Epilysin (MMP-28) is deposited to the basolateral extracellular matrix of epithelial cells

Epilysin (MMP-28) is a conserved member of the matrix metalloproteinase (MMP) family. It is expressed in various normal tissues, and induced in wounds and in developing and regenerating nerves. Epilysin induces TGF-β mediated epithelial to mesenchymal transition, but its other functions are largely unknown. We have characterized the localization of both catalytically active and mutated inactive, overexpressed epilysin in established epithelial cell lines. We found that epilysin was localized abundantly to the basolateral side of the cells and associated with the extracellular matrix (ECM) as verified by immunoblotting and confocal microscopy. Overexpression of epilysin in MDCK cells resulted in a drastic reduction of basolateral ECM, as observed by the disappearance of collagen type IV, laminin and fibronectin. Cultivation of epilysin expressing MDCK cells in defined serum free medium resulted in the restoration of these proteins to the ECM. The levels of fibronectin and collagen IV were, however, reduced in epilysin expressing cells under the serum free conditions, and degradation fragments of collagen IV were detected supporting the activation of proteolysis by epilysin. Epilysin was observed in its unprocessed 50 kDa active form in the ECM of MDCK cells under serum free conditions whereas in cells cultured in serum containing it was processed to the 48 kDa form. Current results indicate that epilysin associates with the basolateral ECM of cultured epithelial cells, where it plausibly plays a role in the regulation of matrix composition and turnover.     

Neural and mechanical responses of the triceps surae muscle group after 1 h of repeated fast passive stretches.

Experiments were carried out to examine interaction between mechanical changes of the muscle-tendon unit and reduced reflex sensitivity after repeated and prolonged passive muscle stretching (RPS). There is some evidence that this interaction might be relevant also during active stretch-shortening cycle type of fatigue tasks. The results demonstrated a clear deterioration of voluntarily and electrically induced muscle contractions after RPS. Maximal voluntary contraction (MVC), average electromyographic activities of the gastrocnemius and soleus muscles, and maximal twitch contraction decreased on average by 13.8, 10.4, 7.6, and 16.8%, respectively. In addition, there was a 14% lengthening in the total duration of the twitch. MVCs measured at different ankle joint angles revealed a downward and rightward shift in the torque-fascicle length curve after RPS. Interestingly, there was a crossing in the torque-fascicle length curves while measured at different activation levels but at the same joint angle before and after RPS. Even though no changes were observed in the activation level during MVCs, all the reflex parameters showed a clear reduction after RPS. This study presents evidence that repeated and prolonged passive muscle stretching can lead to some modification of material behavior of the aponeurosis-tendon system, such as stress relaxation and/or plastic deformation. In addition, altered material properties seem to affect proprioceptive feedback and, therefore, the motor unit activation in proportion to the contractile failure.     

Soil and total ecosystem respiration in agricultural fields: effect of soil and crop type

A study was made of the effect of soil and crop type on the soil and total ecosystem respiration rates in agricultural soils in southern Finland. The main interest was to compare the soil respiration rates in peat and two different mineral soils growing barley, grass and potato. Respiration measurements were conducted during the growing season with (1) a closed-dynamic ecosystem respiration chamber, in which combined plant and soil respiration was measured and (2) a closed-dynamic soil respiration chamber which measured only the soil and root-derived respiration. A semi-empirical model including separate functions for the soil and plant respiration components was used for the total ecosystem respiration (TER), and the resulting soil respiration parameters for different soil and crop types were compared. Both methods showed that the soil respiration in the peat soil was 2–3 times as high as that in the mineral soils, varying from 0.11 to 0.36 mg (CO₂) m^–2 s^–1 in the peat soil and from 0.02 to 0.17 mg (CO₂) m^–2 s^–1 in the mineral soils. The difference between the soil types was mainly attributed to the soil organic C content, which in the uppermost 20 cm of the peat soil was 24 kg m^–2, being about 4 times as high as that in the mineral soils. Depending on the measurement method, the soil respiration in the sandy soil was slightly higher than or similar to that in the clay soil. In each soil type, the soil respiration was highest on the grass plots. Higher soil respiration parameter values (R_s0, describing the soil respiration at a soil temperature of 10°C, and obtained by modelling) were found on the barley than on the potato plots. The difference was explained by the different cultivation history of the plots, as the potato plots had lain fallow during the preceding summer. The total ecosystem respiration followed the seasonal evolution in the leaf area and measured photosynthetic flux rates. The 2–3-fold peat soil respiration term as compared to mineral soil indicates that the cultivated peat soil ecosystem is a strong net CO₂ source.     

