.0% and 351 IU/mL in 1 mL-syringe; from 4.9% and 245 IU/mL in 26G to 7.6% and 380 IU/mL in 20 G with combined 1 mL syringe; from 2.0% and 100 IU/mL in full-filled sample to 34% and 1675 IU/mL in 0.5 mL suctioned sample into 10 mL-syringe. There was no statistical difference in pH; but the percent decreasing in pCO₂, K⁺, iCa²⁺, iMg²⁺; the percent increasing in pO₂ and Na⁺ were statistical significance compared to samples full-filled in syringes. The all changes in pH and pO₂ were acceptable; but the changes in pCO₂, Na⁺, K⁺ and iCa²⁺ were unacceptable according to TEa limits except fullfilled-syringes.

Conclusions:

The changes in PDRs and FHCs due nonstandardized sampling in syringe washed with liquid heparin give rise to erroneous test results for pCO₂ and electrolytes.     

The effect of the surface functionalization and the electrolyte concentration on the electrical conductance of silica nanochannels

It is known that the conductance of nanochannels as a function of electrolyte concentration deviates from a linearly proportional relationship and approaches a value independent of the concentration as the electrolyte concentration is lowered. Most of the proposed models account for this behavior by considering a constant surface charge density and an ideal electrolyte solution. However, at low electrolyte concentrations, the ideal electrolyte approximation is no longer valid because the ions that result from the atmospheric carbon dioxide dissolution in water dominate the ionic concentration. In this paper, arrays of silica nanochannels were electrically characterized via conductance measurements. The conductance at low salt concentrations is modeled by a variable surface charge model that accounts for all ionic species in solution. This model was used to determine the variable surface charge of the bare silica nanochannels as well as of chemically modified nanochannels. The model correctly predicted the variation of the nanochannel conductance observed after silane (aminopropyldimethylethoxysilane) functionalization and single-strand DNA immobilization. Finally, pH modification of bulk KCl solutions was employed as an alternative method of changing the surface charge of silica nanochannels. Surface charge calculated from conductance measurements performed at different bulk pH values confirmed that the surface charge of the silica nanochannel walls is sensitive to the H⁺ concentration.     

Investigating CSI: portrayals of DNA testing on a forensic crime show and their potential effects

The popularity of forensic crime shows such as CSI has fueled debate about their potential social impact. This study considers CSI's potential effects on public understandings regarding DNA testing in the context of judicial processes, the policy debates surrounding crime laboratory procedures, and the forensic science profession, as well as an effect not discussed in previous accounts: namely, the show's potential impact on public understandings of DNA and genetics more generally. To develop a theoretical foundation for research on the "CSI effect," it draws on cultivation theory, social cognitive theory, and audience reception studies. It then uses content analysis and textual analysis to illuminate how the show depicts DNA testing. The results demonstrate that CSI tends to depict DNA testing as routine, swift, useful, and reliable and that it echoes broader discourses about genetics. At times, however, the show suggests more complex ways of thinking about DNA testing and genetics.     

农户仓类设施采纳及其对玉米储存数量和损失的影响

近年来,粮食增产难度提升,减少粮食损失成为保障国家粮食安全的重要内容。中国政府通过实施科学储粮工程,鼓励农户采用更为先进的设施储粮,改善储粮设施和储藏条件,减少损失。本文基于中国23省（区、市）1202户农户调查数据,使用倾向性得分匹配法评估仓类设施采纳对农户玉米储存规模、储存时间、储存损失和鼠害程度的影响。结果表明：①采用仓类设施显著提升农户玉米储存数量,使农户平均玉米储存规模达4655.30 kg,比没有采用的农户高1188.77~1368.55 kg,并延长农户玉米储存时间0.2个季度;②采用仓类设施显著减轻玉米储存过程中的鼠害,使玉米储存损失数量降低60%,减少的损失使农民平均节约玉米28~33 kg,玉米储存损失率由2.75%下降到0.87%。因此,国家应继续实施科学储粮工程,鼓励更多的农户采用科学储粮设施,降低储粮损失。     

Relational effects on knowledge integration: the differential effects on search and transfer

The paper investigates the effect of homophily and status differences on knowledge integration among individuals involved in product development activities. By distinguishing between search and transfer as two integral parts of the knowledge integration process, the paper addresses the question of how cognitive and motivational barriers to knowledge integration operate differently through the search and the transfer processes respectively. A study of 434 knowledge integration activities among 49 participants in four software development teams suggests that while search is directed both by homophily and by status differences among team participants, only status differences affect the perceived value of knowledge transfer activities. Further, the study indicates that there is not necessarily a correspondence between the status cues that direct search activities and the status cues that drive the perceived value of knowledge transfer activities among team participants.     

