Pocket-like Structure Research Articles

Identification of the prebiotic translation apparatus within the contemporary ribosome

AbstractA structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the proto-ribosome emergence hypothesis and show that the tendency for dimerization, a prerequisite for obtaining the catalytic centre, is linked to the fold of its two components, indicating functional selection at the molecular level in the prebiotic era and supporting the existence of dimeric proto-ribosome.

Three-Dimensional Reconstruction of the Xenarthrous Process of the Thoracic and Lumber Vertebrae in the Giant Anteater

Abstract. The presacral vertebra of anteaters was examined by three-dimensional CT image analysis of the xenarthrous processes peculiar to the Order Xenarthra. The anteater is equipped with two following articulations in addition to the normal zygapophysial articulation. The dorsal xenarthrous process of the former vertebra articulates to the ventral area of the base of the mammillary process in the later vertebra. The pocket-like structure in the ventral area of the mammillary process receives the dorsal and ventral xenarthrous processes of the former vertebra. The complicated articulations do not obstruct the ability of the giant anteater to flex dorsally and laterally, however aids flexibility and strengthens the caudal thoracic and lumber regions of the animal. The xenarthrous processes and articulations may function as a supporter of the body weight during the bipedal standing posture when the anteater destroys the nests of ants and termites and protects itself from the enemies.

Keratinophilic Fungi: a microscopic approach by in vitro hair perforation analysis

Nowadays, environmental moulds are often being referred as also being the cause of superficial mycosis. Keratinophilic activity is one of the characteristics involved in the infectious process of some fungal species. With these findings some problems appear: 1) Do these species really act on keratinized tissues?; 2) How do these fungi perform their keratinophilic activity?; 3) Should we validate the results as positives in the case of isolating from the lesions only species considered as environmental? To answer to these questions, the in vitro hair perforation test was performed in 60 different species, including dermatophytes and environmental isolates. In vitro perforation capability, believed to be one of the characteristics involved in some fungal infectious processes, was assessed with aid of optic-, fluorescence-, electron scanning- and transmission-microscopy, followed by calculation of keratinophilic activity. According to Ali-Shtayeh et al., each hair degradation factor has a specific weight in a keratinolytic activity intensity index called “IKA”, which ranges between 0 and 100%. Changes in the hair structure may occur in the two following different ways: (a) Superficial Erosion, where there is an even hair degradation from the outside to the inside (b) Radial Penetration where there is a localized degradation of hair surface, often in a pocket-like structure. Different types of hyphæ are observed: of narrow diameter called boring hyphæ, of larger diameter called wider boring hyphæ) and swollen boring hyphæ (with dilated tips). Hyphæ may also produce highly specialized perforation organs.

Expression of tight junction proteins in epithelium including Ck20-positive M-like cells of human adenoids in vivo and in vitro

The human adenoid epithelium forms a continuous barrier against a wide variety of exogenous antigens. In this study, to elucidate the structures of the epithelial barrier in the human adenoid, including M-cells, we identified M-cells using an anti-cytokeratin 20 (Ck20) antibody and investigated expression of tight junction proteins in human adenoid epithelium in vivo and in vitro. In human adenoid epithelium and primary cultures, mRNAs of occludin, junctional adhesion molecule-A, ZO-1, and claudin-1, -4, -7, and -8 were detected by reverse transcription-polymerase chain reaction, whereas claudin-2 and -9 were expressed in vitro. In the epithelium in vivo, some Ck20-positive cells were randomly observed and indicated pocket-like structures, whereas Ck7 was positive in almost cells. Transmission electron microscopy revealed that Ck20-associated gold particles could be identified in M-like cells which had short microvilli and harboured the lymphocyte in the pocket-like structure. In primary cultures in vitro, Ck20-positive cells were also detected and had a function to take up fluorescent microparticles. In Ck20-positive cells in vivo and in vitro, expression of occludin, ZO-1, claudin-1 and -7 were observed at cell borders. These results indicate that the epithelial barrier of the human adenoid is stably maintained by expression of tight junction proteins in the epithelium including Ck20-positive M-like cells.

