Biotransformation enzyme expression in the nasal epithelium of woodrats

When herbivores come in contact with volatile plant secondary compounds (PSC) that enter the nasal passages the only barrier between the nasal cavity and the brain is the nasal epithelium and the biotransformation enzymes present there. The expression of two biotransformation enzymes Cytochrome P450 2B (CYP2B) and glutathione-S-transferase (GST) was investigated in the nasal epithelia and livers of three populations of woodrats. One population of Neotoma albigula was fed juniper that contains volatile terpenes. Juniper caused upregulation of CYP2B and GST in the nasal epithelium and the expression of CYP2B and GST in the nasal epithelium was correlated to liver expression, showing that the nasal epithelia responds to PSC and the response is similar to the liver. Two populations of Neotoma bryanti were fed creosote that contains less volatile phenolics. The creosote naive animals upregulated CYP2B in their nasal epithelia while the creosote experienced animals upregulated GST. There was no correlation between CYP2B and GST expression in the nasal epithelia and livers of either population. The response of the nasal epithelium to PSC seems to be an evolved response that is PSC and experience dependent.     

Weichselian interstadial pollen stratigraphy from Härjedalen,central Sweden

Weichselian interstadial vegetation history has been studied by means of pollen analysis of organic bearing fine-grained sediments at Dörrsvålen and Brovalltjärnen in a low mountain area in Härjedalen. The composition of the pollen flora suggests treeless vegetation consisting of shrubs and herbs. The interstadial vegetation consisted of Betula nana, Ericaceae, Juniperus and Salix spp. mixed with herbaceous plant communities including Gramineae, Cyperaceae, Caryophyllaceae, Saxifraga, Rumex/Oxyria and Polygonum. Betula and Pinus are represented by long distance-transported pollen. During the interstadial the climatic conditions seem to have been very harsh and continental as (cold) steppe plants reach high frequencies, e.g. Artemisia and Chenopodiaceae. The sediments are thought to have been deposited during an early Weichselian interstadial tentatively correlated with Tärendö in Norrbotten province, northern Sweden, and Odderade in Denmark and north-western Germany. Comparisons are made with other interstadial sites in central and northern Sweden, and in south-eastern Norway.     

Predictive algorithms for adjuvant therapy: TransATAC

Estrogen receptor (ER) positive primary breast cancers have a wide range of clinical outcomes. Prediction of the likely course of the disease aids treatment decision-making. In the translational arm of the ATAC (anastrozole or tamoxifen alone or combined) trial (TransATAC) we have assessed individual and multiparameter biomarkers for their prediction of overall and distant recurrence. None of the biomarkers identified differential benefit for anastrozole versus tamoxifen. Each of ER, PgR, HER2 and Ki67 was associated with risk of recurrence. A combination of these to create a single predictor IHC4 was as informative as the 21-gene recurrence score (RS). Integration of each of these molecular profiles with classical clinicopathologic variables provided the most accurate prediction of outcome.     

Multivariate phenotype analysis enables genome-wide inference of mammalian gene function

The function of the majority of genes in the human and mouse genomes is unknown. Investigating and illuminating this dark genome is a major challenge for the biomedical sciences. The International Mouse Phenotyping Consortium (IMPC) is addressing this through the generation and broad-based phenotyping of a knockout (KO) mouse line for every protein-coding gene, producing a multidimensional data set that underlies a genome-wide annotation map from genes to phenotypes. Here, we develop a multivariate (MV) statistical approach and apply it to IMPC data comprising 148 phenotypes measured across 4,548 KO lines.There are 4,256 (1.4% of 302,997 observed data measurements) hits called by the univariate (UV) model analysing each phenotype separately, compared to 31,843 (10.5%) hits in the observed data results of the MV model, corresponding to an estimated 7.5-fold increase in power of the MV model relative to the UV model. One key property of the data set is its 55.0% rate of missingness, resulting from quality control filters and incomplete measurement of some KO lines. This raises the question of whether it is possible to infer perturbations at phenotype–gene pairs at which data are not available, i.e., to infer some in vivo effects using statistical analysis rather than experimentation. We demonstrate that, even at missing phenotypes, the MV model can detect perturbations with power comparable to the single-phenotype analysis, thereby filling in the complete gene–phenotype map with good sensitivity.A factor analysis of the MV model’s fitted covariance structure identifies 20 clusters of phenotypes, with each cluster tending to be perturbed collectively. These factors cumulatively explain 75% of the KO-induced variation in the data and facilitate biological interpretation of perturbations. We also demonstrate that the MV approach strengthens the correspondence between IMPC phenotypes and existing gene annotation databases. Analysis of a subset of KO lines measured in replicate across multiple laboratories confirms that the MV model increases power with high replicability.

