FWD: black hole from baidu

I searched some knowledge about the black hole in chinese from baidu

http://baike.baidu.com/view/863.htm


黑洞是一种引力极强的天体，就连光也不能逃脱。当恒星的史瓦西半径小到一定程度时，就连垂直表面发射的光都无法逃逸了。这时恒星就变成了黑洞。说它“黑”，是指它就像宇宙中的无底洞，任何物质一旦掉进去，“似乎”就再不能逃出。由于黑洞中的光无法逃逸，所以我们无法直接观测到黑洞。然而，可以通过测量它对周围天体的作用和影响来间接观测或推测到它的存在。黑洞引申义为无法摆脱的境遇。2011年12月，天文学家首次观测到黑洞“捕捉”星云的过程


information in English from wiki


http://en.wikipedia.org/wiki/Black_hole




A black hole is a region of spacetime from which nothing, not even light, can escape.[1] The theory of general relativity predicts that a sufficiently compact mass will deform spacetime to form a black hole. Around a black hole there is a mathematically defined surface called anevent horizon that marks the point of no return. It is called "black" because it absorbs all the light that hits the horizon, reflecting nothing, just like a perfect black body inthermodynamics.[2] Quantum mechanics predicts that black holes emit radiation like a black body with a finite temperature. This temperature is inversely proportional to the mass of the black hole, making it difficult to observe this radiation for black holes of stellar mass or greater.

Objects whose gravity field is too strong for light to escape were first considered in the 18th century by John Michell and Pierre-Simon Laplace. The first modern solution of general relativity that would characterize a black hole was found by Karl Schwarzschild in 1916, although its interpretation as a region of space from which nothing can escape was not fully appreciated for another four decades. Long considered a mathematical curiosity, it was during the 1960s that theoretical work showed black holes were a generic prediction of general relativity. The discovery of neutron stars sparked interest in gravitationally collapsedcompact objects as a possible astrophysical reality.

Black holes of stellar mass are expected to form when very massive stars collapse at the end of their life cycle. After a black hole has formed it can continue to grow by absorbing mass from its surroundings. By absorbing other stars and merging with other black holes, supermassive black holes of millions of solar masses may form. There is general consensus that supermassive black holes exist in the centers of most galaxies. In particular, there is strong evidence of a black hole of more than 4 million solar masses at the center of our galaxy, the Milky Way.

Despite its invisible interior, the presence of a black hole can be inferred through its interaction with other matter and with light and other electromagnetic radiation. From stellar movement, the mass and location of an invisible companion object can be calculated; in a number of cases the only known object capable of meeting these criteria is a black hole. Astronomers have identified numerous stellar black hole candidates in binary systems by studying the movement of their companion stars in this way.

black hole

Today, just discussed with my college about the black hole. I just know there is black hole, but nothing more. there are so many interesting thing I don't know.maybe this is the reason I like to do research ,because I don't know ,after I know something, I realize there are more things I don't know.this is the process of learn.maybe.

龙年大吉

Happy Chinese new year!龙年大吉！！

Derived Cleaved Amplified Polymorphic Sequences (dCAPS)

FROM NCBI

Introduction

The Derived Cleaved Amplified Polymorphic Sequences (dCAPS) assay is a modification of CAPS (or alternatively, PCR-RFLP) technique for detection of Single Nucleotide Polymorphisms (SNPs). In dCAPS assay a mismatches in PCR primer are used to create restriction endonuclease (RE)-sensitive polymorphism based on the target mutation. This technique is useful for genotyping known mutations and genetic mapping of isolated DNAs.

Similar to the CAPS technique, this method is simple, relatively inexpensive, and uses the ubiquitous technologies of PCR, restriction digestion and standard agarose gel electrophoresis

How It Works


The dCAPS technique introduces or destroys a restriction enzyme recognition sites by using primers that containing one or more micmatches to the template DNA. The PCR product modified in this manner is then subjected to restriction enzyme digestion and the presence or absence of the SNP is determined by the resulting restriction pattern.

