Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases

The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M.Pvu II, revealed extended regions of homology. The sequence comparison of the three DNA[cytosine-N4]-methylases using originally developed software revealed two conserved patterns, DPF-GSGT and TSPPY, which were found similar also to those of adenine and DNA[cytosine-C5]-methylases. These data provided a basis for global alignment and classification of DNA-methylase sequences. Structural considerations led us to suggest that the first region could be the binding site of AdoMet, while the second is thought to be directly involved in the modification of the exocyclic amino group.     

Five-stranded β-sheet sandwiched with two α-helices: A structural link between restriction endonucleases EcoRI and EcoRV

Examination of crystal structures of restriction endonucleases EcoRI and EcoRV complexes with their cognate DNA revealed a common structural element, which forms the core of both proteins. This element consists of a five-stranded β-sheet and two α-helices packed against it and could be described as α–β sandwich in which helices and β-strands lie in two stacked layers. While the spatial structure of this α–β sandwich is conserved in both enzymes, there are no detectable similarities between amino acid sequences except of a few residues involved in active site formation. Probably, other restriction endonucleases which have similar organization of the active site might possess similar structural element regardless of DNA sequence recognized and recognition elements in the enzyme used. © 1994 Wiley-Liss, Inc.     

Peripheral and central fatigue after muscle-damaging exercise is muscle length dependent and inversely related

Healthy untrained men performed 10 series of 12 knee eccentric extension repetitions (EE) at 160°/s. The maximal voluntary isometric contraction force of the quadriceps muscle, the maximal rate of electrically induced torque development (RTD) and relaxation (RTR), isokinetic concentric torque at 30°/s, the electrostimulation-induced torque at 20 and 100 Hz frequencies were established before and after EE at shorter and longer muscle lengths. Besides, voluntary activation (VA) index and central activation ratio (CAR) were tested. There was more peripheral fatigue than central after EE. We established more central fatigue as well as low frequency fatigue at a shorter muscle length compared to the longer muscle length. Relative RTD as well as relative RTR, improved after EE and did not depend on the muscle length. Finally, central fatigue is inversely significantly related with the eccentric torque reduction during eccentric exercise and with the changes in muscle torque induced by low frequency stimulation.     

Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations

Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures. The formation of fruiting bodies is a result of collective cell movement on a solid surface. In the course of development, groups of flexible rod-shaped cells form streams and move in circular or spiral patterns to form aggregation centers that can become sites of fruiting body formation. The mechanisms of such cell movement patterns are not well understood. It has been suggested that myxobacterial development depends on short-range contact-mediated interactions between individual cells, i.e. cell aggregation does not require long-range signaling in the population. In this study, by means of a computational mass-spring model, we investigate what types of short-range interactions between cells can result in the formation of streams and circular aggregates during myxobacterial development. We consider short-range head-to-tail guiding between individual cells, whereby movement direction of the head of one cell is affected by the nearby presence of the tail of another cell. We demonstrate that stable streams and circular aggregates can arise only when the trailing cell, in addition to being steered by the tail of the leading cell, is able to speed up to catch up with it. It is suggested that necessary head-to-tail interactions between cells can arise from physical adhesion, response to a diffusible substance or slime extruded by cells, or pulling by motility engine pili. Finally, we consider a case of long-range guiding between cells and show that circular aggregates are able to form without cells increasing speed. These findings present a possibility to discriminate between short-range and long-range guiding mechanisms in myxobacteria by experimentally measuring distribution of cell speeds in circular aggregates.     