Laminae type and possible mechanisms for the formation of laminated sediments in the Shaban Deep, northern Red Sea

Abstract. Laminated sediments in the Shaban Deep, a brine-filled basin in the northern Red Sea, were analyzed with backscattered electron imagery. Here we present possible mechanisms involved in the formation of laminae of various types and homogenous intervals arising from the detailed investigation of multicore GeoB 7805-1 (26°13.9' N and 35°22.6' E; water depth 1447 m) and gravity core GeoB 5836-2 (26°12.61' N, 35°21.56' E; water depth 1475 m). Sediment makeup includes six types: a) a laminated structure with alternating light (mainly coccoliths) and dark (diatom frustules) layers, where the diatom component is indicative of the intra-annual variability between stratification and mixing events; b) a pocket-like structure attributed to the sinking of particles within fecal pellets and aggregates; c) a matrix of tightly packed diatoms that relates to extended stratification/mixing periods of the water column; d) homogenous intervals that result from turbidity deposition; e) silt accumulations which origin may lie in agglutinated foraminifers; and f) pyrite layers with pyrite formation initiated at the seawater-brine interface.

The role of mite pocket-like structures on Agama caudospinosa (Agamidae) infested by Pterygosoma livingstonei sp. n. (Acari: Prostigmata: Pterygosomatidae)

Pterygosoma livingstonei sp. n. collected from the Kenyan lizard Agama caudospinosa Meek shows morphological affinities with other South African congener species parasitizing lizards of the genus Agama, especially with P. triangulare Lawrence, 1936, but it differs in having glabrous genua II and III. P. livingstonei shows affinities with the Lawrence's hispida species group in the characters of genital and peripheral setae. This new species was found concentrated in a nuchal "mite pocket-like structure", a behaviour previously unreported among species belonging to the genus Pterygosoma. Mite pockets (or acarodomatia, acarinaria) of lizards typically house damaging chigger mites, and are usually interpreted as the evolutionary host's response to limit damage caused by parasites. Because scale mites are permanent ectoparasites and less damaging than seasonally occurring larval trombiculids, the heavy infestation by P. livingstonei in the nuchal skin folds of its host is interpreted as a consequence of the best utilisation of an available protected site by these mites that spend their entire life cycle on their host and whose primitive body shape prevents them from seeking shelter beneath the scales of their lizard host.

Crystal engineering of an inclusion coordination polymer with cationic pocket-like structure and its property to form metal–organic nanofibers

The reaction of cobalt nitrate hexahydrate with 4,4 ′-bipyridine (BPY) under hydrothermal conditions produced a new cationic pocket-like coordination polymer built by mixed double-hydrogen-bonded and coordinated 4,4 ′-bipyridine rectangular-grid with inclusion species, and this material has been fabricated into metal–organic nanofibers by electrospinning.

High temperature oxidation of the bicrystals of Incoloy alloy 909 and an Fe-36% Ni alloy in air under tensile stress

The bicrystals of both an Fe-36% Ni alloy and Incoloy alloy 909 were oxidized at 1200 and 1250 K in air respectively with a tensile stress of 2.5, 4.9, or 14.7 MPa. The thickness of external scale, intergranular subscale and intragranular subscale all exhibited linear relationships with the square root of oxidation time, indicating that oxidation followed parabolic law. In oxidized Fe-36% Ni bicrystals, leading cellular oxide nodules formed in intragranular subscale and a tensile stress promoted intergranular oxidation and the formation of cavities at the grain boundary. In oxidized Incoloy alloy 909 bicrystals, intergranular subscale only slightly led the internal subscale. However, intergranular oxidation was obvious in equiaxed specimens of this alloy. The external scale was stratified in Fe-36% Ni alloy, but it exhibited cellular or pocket-like structure in Incoloy alloy 909. The latter alloy possessed a much better resistance to oxidation than the Fe-36% Ni alloy.

High temperature oxidation of the bicrystals of Incoloy alloy 909 and an Fe-36% Ni alloy in air under tensile stress

The bicrystals of both an Fe-36% Ni alloy and Incoloy alloy 909 were oxidized at 1200 and 1250 K in air respectively with a tensile stress of 2.5, 4.9, or 14.7 MPa. The thickness of external scale, intergranular subscale and intragranular subscale all exhibited linear relationships with the square root of oxidation time, indicating that oxidation followed parabolic law. In oxidized Fe-36% Ni bicrystals, leading cellular oxide nodules formed in intragranular subscale and a tensile stress promoted intergranular oxidation and the formation of cavities at the grain boundary. In oxidized Incoloy alloy 909 bicrystals, intergranular subscale only slightly led the internal subscale. However, intergranular oxidation was obvious in equiaxed specimens of this alloy. The external scale was stratified in Fe-36% Ni alloy, but it exhibited cellular or pocket-like structure in Incoloy alloy 909. The latter alloy possessed a much better resistance to oxidation than the Fe-36% Ni alloy.