Applications of dCAPS primers


To create a restriciton site that is dependent on the presence or absence of the SNP allele in question
To introduce a specific restriction site for each of two alleles being analyzed, to positively identify homozygotes for a particular allele without the possibbility of mis-scoring due to partial restriciton enzyme digestion
To disrupt an additional restriction site situated in close proximity to the CAPS polymorphism to be analyzed

REF：
Neff MM, Neff JD, Chory J, Pepper AE. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J. 1998 May;14(3):387-92. PMID: 9628033


http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechDCAPS.shtml

Perfect overlap PCR protocol from Nature

Perfect overlap PCR protocol from Nature


Nature Protocols 2, -924 - 932 (2007) 

Gene splicing and mutagenesis by PCR-driven overlap extension

Karin L Heckman¹ & Larry R Pease¹

ABSTRACT

Extension of overlapping gene segments by PCR is a simple, versatile technique for site-directed mutagenesis and gene splicing. Initial PCRs generate overlapping gene segments that are then used as template DNA for another PCR to create a full-length product. Internal primers generate overlapping, complementary 3′ ends on the intermediate segments and introduce nucleotide substitutions, insertions or deletions for site-directed mutagenesis, or for gene splicing, encode the nucleotides found at the junction of adjoining gene segments. Overlapping strands of these intermediate products hybridize at this 3′ region in a subsequent PCR and are extended to generate the full-length product amplified by flanking primers that can include restriction enzyme sites for inserting the product into an expression vector for cloning purposes. The highly efficient generation of mutant or chimeric genes by this method can easily be accomplished with standard laboratory reagents in approximately 1 week.

Fulltext 

http://www.nature.com/nprot/journal/v2/n4/full/nprot.2007.132.html

JUST ORDERED TWO BOOKS FROM AMAZON

I JUST SENT MY ORDER TO AMAZON. I ORDERED THE BOOK MOLECULARBIOLOGY OF THE CELL AND BIOCHEMISTRY. Try to learn hard..........

Phylogenetic Analysis by Maximum Likelihood (PAML)

Introduction

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.

This document is about downloading and compiling PAML and getting started. See the manual for more information about running programs in the package.

PAML Resources on the web

• PAML discussion group (Old posts are at the Genetics Software Forum)
• Redhat linux rpm in the Biorpms repository
• ML estimation of dN and dS on the web
• Joe Bielawski provided a PAML demo. See the data files and demo for the book chapter by Bielawski & Yang, 2005.
• A step-by-step manual for MCMCtree with an example dataset (MCMCtree.example.tgz) (the manual in English, Japanese, and Chinese)

Download page

Disscussion forum

Fungi Experimental Methods in Biology

Fungi Experimental Methods in Biology

Book Description

ISBN-10: 1574444689 | ISBN-13: 978-1574444681 | Publication Date: June 23, 2005 | Edition: 1

Today’s accelerated pace of research, aided by new instruments and techniques that combine the approaches of genetics, biochemistry, and cell biology, has changed the character of mycology. A new approach is necessary for the organization and study of fungi.
Fungi: Experimental Methods in Biology presents the latest information in fungal biology generated through the application of genetics, molecular biology, and biochemistry. This book analyzes information derived through real experiments, and focuses on unresolved questions in the field. Divided into six sections comprising 14 chapters, the text describes the special features of fungi, interactions of fungi with other organisms, model fungi in research, gene manipulation, adaptations, and natural populations.
Each chapter is self-contained and written in a style that enables the reader to progress from elementary concepts to advanced research, benefiting both beginning research workers and experienced professionals. A comprehensive appendix covers the principles in naming fungi and discusses their broad classification.

Download this book

Fungal biology 4th Edition

 Fungal biology 4th Edition
J. W. Deacon

"Fungal Biology" is the fully updated new edition of this undergraduate text, covering all major areas of fungal biology and providing insights into many topical areas such as:
fungal ultrastructure and the mechanisms of fungal growth
important fungal metabolites, including antibiotics, mycotoxins and immunosuppressants
the molecular techniques used to study fungal populations
fungal genetics and fungal genomes
the significance of fungi in mutualistic and pathogenic interactions
the major methods for controlling fungi, including the fungi that cause diseases of humans and the antifungal drugs used to treat these infections

This edition also focuses on the interactions of fungi that form the basis for developing biological control agents, with several commercial examples of the control of insect pests and plant diseases.

The text is illustrated with many diagrams and tables that summarize key points, and with many high-quality images (available in color to download free via www.blackwellpublishing.com/deacon and for instructors on CD-ROM).

The emphasis throughout is on the functional biology of fungi, with several examples from recent research. The book also includes a clear illustrative account of the features and significance of the main fungal groups.

作者简介 (2006)

Jim Deacon is Senior Lecturer in Microbiology at the University of Edinburgh, and has 35 years of teaching experience in the field of plant–microbe–fungal interactions. He has published over 100 scientific papers in peer-reviewed journals, been an invited keynote speaker at international symposia and congresses around the world, and acted as consultant to biotechnology companies.