基于Lagrangian松弛和Benders分解法的不同渗透率下电网投资运营策略研究

为探讨不同可再生能源渗透情形下的电网投资、再调度与可再生能源(renewable energy source,RES)削减需求,提出一种连续的电力市场、网络模拟方法。市场模拟代表电力交易日前市场每小时的市场清算过程,网络仿真代表了输电系统在确定常规电厂的最优再调度命令和RES的削减命令时所起的作用。通过市场模拟和网络模拟分别迭代计算成本效益和输电网投资需求。此外,利用Benders分解技术和增广拉格朗日松弛法求解目标年的优化问题。最终通过算例分析验证所提方法的有效性。     

Zoom in on DNA Cleavage by Cas9

<正>CRISPR-Cas system is an adaptive immune system of bacteria and archaea to prevent against the foreign nucleic acids. Cas9, the signature Cas protein in type II CRISPR-Cas system, is an RNAguided DNA endonuclease. Cas9 cleaves target ds DNA via its Ruv C and HNH domains, and it is widely used for genome engineering applications.     

Non-coding RNAs and DNA methylation in plants

Cytosine DNA methylation is an epigenetic modiication in eukaryotes that maintains genome integrity and regulates gene expression. he DNA methylation paterns in plants are more complex than those in animals,and plants and animals have common as well as distinct pathways in regulating DNA methylation. Recent studies involving genetic, molecular, biochemical and genomic approaches have greatly expanded our knowledge of DNA methylation in plants. he roles of many proteins as well as non-coding RNAs in DNA methylation have been uncovered.     

产业集群中的知识溢出及其效应研究

从知识的溢出、知识溢出的吸收与转化、知识的再扩散三个阶段分析集群中的知识溢出机理。在此基础上,分析知识溢出的创新提升效应:降低创新成本与风险、提升创新效率,整体提高知识积累水平、激发集群内部的创新活动,激活集群内部的默会性知识、形成独特的创新优势。     

Technological and non-technological innovation effects on firm performance

The effects of technological and non-technological innovation affecting firm performance are investigated. Technological innovation involves new product development, while non-technological innovation involves strategy and leadership, culture and climate, innovation and collaboration, and organizational and environmental evolution. 342 firms participated in the research; thirteen hypotheses are tested; eleven are significant. Demographic analyses on job roles, firm types, industry groupings and firm size are also conducted. The majority of the demographic factors were not significant. However a small number of significant results are confirmed. Structural equation modelling is used to test the model. Important lessons for managers and future research areas are suggested.     

DNA计算在信息安全领域的影响与应用

基于DNA纳米技术的各种超分子体(功能单元),能实现信息存储、计算、移动和靶向送药等功能,其纳米结构的控制精度达到了原子级。基于DNA纳米技术的信息存储和计算模式,具有高度并行性、高密度和低能耗,天生适用于大量信息的存储和并行处理。面对这种新兴的计算模式,人们研究和开发了各种计算模型,讨论其对传统密码体系的影响和DNA存储信息的安全问题,包括密钥搜索、信息加密、信息隐藏及认证等。文章综述了基于DNA纳米技术的各种计算模型对传统加密算法的影响,概述了利用DNA纳米技术进行加密解密、认证签名的方案和技术,总结了当前基于DNA纳米技术的信息安全领域研究中存在的问题并展望了DNA计算及其在信息安全和存储领域的应用前景。     

中国人口年龄结构对碳排放的影响

近年来,将人口年龄结构作为温室气体排放驱动因素的研究很少,已有的研究也只是将人口年龄做简单分类,由此导致对年龄结构影响碳排放的考察不够深入和具体。本文细化了人口年龄结构,将人口年龄划分为0~14岁、15~29岁、30~44岁、45~59岁和60岁及以上五个组别,并基于扩展的随机STIRPAT模型考察了人口年龄结构对碳排放的影响,以达到更好地解释人口年龄结构对中国碳排放影响机制的目的。研究结果表明,人口年龄结构对碳排放影响显著。不同年龄人口所占比重不同,对碳排放影响不同。其中,30~44岁人口对碳排放的影响最大,15~29岁人口的影响不显著,60岁及以上人口比重对碳排放的影响为负。分析还表明,随着中国老龄化进程的加快,无论从生产还是消费渠道看,未来中国人口年龄结构变化都有减缓碳排放加速的可能。本文最后提出了从消费渠道降低碳排放的对策建议。     

科技成果价值的分析及对评估的影响

当前 ,科学技术发展的重要标志是科学技术日益成为生产力发展的主导因素 ,同时又是生产力体系中其他重大变化的起点。而科技成果的价值怎样体现又如何评估 ,是当前科技界和产业界关注的问题。本文分析了科技成果价值的科学性、经济性和社会性 ,科技成果价值在时间和空间上的表现。以及这些因素和科技成果评估者对科技成果价值评估的影响。     

Radioprotective effects of ocimum flavonoids on leukocyte oxidants and antioxidants in oral cancer

Oxidants (NADPH oxidase and myeloperoxidase) and antioxidants (GSH,GSH peroxidase, SOD and glucose 6 phosphate dehydrogenase, that provides NADPH for antioxidants) were assayed in the neutrophils from oral cancer patients, in three stages viz, baseline samples,15 days after radiation and 30 days following radiation. These samples were obtained from 2 groups of patients. Group A that received radiation alone and Group B that received radiation and ocimum flavonoids,a radioprotector. The results showed a significant fall in the SOD levels in the second follow up of group B.Glucose 6 phosphate dehydrogenase showed significant increase only in the first follow up of patients who received Ocimum flavonoids. Except for these findings all other parameters remained statistically nonsignificant.