基于PC/Linux蛋白序列分析系统的构建及应用

介绍利用常见的x86PC,Linux操作系统配合BLAST、PHYLIB和EMBOSS等常见的生物分析软件构建可以完成多种蛋白数据分析的大规模自动分析系统。该系统可自动完成从DNA序列中获取读码框、核酸序列向蛋白序列的转化、在蛋白序列数据库中查找同源序列、序列录入数据库以及蛋白序列的等电点、亲 疏水位点、二级结构等性质的分析、多个序列之间相似度和进化地位的分析,并对输出的结果数据利用Web服务器进行发布。与传统的序列分析模式相比,此分析系统大大加速了对大规模数据信息的分析和利用。

EMBOSS软件包序列分析程序应用实例

本文介绍欧洲分子生物学开放软件包EMBOSS序列分析程序应用实例。第1节简单介绍EMBOSS软件包的概况和基本用法。第2节介绍格式转换、序列提取、序列变换和序列显示等常用序列处理程序。第3节介绍序列比对程序,包括双序列比对、多序列比对和点阵图程序。第4节介绍常用核酸序列分析程序,可用于核苷酸组分统计、开放读码框分析、CpG岛识别、密码子使用统计和重复序列寻找等。第5节介绍常用蛋白质序列分析程序,包括氨基酸组分统计、序列特征位点识别、二级结构分析等。文中结合教学实例,选择部分常用程序,给出具体运行方式,并扼要说明分析结果的生物学意义。文末对程序运行过程中需要注意的地方加以讨论,并用表格列出部分常用程序的名称和用途,以便读者查阅。

EMBOSS和EMBnet

笔者撰写的“EMBOSS软件包序列分析程序实例”一文,已经在《生物信息学》期刊2021年第19卷第1期发表。此文介绍欧洲分子生物学开放软件包(European Molecular Biology Open Software Suite,EMBOSS)。EMBOSS是欧洲分子生物学网络组织(European Molecular Biology Network,EMBnet)于上世纪九十年代末启动的以欧洲国家为主的国际合作项目,是生物信息学领域中较早投入使用的大型开源软件包。本文基于笔者亲身经历,回顾EMBOSS项目的来龙去脉,讲述EMBnet三十多年来的发展历程,及其对生物信息开发、服务和教育培训等方面的贡献,从某个侧面为读者特别是年轻读者展示生物信息学发展早期的一段历史。

生物信息处理中心的建立

本文提出了一套生物信息处理中心的建立方案,具有实用、建设成本低廉、构建方便、全面共享和可扩展性强等特点。生物信息处理中心以数据库相似性搜索、数据库资源检索和生物序列分析为主线,建立了软硬件环境和应用程序及数据库,能够满足绝大多数科研人员的生物信息学分析需求。

EXPERIMENTAL STUDY ON THE HOT EMBOSSING POLYMER MICROFLUIDIC CHIP

Experiments are used to study the fabrication of polymer microfluidic chip with hot embossing method. The pattern fidelity with respect to the process parameters is analyzed. Experiment results show that the relationship between the imprint temperature and the microchannel width is approximately exponential. However, the depth of micro channel isn＇t sensitive to the imprint temperature. When the imprint pressure is larger than 1 MPa and the imprint time is longer than 2 min, the increasing of imprint pressure and holding time has little impact on the microchannel width. So over long holding time is not needed in hot embossing. Based on the experiment analysis, a series of optimization process parameters is obtained and a fine microfluidic chip is fabricated. The electrophoresis separation experiment are used to verify the microfluidic chip performance after bonding. The results show that 100bp-ladder DNA sample can be separated in less than 5 min successfully.

HOT EMBOSSING METHODS FOR PLASTIC MICROCHANNEL FABRICATION

Fabrication of microchannels on polymethylmethacrylate （PMMA） substrates using novel microfabrication methods is demonstrated. The image of microchannels is transferred from a silicon master possessing the inverse image of the microchannel to a PMMA plate by using hot embossing methods. The silicon master is electrostatically bonded to a Pyrex 7740 glass wafer, which improves the device yield from about 20 devices to hundreds of devices per master. Effects of embossing temperature, pressure and time on the accuracy of replication are systematically studied using the orthogonal factorial design. According to the suggested experimental model, the time for the whole embossing procedure is shorten from about 20 min to 6 min, and the accuracy of replication is 99.3%. The reproducibility of the hot embossing method is evaluated using 10 channels on different microfluidic devices, with variations of 1.4 % in depth and 1.8% in width.

