Quarterly literature reviews in applied microbiology

These quarterly literature reviews are a listing of selected references from various sources. The selection has been made by a panel of 'reviewers' and is compiled by S.P. Denyer, Department of Pharmacy, Brighton Polytechnic. This current selection includes some references published prior to this quarter which have only recently come to the attention of the 'reviewers'. The listing is not intended to be exhaustive. We regret that reprints and photocopies are not available from the Journal or from the 'review' panel.     

Database of mutations that alter the large tumor antigen in simian virus 40.

The SV40 T antigen database is a listing of plasmids and/or viruses that express mutant forms of the virus-encoded large T antigen protein. The parental virus strain, nucleic acid sequence of the mutations, the effect of the mutation on the T antigen amino acid sequence, and key references are included in the listing. The database is available from the authors as a Macintosh FileMaker Pro file, and as a hard copy printout.     

Physiological pharmacokinetics

A discussion of the bases of physiological pharmacokinetics is followed by a brief review of the fundamental mass balance equations of the models. Some examples are outlined, together with a listing of published reviews which give many more references and detailed examples. Finally, some thoughts on future research directions are presented.     

Genomic selection using low density marker panels with application to a sire line in pigs

Background

Genomic selection has become a standard tool in dairy cattle breeding. However, for other animal species, implementation of this technology is hindered by the high cost of genotyping. One way to reduce the routine costs is to genotype selection candidates with an SNP (single nucleotide polymorphism) panel of reduced density. This strategy is investigated in the present paper. Methods are proposed for the approximation of SNP positions, for selection of SNPs to be included in the low-density panel, for genotype imputation, and for the estimation of the accuracy of genomic breeding values. The imputation method was developed for a situation in which selection candidates are genotyped with an SNP panel of reduced density but have high-density genotyped sires. The dams of selection candidates are not genotyped. The methods were applied to a sire line pig population with 895 German Piétrain boars genotyped with the PorcineSNP60 BeadChip.

Results

Genotype imputation error rates were 0.133 for a 384 marker panel, 0.079 for a 768 marker panel, and 0.022 for a 3000 marker panel. Error rates for markers with approximated positions were slightly larger. Availability of high-density genotypes for close relatives of the selection candidates reduced the imputation error rate. The estimated decrease in the accuracy of genomic breeding values due to imputation errors was 3% for the 384 marker panel and negligible for larger panels, provided that at least one parent of the selection candidates was genotyped at high-density.Genomic breeding values predicted from deregressed breeding values with low reliabilities were more strongly correlated with the estimated BLUP breeding values than with the true breeding values. This was not the case when a shortened pedigree was used to predict BLUP breeding values, in which the parents of the individuals genotyped at high-density were considered unknown.

Conclusions

Genomic selection with imputation from very low- to high-density marker panels is a promising strategy for the implementation of genomic selection at acceptable costs. A panel size of 384 markers can be recommended for selection candidates of a pig breeding program if at least one parent is genotyped at high-density, but this appears to be the lower bound.     

National mammal guides: a review of references to Recent faunas

Over four hundred reference guides to the mammalian faunas of almost one hundred and fifty countries, dependencies, and well known, geographically isolated areas are listed, including approximately 60% of the total number of countries found in a current atlas.
Although guides to national mammalian faunas have served as useful synopses for large countries and a useful sub-division for large physiographic/ecological areas, most countries either lack a comprehensive reference to the identity, distribution, behaviour, and local literature on mammals, or the existing work has long required revision. Included in this report is a reference list of some important supra-national areas, preceeding a cross-referenced national listing (by current names, with a chronological listing of references within the country).
National mammal guides are not only an invaluable reference source for the professional, but are also an important stimulus to the layman and government at all levels to take an interest in and appreciate the faunal heritage of mammals found within a country.     

