Preparation and properties of a complex from rat liver of polyribosomes with components of the cytoskeleton.

Gel filtration with 1% agarose (Bio-Gel A-150m) separates polyribosomes bound to microsomal membranes from 'free' polyribosomes when these fractions are prepared by standard centrifugal techniques. However, when polyribosomes contained in an unfractionated postmitochondrial supernatant are run on an identical column, over 90% of the total polyribosomes are present as aggregates, designated 'membrane-cytomatrix', which are eluted in the column void volume. Polyribosomes are not released from these aggregates on removal of microsomal phospholipids by treatment of postmitochondrial supernatant with 1% Triton X-100, a neutral detergent. The aggregates are disrupted by the usual ultracentrifugation techniques used in subcellular fractionation. After treatment of membrane-cytomatrix with Triton X-100 to remove phospholipids and membrane proteins, 58% of the polyribosomes still remain associated with protein-containing complexes in the form of a cytomatrix and are not 'free'. Preparations of both membrane-cytomatrix and cytomatrix are capable of sustained protein synthesis. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis revealed that the cytoskeletal proteins actin and myosin are present in the cytomatrix. Incubation of cytomatrix preparations with the actin-depolymerizing agent deoxyribonuclease I caused release of the polyribosomes. Polyribosome release by deoxyribonuclease I was prevented by prior incubation with phalloidin, which is known to stabilize F-actin. Thus polyribosomes are associated with cytoskeletal elements in rat liver, and this association is dependent on polymeric forms of actin.     

The protein-lipid interface: perspectives from magnetic resonance and crystal structures

Lipid-protein interactions in membranes are dynamic, and consequently are well studied by magnetic resonance spectroscopy. More recently, lipids associated with integral membrane proteins have been resolved in crystals by X-ray diffraction, mostly at cryogenic temperatures. The conformation and chain ordering of lipids in crystals of integral proteins are reviewed here and are compared and contrasted with results from magnetic resonance and with the crystal structures of phospholipid bilayers. Various aspects of spin-label magnetic resonance studies on lipid interactions with single integral proteins are also reviewed: specificity for phosphatidylcholine, competition with local anaesthetics, oligomer formation of single transmembrane helices, and protein-linked lipid chains. Finally, the interactions between integral proteins and peripheral or lipid-linked proteins, as reflected by the lipid-protein interactions in double reconstitutions, are considered.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Cytochemical and fine structural analysis of oogenesis in the gastropod, Ilyanassa obsoleta

An analysis of differentiating oocytes of the gastropod, Ilyanassa obsoleta, has been made by techniques of light and electron microscopy. Early previtellogenic oocytes are limited by a smooth surfaced oolemma and are associated with each other by maculae adhaerentes. Previtellogenic oocytes are also distinguished by a large nucleus containing randomly dispersed aggregates of chromatin. Within the ooplasm are Golgi complexes, mitochondria and a few cisternae of the rough endoplasmic reticulum. When vitellogenesis begins, the oolemma becomes morphologically specialized by the formation of microvilli. One also notices an increase in the number of organelles and inclusions such as lipid droplets. During vitellogenesis there is a dilation of the saccules of the Golgi complexes and cisternae of the endoplasmic reticulum. Associated with the Golgi complexes are small protein-carbohydrate yolk precursors encompassed by a membrane. These increase in size by fusing with each other. The “mature” yolk body is a membrane-bounded structure with a central striated core and a granular periphery. At maturity a major portion of the ooplasmic constituents such as as mitochondria and lipid droplets occupy the animal region while the bulk of the population of yolk bodies are situated in the vegetal hemisphere. The follicle cells incompletely encompass the developing oocyte. In addition to the regularly occurring organelles, follicle cells are characterized by the presence of large quantities of rough endoplasmic reticulum and Golgi complexes whose saccules are filled with a dense substance. Associated with the Golgi saccules are secretory droplets of varied size. Amongst the differentiating oocytes and follicle cells are Leydig cells. These cells are characterized by a large vacuole containing glycogen. A possible function for the follicle and Leydig cells is discussed.     

