Alignment of chain-like molecules

The steric obstruction model, that describes the enhanced alignment of folded proteins by anisotropic medium, is extended to account for the residual dipolar couplings of chain-like polypeptides. The average alignment of each chain segment is calculated from an ensemble of conformations represented by a spatial probability distribution. The segmental alignment depends on chain length, flexibility and segment's position in the chain. Residual dipolar couplings in turn depend on internuclear vector directions within each fragment. The results of calculations and simulations explain salient features of the experimental data. With this insight residual dipolar couplings can be interpreted to assess the degree of denaturation, local structures and spatial organization of weakly structured proteins.     

NuMA in rat testis--evidence for roles in proliferative activity and meiotic cell division

NuMA is a well-characterized organizer of the mitotic spindle, which is believed to play a structural role in interphase nucleus. We studied the expression of NuMA in rat seminiferous epithelium in detail. Different stages of the cycle of the seminiferous epithelium were identified using transillumination. Corresponding areas were microdissected and analysed using immunofluorescence, immunohistochemistry, or immunoblotting. NuMA was expressed in Sertoli cells, proliferating type A and B spermatogonia, and early spermatids but it was absent in late spermatids and mature spermatozoa. Interestingly, NuMA-positive primary spermatocytes lost their nuclear NuMA at the beginning of long-lasting prophase of the first meiotic division. A strong expression was again observed at the end of the prophase and finally, a redistribution of NuMA into pole regions of the meiotic spindle was observed in first and second meiotic divisions. In immunoblotting, a single 250-kDa protein present in all stages of the rat seminiferous epithelial cycle was detected. Our results show that NuMA is not essential for the organization of nuclear structure in all cell types and suggest that its presence is more likely connected to the proliferation phase of the cells. They also suggest that NuMA may play an important role in meiotic cell division.     

Hearing impairment in patients with 3243A→G mtDNA mutation: phenotype and rate of progression

The relationship between the phenotype and the genotype is complex in diseases caused by mutations in mitochondrial DNA (mtDNA). The 3243A-->G mutation in mtDNA frequently leads to sensorineural hearing impairment (HI), a phenotype that can be assessed in severity by audiometry; hence, consecutive audiograms can give an estimate of the rate of HI progression.We examined the audiological phenotype of 38 patients (14 men, 24 women; mean age: 45+/-14 years) who possessed the 3243A-->G mutation and who belonged to a population-based cohort ascertained in the province of Northern Ostrobothnia, Finland. The subjects took part in an otorhinolaryngologic examination, including audiometry. Factors modulating the severity of HI were analyzed, and the rate of HI progression was calculated. The better ear hearing level (BEHL) at frequencies 0.5, 1, 2, and 4 kHz (BEHL0.5-4kHz) was greater than 20 dB suggesting HI in 28 patients (74%). A good correlation (r=0.428, P=0.009) was found between BEHL0.5-4kHz and the degree of the mutant heteroplasmy. BEHL0.5-4kHz was worse in men than in women, and women outnumbered men among patients with normal hearing or mild HI. In addition, 181 consecutive audiograms were reviewed from 24 patients with HI. The rate of HI progression was calculated to be 2.9 dB/year in men and 1.5 dB/year in women, being clearly faster than the rates that have been observed in the corresponding age group in the general population. A high degree of mutant heteroplasmy, male gender, and age were found to increase the severity of HI. Phenotypic difference by gender may thus be a more universal phenomenon in mitochondrial diseases, not only being associated with Leber's hereditary optic neuropathy. This study provides the first estimate of the rate of disease progression among patients with the 3243A-->G mutation.     

Genome-wide selection of unique and valid oligonucleotides

Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other location of the whole genome. By using probe size 25, we analyzed 17 complete genomes representing a wide range of both prokaryotic and eukaryotic organisms. More than 92% of all the genes in the investigated genomes contained valid oligonucleotides. Extensive statistical tests were performed to characterize the properties of unique and valid oligonucleotides. Unique and valid oligonucleotides were relatively evenly distributed in genes except for the beginning and end, which were somewhat overrepresented. The flanking regions in eukaryotes were clearly underrepresented among suitable oligonucleotides. In addition to distributions within genes, the effects on codon and amino acid usage were also studied.     