Genomic Selection Using Low-Density Marker Panels

Genomic selection (GS) using high-density single-nucleotide polymorphisms (SNPs) is promising to improve response to selection in populations that are under artificial selection. High-density SNP genotyping of all selection candidates each generation, however, may not be cost effective. Smaller panels with SNPs that show strong associations with phenotype can be used, but this may require separate SNPs for each trait and each population. As an alternative, we propose to use a panel of evenly spaced low-density SNPs across the genome to estimate genome-assisted breeding values of selection candidates in pedigreed populations. The principle of this approach is to utilize cosegregation information from low-density SNPs to track effects of high-density SNP alleles within families. Simulations were used to analyze the loss of accuracy of estimated breeding values from using evenly spaced and selected SNP panels compared to using all high-density SNPs in a Bayesian analysis. Forward stepwise selection and a Bayesian approach were used to select SNPs. Loss of accuracy was nearly independent of the number of simulated quantitative trait loci (QTL) with evenly spaced SNPs, but increased with number of QTL for the selected SNP panels. Loss of accuracy with evenly spaced SNPs increased steadily over generations but was constant when the smaller number individuals that are selected for breeding each generation were also genotyped using the high-density SNP panel. With equal numbers of low-density SNPs, panels with SNPs selected on the basis of the Bayesian approach had the smallest loss in accuracy for a single trait, but a panel with evenly spaced SNPs at 10 cM was only slightly worse, whereas a panel with SNPs selected by forward stepwise selection was inferior. Panels with evenly spaced SNPs can, however, be used across traits and populations and their performance is independent of the number of QTL affecting the trait and of the methods used to estimate effects in the training data and are, therefore, preferred for broad applications in pedigreed populations under artificial selection.     

TRAINING, VALIDATION AND MAINTENANCE OF A PANEL TO EVALUATE THE TEXTURE OF DRY BEANS (PHASEOLUS VULGARIS L.)

The inclusion of dry beans in diets has clear health benefits. However, consumers in developed countries mainly choose beans for their sensory qualities, especially for their texture. This article describes the constitution, training and validation of a panel of judges to evaluate the texture of dry beans. The judges were trained in the perception of different textures, analyzed a wide range of beans and selected seed-coat roughness, seed-coat perceptibility and creaminess/mealiness of the cotyledon as the main attributes to be scored. After training, the panel was capable of discriminating between different varieties of beans and even between beans of the same variety grown at different locations. The analysis of the behavior of the panel in a standard tasting session 2 years after its formation showed that periodic inclusion of samples from the extremes of the scales for the attributes during tasting sessions was sufficient to keep the panel trained.

PRACTICAL APPLICATIONS

This article could serve as a guide for the training of sensory panels to evaluate the texture of dry beans. It describes the selection of the attributes on which the analysis is based, references for the extreme values of the attributes and how to train the panel. It also provides a practical example of the analysis of the behavior of the panel some time after training.     

Comparison of genotype imputation strategies using a combined reference panel for chicken population

Using whole-genome sequence (WGS) data are supposed to be optimal for genome-wide association studies and genomic predictions. However, sequencing thousands of individuals of interest is expensive. Imputation from single nucleotide polymorphisms panels to WGS data is an attractive approach to obtain highly reliable WGS data at low cost. Here, we conducted a genotype imputation study with a combined reference panel in yellow-feather dwarf broiler population. The combined reference panel was assembled by sequencing 24 key individuals of a yellow-feather dwarf broiler population (internal reference panel) and WGS data from 311 chickens in public databases (external reference panel). Three scenarios were investigated to determine how different factors affect the accuracy of imputation from 600 K array data to WGS data, including: genotype imputation with internal, external and combined reference panels; the number of internal reference individuals in the combined reference panel; and different reference sizes and selection strategies of an external reference panel. Results showed that imputation accuracy from 600 K to WGS data were 0.834±0.012, 0.920±0.007 and 0.982±0.003 for the internal, external and combined reference panels, respectively. Increasing the reference size from 50 to 250 improved the accuracy of genotype imputation from 0.848 to 0.974 for the combined reference panel and from 0.647 to 0.917 for the external reference panel. The selection strategies for the external reference panel had no impact on the accuracy of imputation using the combined reference panel. However, if only an external reference panel with reference size >50 was used, the selection strategy of minimizing the average distance to the closest leaf had the greatest imputation accuracy compared with other methods. Generally, using a combined reference panel provided greater imputation accuracy, especially for low-frequency variants. In conclusion, the optimal imputation strategy with a combined reference panel should comprehensively consider genetic diversity of the study population, availability and properties of external reference panels, sequencing and computing costs, and frequency of imputed variants. This work sheds light on how to design and execute genotype imputation with a combined external reference panel in a livestock population.     

