The solution structure of the amino-terminal domain of human DNA polymerase epsilon subunit B is homologous to C-domains of AAA+ proteins

DNA polymerases α, δ and ε are large multisubunit complexes that replicate the bulk of the DNA in the eukaryotic cell. In addition to the homologous catalytic subunits, these enzymes possess structurally related B subunits, characterized by a carboxyterminal calcineurin-like and an aminoproximal oligonucleotide/oligosaccharide binding-fold domain. The B subunits also share homology with the exonuclease subunit of archaeal DNA polymerases D. Here, we describe a novel domain specific to the N-terminus of the B subunit of eukaryotic DNA polymerases ε. The N-terminal domain of human DNA polymerases ε (Dpoe2NT) expressed in Escherichia coli was characterized. Circular dichroism studies demonstrated that Dpoe2NT forms a stable, predominantly α-helical structure. The solution structure of Dpoe2NT revealed a domain that consists of a left-handed superhelical bundle. Four helices are arranged in two hairpins and the connecting loops contain short β-strand segments that form a short parallel sheet. DALI searches demonstrated a striking structural similarity of the Dpoe2NT with the α-helical subdomains of ATPase associated with various cellular activity (AAA+) proteins (the C-domain). Like C-domains, Dpoe2NT is rich in charged amino acids. The biased distribution of the charged residues is reflected by a polarization and a considerable dipole moment across the Dpoe2NT. Dpoe2NT represents the first C-domain fold not associated with an AAA+ protein.     

Genetic approaches to the cellular functions of polyamines in mammals.

The polyamines putrescine, spermidine and spermine are organic cations shown to participate in a bewildering number of cellular reactions, yet their exact functions in intermediary metabolism and specific interactions with cellular components remain largely elusive. Pharmacological interventions have demonstrated convincingly that a steady supply of these compounds is a prerequisite for cell proliferation to occur. The last decade has witnessed the appearance of a substantial number of studies, in which genetic engineering of polyamine metabolism in transgenic rodents has been employed to unravel their cellular functions. Transgenic activation of polyamine biosynthesis through an overexpression of their biosynthetic enzymes has assigned specific roles for these compounds in spermatogenesis, skin physiology, promotion of tumorigenesis and organ hypertrophy as well as neuronal protection. Transgenic activation of polyamine catabolism not only profoundly disturbs polyamine homeostasis in most tissues, but also creates a complex phenotype affecting skin, female fertility, fat depots, pancreatic integrity and regenerative growth. Transgenic expression of ornithine decarboxylase antizyme has suggested that this unique protein may act as a general tumor suppressor. Homozygous deficiency of the key biosynthetic enzymes of the polyamines, ornithine and S-adenosylmethionine decarboxylase, as achieved through targeted disruption of their genes, is not compatible with murine embryogenesis. Finally, the first reports of human diseases apparently caused by mutations or rearrangements of the genes involved in polyamine metabolism have appeared.     

Comparison of Different Standard Methods to Evaluate the Total Concentrations of Heavy Metals in Waste Rock

The mining industry is a very rapidly increasing production sector in Finland. Many new mines have been opened recently and others are in the planning phase. Mining legislation has been recently revised and compilation of an ID-directive (Industrial Emission Directive, 2010) required to implement environmental law revision is in progress. The aim of this study was to compare different digestion methods recommended by the Finnish Environmental Administration for threshold and guideline value determinations in the Finnish PIMA Decree (214/2007) and Government Decree (591/2006) concerning recovery of certain wastes in earth construction. Altogether six methods were tested, of which five were microwave-assisted acid digestion methods: ISO 11466, EPA Method 3051A (aqua region), EPA Method 3051A (HNO₃), EPA Method 3051A (HNO₃/HCl), and SFS-EN 13656, while one was a fusion method with lithium tetraborate (ASTM C 1391 - 95). The results showed that concentrations of heavy metals (As, Cd, Co, Cu, Ni, Pb, Sb, V, and Zn) can be determined reproducibly with standard methods, but the chemical method used can have a significant impact on the results. This conclusion is very important, because the measured heavy metal values can affect the classification and processing of waste materials, and thereby can significantly impact the cost of treatment.     

The breeding biology of the starling Sturnus vulgaris in northern Finland

The breeding biology of the starling Sturnus vulgaris was studied in three populations in northern Finland, with additional reference localities in nearby areas. Results from a total of 329 nests are presented from years 1962-1976.
The onset of laying in the Oulu area took place on 5 May, the median date being 10 May, about one week later than in southern Finland and 2–3 weeks later than in central Europe. The clutch-size was 5.29 ± 0.05 in the first nests and 5.06 ± 0.26 in later ones. Incubation time was 12.1 ± 0.6 d. An average of 3.31 ± 0.10 fledglings was produced per pair, 3.69 ± 0.08 in succesful clutches, which is significantly less than usually reported from central Europe. Most of the losses were due to starvation of the young.
No second broods were observed in the Oulu area, and repeated nesting was not common, probably because of the general late start of laying.
The reasons for the recent decline in several Finnish starling populations do not lie in the production capacity but must be sought for elsewhere.     