Floral bract function, flowering process and breeding systems ofSarcandra andChloranthus (Chloranthaceae)

Structure and function of floral bracts, anthesis and breeding systems were investigated in greenhouse plants ofSarcandra chloranthoides, Sarcandra glabra, andChloranthus spicatus (Chloranthaceae). In early developmental stages the floral bract replaces the lacking perianth as a protective structure by enclosing the floral organs completely in a pocket-like structure, which is formed by the u-shaped attachment zone of the floral bract to the spike axis. The floral bract has a tip with an epithem tissue, from which traces of secretion seem to be released by the stomata. All species investigated have protogynous and longlasting flowers. The female phase begins five to seven days earlier than the male phase. It continues during the male phase and for some time thereafter. The male phase lasts between one day (Chloranthus spicatus) and seven days (Sarcandra chloranthoides). This is the first study on breeding systems of Chloranthaceae. They are of special interest in such a basal family of the angiosperms. Although the investigatedSarcandra andChloranthus species have similar flowers with entomophilous features, surprisingly their breeding systems are diverse:Sarcandra glabra is self-compatible,S. chloranthoides is agamospermous andChloranthus spicatus is self-incompatible.

Structural specializations of immunoglobulin superfamily members for adhesion to integrins and viruses.

The circulation and migration of leukocytes are critical for immune surveillance and immune response to infection or injury. The key step of leukocyte recruitment involves the adhesion between immunoglobulin superfamily (IgSF) proteins on endothelium and integrin molecules on leukocyte surfaces. Some of the IgSF members are subverted as virus receptors. Four crystal structures of N-terminal two-domain fragments of these IgSF proteins have been determined: intercellular adhesion molecule-1 (ICAM-1), ICAM-2, vascular adhesion molecule-1 (VCAM-1), and mucosal addressin cell adhesion molecule-1 (MAdCAM-1). An acidic residue near the bottom of domain 1 plays a key role in integrin binding. For ICAM-1 and ICAM-2, this glutamic acid residue is located on a flat surface, complementary to the flat surface of the I domain of the integrin to which they bind, lymphocyte function-associated antigen-1 (LFA-1). For VCAM-1 and MAdCAM-1, the acidic residue is aspartic acid, and it resides on a protruded CD loop which may be complementary to a more pocket-like structure in the alpha 4 integrins to which they bind, which lack I domains. A number of unique structural features of this subclass of IgSF have been identified which are proposed to consolidate the domain structure to resist force during adhesion to integrins. Different mechanisms are proposed for the different CAMs to present the integrin-binding surface toward the opposing cell for adhesion, and prevent cis interaction with integrins on the same cell. Finally, CD4 and ICAM-1 are compared in the context of ligand binding and virus binding, which shows how human immunodeficiency virus and rhinovirus fit well with the distinct structural feature of their cognate receptors.

A novel galactosyl-binding lectin from the plasma of the blood clam, Anadara granosa (L) and a study of its combining site

The marine blood clam species Anadara granosa (L) belong to arcidae, a family with some extraordinary haematological features. The plasma of this species exhibited strong haemagglutinating activities, from which a galactosyl binding lectin, Anadarin P, was purified in a single step affinity chromatography using Sepharose 4B-asialofetuin as an affinity matrix. The purified lectin, eluted with lactose, was found to be homogeneous by alkaline polyacrylamide disc gels, gel-filtration and isoelectric focusing. Native M(r) of the lectin was 130,000 having a PI value of 6.82 and was composed of two subunits of M(r) 17,000 and M(r) 16,000 which were noncovalently bound. The lectin was remarkably thermostable; the agglutinating titre remained unchanged over a wide range of pH (from 5 to 10) but increased with neuraminidase treated rabbit erythrocytes. Anadarin P combining site has been proposed to be small pocket-like structure which recognised only C-3 and C-4 hydroxyl groups of D-galactose. Presence of bulky groups at C-2 and C-6 exert strong steric hindrance as L-arabinose, 2-deoxy-D-galactose and D-xylose are better inhibitors than D-galactose. The lectin fails to differentiate methyl substituted galactosides as both alpha- and beta- methyl galactosides are equally active; but in case of substituted phenyl glycosides, the lectin shows different affinity towards alpha and beta anomers. The avidity of the lectin to bind the aromatic aglycons of galactosides suggests the presence of a hydrophobic region in the combining site. Interactions with some disaccharides indicate the presence of an extended area near the monosaccharide binding site.

