A primer in epidemiologic methodology

Epidemiology is defined as the study of the distribution and determinants of disease within populations. In addition to the requirements for disease surveillance, epidemiologic methods have numerous applications in laboratory animal science and can reveal important insights into the multifactoral mechanisms of disease, thereby aiding in the design of optimized intervention strategies. Observational approaches to data collection can be used to quantify the role of causal factors under natural circumstances, complementing the value of experimental studies in this field. The meaning and appropriate use of standard measures of disease frequency and exposure-disease relationships are reviewed, along with explanations of bias and confounding. Recommendations for reporting the methods and findings from this type of work in comparative medicine literature are presented. Aspects of model-based approaches to data analysis are introduced, offering further opportunities for gaining needed information from epidemiologic study of problems in laboratory animal medicine and management.     

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.     

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.     

Releaser and primer pheromones in Collembola

In Collembola, pheromones appear to be present in the faecal pellets. Pheromone release after cessation of faeces production points to the digestive tract as a possible site of biosynthesis.During the pre-moulting periods Collembola do not react to pheromones, possibly due to their low activity at that time, whereas the production of the pheromones continues.Starvation periods of up to 14 days diminish pheromone release but do not cause complete cessation. Production per animal seems to decrease at increasing densities.The effect of pheromones on the reproductive efficiency of Collembola is discussed in the context of their physiological and behavioural ecology.     

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 on peroxiredoxin biochemistry

Peroxiredoxins were not recognized as a family of enzymes until the 1990s but are now known to be the dominant peroxidases in most organisms. Here, the history and fundamental properties of peroxiredoxins are briefly reviewed, with a special focus on describing how an exquisitely tunable balance between fully folded and locally unfolded conformations plays a large role in peroxiredoxin catalytic properties.     

The degenerate primer design problem

A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part, or is known in a related species. We prove that various simplified versions of the problem are hard, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant. Based on these algorithms, we implemented a program called HYDEN for designing highly-degenerate primers for a set of genomic sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.     

Animal linguistics: a primer

The evolution of language has been investigated by several research communities, including biologists and linguists, striving to highlight similar linguistic capacities across species. To date, however, no consensus exists on the linguistic capacities of non-human species. Major controversies remain on the use of linguistic terminology, analysis methods and behavioural data collection. The field of ‘animal linguistics’ has emerged to overcome these difficulties and attempt to reach uniform methods and terminology. This primer is a tutorial review of ‘animal linguistics’. It describes the linguistic concepts of semantics, pragmatics and syntax, and proposes minimal criteria to be fulfilled to claim that a given species displays a particular linguistic capacity. Second, it reviews relevant methods successfully applied to the study of communication in animals and proposes a list of useful references to detect and overcome major pitfalls commonly observed in the collection of animal behaviour data. This primer represents a step towards mutual understanding and fruitful collaborations between linguists and biologists.