Production of Estonian case-inflected nouns shows whole-word frequency and paradigmatic effects

Most psycholinguistic models of lexical processing assume that the comprehension and production of inflected forms is mediated by morphemic constituents. Several more recent studies, however, have challenged this assumption by providing empirical evidence that information about individual inflected forms and their paradigmatic relations is available in long-term memory (Baayen et al. 1997; Milin et al. 2009a, 2009b). Here, we investigate how whole-word frequency, inflectional paradigm size and morphological family size affect production latencies and articulation durations when subjects are asked to read aloud isolated Estonian case-inflected nouns. In Experiment 1, we observed that words with a larger morphological family elicited shorter speech onset latencies, and that forms with higher whole-word frequency had shorter acoustic durations. Experiment 2, for which we increased statistical power by using 2,800 words, revealed that higher whole-word frequency, inflectional paradigm size, and morphological family size reduced both speech onset times and acoustic durations. These results extend our knowledge of morphological processing in three ways. First, whole-word frequency effects of inflected forms in morphologically rich languages are not restricted to a small number of very high-frequency forms, contrary to previous claims (Niemi et al. 1994; Hankamer 1989; Yang 2016). Second, we replicated the morphological family size effect in a new domain, the acoustic durations of inflected forms. Third, we showed that a novel paradigmatic measure, inflectional paradigm size, predicts word naming latencies and acoustic durations. These results fit well with Word-and-Paradigm morphology (Blevins 2016) and argue against strictly (de)compositional models of lexical processing.     

Separation and partial characterization of two alkaline peptidases from cotyledons of resting kidney beans, Phaseolus vulagaris

Extracts prepared from cotyledons of resting kidney beans ( Phaseolus vulgaris L., cv. Processor) rapidly hydrolyzed two dipeptides, Leu-Tyr and Ala-Gly, with pH optima at 9.2 and 8.5, respectively. On ion exchange chromatography on DEAE-Sephacel the two activities eluted as separate peaks, showing that they were due to two different peptidases. The extracts also hydrolyzed Leu-β-naphthylamide optimally at pH 6.4; this activity eluted as a third peak berween the other peaks. The activity peak acting on Leu-Tyr and Ala-Gly rapidly hydrolized two tripeptides, showing that it was an aminopeptidase, whereas the Ala-Gly hydrolyzing peak acted only on dipeptides. The activities against Leu-Tyr and Ala-Gly were also separated by gel chromatography on Sephacryl S-300 with elution positions corresponding to M, values of about 360 000 and 105 000. The aminopeptidase was inhibited by bestatin, and the dipeptidase was inhibited by p-hydroxymercuribenzoate. Both enzymes were inhibited by o-phenanthroline. In most of their properties the two kidneys bean enzymes resembled the alkaline aminopeptidase and the dipeptidase earlier characterized from barley grains.     

Relationship between local perfusion and FFA uptake in human skeletal muscle-no effect of increased physical activity and aerobic fitness.

We investigated heredity-independent effects of increased physical activity and aerobic fitness on skeletal muscle free fatty acid (FFA) uptake, perfusion, and their heterogeneity at rest and during exercise. Also, the relationship between local skeletal muscle FFA uptake and perfusion was studied. Nine young adult male monozygotic twin pairs with significant difference in physical activity [229 min (SD 156) average time spent for conditioning exercise per week in more and 98 min (SD 71) in less active twins, P = 0.013] and aerobic fitness [18% (SD 10) difference in maximum O2 uptake] between brothers were studied using positron emission tomography. Submaximal knee-extension exercise increased perfusion, FFA uptake, and oxygen uptake in quadriceps femoris muscles 6-10 times compared with resting values (P < 0.001). More active twins tended to utilize more oxygen, while no differences were found in muscle perfusion or FFA uptake between groups. Mean perfusion and FFA uptake correlated strongly at a whole muscle level, both at rest (r = 0.97, P = 0.03 in more and r = 0.98, P = 0.02 in less active twins) and during exercise (r = 0.99, P = 0.01 and r = 0.94, P = 0.06), but at the voxel level (87 mm3) correlation was only moderate during exercise [r = 0.73 (SD 0.08) vs. r = 0.74 (SD 0.10), P = 0.92] and weak at rest [r = 0.28 (SD 0.13) vs. r = 0.33 (SD 0.21), P = 0.58]. Exercise decreased both perfusion and FFA uptake heterogeneity within the muscles (P < 0.001) similarly in both groups. In conclusion, long-term history of moderately increased physical activity tends to enhance muscle oxidative metabolism, but it does not have any significant influence on the FFA uptake or perfusion rates or their heterogeneity in skeletal muscle. Submaximal knee-extension exercise decreases heterogeneity of muscle FFA uptake and perfusion and improves matching between local muscle perfusion and FFA uptake. Thus it seems that the genetic influence is more important to determine the heterogeneity of perfusion and FFA uptake in skeletal muscle than exercise training.     

Particle-induced myeloperoxidase release in serially diluted whole blood quantifies the number and the phagocytic activity of blood neutrophils and opsonization capacity of plasma.

Luminol-amplified chemiluminescence (CL) from phagocytes has previously been shown to be almost completely dependent on the release of myeloperoxidase (MPO) from azurophilic granules. We measured the luminol-amplified chemiluminescence response (WBCL) by using serially diluted whole blood. In these experiments, non-opsonized and serum-opsonized zymosan (NWBCL and OWBCL, respectively) were used concurrently as phagocytosable particles. We found two whole-blood dilution ranges with clinical significance: first, <0.04% of whole blood in the reaction volume, where MPO released by the zymosan-activated leukocyte population came almost totally from neutrophils and the OWBCL response could be exploited as a measure of a neutrophil count in a given blood specimen, despite the pathophysiological state of the host. In contrast, the NWBCL response was two-fold in blood samples from bacterial infection patients compared to those of controls and patients with viral infection, suggesting the use of NWBCL for the differential diagnosis of bacterial infections from viral infections; second, 0.16-1.2% of whole blood in the reaction volume, where the opsonization capacity of plasma (OC(50)) can be determined. We also found that at whole blood content >0.04%, erythrocytes quickly start to absorb chemiluminescence light, and that at whole blood content >1.2%, plasma proteins, most probably albumin and fibrinogen, start to inhibit MPO release.