URL:

GOOGLE

DOWNLOAD THIS BOOK

Vector NTI® Software

Vector NTI^® software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publicize diverse types of molecular biology data, all within one graphically rich analysis environment. Vector NTI^®Software allows you to:

• Curate—store and manage collections, visualize maps, and search sequences
• Discover—analyze, compare, and contrast sequences
• Design—cloning strategy; primers for PCR, cloning, and
  resequencing; and gel simulations of sequences
• Confirm—contig assembly, sequence validation, and
  literature validation

Watch Vector NTI Advance® in Action!

What is Vector NTI Advance® Software?

Vector NTI Advance® 11.5—The Industry Standard for Sequence Analysis

Vector NTI Advance® offers unparalleled, multi-modular, integrated sequence analysis and data management tools. The software contains a comprehensive set of data analysis and management tools, implemented across five application modules.

For Mac users, Vector NTI Advance® 11.5 can be run using Parallels Desktop® and on Windows® XP Pro on Intel®-based Macs. For PC users, Vector NTI Advance® runs on Windows® 7, Windows Vista®, and XP Pro operating systems, including in Japanese language editions.

Vector NTI®                   Sequence analysis, annotation, and illustration; restriction mapping; recombinant molecule design, including Gateway® and TOPO® cloning; in silico gel electrophoresis; synthetic biology workflows support and data management ContigExpress®                   DNA sequence assembly and editing, contig building, SNP and mutation detection, genotype analysis Chromatogram data analysis and editing; consensus creation using Quality Values Automatic sequence trimming, vector contamination trimming BioAnnotator™                   Protein motif mapping and annotation using Pfam, PROSITE, BLOCKS motif databases Physiochemical analyses of DNA sequences		AlignX®                   Multiple sequence alignment of proteins and DNAs Alignment statistics, cladograms, alignment editing, annotation, repeat identification, etc. GenomBench™                   Visualization and analysis of megabase-sized genomic DNA fragments from numerous DAS servers Chromosomal views, cDNA-to-gene alignment, intron-exon boundary mapping, annotation

For a detailed summary of Vector NTI Advance® key applications, click here.

The Vector NTI® multi-modular, integrated sequence analysis and data management tools enable seamless workflows.

Cloning Tools

	Clone2Seq™ is designed for those who already know how they wish to recombine two restriction fragments, e.g., cloning a BamHI-EcoRI insert into an appropriately digested vector. The interface makes it easy to select molecules and fragments for cloning, to modify fragment ends for compatibility (if necessary), and to create the desired recombinant, whether circular or linear. Despite the simplicity of the workflow, Clone2Seq™ retains all the power of the cloning functionality in Vector NTI Advance®, including our renowned graphical map creation and parent-descendant lineage tracking.
	VectorSelector™ enables you to search for cloning vectors based on eight different criteria such as one or two different restriction sites, with annotated coding DNA sequence (CDS) features that confer drug resistance, by linear or circular form and by having specific attB sites that are used in Gateway® cloning. Results are captured in a spreadsheet-style format, and any group of results can be saved to a subset in the Local Database. Any individual search result can be opened in the Molecule Viewer or even sent to Clone2Seq™ for use in a rapid cloning experiment.
	Gene Synthesis with ReGENerator™ allows you to design specific DNAs in silico. Start with your protein sequence, and if required, mutate it by substituting, adding, or deleting amino acids by simply typing in new resides. Any number and type of mutation can be made in this step. Choose a codon-usage table that best reflects your experimental expression system, and ReGENerator™ will calculate a DNA sequence that encodes your desired protein. You can add any number of flanking sequences to the 5′ and 3′ ends of the newly-created DNA—such as restriction sites, Gateway® cloning sites, and expression or purification tags. With the simple click of a button you'll be directed to the GENEART website for the best products and services in gene synthesis.

Robust Data Management and Usability

Vector NTI Advance® software includes the Vector NTI® Local Database, to help you store and manage many types of molecular biology data. The local database allows sophisticated levels of integration of analysis tools and raw data. You can also store the results of many analyses in the database as well.

Vector NTI Advance® uses open file format to manage the molecule data, meaning all data files for storage and export are all readable by a text editor (e.g., Microsoft Windows® Notepad). Unlike other programs of this type that use a proprietary data format that locks users into a single software solution, Vector NTI Advance® allows the data files to be openly exchangeable.

In a world with growing global collaboration, we believe open data exchange is critical for success. Even if you cease using Vector NTI®, you are assured that your data remains accessible to you and can be imported to a different software program of your choice.