Pellet manufacturing by extrusion-spheronization using process analytical technology

The aim of this study was to investigate the phase transitions occurring in nitrofurantoin and theophylline formulations during pelletization by extrusion-spheronization. An at-line process analytical technology (PAT) approach was used to increase the understanding of the solid-state behavior of the active pharmaceutical ingredients (APIs) during pelletization. Raman spectroscopy, near-infrared (NIR) spectroscopy, and X-ray powder diffraction (XRPD) were used in the characterization of polymorphic changes during the process. Samples were collected at the end of each processing stage (blending, granulation, extrusion, spheronization, and drying). Batches were dried at 3 temperature levels (60°C, 100°C, and 135°C). Water induced a hydrate formation in both model formulations during processing. NIR spectroscopy gave valuable real-time data about the state of water in the system, but it was not able to detect the hydrate formation in the theophylline and nitrofurantoin formulations during the granulation, extrusion, and spheronization stages because of the saturation of the water signal. Raman and XRPD measurement results confirmed the expected pseudopolymorphic changes of the APIs in the wet process stages. The relatively low level of Raman signal with the theophylline formulation complicated the interpretation. The drying temperature had a significant effect on dehydration. For a channel hydrate (theophylline), dehydration occurred at lower drying temperatures. In the case of isolated site hydrate (nitrofurantoin), dehydration was observed at higher temperatures. To reach an understanding of the process and to find the critical process parameters, the use of complementary analytical techniques are absolutely necessary when signals from APIs and different excipients overlap each other. Published: September 30, 2005     

Whitefish stocking in acidified lakes: ecological and physiological responses

In autumn 1986, six small lakes at different stages of acidification were stocked with one-summer-old whitefish, Coregonus pallasi Valenciennes 1848, in order to see whether whitefish stocking would be a suitable method for the mitigation of acidification effects. In two of the lakes the introduction was a complete failure: the whitefish did not survive, evidently due to high acidity and high aluminium concentrations of the lake waters. In one of the most acidified lakes (pH 4.3–4.8, Al_lab 29–125 g 1^–1) and in two less acidic lakes (pH 5.0–5.2 and 5.4–6.4), introduction was successful. Three years after the introduction, the mean weights of the fish in those three lakes were 580, 250 and 360 g respectively, with the weight and also the condition factor of stocked whitefish being highest in the most acidified lake. In that lake there were few or no fish present during the introduction, whereas in the less acid lakes there were dense populations of perch and therefore a potential interspecific competition for food. Different availability of food in the lakes was presumed to be the main reason for the growth differences. Plasma Na⁺ and Cl^– concentrations of whitefish were lower in the acidic lakes than in the lake with pH around 6 three years after stocking. This suggests that, despite the good growth and highest condition factor of whitefish in the most acid lake, the fish still experienced some acid stress.     

Some Factors Causing Mortality among Female Minks during the Puerperium and Lactation Periods

The purpose of this study, in which the farm was used as the statistical unit, was to find factors affecting mink mortality under farm conditions. Mortality was hypothesised to be affected by factors including, among others, variables describing the amount (level) and variation in composition and quality of the feed. Other explanatory variables applied in the study included farm size and age. Factor analyses were performed for variables of feed composition and quality in order to condense the variable information and to facilitate the selection of explanatory variables. This report presents a preliminary regression model for female mink mortality factors describing feed level and variation, and farm size, as explanatory variables. The regression model emphasized among other factors the importance of a constant albumin quality and a constant energy level.     

Non-native Fish Occurrence and Biomass in 1943 Western Palearctic Lakes and Reservoirs and their Abiotic and Biotic Correlates

Invasion of non-native species is considered a major threat to global biodiversity. Here we present a comprehensive overview of the occurrence, richness and biomass contribution of non-native fish species in 1943 standing water bodies from 14 countries of the Western Palearctic, based on standardised fish catches by multi-mesh gillnetting. We expected strong geographical gradients to emerge in the occurrence of non-natives. We further hypothesised that the contribution by non-natives to the local fish community biomass was correlated with local richness and the trophic level of native and non-native species. Non-native fish species occurred in 304 of 1943 water bodies (16%). If the average number of occupied water bodies per country was weighted by number of water bodies per country, the grand mean occurrence of non-natives in Western Palearctic water bodies was 10%. Exotic (non-native to the Palearctic) and translocated (non-native only to parts of the Palearctic) species were found in 164 (8.4%) or 235 (12.1%) of the water bodies, respectively. The occurrence and local richness of non-native fish species increased with temperature, precipitation and lake area and were substantially higher in reservoirs than in natural lakes. High local biomass contributions of non-native species were strongly correlated with low richness of native species and high richness of non-native species, whereas the trophic level of the fish species had only a weak effect. Single non-native species rarely dominated community biomass, but high biomass contributions and thus strong community and ecosystem impacts can be expected if several non-native species accumulate in a water body.