Time Course of Physiological and Psychological Responses in Humans during a 20-Day Severe-Cold–Acclimation Programme

The time course of physiological and psychological markers during cold acclimation (CA) was explored. The experiment included 17 controlled (i.e., until the rectal temperature reached 35.5°C or 170 min had elapsed; for the CA-17 session, the subjects (n = 14) were immersed in water for the same amount of time as that used in the CA-1 session) head-out water immersions at a temperature of 14°C over 20 days. The data obtained in this study suggest that the subjects exhibited a thermoregulatory shift from peripheral-to-central to solely central input thermoregulation, as well as from shivering to non-shivering thermogenesis throughout the CA. In the first six CA sessions, a hypothermic type of acclimation was found; further CA (CA-7 to CA-16) led to a transitional shift to a hypothermic–insulative type of acclimation. Interestingly, when the subjects were immersed in water for the same time as that used in the CA-1 session (CA-17), the CA led to a hypothermic type of acclimation. The presence of a metabolic type of thermogenesis was evident only under thermoneutral conditions. Cold-water immersion decreased the concentration of cold-stress markers, reduced the activity of the innate immune system, suppressed specific immunity to a lesser degree and yielded less discomfort and cold sensation. We found a negative correlation between body mass index and Δ metabolic heat production before and after CA.     

Compartment volume influences microtubule dynamic instability: a model study

Microtubules (MTs) are cytoskeletal polymers that exhibit dynamic instability, the random alternation between growth and shrinkage. MT dynamic instability plays an essential role in cell development, division, and motility. To investigate dynamic instability, simulation models have been widely used. However, conditions under which the concentration of free tubulin fluctuates as a result of growing or shrinking MTs have not been studied before. Such conditions can arise, for example, in small compartments, such as neuronal growth cones. Here we investigate by means of computational modeling how concentration fluctuations caused by growing and shrinking MTs affect dynamic instability. We show that these fluctuations shorten MT growth and shrinkage times and change their distributions from exponential to non-exponential, gamma-like. Gamma-like distributions of MT growth and shrinkage times, which allow optimal stochastic searching by MTs, have been observed in various cell types and are believed to require structural changes in the MT during growth or shrinkage. Our results, however, show that these distributions can already arise as a result of fluctuations in the concentration of free tubulin due to growing and shrinking MTs. Such fluctuations are possible not only in small compartments but also when tubulin diffusion is slow or when many MTs (de)polymerize synchronously. Volume and all other factors that influence these fluctuations can affect MT dynamic instability and, consequently, the processes that depend on it, such as neuronal growth cone behavior and cell motility in general.     

Muscle-damaging exercise affects isokinetic torque more at short muscle length

The aim of this study was to investigate the differences in the length-dependent changes in quadriceps muscle torque during voluntary isometric and isokinetic contractions performed after severe muscle-damaging exercise. Thirteen physically active men (age = 23.8 ± 3.2 years, body weight = 77.2 ± 4.5 kg) performed stretch-shortening cycle (SSC) exercise comprising 100 drop jumps with 30-second intervals between each jump. Changes in the voluntary and electrically evoked torque in concentric and isometric conditions at different muscle lengths, muscle soreness, and plasma creatine kinase (CK) activity were assessed within 72 hours after SSC exercise. Isokinetic knee extension torque decreased significantly (p < 0.05) at all joint angles after SSC exercise. At 2 minutes and at 72 hours after SSC exercise, the changes in knee torque were significantly smaller at 80° (where 180° = full knee extension) than at 110-130°. At 2 minutes after SSC exercise, the optimal angle for isokinetic knee extension torque shifted by 9.5 ± 8.9° to a longer muscle length (p < 0.05). Electrically induced torque at low-frequency (20-Hz) stimulation decreased significantly more at a knee joint angle of 130° than at 90°. The subjects felt acute muscle pain and CK activity in the blood increased to 1,593.9 ± 536.2 IU·L?1 within 72 hours after SSC exercise (p < 0.05). This study demonstrates that the effect of muscle-damaging exercise on isokinetic torque is greatest for contractions at short muscle lengths. These findings have practical importance because the movements in most physical activities are dynamic in nature, and the decrease in torque at various points in the range of motion during exercise might affect overall performance.     

Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes

The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set.