Symmetries of the superconducting order parameters in the doped spin-liquid state.

We show that the Fermi surfaces of the doped holes in the spin-liquid state consist of pairs of pockets separated by crystal momentum Q, in the low-doping limit. Due to the pocketlike structure of the Fermi surface and the A-B sublattice pairing, the spin-singlet superconducting order parameters have unusual symmetry properties. The order parameters are found to have nontrivial quantum numbers of 90\ifmmode^\circ\else\textdegree\fi{} rotation and, sometimes, nonzero crystal momenta. The nonzero crystal momenta carried by the order parameters can be detected by measuring the unusual values (e.g., hc/4e) of the flux confined to various dislocations in superconducting thin films.

Intraluminal Diverticulum of the Duodenum demonstrated by Intravenous Cholangiography

An intraluminal diverticulum of the duodenum is a congenital sac or pocket-like structure lying within the lumen of the duodenum, generally near the level of the ampulla of Vater. We have been able to find only 13 reported cases showing the characteristics of true intraluminal diverticula. We report here an additional case which presents the unique feature of the termination of the common bile duct within the diverticulum. This was demonstrated and diagnosed preoperatively by intravenous cholangiography. Such a case has to the best of our knowledge not been previously recorded. An 18-year-old youth, born in Algeria, was admitted because of attacks of diffuse upper abdominal pain and vomiting of six months duration. There was no definite relationship to meals but some of the attacks occurred at night. He had lost about ten kg in weight during this period. His past history was negative and he did not remember similar attacks in childhood. Physical examination revealed nothing abnormal except some epigastric tenderness. Laboratory examinations were normal. A barium meal revealed an oval-shaped defect in the lower part of the descending duodenum. The defect was well defined at its upper, lateral and lower aspect; its longitudinal diameter was about 5 cm reaching from the region of the papilla of Vater to the inferior genu of the duodenum (Figs. 1, 2 and 3).

Intraluminal diverticulum: a form of duplication.

Intraluminal diverticulum of the duodenum is an unusual congenital anomaly that can be readily recognized by its striking and characteristic roentgen appearance. The abnormality, which so far has been reported only in the second portion of the duodenum, consists of a pocket-like structure, open proximally and closed distally, attached to the inner wall of the gut. A portion of its wall is contiguous with that of the normal duodenum, while the remainder is formed by a thin membrane covered on both sides by typical duodenal mucosa. Although Silcock (6) demonstrated the lesion at autopsy in 1895, it was not until 1947 that Nelson (5) first described its roentgen appearance. Four additional articles on the subject have since appeared in the literature, each reporting a single case (2, 3, 4, 7). All authors except Köhler (3) have attributed the lesion to an incomplete duodenal diaphragm which has become pouch-like as a result of peristaltic activity. We believe that the embryological theory proposed by Bremer (1), to explain duplication of the intestinal tract, is equally applicable to the genesis of intraluminal diverticulum. Thus, as postulated by Köhler, this anomaly may actually represent a form of intestinal duplication rather than a distorted incomplete duodenal diaphragm. Recently we have encountered 2 patients at the University of Cincinnati Medical Center with intraluminal diverticulum of the duodenum demonstrated roentgenologically. In one, surgical correction was complicated by injury to the ampulla of Vater. Case I: I. W., a 47-year-old white male, was first seen at the Cincinnati Veterans Hospital complaining of the sensation of a lump in the epigastrium for six months. This occurred only after eating or drinking and was sometimes accompanied by nausea. The past history was non-contributory. The patient had had no gastrointestinal complaints prior to the present illness. Physical examination and laboratory studies were normal. An upper gastrointestinal series (Figs. 1A and 1B) demonstrated a peculiar defect extending from the mid-descending duodenum well into the third portion. This defect had a large, smooth lumen, the mucosa of which showed a longitudinal linear pattern. The lumen filled with barium from its proximal end. In the upright position it contained entrapped gas. The pocket-like structure impinged upon the main duodenal channel, from which it was separated by a thin, smooth radiolucent membrane. On fluoroscopy the lumen was seen to fill and empty with duodenal peristalsis. At times a mild degree of intussusception appeared to occur, but this did not reproduce the patient's symptoms. The remainder of the gastrointestinal tract was normal. At operation the duodenum appeared normal externally, but when it was opened, several large pieces of pineapple were found free in the lumen. In the distal descending and proximal transverse portions of the duodenum two separate lumens were identified. The more medial of these was about 6 cm.