Homologous recombination in prokaryotes: enzymes and controlling sites

A common step in prokaryotic recombination appears to be the synapsis of the 3'-end of single-stranded DNA with duplex DNA to form a D-loop. The enzymatic mechanisms by which 3'-ends are produced and by which D-loops are converted into recombinant molecules are illustrated by proposed mechanisms of recombination by the Escherichia coli RecBCD pathway and the phage lambda Red pathway. The enzymes promoting recombination and the special DNA sites at which they act are emphasized. Recombination by other E. coli pathways and in other prokaryotes is compared with these mechanisms.     

rab GTP-binding proteins with three different carboxyl-terminal cysteine motifs are modified in vivo by 20-carbon isoprenoids.

p21ras and several other ras-related GTP-binding proteins are modified post-translationally by addition of 15-carbon farnesyl or 20-carbon geranylgeranyl isoprenoids to cysteines within a conserved carboxyl-terminal sequence motif, Caa(M/S/L), where a is an aliphatic amino acid. Proteins ending with M or S are substrates for farnesyltransferase, whereas those ending with L are modified preferentially by geranylgeranyltransferase. We recently reported that GTP-binding proteins encoded by rab1B (GGCC), rab2 (GGCC), and rab5 (CCSN) are modified by 20-carbon isoprenyl derivatives of [3H]mevalonate when translated in vitro, despite having carboxyl-terminal sequences distinct from the Caa(M/S/L) motif. We now show that these proteins function as specific acceptors for geranylgeranyl in vitro and are modified by 20-carbon isoprenyl groups in COS cells metabolically labeled with [3H]mevalonate. Proteins encoded by rab4 and rab6, with yet another distinct carboxyl-terminal motif (xCxC), are similarly modified by 20-carbon isoprenoids in vitro and in vivo. The geranylgeranyl modification of rab5 protein (CCSN) is catalyzed by an enzyme in brain cytosol but not by a purified geranylgeranyltransferase that modifies GTP-binding proteins with the CaaL motif. Unlike the prenylation of proteins with Caa(M/S/L) termini, the prenylation of rab5 protein is not inhibited by a synthetic peptide based on its carboxyl-terminal sequence (TRNQCCSN). When cellular isoprenoid synthesis is blocked by treatment of cells with lovastatin, rab proteins that are normally localized in membranes of the endoplasmic reticulum, Golgi apparatus, and endosomes accumulate in the cytosol. This change in rab protein localization is reversed by providing cells with mevalonate. These findings suggest that geranylgeranyl modification underlies the ability of rab GTP-binding proteins to associate with intracellular membranes, where they are postulated to function as mediators of vesicular traffic.     

酵母基因内含子中二聚体寡核苷酸转录调控位点的统计分析

对高效和低效转录酵母基因内含子序列中寡核苷酸的出现频率进行对照分析, 结果显示高效和低效内含子序列的结构有差异, 而且高效转录内含子序列含有较多潜在的转录因子结合位点. 观察实验获得的转录调控位点, 发现许多调控位点不是相邻接的寡核苷酸,而是由一对保守寡核苷酸构成, 这对寡核苷酸被一段长度固定的非保守区域间隔开. 于是对此形式的二聚体寡核苷酸(dyad)在高效和低效内含子序列中出现的频率进行统计比较分析,抽提出在高效内含子组出现的频率显著高于在低效内含子组出现频率的二聚体寡核苷酸, 分析这些二聚体寡核苷酸在两组内含子序列中的分布特征, 并对照实验结果, 这些二聚体寡核苷酸可能与基因转录的正调控有关.     

Organization of sympathetic neuronal plexuses in culture according to the results of scanning electron microscopy

Nervous cells obtained by dissociation of the rat cranial cervical ganglion cultivated in vitro, are demonstrated to form a network in which spontaneous and provoked electric activity is registered. The structural base for transmission the electrical activity in the plexus are complex divergent-convergent complexes, formed by elementary morphofunctional units: contacts of varicose terminals with each other, with cell bodies and terminal boutons, contacts of the boutons with each other and with the cell bodies, etc. The phenomena are revealed by means of raster electron microscopy.     

Convective Flow of Sisko Fluid over a Bidirectional Stretching Surface

The present investigation focuses the flow and heat transfer characteristics of the steady three-dimensional Sisko fluid driven by a bidirectional stretching sheet. The modeled partial differential equations are reduced to coupled ordinary differential equations by a suitable transformation. The resulting equations are solved numerically by the shooting method using adaptive Runge Kutta algorithm in combination with Newton''s method in the domain [0,∞). The numerical results for the velocity and temperature fields are graphically presented and effects of the relevant parameters are discussed in detail. Moreover, the skin-friction coefficient and local Nusselt number for different values of the power-law index and stretching ratio parameter are presented through tabulated data. The numerical results are also verified with the results obtained analytically by the homotopy analysis method (HAM). Additionally, the results are validated with previously published pertinent literature as a limiting case of the problem.     

