Microbiological, Biochemical, and Electron Microscopic Characterization of a Pectinatus Strain

A spoilage organism isolated from turbid beer is described. The bacterium was gram negative, catalase negative, strictly anaerobic, and rod shaped, having flagella only on one side of the cell. The main metabolic product was propionic acid. In addition acetic, succinic, and lactic acids and acetoin were formed. Malonate inhibited the production of propionic acid by the strain studied and by both Pectinatus and Propionibacterium strains. The guanine-plus-cytosine content of deoxyribonucleic acid was 36 mol%. Differences between this strain and Pectinatus strains were 2 to 5 percentage points. Immunofluorescent staining and gel diffusion precipitin tests revealed that the antigenic structure differed from those of Pectinatus strains. The isolated organism can, despite some differences, be regarded as belonging to the genus Pectinatus.     

Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays

MOTIVATION: Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer. RESULTS: We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments. AVAILABILITY: R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/     

Responses in the start of Betula (birch) pollen seasons to recent changes in spring temperatures across Europe

A shift in the timing of birch pollen seasons is important because it is well known to be a significant aeroallergen, especially in NW Europe where it is a notable cause of hay fever and pollen-related asthma. The research reported in this paper aims to investigate temporal patterns in the start dates of Betula (birch) pollen seasons at selected sites across Europe. In particular it investigates relationships between the changes in start dates and changes in spring temperatures over approximately the last 20 years. Daily birch pollen counts were used from Kevo, Turku, London, Brussels, Zurich and Vienna, for the core period from 1982 to 1999 and, in some cases, from 1970 to 2000. The sites represent a range of biogeographical situations from just within the Arctic Circle through to North West Maritime and Continental Europe. Pollen samples were taken with Hirst-type volumetric spore traps. Weather data were obtained from the sites nearest to the pollen traps. The timing of birch pollen seasons is known to depend mostly on a non-linear balance between the winter chilling required to break dormancy, and spring temperatures. Pollen start dates and monthly mean temperatures for January through to May were compiled to 5-year running means to examine trends. The start dates for the next 10 years were calculated from regression equations for each site, on the speculative basis that the current trends would continue. The analyses show regional contrasts. Kevo shows a marked trend towards cooler springs and later starts. If this continues the mean start date will become about 6 days later over the next 10 years. Turku exhibits cyclic patterns in start dates. A current trend towards earlier starts is expected to continue until 2007, followed by another fluctuation. London, Brussels, Zurich and Vienna show very similar patterns in the trends towards earlier start dates. If the trend continues the mean start dates at these sites will advance by about 6 days over the next 10 years. Following this work, amendments will be needed to pollen calendars and local predictive models. It will also be important to assess the implications of earlier seasons for allergy sufferers.     

Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer

Hereditary factors are presumed to play a role in one third of colorectal cancer (CRC) cases. However, in the majority of familial CRC cases the genetic basis of predisposition remains unexplained. This is particularly true for families with few affected individuals. To identify susceptibility genes for this common phenotype, we examined familial cases derived from a consecutive series of 1514 Finnish CRC patients. Ninety-six familial CRC patients with no previous diagnosis of a hereditary CRC syndrome were included in the analysis. Eighty-six patients had one affected first-degree relative, and ten patients had two or more. Exome sequencing was utilized to search for genes harboring putative loss-of-function variants, because such alterations are likely candidates for disease-causing mutations. Eleven genes with rare truncating variants in two or three familial CRC cases were identified: UACA, SFXN4, TWSG1, PSPH, NUDT7, ZNF490, PRSS37, CCDC18, PRADC1, MRPL3, and AKR1C4. Loss of heterozygosity was examined in all respective cancer samples, and was detected in seven occasions involving four of the candidate genes. In all seven occasions the wild-type allele was lost (P = 0.0078) providing additional evidence that these eleven genes are likely to include true culprits. The study provides a set of candidate predisposition genes which may explain a subset of common familial CRC. Additional genetic validation in other populations is required to provide firm evidence for causality, as well as to characterize the natural history of the respective phenotypes.     

Pollen concentrations inside private cars during the Poaceae and Artemisia spp. pollen season – a case study

A growing number of studies are researching indoor air concentrations of pollen in buildings, but to our knowledge no studies have dealt with the precise concentration of pollen inside private cars. The aim of this study was to assess the risk of exposure to pollen in private cars throughout the Poaceae and Artemisia spp. pollen season.

The study was conducted in the town of Lappeenranta and along Highway 6 in south‐east Finland between July 14 and August 17, 2003. The pollen concentrations were measured inside two moving and parked cars using rotorod‐type samplers. Surface and ambient Burkard samples were also collected.

Both Poaceae and Artemisia spp. pollen were recorded only on one day and in low concentrations (<10 pollen grains per cubic meter, pg/m³) inside moving and parked cars, whereas the concentrations of Betula spp. (0–15 vs. 0–12?pg/m³) and Pinus (0–41 vs. 0–80?pg/m³) ranged from low to moderate, respectively. The number of pollen grains on the inside surfaces of cars ranged from zero to 72?pg/cm² during the measurement periods.

The concentrations of Poaceae and Artemisia spp. pollen in the indoor air of the car during the flowering period were low, therefore, likely to cause reactions only in the most sensitive people. By contrast, even after the main flowering period the concentrations of Betula spp. pollen were on a level high enough to cause reactions in individuals with allergies.     