Fluctuations of Hi-Hat Timing and Dynamics in a Virtuoso Drum Track of a Popular Music Recording

Long-range correlated temporal fluctuations in the beats of musical rhythms are an inevitable consequence of human action. According to recent studies, such fluctuations also lead to a favored listening experience. The scaling laws of amplitude variations in rhythms, however, are widely unknown. Here we use highly sensitive onset detection and time series analysis to study the amplitude and temporal fluctuations of Jeff Porcaro’s one-handed hi-hat pattern in “I Keep Forgettin’”—one of the most renowned 16th note patterns in modern drumming. We show that fluctuations of hi-hat amplitudes and interbeat intervals (times between hits) have clear long-range correlations and short-range anticorrelations separated by a characteristic time scale. In addition, we detect subtle features in Porcaro’s drumming such as small drifts in the 16th note pulse and non-trivial periodic two-bar patterns in both hi-hat amplitudes and intervals. Through this investigation we introduce a step towards statistical studies of the 20th and 21st century music recordings in the framework of complex systems. Our analysis has direct applications to the development of drum machines and to drumming pedagogy.     

Genes coding for cytochromec oxidase inParacoccus denitrificans

Several loci on theParacoccus denitrificans chromosome are involved in the synthesis of cytochromec oxidase. So far three genetic loci have been isolated. One of them contains the structural genes of subunits II and III, as well as two regulatory genes which probably code for oxidase-specific assembly factors. In addition, two distinct genes for subunit I have been cloned, one of which is located adjacent to the cytochromec ₅₅₀ gene. An alignment of six promoter regions reveals only short common sequences.     

Land use indicators in life cycle assessment

Purpose  

Inclusion of land use-related environmental aspects into LCA methodology has been under active development in recent years. Although many indicators have been developed and proposed for different aspects of land use (climate change, biodiversity, resource depletion and soil quality), many of indicators have, as yet, not been tested and compared in LCA applications. The aim of this study is to test the different LCIA indicators in practice in a case study of beer production.     

Primer extension mutagenesis powered by selective rolling circle amplification

Primer extension mutagenesis is a popular tool to create libraries for in vitro evolution experiments. Here we describe a further improvement of the method described by T.A. Kunkel using uracil-containing single-stranded DNA as the template for the primer extension by additional uracil-DNA glycosylase treatment and rolling circle amplification (RCA) steps. It is shown that removal of uracil bases from the template leads to selective amplification of the nascently synthesized circular DNA strand carrying the desired mutations by phi29 DNA polymerase. Selective RCA (sRCA) of the DNA heteroduplex formed in Kunkel's mutagenesis increases the mutagenesis efficiency from 50% close to 100% and the number of transformants 300-fold without notable diversity bias. We also observed that both the mutated and the wild-type DNA were present in at least one third of the cells transformed directly with Kunkel's heteroduplex. In contrast, the cells transformed with sRCA product contained only mutated DNA. In sRCA, the complex cell-based selection for the mutant strand is replaced with the more controllable enzyme-based selection and less DNA is needed for library creation. Construction of a gene library of ten billion members is demonstrated with the described method with 240 nanograms of DNA as starting material.     

Conserved C-terminal charge exerts a profound influence on the aggregation rate of α-synuclein

α-Synuclein (α-syn) is the major component of filamentous Lewy bodies found in the brains of patients diagnosed with Parkinson's disease (PD). Recent studies demonstrate that, in addition to the wild-type sequence, α-syn is found in several modified forms, including truncated and phosphorylated species. Although the mechanism by which the neuronal loss in PD occurs is unknown, aggregation and fibril formation of α-syn are considered to be key pathological features. In this study, we analyze the rates of fibril formation and the monomer-fibril equilibrium for eight disease-associated truncated and phosphorylated α-syn variants. Comparison of the relative rates of aggregation reveals a strong monotonic relationship between the C-terminal charge of α-syn and the lag time prior to the observation of fibril formation, with truncated species exhibiting the fastest aggregation rates. Moreover, we find that a decrease in C-terminal charge shifts the equilibrium to favor the fibrillar species. An analysis of these findings in the context of linear growth theories suggests that the loss of the charge-mediated stabilization of the soluble state is responsible for the enhanced aggregation rate and increased extent of fibril fraction. Therefore, C-terminal charge is kinetically and thermodynamically protective against α-syn polymerization and may provide a target for the treatment of PD.