Groupamatic 360 C1 and automated blood donor processing in a transfusion center

Automation of donor management flow path is controlled by: --a 3 slip "port a punch" card, --the groupamatic unit with a result sorted out on punch paper tape, --the management computer off line connected to groupamatic. Data tracking at blood collection time is made by punching a card with the donor card used as a master card. Groupamatic performs: --a standard blood grouping with one run for registered donors and two runs for new donors, --a phenotyping with two runs, --a screening of irregular antibodies. Themanagement computer checks the correlation between the data of the two runs or the data of a single run and that of previous file. It updates the data resident in the central file and prints out: --the controls of the different blood group for the red cell panel, --The listing of error messages, --The listing of emergency call up, --The listing of collected blood units when arrived at the blood center, with quantitative and qualitative information such as: number of blood, units collected, donor addresses, etc., --Statistics, --Donor cards, --Diplomas.     

EXPERTS VERSUS CONSUMERS: A CRITIQUE

In a recent paper Moskowitz (1996) refuted the notion that consumers are incapable of validly rating the sensory aspects of products. An analysis of this paper reveals that references are not presented to support his introduction, there is lack of experimental detail, parameters to compare panels were questionable, the degree of expertise of the expert panel is put to doubt and the model proposed to relate data between panels was not compared to existing models.     

Measuring Preferences on Environmental Damages in LCIA. Part 1: Cognitive Limits in Panel Surveys (9 pp)

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Part 1: Cognitive Limits in Panel Surveys · Part 2: The Question Format in Panel Surveys This series of two papers discusses the elicitation of weights for damage categories in LCIA with the aid of panel surveys. The papers focus especially on methodological aspects in panel surveys. Part 1 discusses potential cognitive limits of the panel members to understand the reference that is weighted. Part 2 focuses on the influence of the question format and compares results from two different weighting tasks: discrete choice (between alternatives) and score allocation.

Goal, Scope and Background

The weighting of environmental impacts and damages on the safeguard subjects Human Health, Ecosystems, and Resources is a significant step of full aggregated LCIA. Panel surveys have become a common approach in LCIA research to investigate the preferences of stakeholders on environmental impacts and damages. Despite the numerous studies, the knowledge on how to elicit reliable weights is still poor and inconsistent. We present a questionnaire study with 58 environmental science students to investigate so-called framing effects in panel surveys.

Main Features

The study investigates the significance of different framings, which were provided by three references. In addition, the significance of quantitative information provided in the questionnaire is tested. The references are (a1) safeguard subjects without specified additional information, (a2) damages in Europe as they are perceived by the panelist, and (a3) quantified scenarios derived from Eco-indicator99. All participants ranked and rated the importance of the safeguard subjects three times, once within each reference system. According to a test-of-scope study, quantitative information given to the panelist was varied. One level (b1) included data from the Ecoindicator99 methodology, whereas the other group (b2) received data with significantly higher Human Health damages and lower Ecosystem damages, ceteris paribus. This design allows testing the influence of quantitative data on the rating.

Results

The weighting of the safeguard subjects (a1) reveals that Human Health is considered a slightly more important safeguard subject than Ecosystems. However, both are judged to be significantly more important than Resources. This picture changes for the references (a2) and (a3) where damages were weighted. For both references, the respondents rated damages to Ecosystems as most important followed by Resources and Human Health, showing by far the lowest weights. Therefore, the framing of the reference that was weighted played a significant role. The ratings of the subgroups (b1) and (b2) did not differ with respect to the importance of damages, though substantially different quantitative information was given.

Conclusion and Outlook

The participants of the study were obviously insensitive with respect to quantitative information provided. This raises three questions, which are discussed. What is the mental model upon which respondents base their beliefs and values? Can we expect that 'more sophisticated' subjects would respond differently? Which prerequisites should an empirical weighting procedure fulfill in order to incorporate numerical data? We propose different approaches for future procedures in order to accurately analyze these questions.     