Find out how easy it is using Notepad to take a look at the sequences and molecule descriptions in the database folder of Vector NTI (C:\Vector NTI Database) by opening up the .mol, .seq, and .ma4 files upon which the database is built.

Vector NTI^® Express

Completely redesigned to be faster, more intuitive and with a dedicated Mac OS® X version Vector NTI® Express Software retains the core, trusted tools of Vector NTI Advance®Software with a brand new interface. Built on a new platform, Vector NTI® Express Software supports the future of bioinformatics and synthetic biology with a plug-in architecture to consistently deliver new tools and functionality.

What's New in Vector NTI® Express Software

Performing multiple sequence alignments with the new interface of Vector NTI^® Express

Click to enlarge and see a full-screen view.

• Brand New Interface. Find and use tools quickly and easily with an intuitive and streamlined interface. Vector NTI^® Express introduces an internet browser-like functionality to switch between projects in a tabular view.

• Dedicated Mac OS^® X Support. Vector NTI^® Express runs on Mac OS^® X without the need for emulation solutions. Windows^® 7 and Windows^® XP operating systems are also supported.

• Plug-In Architecture. New Bioinformatics tools from Life Technologies will be delivered seamlessly through automatic updates to the existing software. Vector NTI^® Express will check for these new tools automatically in addition to refinements to existing tools so you can have full confidence your software is up to date. Vector NTI^® Expresswill check for these new tools automatically in addition to refinements to existing tools so you can have full confidence your software is up to date.

Prescribed workflows make projects such as Contig-Assembly and Gateway^®cloning easy to perform, step-by-step.

Click to enlarge and see a full-screen view.

• Prescribed Workflows. Projects such as Contig-assembly and Gateway^® and TOPO^® cloning are now performed in a step-by-step workflow. Quickly identify suitable Gateway^® or TOPO^® vectors from your library and build your clones with ease.

• Next-Generation Sequencing (NGS) Support. Bam File outputs from NGS platforms such as Ion Torrent PGM™, SOLiD^®, and Illumina^®HiSeq^® platforms that have been processed into FASTA File format (we recommend tools such as SAM tools and Picard) can be read into Vector NTI^® Express for analysis.

• EMBOSS Algorithms. Standards-Based Bioinformatics Algorithms, Import Support for Analysis File Types (BED, GFF, GTF), Compare Annotation on a Genome—Multi-Track Analysis (Gene, Promoter, Multiple Splice Variants, Transcript, Protein, and Terminator), and intersections to create new annotations.

• Molecule Relationships. New tools for studying DNA-protein relationships, including translation, reverse-translation, and codon optimization.

URL：

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/vector-nti-software.html


也许你对这个软件也感兴趣，这个网址可能对你有用： 下载地址

PCR Overlap Extension

This protocol from internet, it looks very good. here are some comments from me :)
4.2, I have used phusion, there is no problem for fragment under 3kb. I don't know why the author state this, I am not sure the reason. but one good point if you don't use phusion, is that you can do TA cloning after purification.

Overview

Create long DNA fragments from shorter ones. This method is also called "Splicing by Overlap Extension" or SOEing.

Procedure

1. Design Primers:
   1. These primers are like bridges between the two parts you want to assemble together.
   2. You will order two primers which are complements of one another.
   3. These primers will each have a 60°C Tm with one part and a 60°C Tm with the other part.
   4. The "end primers" will not have any complements and will likely only have restriction sites.
2. "Extension PCR" PCR amplify the necessary fragments separately
   1. Use a proofreading polymerase enzyme.
   2. Use an annealing temp of 60°C.
3. Clean up the product using a DNA column.
4. "Overlap PCR" Use cleaned up fragments as template in a PCR reaction:
   1. About 1/2 to 3/4 volume of the Overlap PCR reaction should be equimolar amounts of purified fragments.
   2. Do not use Phusion polymerase. Try Pfu Turbo.
   3. Do not add any primers; the templates will prime each-other.
   4. Run 15 PCR cycles without primers.
   5. Use an annealing temp of 60°C.
5. "Purification PCR" Add end primers to the Overlap PCR reaction:
   1. Continue cycling for another 15-20 rounds.
   2. Use an annealing temp of 72°C
6. Gel extract the correct size fragment.
7. Clone into the desired vector.
1. Digest
2. Ligate
3. Transform
4. Select
5. Sequence

From:    http://openwetware.org/wiki/PCR_Overlap_Extension