Minor promoters of phage phi X174 are controlled by CRP-cAMP, lexA, glnG and several other common common regulatory systems of the host cell

It was found that CRP-cAMP-recognized sequences in DNA being suggested as GTGN7-11CAC (with variability both in domain's structures and in spacer's length) are located non-randomly in promoters. In CRP-cAMP-stimulated promoters they lie upstream the "-35" box and are separated from it by a whole number of DNA turns, whereas in CRP-cAMP-repressed ones they are located downstream "-35" in a half-whole-turn-number distance. Several CRP-, SOS- and NR1-sites in the phi X174 DNA sequence were found and a few new promoters were deduced from it. PCRP1 lies within gene F and has both CRR and ntrC sites and one SOS-operator, PCRP3 (in gene A) has a CRP site which overlaps with the SOS-operator, PA and PCRP2 (in gene G) have sCRP and PD has a stringent discriminator. Four promotors, PCRP1, PCRP2, PA and PB are cloned in the pBR322 plasmid. For cloned PCRP1 the activation by exogenous cAMP and the SOS-induction by the mitomycin C were observed in vivo in pVYB215-containing cells by increasing the levels of beta-lactamase up to 27-fold. The new gene L of the phi X174 is deduced from the DNA sequence. It has two start points, overlaps the gene F inside it and codes for peptides 23 or 19 amino acids in length. These lethal peptides have strong homology in sequence to the cellular protein sulA(sfiA) of E. coli, and L* can cause observed filamentation and death of pVYB215- bearing cells after PCRP1 induction. In the A and A* protein sequences two domains "helix-turn-helix" were found that are homologous to those in CRP and repressors; this makes possible the competition between A* and CRT for its DNA sites that also have some homology. The model of the phi X174 infection cycle control and mechanisms of DNA recognition by CRP-CAMP are discussed. PCRP1 is the first promotor controlled by both three global regulons of E. coli cell.     

A simple quantitative method of estimation of cell-intactness based on ethidium bromide fluorescence

A quantitative method based on fluorescence generated by the binding of ethidium bromide (EB) to DNA has been developed for estimation of the intactness of the plasma membrane of a mammalian cell type (goat epididymal spermatozoon). The method consists of mixing of sperm preparations with EB in a modified Ringer's solution followed by immediate measurement of fluorescence intensity at 365-580 nm (excitation-emission). The data were corrected for non-specific values of fluorescence due to intact cells only. The percentage of damaged cells in a sperm population was calculated by comparing the corrected fluorescence values of the cell preparations with those of the sonicated cells. The values of sperm intactness obtained by this method (99.5 +/- 0.3) compared well with those obtained by the widely used "marker enzyme" method (97 +/- 0.8) based on estimation of lactic dehydrogenase in the extracellular medium. The validity of this method has been confirmed by using cells of defined intactness i.e. preparations of vigorously forward-motile spermatozoa that showed nearly 100% intactness. The method can detect as low as 0.5% "leaky" or damaged cells in a cell preparation. The "EB-fluorescence" method is simpler and more rapid and reliable than the conventional "marker enzyme" method for estimation of cellular intactness.     

The suprachiasmatic nucleus: a clock of multiple components

Although impressive progress has been made in understanding the molecular basis of pacemaker function in the suprachiasmatic nucleus (SCN), fundamental questions about cellular and regional heterogeneity within the SCN, and how this heterogeneity might contribute to SCN pacemaker function at a tissue level, have remained unresolved. To reexamine cellular and regional heterogeneity within the SCN, the authors have focused on two key questions: which SCN cells are endogenously rhythmic and/or directly light responsive? Observations of endogenous rhythms of electrical activity, gene/protein expression, and protein phosphorylation suggest that the SCN in mammals examined to date is composed of anatomically distinct rhythmic and nonrhythmic components. Endogenously rhythmic neurons are primarily found in rostral, dorsomedial, and ventromedial portions of the nucleus; at mid and caudal levels, the distribution of endogenously rhythmic cells in the SCN has the appearance of a "shell." The majority of nonrhythmic cells, by contrast, are located in a central "core" region of the SCN, which is complementary to the shell. The location of light-responsive cells, defined by direct retinohypothalamic input and light-induced gene expression, largely overlaps the location of nonrhythmic cells in the SCN core, although, in hamsters and mice light-responsive cells are also present in the ventral portion of the rhythmic shell. While the relative positions of rhythmic and light-responsive components of the SCN are similar between species, the precise boundaries of these components, and neurochemical phenotype of cells within them, are variable. Intercellular communication between these components may be a key feature responsible for the unique pacemaker properties of the SCN observed at a tissue and whole animal level.     