Histological Preparation of the Undecalcified Rat Otic Bulla for Mesoscopic Observations

Otic bullas of the rat, obtained by excision and formalin fixed, are successfully embedded in methylmethacrylate by dehydration and subsequent infiltration with plastic under vacuum. Sections 10 μm thick are obtained by cutting the trimmed and sandpapered acrylic blocks on an LKB multirange microtome. The sections are collected on adhesive tape and stained with a Trichrome stain (modified Weigert-van Gieson). Finally, the sections attached to the tape are mounted on microscope slides with glycerin-gelatin and sealed in the same medium. Serial sections are used for three-dimensional graphic reconstruction.     

Turn of promotor DNA by cAMP receptor protein characterized by bead model simulation of rotational diffusion

The rotation diffusion of DNA double helices and their complexes with the cAMP receptor protein (CRP) has been simulated by bead models, in order to derive information on their structure in solution by comparison with results obtained from dichroism decay measurements. Straight DNA double helices are simulated by linear, rigid strings of overlapping beads. The radius of the beads and the length of the string are increased simultaneously by the same increments from initial outer dimensions derived from crystallographic data to final values, which are fitted to experimental rotation time constants observed for short DNA fragments (less than 100 bp). The final values reflect the solvated structure with the same 'solvation layer' added in all three dimensions. The protein is simulated by overlapping beads, which are assembled to a structure very similar to that found by x-ray crystallography. Complexes of the protein with DNA are formed with the centres of palindromic DNA sites at the centre of the two helix-turn-helix-motifs of the protein with some overlap of the two components. Simulation of the experimental data obtained for CRP complexes with specific DNA in the presence of cAMP requires strong bending of the double helices. According to our simulation the DNA is almost completely wrapped around the protein both in the complexes with a 62 bp fragment containing the standard CRP site and with a 80 bp fragment containing the second binding site of the lac operon. Simulations of the data obtained for a 203 bp fragment with both binding sites suggest that the two bound CRP proteins are in contact with each other and that the DNA is wrapped around the two protein dimers. A stereochemical model is suggested with a tetrahedral arrangement of the four protein subunits, which provides the advantage that two binding sites of the protein formed by two subunits each are located favorable for tight contacts to two binding sites on bent DNA, provided that the DNA sites are separated by an integer number of helix turns. In summary, the simulations demonstrate strong bending, which can be reflected by an arc radius in the range around 50 A. According to these data the overall bending angle of our longest DNA fragment is approximately 180 degrees, and thus the protruding ends are sufficiently close to each other such that RNA polymerase, for example, could contact both helical segments.     

Turn of Promotor DNA by cAMP Receptor Protein Characterized by Bead Model Simulation of Rotational Diffusion

Abstract

The rotation diffusion of DNA double helices and their complexes with the cAMP receptor protein (CRP) has been simulated by bead models, in order to derive information on their structure in solution by comparison with results obtained from dichroism decay measurements. Straight DNA double helices are simulated by linear, rigid strings of overlapping beads. The radius of the beads and the length of the string are increased simultaneously by the same increments from initial outer dimensions derived from crystallographic data to final values, which are fitted to experimental rotation time constants observed for short DNA fragments (< 100 bp). The final values reflect the solvated structure with the same ‘solvation layer’ added in all three dimensions. The protein is simulated by overlapping beads, which are assembled to a structure very similar to that found by x-ray crystallography. Complexes of the protein with DNA are formed with the centres of palindromic DNA sites at the centre of the two helix- turn-helix-motifs of the protein with some overlap of the two components. Simulation of the experimental data obtained for CRP complexes with specific DNA in the presence of cAMP requires strong bending of the double helices. According to our simulation the DNA is almost completely wrapped around the protein both in the complexes with a 62 bp fragment containing the standard CRP site and with a 80 bp fragment containing the second binding site of the lac operon. Simulations of the data obtained for a 203 bp fragment with both binding sites suggest that the two bound CRP proteins are in contact with each other and that the DNA is wrapped around the two protein dimers. A stereochemical model is suggested with a tetrahedral arrangement of the four protein subunits, which provides the advantage that two binding sites of the protein formed by two subunits each are located favorable for tight contacts to two binding sites on bent DNA provided that the DNA sites are separated by an integer number of helix turns. In summary, the simulations demonstrate strong bending, which can be reflected by an arc radius in the range around 50 Å. According to these data the overall bending angle of our longest DNA fragment is approximately 180°, and thus the protruding ends are sufficiently close to each other such that RNA polymerase, for example, could contact both helical segments.     

