Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli

Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these characters yielded a unique phylogenetic tree. This analysis not only distinguished among bacterial strains that were otherwise identical in their biochemical characteristics and enzyme electrophoretic mobilities, but certain aspects of the topology of the tree were consistent across several unrelated insertion elements. The distribution of IS elements was then reexamined in light of the inferred phylogenetic relationships to investigate the biological properties of the elements, such as rates of insertion and deletion, and to discover apparent recombinational events. The analysis shows that the pattern of distribution of insertion elements in the bacterial genome is sufficiently stable for epidemiological studies. Although the rate of recombination by conjugation has been postulated to be low, at least two such events appear to have taken place.      

Conserved residues of the Pro103–Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase

The synthesis of glycogen in bacteria and starch in plants is allosterically controlled by the production of ADP-glucose by ADP-glucose pyrophosphorylase. Using computational studies, site-directed mutagenesis, and kinetic characterization, we found a critical region for transmitting the allosteric signal in the Escherichia coli ADP-glucose pyrophosphorylase. Molecular dynamics simulations and structural comparisons with other ADP-glucose pyrophosphorylases provided information to hypothesize that a Pro103–Arg115 loop is part of an activation path. It had strongly correlated movements with regions of the enzyme associated with regulation and ATP binding, and a network analysis showed that the optimal network pathways linking ATP and the activator binding Lys39 mainly involved residues of this loop. This hypothesis was biochemically tested by mutagenesis. We found that several alanine mutants of the Pro103–Arg115 loop had altered activation profiles for fructose-1,6-bisphosphate. Mutants P103A, Q106A, R107A, W113A, Y114A, and R115A had the most altered kinetic profiles, primarily characterized by a lack of response to fructose-1,6-bisphosphate. This loop is a distinct insertional element present only in allosterically regulated sugar nucleotide pyrophosphorylases that could have been acquired to build a triggering mechanism to link proto-allosteric and catalytic sites.     

Oligopeptidase B from <Emphasis Type="Italic">Serratia proteamaculans</Emphasis>. II. Enzymatic characteristics: Substrate analysis,influence of calcium ions,pH and temperature dependences

Enzymatic properties of a novel oligopeptidase B from psychrotolerant gram-negative microorganism Serratia proteamaculans (PSP) were studied. The substrate specificity of PSP was analyzed using p-nitroanilide substrates, and the influence of calcium ions on the enzyme activity was studied. Hydrolysis of oligopeptides by PSP was studied using melittin as the substrate. Optimal conditions for the PSP activity (pH and temperature) have been established. It was found that PSP shares some properties with oligopeptidases B from other sources containing two Asp/Glu residues in the S2 site, but it differs significantly in some characteristics. The S2 site of PSP contains only one Asp460 residue. The secondary specificity of PSP has a number of specific features: an unusual substrate inhibition by peptides with hydrophobic residues at the P2 position, as well as the drastic influence of calcium ions on substrate characteristics of the enzyme. It is assumed that the PSP molecule contains a large hydrophobic substrate-binding site, and significant conformational rearrangements of the enzyme active site are induced by Ca²⁺ binding and by the formation of the enzyme-substrate complex. The temperature characteristics of PSP (high activity at low temperature as well as low apparent temperature optimum (25°C)) confirm that PSP is a psychrophilic enzyme.     

Major morphological effects of a regulatory gene: Pgm1-t in rainbow trout

We have investigated the morphological effects of a genetic locus, Pgm1- t, that affects the expression of a phosphoglucomutase locus (Pgm1) in liver of rainbow trout (Salmo gairdneri). We have previously shown that embryos with liver Pgm1 expression hatch earlier than those without liver Pgm1 expression. We predicted that this difference in developmental rate should cause a reduction in meristic counts in the more rapidly developing fish with liver Pgm1 expression. Eight meristic (countable) characters in nine full-sib groups segregating for the presence or absence of liver Pgm1 expression are in agreement with this prediction. In eight of the nine families, there is a significant difference in the multivariate distribution of the eight meristic counts between full sibs with and without liver Pgm1 expression. This separation in multivariate space is based on a tendency for lower meristic counts in fish with liver Pgm1 expression. The magnitude of these morphological differences is similar to that between two subspecies of cutthroat trout (Salmo clarki) that show substantial genetic divergence at structural loci encoding enzymes (Nei's D = 0.34). These data support the view that small changes in the developmental process caused by genetic differences at regulatory genes can have large effects on morphology.      

Changes in the Levels of IAA,ABA, and Cytokinins in Wheat Seedlings Infected with Tilletia caries

The seedling growth and the content of endogenous phytohormones in wheat seedlings were estimated 3, 6, and 9 days after infection with the bunt pathogen (Tilletia caries) (DC.)TUL. The infection of a pathogen-susceptible species Triticum aestivum L. and a resistant species T. timopheevii Zhuk. resulted, respectively, in an increase and a decrease in the seedling growth and the IAA content as compared to the control. The cytokinin content increased in both species, and the increase in T. timopheevii was more rapid. The pathogen-induced increase in auxin content is suggested to enhance fungal invasion of plants. In the susceptible species, a high ABA concentration was retained for a longer period of time and could act as a factor of virulence. At the same time, in the resistant species, an increase in ABA content was transient and seems to trigger plant defense mechanisms.     

Comparison of influenza outbreaks in the Republic of Kazakhstan and Russia induced by 2009 yearly new variant of A(H1N1) influenza virus

The aim of the work is the comparison of the epidemiology of influenza and acute respiratory virus infections(ARVI)in the Republic of Kazakhstan with the corresponding influenza epidemic in Russia induced by influenza pandemic virus A/California/07/2009 in 2009. Data on influenza and ARVI from the Republic of Kazakhstan and Federal Center of influenza was collected and investigated over the course of several weeks from hospitalized patients with the same diagnosis among all population and in age groups on 16 territories of Kazakhstan and in 49 major cities of Russia. The epidemic in Kazakhstan resembled the Russian epidemic in terms of its abnormally early beginning,expression of monoaetiology,the spread of the epidemic into all territories and start of the epidemics among adult population. High percentage of hospitalized people and lethal outcome were registered in this epidemic. Similarity of epidemic process character in corresponding border-line territories of both countries was found out.     

Purinergic Mechanisms of Adaptation of Different Types of Motor Units under Conditions of Allergic Reorganization

Biophysics - A role for presynaptic signaling was found in the processes of adaptation to allergies during isometric contractions of mouse EDL (fast) and soleus (slow) muscles evoked by electrical...     

A High Calcium Level-Based Model for Identifying Postsynaptic Effects of ATP

Biophysics - Identification of the pre- and postsynaptic effects of ATP is a methodological challenge. In our previous study, the role of P2 receptor signaling in synaptic transmission processes...