Nucleotide sequence of a regulatory region of the uidA gene in Escherichia coli K12

Summary Multiple regulatory events are involved in the expression of the uidA gene. A regulatory region of this gene has been located on a 460 base pair Sau3A-EcoRI fragment and its nucleotide sequence was determined by the dideoxy method using pEMBL plasmids. A preliminary analysis of this sequence revealed the presence of numerous palindromic structures with some overlaps.     

A Stereological Approach for Estimation of Cellular Immunogold Labeling and Its Spatial Distribution in Oriented Sections Using the Rotator

Particulate gold labeling applied to ultrathin sections is a powerful approach for locating cellular proteins and lipids on thin sections of cellular structures and compartments. Effective quantitative methods now allow estimation of both density and distribution of gold labeling across aggregate organelles or compartment profiles. However, current methods generally use random sections of cells and tissues, and these do not readily present the information needed for spatial mapping of cellular quantities of gold label. Yet spatial mapping of gold particle labeling becomes important when cells are polarized or show internal organization or spatial shifts in protein/lipid localization. Here we have applied a stereological approach called the rotator to estimate cellular gold label and proportions of labeling over cellular compartments at specific locations related to a chosen cell axis or chosen cellular structures. This method could be used in cell biology for mapping cell components in studies of protein translocation, cell polarity, cell cycle stages, or component cell types in tissues. (J Histochem Cytochem 57:709–719, 2009)     

The concept of a changing receptor concentration: implications for the theory of drug action

Drugs are considered to produce their effects on biological tissues either by altering some physical property of cells or by interacting with specific cellular components, called receptors. Most drugs and endogenous neurotransmitters act on highly selective receptors located on the outer surface membrane of cells. These receptors were believed, until recently, to be stationary on the cell surface and to be present in unvarying numbers. Consequently, most early theorists modeled the drug-receptor interaction on the basis of stationary and static receptor molecules. The substantial advances in our understanding of drug action based on these models have partly justified this view. However, recent electron microscopic studies have revealed the presence of structures, including "coated" pits and vesicles, that appear to provide a mechanism by which cell surface receptors might be internalized in a process of endocytosis. The precise intracellular fate of these internalized receptors is unknown, but based on present understanding, it seems reasonable to believe that some are destroyed intracellularly whereas others are recycled to the cell surface. The importance of such processes to pharmacologic theory is a new awareness of a cellular pathway that is capable of internalizing drugs, receptors, or both. The implications of such a process to the theory of drug action extends to some unexplained drug phenomena such as down regulation, drug tolerance, tachyphyllaxis, and partial agonism. We present herein the theoretical framework for a model of drug action that incorporates the possibility of receptor internalization and subsequent degradation, recycling, or replacement.     

Ultrastructural and cytochemical study on the epithelium lining ductuli efferentes in Equus asinus

The ultrastructure and cytochemistry of the epithelium lining ductuli efferentes in adult Equus asinus was studied. The epithelium is constituted of randomly distributed ciliated and non-ciliated cells extending from the basement membrane to the lumen. A third cellular type appearing to be in a degenerating state may also occur with variable frequency and is basally located. Mainly "non-ciliated cells" display ultrastructural and cytochemical features which can be related to strong resorptive activity; lysosomes and pigment granules, lipofuscinic in nature, are also present. Pigment masses exhibiting the same morphological and histochemical features fill the cytoplasm of degenerating cells. The results are compared with those obtained by previous authors in other Mammals and in Birds and are related to the functions commonly attributed to ductuli efferentes. The origin of degenerating cells, which are peculiar of Equidae, is discussed.     

Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody

Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2.9 and 1.9 Å, respectively. The IL-23 structure closely resembles that of IL-12. They share the common p40 subunit, and IL-23 p19 overlaps well with IL-12 p35. Along the hydrophilic heterodimeric interface, fewer charged residues are involved for IL-23 compared with IL-12. The binding site of the Fab is located exclusively on the p19 subunit, and comparison with published cytokine-receptor structures suggests that it overlaps with the IL-23 receptor binding site.     