The function of the majority of genes in the human and mouse genomes is unknown, and illuminating this "dark genome" is a major challenge for the biomedical sciences. This study shows that multi-dimensional phenotypes from single-gene knockout mouse lines can be analysed at a genome-wide scale both to increase power and infer missing phenotypes.     

Production of cloned pigs from in vitro systems

Here we describe a procedure for cloning pigs by the use of in vitro culture systems. Four healthy male piglets from two litters were born following nuclear transfer of cultured somatic cells and subsequent embryo transfer. The initiation of five additional pregnancies demonstrates the reproducibility of this procedure. Its important features include extended in vitro culture of fetal cells preceding nuclear transfer, as well as in vitro maturation and activation of oocytes and in vitro embryo culture. The cell culture and nuclear transfer techniques described here should allow the use of genetic modification procedures to produce tissues and organs from cloned pigs with reduced immunogenicity for use in xenotransplantation.     

Differences Among Helicobacter pylori Strains Isolated from Three Different Populations and Demonstrated by Restriction Enzyme Analysis of an Internal Fragment of the Conserved Gene hpaA

Background. Our goal was to test the idea that Helicobacter pylori genotypes vary from one population to another. Methods. Analysis of Sau3A and Hinf I restriction fragment–length polymorphism (RFLP) in a 375-bp polymerase chain reaction amplicon of hpaA was used to compare 31 H. pylori isolates from a relatively small and genetically homogeneous population (Goteborg, Sweden) with those of large, genetically heterogeneous populations located in two different countries (50 isolates from Houston, TX, and 69 isolates from Minas Gerais, a state in the southeastern region of Brazil). Results. Five different Sau3A and three different Hinf I restriction patterns were found; different combinations of these comprise 10 different RFLP types, I through X. The RFLP types found in the United States and Brazil collections were very similar, except for two Brazil isolates belonging to type VIII and five Brazil isolates belonging to type X, neither type found in the United States. The overall profile of H. pylori isolates from Sweden was remarkably different, with 18 of 31 (58%) having a new Sau3A restriction pattern, termed gS; 10 of these 18 isolates had Hinf I restriction pattern E (RFLP type VIII), and 8 had Hinf I restriction pattern F (RFLP type IX). No isolates from Sweden belonged to RFLP type III or type X. Conclusions. RFLP typing of a 375-bp polymerase chain reaction–amplified DNA fragment of H. pylori hpaA revealed that H. pylori genotypes can and do vary from one population to another. We conclude that the unique RFLP profile shown by the group of H. pylori isolates from Goteborg is the result of a cohort effect in this relatively small, stable, genetically homogeneous population. Also, the overall similarity between RFLP profiles of the H. pylori isolates from Texas and Minas Gerais coincides with the fact that although geographically distanced, these populations are similar in being large, dynamic, and genetically heterogeneous.     

Determining biological tissue turnover using stable isotopes: the reaction progress variable

The reaction progress variable is applied to stable isotope turnover of biological tissues. This approach has the advantage of readily determining whether more than one isotope turnover pool is present; in addition, the normalization process inherent to the model means that multiple experiments can be considered together although the initial and final isotope compositions are different. Consideration of multiple isotope turnover pools allows calculation of diet histories of animals using a time sequence of isotope measurements along with isotope turnover pools. The delayed release of blood cells from bone marrow during a diet turnover experiment can be quantified using this approach. Turnover pools can also be corrected for increasing mass during an experiment, such as when the animals are actively growing. Previous growth models have been for exponential growth; the approach here can be used for several different growth models. Electronic Supplementary Material The online version of this article () contains supplementary material, which is available to authorized users.