A Transparent Polyimide Film as a Biological Cell Culture Sheet with Microstructures

The research on stem cell cultures has attracted much attention due to the recent development of regenerative medicine. Therefore, higher functionalities for devices used for culturing cells are strongly demanded. In this study, we fabricated cell culture sheets using transparent polyimide (PI), parylene (PA), and polyetheretherketone (PEEK) to make polymer materials that had microstructures. We then cultured stromal marrow cells (OP9) on them and investigated the cell alignment within the microstructures. Hot embossing was used to fabricate the microstructures with a width and depth of 5 μm on the polymer substrates. Cultivation of the cells was confirmed on the transparent PI and PA sheets, however, it was not observed on the PEEK sheet. Slight alignment of the cells was also observed along with the microstructures.

OPTIMUM DESIGN OF PROCESSING CONDITION AND EXPERIMENTAL INVESTIGATION OF GRATING FABRICATION WITH HOT EMBOSSING LITHOGRAPHY

The cross-section profiles of polymer deformation in the hot embossing lithography process were studied by finite element method for various temperature, time and pressure. In order to successfully fabricate high-frequency grating lines, an optimal imprint condition was selected and the related experiments were carried out. The fabricated gratings were illuminated by the SEM image and AFM analysis, which agree well with the simulated results. Therefore, the finite element methods are helpful for a better comprehension of the polymer flow phenomena governing the pattern definition and the design of optimum processing conditions for successful grating fabrication.

A novel method to mass-produce PDMS stamps based on nanoimprint

Soft lithography is a low-cost and convenient method for the forming and manufacturing of micro/ nanostructures compared to the traditional optical lithography. In soft lithography, poly（dimethylsiloxane） （PDMS） stamps with relief structures have been widely used to transfer patterns. The traditional fabrication approach of PDMS stamps is time-consuming since the master has been occupied during the curing process. By adding and repeating fast nanoimprint step, many intermediate polymeric molds can be produced from the master and these molds can then be employed to replicate more PDMS stamps while the time used is close to that of the common way. We demonstrated this idea by three masters which were made by the DEM （Deepetching, Electroforming and Microreplicating） and FIB （Focused Ion Beam） techniques. The photos show that the patterns on the PMDS stamps successfully duplicated patterns on the origin masters.

Hot embossing of micro energy director for micro polymer fusion ultrasonic bonding

In order to use micro ultrasonic bonding technique to package polymer microfluidic chips, an auxiliary microstructure named micro energy director is designed and fabricated. The hot embossing process for PMMA （ polymethyl methacrylate） substrates with both concave micro channel and convex micro energy director for ultrasonic bonding is studied. The embossing processes with different embossing temperatures are simulated using Finite Element Method （FEM）. The optimized parameters are： the embossing temperature of 135 ℃ , holding time of 200 s, and the embossing pressure of 1.65 MPa. The experimental results show that the replication error between experiments and simulations is less than 2% and the replication accuracy of the microstrueture is more than 96%. The study offers a method for quick optimizing parameters for hot embossing both concave and convex microstructures.

A Novel Extrusion Microns Embossing Method of Polymer Film

A continuous hot embossing method is reported in this paper. The continuous means that the extruder and the hot embossing equipment is used in series, the polymer film is embossed after extrusion immediately. The basic principle of this method, the key design point and the corresponding operate process of the embossing equipment is described in this paper. The polymer diffuser with micro-lens matrix on its surface is designed and the optical properties are simulated. Then, the diffuser is fabricated by the embossing equipment. The optical properties of the diffuser are tested and compared with the results of the simulation to verify the reproducibility of the equipment. By this method, the diffuser with large area can be fabricated with high precision of graphic replication, high efficiency and low cost.