Integrative analysis of genetical genomics data incorporating network structures

In a living organism, tens of thousands of genes are expressed and interact with each other to achieve necessary cellular functions. Gene regulatory networks contain information on regulatory mechanisms and the functions of gene expressions. Thus, incorporating network structures, discerned either through biological experiments or statistical estimations, could potentially increase the selection and estimation accuracy of genes associated with a phenotype of interest. Here, we considered a gene selection problem using gene expression data and the graphical structures found in gene networks. Because gene expression measurements are intermediate phenotypes between a trait and its associated genes, we adopted an instrumental variable regression approach. We treated genetic variants as instrumental variables to address the endogeneity issue. We proposed a two‐step estimation procedure. In the first step, we applied the LASSO algorithm to estimate the effects of genetic variants on gene expression measurements. In the second step, the projected expression measurements obtained from the first step were treated as input variables. A graph‐constrained regularization method was adopted to improve the efficiency of gene selection and estimation. We theoretically showed the selection consistency of the estimation method and derived the bound of the estimates. Simulation and real data analyses were conducted to demonstrate the effectiveness of our method and to compare it with its counterparts.     

Assemblons: nuclear structures defined by aggregation of immature capsids and some tegument proteins of herpes simplex virus 1.

In cells infected with herpes simplex virus 1 (HSV-1), the viral proteins ICP5 (infected-cell protein 5) and VP19c (the product of UL38) are associated with mature capsids, whereas the same proteins, along with ICP35, are components of immature capsids. Here we report that ICP35, ICP5, and UL38 (VP19c) coalesce at late times postinfection and form antigenically dense structures located at the periphery of nuclei, close to but not abutting nuclear membranes. These structures were formed in cells infected with a virus carrying a temperature-sensitive mutation in the UL15 gene at nonpermissive temperatures. Since at these temperatures viral DNA is made but not packaged, these structures must contain the proteins for immature-capsid assembly and were therefore designated assemblons. These assemblons are located at the periphery of a diffuse structure composed of proteins involved in DNA synthesis. This structure overlaps only minimally with the assemblons. In contrast, tegument proteins were located in asymmetrically distributed structures also partially overlapping with assemblons but frequently located nearer to nuclear membranes. Of particular interest is the finding that the UL15 protein colocalized with the proteins associated with viral DNA synthesis rather than with assemblons, suggesting that the association with DNA may take place during its synthesis and precedes the involvement of this protein in packaging of the viral DNA into capsids. The formation of three different compartments consisting of proteins involved in viral DNA synthesis, the capsid proteins, and tegument proteins suggests that there exists a viral machinery which enables aggregation and coalescence of specific viral protein groups on the basis of their function.     

Studies on pancreatic acinar cells in tissue culture: basal lamina (basement membrane matrix promotes three-dimensional reorganization

Rat pancreatic acinar cells have been dissociated and maintained in culture under specific conditions which allow the retention of their differentiated state and three-dimensional organization. When cultured on a basal lamina (basement membrane) matrix, the cells first formed large monolayer patches and then reorganized themselves into acini-like structures. The cells regained their polarity around luminal spaces which appeared to be sealed off by well developed junctional complexes. Typical microvilli appeared at the "apical" plasma membrane projecting themselves into the luminal spaces. The intracellular organization resembled that of the cells in situ: a well developed rough endoplasmic reticulum located towards the "base" of the cell around a nucleus; a supranuclearly positioned Golgi apparatus and numerous secretory granules located in the "apical" region of the cell. Immunocytochemistry has revealed the presence of two pancreatic enzymes, amylase and chymotrypsinogen, in the various cellular compartments involved in secretion; the rough endoplasmic reticulum and Golgi cisternae as well as in the secretory granules. Biochemical evaluations have also shown the presence of amylase in the acinar cells and culture medium. These results thus demonstrate that dissociated pancreatic acinar cells maintained in culture under specific conditions reaggregate themselves into acini-like structures and retain their differentiated morphology as well as their ability to secrete.     