Experimental assessment of the accuracy of genomic selection in sugarcane

Sugarcane cultivars are interspecific hybrids with an aneuploid, highly heterozygous polyploid genome. The complexity of the sugarcane genome is the main obstacle to the use of marker-assisted selection in sugarcane breeding. Given the promising results of recent studies of plant genomic selection, we explored the feasibility of genomic selection in this complex polyploid crop. Genetic values were predicted in two independent panels, each composed of 167 accessions representing sugarcane genetic diversity worldwide. Accessions were genotyped with 1,499 DArT markers. One panel was phenotyped in Reunion Island and the other in Guadeloupe. Ten traits concerning sugar and bagasse contents, digestibility and composition of the bagasse, plant morphology, and disease resistance were used. We used four statistical predictive models: bayesian LASSO, ridge regression, reproducing kernel Hilbert space, and partial least square regression. The accuracy of the predictions was assessed through the correlation between observed and predicted genetic values by cross validation within each panel and between the two panels. We observed equivalent accuracy among the four predictive models for a given trait, and marked differences were observed among traits. Depending on the trait concerned, within-panel cross validation yielded median correlations ranging from 0.29 to 0.62 in the Reunion Island panel and from 0.11 to 0.5 in the Guadeloupe panel. Cross validation between panels yielded correlations ranging from 0.13 for smut resistance to 0.55 for brix. This level of correlations is promising for future implementations. Our results provide the first validation of genomic selection in sugarcane.     

Database of mutations within the adenovirus 5 E1A oncogene.

The Ad5 E1A database is a listing of mutations affecting the early region 1A (E1A) proteins of human adenovirus type 5. The database contains the name of the mutation, the nucleic acid sequence changes, the resulting alterations in amino acid sequence and reference. Additional notes and references are provided on the effect of each mutation on E1A function. The database is contained within the Adenovirus 5 E1A page on the World Wide Web at: http://www.geocities.com/CapeCanaveral/Hangar /2541/     

Reference bias in reports of drug trials.

Articles published before 1985 describing double blind trials of two or more non-steroidal anti-inflammatory drugs in rheumatoid arthritis were examined to see whether there was any bias in the references they cited. Althogether 244 articles meeting the criteria were found through a Medline search and through examining the reference lists of the articles retrieved. The drugs compared in the studies were classified as new or as control drugs and the outcome of the trial as positive or not positive. The reference lists of all papers with references to other trials on the new drug were then examined for reference bias. Positive bias was judged to have occurred if the reference list contained a higher proportion of references with a positive outcome for that drug than among all the articles assumed to have been available to the authors (those published more than two years earlier than the index article). Altogether 133 of the 244 articles were excluded for various reasons--for example, 44 because of multiple publication and 19 because they had no references. Among the 111 articles analysed bias was not possible in the references of 35 (because all the references gave the same outcome); 10 had a neutral selection of references, 22 a negative selection, and 44 a positive selection--a significant positive bias. This bias was not caused by better scientific standing of the cited articles over the uncited ones. Thus retrieving literature by scanning reference lists may produce a biased sample of articles, and reference bias may also render the conclusions of an article less reliable.     

A high-resolution molecular-based panel of assays for identification and characterization of human embryonic stem cell lines

Meticulous characterization of human embryonic stem cells (hESC) is critical to their eventual use in cell-based therapies, particularly in view of the diverse methods for derivation and maintenance of these cell lines. However, characterization methods are generally not standardized and many currently used assays are subjective, making dependable and direct comparison of cell lines difficult. In order to address this problem, we selected 10 molecular-based high-resolution assays as components of a panel for characterization of hESC. The selection of the assays was primarily based on their quantitative or objective (rather than subjective) nature. We demonstrate the efficacy of this panel by characterizing 4 hESC lines, derived in two different laboratories using different derivation techniques, as pathogen free, genetically stable, and able to differentiate into derivatives of all three germ layers. Our panel expands and refines a characterization panel previously proposed by the International Stem Cell Initiative and is another step toward standardized hESC characterization and quality control, a crucial element of successful hESC research and clinical translation.     

The Molecular Biology Database Collection: an updated compilation of biological database resources

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www. nar.oupjournals.org.     

The Molecular Biology Database Collection: 2003 update

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the jumping-off point from which to find specialized databases that may be of use in advancing biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in this Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org.