Intravenous endotoxin recruits a distinct subset of human neutrophils, defined by monoclonal antibody 31D8, from bone marrow to the peripheral circulation

Human neutrophils label with fluorochrome-labeled monoclonal antibody 31D8 as bright or dull. We determined the source and fate of 31D8 dull neutrophils by studying volunteers injected with endotoxin, epinephrine, or hydrocortisone, by examining bone marrow, and by examining skin blister exudate. We find that 31D8 dull neutrophils are normally not present in significant numbers in the circulation, are present in large numbers in normal marrow, and are recruited from the marrow by endotoxin, to a lesser extent by steroid, but not at all by epinephrine. 31D8 dull pattern correlates with morphologic immaturity in postendotoxin peripheral blood and bone marrow; however, blister exudate neutrophils contain only morphologically mature neutrophils, of which a significant number are 31D8 dull. We conclude that 31D8 dull neutrophils reside primarily in bone marrow and are released by agents which enhance bone marrow release of neutrophils. Their accumulation in skin blister exudate is unexplained, but suggests a special role in the inflammatory process.     

N-acetylimidazole inactivates renal Na,K-ATPase by disrupting ATP binding to the catalytic site

Treatment of renal Na,K-ATPase with N-acetylimidazole (NAI) results in loss of Na,K-ATPase activity. The inactivation kinetics can be described by a model in which two classes of sites are acetylated by NAI. The class I sites are rapidly reacting, the acetylation is prevented by the presence of ATP (K0.5 congruent to 8 microM), and the inactivation is reversed by incubation with hydroxylamine. These data suggest that the class I sites are tyrosine residues at the ATP binding site. The second class of sites are more slowly reacting, not protected by ATP, nor reversed by hydroxylamine treatment. These are probably lysine residues elsewhere in the protein. The associated K-stimulated p-nitrophenylphosphatase activity is inactivated by acetylation of the class II sites only; thus the tyrosine residues associated with ATP binding to the catalytic center are not essential for phosphatase activity. Inactivated enzyme no longer has high-affinity ATP binding associated with the catalytic site, although low-affinity ATP effects (inhibition of phosphatase and deocclusion of Rb) are still present. The inactivated enzyme can still be phosphorylated by Pi, occlude Rb+ ions, and undergo the major conformational transitions between the E1 Na and E2 K forms of the enzyme. Thus acetylation of the Na,K-ATPase by NAI inhibits high-affinity ATP binding to the catalytic center and produces inactivation.     

THE RECOGNITION AND TREATMENT OF VENOMOUS AND NON-VENOMOUS INSECTS BY SMALL BEE-EATERS

The manner in which bee-eaters cope with the stinging honey-bees which comprise their principal food was investigated by aviary studies of Merops bullocki. Worker Apis are de-venomed by an innate sequence of beating the insect and rubbing its abdomen against the perch. Treatment improves with experience. Drone bees are distinguished by the birds from workers but are not instantly recognised as non-venomous; they are subjected to low intensity rubbing combined with non-venomous prey treatment concomitant with their size. Non-Hymenoptera, including some insects which superficially resemble bees, are recognised as non-venomous and are not rubbed, but are beaten until immobilized. Bee-eaters appear to have partial immunity to venom.     

Evidence that tubulobulbar complexes in the seminiferous epithelium are involved with internalization of adhesion junctions