Probing compressibility of the nuclear interior in wild-type and lamin deficient cells using microscopic imaging and computational modeling

Mechanical properties of the cell nucleus play an important role in maintaining the integrity of the genome and controlling the cellular force balance. Irregularities in these properties have been related to disruption of a variety of force-dependent processes in the cell, such as migration, division, growth or differentiation. Characterizing mechanical properties of the cell nucleus in situ and relating these parameters to cellular phenotypes remain challenging tasks, as conventional micromanipulation techniques do not allow direct probing of intracellular structures. Here, we present a framework based on light microscopic imaging and automated mechanical modeling that enables characterization of the compressibility of the nuclear interior in situ. Based entirely on optical methods, our approach does not require application of destructive or contacting techniques and it enables measurements of a significantly larger number of cells. Compressibility, in this paper represented by Poisson's ratio ν, is determined by fitting a numerical model to experimentally observed time series of microscopic images of fluorescent cell nuclei in which bleached patterns are introduced. In a proof-of-principle study, this framework was applied to estimate ν in wild type cells and cells lacking important structural proteins of the nuclear envelope (LMNA(-/-)). Based on measurements of a large number of cells, our study revealed distinctive changes in compressibility of the nuclear interior between these two cell types. Our method allows an automated, contact-free estimation of mechanical properties of intracellular structures. Combined with knockdown and overexpression screens, it paves the way towards a high-throughput measurement of intracellular mechanical properties in functional phenotyping screens.     

Coexpression of ecto-5'-nucleotidase/CD73 with specific NTPDases differentially regulates adenosine formation in the rat liver

Ectonucleotidases modulate purinergic signaling by hydrolyzing ATP to adenosine. Here we characterized the impact of the cellular distribution of hepatic ectonucleotidases, namely nucleoside triphosphate diphosphohydrolase (NTPDase)1/CD39, NTPDase2/CD39L1, NTPDase8, and ecto-5'-nucleotidase/CD73, and of their specific biochemical properties, on the levels of P1 and P2 receptor agonists, with an emphasis on adenosine-producing CD73. Immunostaining and enzyme histochemistry showed that the distribution of CD73 (protein and AMPase activity) overlaps partially with those of NTPDase1, -2, and -8 (protein levels and ATPase and ADPase activities) in normal rat liver. CD73 is expressed in fibroblastic cells located underneath vascular endothelial cells and smooth muscle cells, which both express NTPDase1, in portal spaces in a distinct fibroblast population next to NTPDase2-positive portal fibroblasts, and in bile canaliculi, together with NTPDase8. In fibrotic rat livers, CD73 protein expression and activity are redistributed but still overlap with the NTPDases mentioned. The ability of the observed combinations of ectonucleotidases to generate adenosine over time was evaluated by reverse-phase HPLC with the recombinant rat enzymes at high "inflammatory" (500 μM) and low "physiological" (1 μM) ATP concentrations. Overall, ATP was rapidly converted to adenosine by the NTPDase1+CD73 combination, but not by the NTPDase2+CD73 combination. In the presence of NTPDase8 and CD73, ATP was sequentially dephosphorylated to the CD73 inhibitor ADP, and then to AMP, thus resulting in a delayed formation of adenosine. In conclusion, the specific cellular cocompartmentalization of CD73 with hepatic NTPDases is not redundant and may lead to the differential activation of P1 and P2 receptors, under normal and fibrotic conditions.     

A multinomial model for estimating the size of a whale population from incomplete census data

This paper adapts the removal method of population size estimation to the problem of estimating the size of the western Arctic stock of bowhead whales. The whales are counted during their spring migration as they pass two census camps located near Point Barrow, Alaska. Whales seen at the first camp are "removed" from the population of concern to the second camp, where only whales missed by the first camp are counted. If both camps were in operation throughout the migration and if the probability of missing a whale were constant, the removal method would provide a population size estimate based on a trinomial model in which the size of the population would be the number of trials, whales counted by each camp would provide the observed cell totals, and whales missed by both camps would represent an unobserved cell total. Since the probability of missing a whale depends on visibility, we model the population size as the sum of the number of trials of several independent trinomial distributions, each of which represents a particular visibility condition occurring during the census. To account for the fact that watch cannot be maintained at both camps throughout the migration, we derive a confidence interval estimate of the number of trials under a more general model allowing for incomplete observation of totals within particular cells as well as for completely unobserved cells.     

Methodology for determination of the state of microbial culture by degree of spatial organization of whole cells and their external structures

The proposed methodology for determination of biosystems state is based on registration of changes in the space-time parameters of cells and their external structures in a population of microorganisms from different taxonomic groups by the method of noninvasive layer-by-layer analysis using internal reflection spectroscopy. The dependence between the state of an organism and the changes in spatial organization of whole cells and their surface layers have been revealed. The proposed method allows estimation of the character and degree of dynamics of biosystem variations irrespective of the kind of influence. This method can be used for assessing the state of other organisms by the differences between values A for the surface structures and cells of these organisms.