A numerical model of birch pollen emission and dispersion in the atmosphere. Model evaluation and sensitivity analysis

An evaluation of performance of the System for Integrated modeLling of Atmospheric coMposition (SILAM) in application to birch pollen dispersion is presented. The system is described in a companion paper whereas the current study evaluates the model sensitivity to details of the pollen emission module parameterisation and to the meteorological input data. The most important parameters are highlighted. The reference year considered for the analysis is 2006. It is shown that the model is capable of predicting about two-thirds of allergenic alerts, with the odds ratio exceeding 12 for the best setup. Several other statistics corroborate with these estimations. Low-pollen concentration days are also predicted correctly in more than two-thirds of cases. The model experiences certain difficulties only with intermediate pollen concentrations. It is demonstrated that the most important input parameter is the near-surface temperature, the bias of which can easily jeopardise the results. The model sensitivity to random fluctuations of temperature is much lower. Other parameters important at various stages of pollen development, release, and dispersion are precipitation and ambient humidity, as well as wind direction.     

Indoor and outdoor pollen concentrations in private and public spaces during the <Emphasis Type="Italic">Betula</Emphasis> pollen season

Although the number of studies of pollen concentrations inside and outside buildings is increasing, little is known about the efficiency of penetration of pollen from outdoor to indoor air, and further. We studied indoor and outdoor pollen concentrations in the town of Lappeenranta and in the municipality of Rautjärvi in SE Finland from May 3–23, 2004, i.e. throughout the Betula pollen season, and assessed the risk of exposure to pollen grains. Pollen concentrations were measured inside and outside a block of flats, a detached house, and the regional central hospital, using rotorod-type samplers; in the town of Joutseno data were compared with Burkard counts. Outdoor concentrations of Betula pollen grains ranged between low and abundant (0–855 grains m^?3). The corresponding indoor concentrations near the main front doors varied from low to moderate (0–17 grains m^?3) in the central hospital and were low (<10 grains m^?3) in both residential buildings. Indoor concentrations further from the main front door were low (<10 grains m^?3) at all study sites. The concentrations of Betula pollen decreased substantially from outdoors to indoors, and further toward the centre of the building, probably indicating relatively poor penetrating properties of the pollen grains and/or the short-lived presence of pollen grains in indoor air. The concentrations of Betula pollen inside the buildings during the peak flowering period were mostly at a level barely inducing reactions even in the most sensitive persons.     

Persisting chronic gastritis and elevated Helicobacter pylori antibodies after successful eradication therapy

AIM: The persistence of chronic inflammation in gastric mucosa and elevated Helicobacter pylori antibodies after successful eradication therapy are common findings in clinical practice. We studied their possible association with each other and disappearance in long-term follow up, as well as their possible connection with gastric atrophy. PATIENTS AND METHODS: The study population consisted of 108 dyspeptic patients with successful eradication therapy median 6.4 years earlier. The patients underwent gastroscopy, and biopsies from antrum and corpus were evaluated by an experienced pathologist. Serum samples collected from 77 patients were studied for H. pylori antibodies, parietal cell antibodies, as well as for pepsinogen I, pepsinogen II, and gastrin-17 levels. RESULTS: The prevalence of chronic gastric inflammation and elevated H. pylori antibodies after successful eradication therapy decreased by time, but still after 5 years, 17 of 51 (33%) subjects had elevated H. pylori antibodies and 14 of 68 (21%) had a mild inactive chronic inflammation in gastric mucosa. In patients with and without chronic inflammation in gastric mucosa, elevated H. pylori antibodies were detected in three of 10 (30%) and 14 of 41 (34%), elevated parietal cell antibodies in one of 10 (10%) and six of 41 (15%), low pepsinogen I in one of 10 (10%) and none of 41, and elevated gastrin-17 in three of 10 (30%) and six of 41 (15%), respectively. CONCLUSION: More than 5 years after successful H. pylori eradication therapy, mild persistent chronic inflammation may occur in gastric mucosa in up to one-fifth and elevated H. pylori antibodies even in one-third of patients, although these two are independent phenomena.     

A longitudinal assessment of miR-122 and GLDH as biomarkers of drug-induced liver injury in the rat

Context: There is an ongoing search for specific and translational biomarkers of drug-induced liver injury (DILI). MicroRNA-122 (miR-122) has previously shown potential as a sensitive, specific, and translational biomarker of DILI in both rodent, and human studies.

Objective: To build on previous work within the field, we examined biomarker kinetics in a rat model of acetaminophen (APAP)-induced liver injury to confirm the sensitivity, and specificity of miR-122 and glutamate dehydrogenase (GLDH).

Materials and methods: qRT-PCR and a standard enzymatic assay were used for biomarker analysis.

Results: Both miR-122 and GLDH were demonstrated to be more readily-detectable biomarkers of APAP-DILI than alanine aminotransferase (ALT). Peak levels for all biomarkers were detected at 2 days after APAP. At day 3, miR-122 had returned to baseline; however, other biomarkers remained elevated between 3 and 4 days. We were also able to demonstrate that, although miR-122 is present in greater quantities in exosome-free form, both exosome-bound and non-vesicle bound miR-122 are released in a similar profile throughout the course of DILI.

Discussion and conclusions: Together, this study demonstrates that both GLDH and miR-122 could be used during preclinical drug-development as complementary biomarkers to ALT to increase the chance of early detection of hepatotoxicity.