Biologically-generated primer for PCR: PCR primer of unknown sequence.

We describe a method for producing specific PCR primers directly from PCR product, bypassing the usual need to know the primer sequence. Lack of abundance of primers derived from a PCR product is compensated for by the incorporation of an arbitrary 5'TAG sequence which acts as a surrogate template target for the bulk amplification phase. We use the technique to amplify clonospecific rearranged immunoglobulin genes, which have applications as markers of lymphoid neoplasms for tracing the success of therapy. The principle may have wider application wherever conserved and variable regions of DNA are juxtaposed.     

A prion primer

By biological and medical criteria, prions are infectious agents; however, many of their properties differ profoundly from those of conventional microbes. Prions are "encoded" by alterations in protein conformation rather than in nucleic acid or amino acid sequence. New epidemic prion diseases (bovine spongiform encephalopathy and new variant Creutzfeldt-Jakob disease) have recently emerged under the active surveillance of the modern world. The risk of contracting prion disease from blood products or other biologicals is now a focus of worldwide concern. Much has been discovered about prions and prion diseases, but much remains to be done.     

On the mechanism of the modular primer effect.

Modular primers are strings of three contiguously annealed unligated oligonucleotides (modules) as short as 5- or 6-mers, selected from a presynthesized library. It was previously found that such strings can prime DNA sequencing reactions specifically, thus eliminating the need for the primer synthesis step in DNA sequencing by primer walking. It has remained largely a mystery why modular primers prime uniquely, while a single module, used alone in the same conditions, often shows alternative priming of comparable strength. In a puzzling way, the single module, even in a large excess over the template, no longer primes at the alternative sites, when modules with which it can form a contiguous string are also present. Here we describe experiments indicating that this phenomenon cannot be explained by cooperative annealing of the modules to the template. Instead, the mechanism seems to involve competition between different primers for the available polymerase. In this competition, the polymerase is preferentially engaged by longer primers, whether modular or conventional, at the expense of shorter primers, even though the latter can otherwise prime with similar or occasionally higher efficiency.     

Retinal vasculitis--a primer.

Retinal vasculitis is a diagnosis that is generally suggested by an ophthalmologist. Frequently patients with the disorder are referred to nonophthalmologists for further diagnostic evaluation or treatment. The criteria for defining vasculitis differ greatly between ophthalmologists and other physicians. To facilitate collaboration between ophthalmologists and their colleagues, we have sought to clarify the term "retinal vasculitis" by discussing its subcategories, the potential role of antiphospholipid antibodies, and the etiology of retinal vasculitis. We offer guidelines for evaluating the disorder and treating patients.     

Efficient primer design algorithms

MOTIVATION: Primer design involves various parameters such as string-based alignment scores, melting temperature, primer length and GC content. This entails a design approach from multicriteria decision making. Values of some of the criteria are easy to compute while others require intense calculations. RESULTS: The reference point method was found to be tractable for trading-off between deviations from ideal values of all the criteria. Some criteria computations are based on dynamic programs with value iteration whose run time can be bounded by a low-degree polynomial. For designing standard PCR primers, the scheme offers in a relative gain in computing speed of up to 50: 1 over ad-hoc computational methods. Single PCR primer pairs have been used as model systems in order to simplify the quantization of the computational acceleration factors. The program has been structured so as to facilitate the analysis of large numbers of primer pairs with minor modifications. The scheme significantly increases primer design throughput which in turn facilitates the use of oligonucleotides in a wide range of applications including: multiplex PCR and other nucleic acid-based amplification systems, as well as in zip code targeting, oligonucleotide microarrays and nucleic acid-based nanoengineering.     

特异性单引物PCR

建立特异性单引物PCR,并用于筛选基因克隆重组子。根据α－globin的一段序列设计引物,按照设计好的特性单引物PCR扩增条有α－globin的重组质粒PLNSX－aglobin,具体扩增条件如下：（1）97℃5min变性后,94℃30s,70℃2min30s,30个循环,制备单链模板;（2）94℃1min,12℃5min,16℃3min,18℃3min,20℃3min,22℃3min,25℃1min,30℃3min,37℃3min,72℃6min,低温条件下引物3′端4－5个碱基与所扩单链模板退火配对,扩增得到一系列不同起始位点但同一序列末端长短一的核酸片段;（3）以上述所得片段为模版进行如下条件的扩增：94℃30min,70℃2min,70℃2min,72℃2min,每个循环增加1s）,45个循环。结果,特异性单引物PCR能够从pLNSX－αglobin上扩增出特异带,可有效用于筛选基因克隆重组子。     

Protein sulfation analysis--A primer

The aim of this review is to present an overview of protein sulfation in the context of 'modificomics', i.e. post-translational modification-specific proteome research. In addition to a short introduction to the biology of protein sulfation (part 1), we will provide detailed discussion regarding (i) methods and tools for prediction of protein tyrosine sulfation sites (part 2), (ii) biochemical techniques used for protein sulfation analysis (part 3.1), and (iii) mass spectrometric strategies and methods applied to protein sulfation analysis (part 3.2). We will highlight strengths and limitations of different strategies and approaches (including references), providing a primer for newcomers to protein sulfation analysis.     

A primer of community ecology using the R language

Community ecology beginners often struggle to understand theories expressed in complex mathematical formulas and to master computer programming. To remedy this situation, this article provides a practical, R-based introduction to community ecology by illustrating core concepts (vital rates, carrying capacity, and density dependence) and models that can be used to explore the patterns of species abundance and diversity. The structure of this article consists of three modeling exercises, each asking a general question that can be answered by a combination of theory and R programming: (1) what determines the abundance of species, and what makes a population persist and go extinct?; (2) what determines the distribution of species and species diversity?; (3) what determines the relative abundance of species and what allows species to coexist? Through the exercises, I discuss the following five concepts and ideas that provide valuable insights into the questions: (i) the tragedy of the commons, (ii) the theory of island biogeography, (iii) competitive exclusion, (iv) the neutral theory of biodiversity, and (v) frequency dependence. These materials are thus designed to guide the reader in developing an intuition for ecological thinking that will help capture the essence of the global environmental and biodiversity crisis. Although this article does not delineate the scope and depth of the vast field of community ecology, I hope that it will motivate the reader to step up to a more formal introduction to community ecology.     

Claude Bernard: primer of the second biomedical revolution

Claude Bernard, the son of a Beaujolais winegrower, moved to Paris to pursue his literary ambitions and went on to become one of the fathers of modern life sciences. What did Bernard do to earn universal renown? And are his teachings relevant to modern science?     

Olga--oligonucleotide primer design program for the Atari ST

A program to facilitate the design of oligonucleotide primnershas been devised. Olga is written in draft ANSI standard ‘C’and makes use of the implementation of Digital Research GEM(Graphics Environment Manager) on the Atari ST Olga is specificallysuited to the polymnerase chain reaction (PCR) allowing si analysisof two primer sequences. The advantage of Olga is that it providesin one program analyses for direct repeats, secondary structuresand primer dimerization as well as several useful ‘finishing’tools for workers engaged in PCR optimization and oligonucleotidesyntheses.     

Specific primer design for the polymerase chain reaction

The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and characteristics for PCR primer design. Recent primer design tools based on Primer3, along with several computational intelligence-based primer design methods which have been applied in primer design, are also reviewed. In addition, characteristics of population-based methods used in primer design are discussed in detail.