Tubulobulbar complexes may be part of the mechanism by which intercellular adhesion junctions are internalized by Sertoli cells during sperm release. These complexes develop in regions where Sertoli cells are attached to adjacent cells by intercellular adhesion junctions termed ectoplasmic specializations. At sites where Sertoli cells are attached to spermatid heads, tubulobulbar complexes consist of fingerlike processes of the spermatid plasma membrane, corresponding invaginations of the Sertoli cell plasma membrane, and a surrounding cuff of modified Sertoli cell cytoplasm. At the terminal ends of the complexes occur clusters of vesicles. Here we show that tubulobulbar complexes develop in regions previously occupied by ectoplasmic specializations and that the structures share similar molecular components. In addition, the adhesion molecules nectin 2 and nectin 3, found in the Sertoli cell and spermatid plasma membranes, respectively, are concentrated at the distal ends of tubulobulbar complexes. We also demonstrate that double membrane bounded vesicles are associated with the ends of tubulobulbar complexes and nectin 3 is present on spermatids, but is absent from spermatozoa released from the epithelium. These results are consistent with the conclusion that Sertoli cell and spermatid membrane adhesion domains are internalized together by tubulobulbar complexes. PKCalpha, a kinase associated with endocytosis of adhesion domains in other systems, is concentrated at tubulobulbar complexes, and antibodies to endosomal and lysosomal (LAMP1, SGP1) markers label the cluster of vesicles associated with the ends of tubulobulbar complexes. Our results are consistent with the conclusion that tubulobulbar complexes are involved with the disassembly of ectoplasmic specializations and with the internalization of intercellular membrane adhesion domains during sperm release.     

Color Term Salience

Eleven focal colors are named by basic color terms in many languages. The most salient colors (black, white, and perhaps red) are named in all languages; the least salient of the set are named in fewer languages. Salience correlates with earliness of introduction, as measured by a scale of social evolution; with brevity of expression, as measured by phonemic length of basic color terms; with frequency of use, as measured by frequency of basic color terms in literary languages; and with frequency of mention in ethnographic literature. None of these correlations are established in the pioneer study of Berlin and Kay (1969), a study whose defects are well exposed by Durbin (1972) and Wescott (1970). The first two were documented respectively in Naroll (1970) and Durbin (1972); the last two are documented here. These four correlations independently support the Berlin-Kay color salience theory. They furnish a sound basis for further research on color term salience in particular and indeed on salience phenomena in general. We speculate that salience may be an important general principle of cultural evolution.     

Recommendations for naming plant pathogenesis-related proteins

Pathogenesis-related proteins (abbreviated PRs) are defined as plant proteins that are induced in pathological or related situations. We propose a unifying nomenclature for PRs based on their grouping into families sharing amino acid sequences, serological relationship, and/or enzymatic or biological activity. The nomenclature classifies novel proteins identified by electrophoresis or chromatography along with those established by other workers. The previously proposed system of the five well-established families from tobacco is extended to accommodate a further six families. Families are indicated by arabic numerals and individual members are named by lower case letters in the order in which they are described. Additional rules are proposed to deal with forms containing more than a single polypeptide and as yet unclassified PRs. PR genes whose sequences are conserved but whose designations are not based on function are to be designated Ypr in accordance with the recommendations of the Commission on Plant Gene Nomenclature.     

Effects of phalloidin and cytochalasin B on cytoskeletal structures in cultured rat hepatocytes

Summary In short-term cultures of rat hepatocytes, bile canaliculi enclosed between unseparated cell couplets are able to perform periodical contractions resulting in expulsion of bile. Pericanalicular cytoskeletal proteins are involved in canalicular contractility: F-actin, myosin and tropomyosin are associated around bile canaliculi, as revealed by staining with tetramethylrhodaminyl-phalloidin and by immunofluorescence. Bile canalicular contractility is distributed by cholestatic agents that are known to interfere with actin polymerization; e.g., phalloidin and also cytochalasin B inhibit canalicular contractility and cause pericanalicular vacuolization and formation of blebs. Whereas the association of the cytoskeletal proteins is not affected by treatment with cytochalasin B, treatment with phalloidin results in dissociation of F-actin and myosin, indicating that binding of phalloidin to F-actin impairs its molecular interaction with myosin.     

Hemostatic mechanisms and malignant tumors

The mutual relationships between malignant tumours and mechanisms of blood coagulation are presented in a brief survey. In this connection, the mechanisms of a tumour cell entering the circulation through the vessel well and its leaving into the tissues are discussed, the theory of microtrauma being used for explaining these processes. Subsequently, the alterations to be found in the count and function of thrombocytes after contact with a malignant cell and the impact on this cell by blood platelets are represented. As a third factor the activation of blood coagulation which is exercised by substances with a procoagulatory effect produced by the malignant tissue and the frequently observed thrombosis in the course of neoplastic diseases are dealt with in connection with blood level changes of some coagulation factors. In a fourth section the significance of fibrinolysis, its activation and inhibition as well as the production of fibrinolytic activators by neoplasms are discussed.