PRESSURE FORCE CONTROL FOR FABRICATION OF PLASTIC MICROFLUIDIC CHIPS WITH HOT EMBOSSING METHOD

A pressure force control system for hot embossing of microfluidic chips is designed with a moment motor and a ball bearing lead screw. Based on the numeric PID technique, the algorithm of pulsant integral accelerated PID control is presented and the negative effects of nonlinearity from friction, clearance and saturation are eliminated. In order to improve the quick-resixmse characteristic, independent thread technique is adopted. The method of pressure force control based on pulsant integral accelerated PID control and independent thread technique is applied with satisfactory control performance.

Hot-embossing fabrication of chalcogenide glasses rib waveguide for mid-infrared molecular sensing

Chalcogenide glasses have shown promise in fabricating mid infrared（MIR） photonic sensing devices due to their excellent optical properties in MIR. In addition, the glass transition temperature of chalcogenide glasses are generally low,making them ideal to create the high-throughput patterns of micro-scale structures based on hot embossing that is alternative to the standard lithographic technology. In this paper, we outline the research progress in the chalcogenide waveguide based on the hot embossing method, and discuss the problems remaining to be solved and the possible solutions.

Finite Element Analysis (FEA) and Thermal Gradient of a Solid Rectangular Fin with Embossing’s for Aerospace Applications

Fins are the extended surfaces through which heat transfer takes place by conduction and convection to keep the base surface cool. Fins of various configurations are presently used ranging from automobile engines to cooling of chip in a computer. Fins used presently are solid with different shapes but in the present research such solid fins are compared with solid fins having maximum of 10 numbers of embossing’s that further increases the surface area for maximum heat transfer. Importance in this research is given to variation of temperature along the length of the fins which in turn gives rate of heat transfer. Thus this research is under taken to increase the efficiency of fins (by extracting heat from the base surface) which is highly demanded today for air cooled engines, compressors, refrigerators etc. In the present research, SOLID70 element and SURF152 elements are used for FE analysis. Methodology involves 3D rectangular fin modelling and meshing, creation of surf elements for the modeling, applying the boundary conditions and source temperature, applying the material property (aluminum) to obtain the steady state thermal contours. FEA results are finally compared with analytic and experimental values for validity. In the present research, a solid rectangular aluminum fin and the same rectangular fin with 2, 4, 8 and 10 embossing’s were compared through finite element analysis for its temperature distribution along the length. FEA analysis of the present research showed that fins having embossing’s were more efficient compared to that a simple solid fin. Hence it is concluded from the present research that embossing’s at preferred locations further increases the rate of heat transfer. From the present analysis it is concluded that the mathematical and FEA for a solid rectangular fin without embossing’s are converging within ±1.2°C and rectangular fin with 10 embossing’s is converging within ±1.4°C and hence the validity.

凹印倒立字符改造

该文解决了DATACARD公司DC7000凸字/凹字模块一种特殊字符的打印需求。

High-fidelity replication of thermoplastic microneedles with open microfluidic channels

Development of microneedles for unskilled and painless collection of blood or drug delivery addresses the quality of healthcare through early intervention at point-of-care.Microneedles with submicron to millimeter features have been fabricated from materials such as metals,silicon,and polymers by subtractive machining or etching.However,to date,large-scale manufacture of hollow microneedles has been limited by the cost and complexity of microfabrication techniques.This paper reports a novel manufacturing method that may overcome the complexity of hollow microneedle fabrication.Prototype microneedles with open microfluidic channels are fabricated by laser stereolithography.Thermoplastic replicas are manufactured from these templates by soft-embossing with high fidelity at submicron resolution.The manufacturing advantages are(a)direct printing from computeraided design(CAD)drawing without the constraints imposed by subtractive machining or etching processes,(b)high-fidelity replication of prototype geometries with multiple reuses of elastomeric molds,(c)shorter manufacturing time compared to three-dimensional stereolithography,and(d)integration of microneedles with open-channel microfluidics.Future work will address development of open-channel microfluidics for drug delivery,fluid sampling and analysis.