Shell structure and affinity of the Carboniferous microproblematicurn Saccamminopsis

Extremely well preserved specimens of the Carboniferous microproblematicum Saccamminopsis Sollas, 1921, from the Visean of Poland reveal a primary structure of the chamber wall, different from that hitherto suggested in hypothetical reconstructions. The calcareous wall is regularly perforated by fine pores which sometimes appear to be bifurcated, but no larger holes are present. The new observations, however, do not resolve the question of affiliation to algae or foraminifers. Similarity of general morphology and shell microstructure justifies a synonymization of Saccam-minopsis the Famennian genus Baculella Conil & Dreesen, 1985. Saccamminopsis is indicative of an extremely shallow marine sedimentary environment.□ Algae, Carboniferous, Foraminifera, problematica , Saccamminopsis.     

Shell structure,ornamentation and affinity of the problematic early Cambrian brachiopod Heliomedusa orienta

The origin of the Brachiopoda has long been a hotly debated topic, and various models have been proposed following the latest finds of exceptionally preserved material. The lower Cambrian (Stage 3) Heliomedusa orienta from the Chengjiang Konservat-Lagerstätte, eastern Yunnan of South China, is an important example of exceptional preservation. A wide variety of affinities have been proposed for Heliomedusa, but recently it has been suggested to reside within the mickwitziids, which may form a stem group to the Brachiopoda. Detailed studies of exceptionally preserved Heliomedusa have increased our knowledge of the soft-part anatomy of this important early brachiopod, but unfortunately, almost nothing is known about its shell structure. Here, we describe new exceptionally preserved specimens from the Chengjiang biota to better reveal both shell structure and ornamentation. Its reticulate–pustulose ornament and tubular structure are reminiscent of traits seen in other mickwitziid brachiopods. In addition, two types of setae can be observed. Apart from the pyritized marginal mantle setae, some tubules are filled with iron oxides, potentially representing thinner and shorter penetrative setae. Both valves of H. orienta appear to have been less mineralized as compared to Mickwitzia monilifera, and the two species differ in diameter and density of tubules and pustules, and in terms of slightly less projected profile of ventral valve with lower umbo posteromedially placed. Although Heliomedusa clearly is closely related to Mickwitzia, their different preservational modes (compacted poorly mineralized/noncompacted mineralized) make detailed comparison difficult; they are provisionally kept as separate genera pending further studies of better-preserved Chinese material.     

Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking

The PI-SceI protein is an intein-encoded homing endonuclease that initiates the mobility of its gene by making a double strand break at a single site in the yeast genome. The PI-SceI protein splicing and endonucleolytic active sites are separately located in each of two domains in the PI-SceI structure. To determine the spatial relationship between bases in the PI-SceI recognition sequence and selected PI-SceI amino acids, the PI-SceI-DNA complex was probed by photocross-linking and affinity cleavage methods. Unique solvent-accessible cysteine residues were introduced into the two PI-SceI domains at positions 91, 97, 170, 230, 376, and 378, and the mutant proteins were modified with either 4-azidophenacyl bromide or iron (S)-1-(p-bromoacetamidobenzyl)-ethylenediaminetetraacetate (FeBABE). The phenyl azide-coupled proteins cross-linked to the PI-SceI target sequence, and the FeBABE-modified proteins cleaved the DNA proximal to the derivatized amino acid. The results suggest that an extended beta-hairpin loop in the endonuclease domain that contains residues 376 and 378 contacts the major groove near the PI-SceI cleavage site. Conversely, residues 91, 97, and 170 in the protein splicing domain are in close proximity to a distant region of the substrate. To interpret our results, we used a new PI-SceI structure that is ordered in regions of the protein that bind DNA. The data strongly support a model of the PI-SceI-DNA complex derived from this structure.     

Properties of flaky affinity resin with co-continuous structure

A new type of flaky affinity resin for capture of the target proteins was prepared to discuss its properties compared with those of a particulate affinity resin. The resin prepared had totally co-continuous structure (monolith) and was utilized in the shape of flake. The concentration of surface amino groups for immobilization of ligand was determined to be 22.3 micromol/ml. Immobilizations of ligand such as Sulfonamide, Ketoprofen, Captopril, or Methotrexate (MTX) on the affinity resin were quantitatively proceeded to afford fully covered (100%) affinity resins. Control of the immobilization rate of affinity resin using Sulfonamide or Ketoprofen was successfully achieved with the calculated immobilization rate. The flaked shape of affinity resin (100-400 microm) presumably simplified affinity experimental procedures and the affinity resin immobilizing Sulfonamide effectively captured one of the target proteins, CAII, without non-specifically bound proteins. The observed properties of the flaky affinity resin as well as ease in handling are really useful for capture of the target proteins of possible rare ligands.     

Pregna-D'-pentarane structure influences progesterone receptor affinity for DNA

Electrophoretic mobility shift assay was used to determine whether pregna-D'-pentaranes allow progesterone receptor (PR) from rat uterine cytosol to bind hormone response element (HRE)-containing oligonucleotide duplexes and to measure the affinity of this interaction. The formation of DNA-protein complexes in low salt medium was progesterone-related ligand-, temperature-, and PR-dependent, and specific for HRE. The highest affinity of PR to DNA (equilibrium K(a) = 0.420 +/- 0.185 nM(-1)) was found in the presence of the partial agonist/antagonist RU486, while the lowest affinity (K(a) = 0.074 +/- 0.013 nM(-1)) was demonstrated with the full agonist 6alpha-methyl-16alpha,17alpha-cyclohexanoprogesterone. With the exception of the strong full agonist R5020, there was a tendency toward correlation between the induced lower affinity of PR for DNA in the context of tyrosine aminotransferase HRE and the full agonistic activity of tested compounds.     

Influence of canonical structure determining residues on antibody affinity and stability

A number of light and heavy chain canonical residue core redesigns were made in a therapeutic antibody (AQC2, anti-VLA1) Fab to explore the consequences to binding affinity and stability. These positions are all loop supporting, primarily CDR1 residues which do not directly contact the antigen. Structure based methods were used with and without consensus sequence information. 30 constructs were made, 24 expressed, and 70% of the designs using consensus sequence information retained binding affinity. Some success maintaining stability with more extreme redesigns suggests a surprising tolerance to mutation, though it often comes at the cost of loss of binding affinity and presumed loop conformation changes. In concordance with the expected need to present an ordered surface for binding, a relationship between decreased affinity and decreased stability was observed. Overpacking the core tends to destabilize the molecule and should be avoided.     

Hemoglobin affinity and structure in high-altitude and sea-level carnivores from Peru

We compared hemoglobin affinity (P₅₀) and structure of high altitude (HA) carnivores with populations of the same species or genus living at sea level (SL). P₅₀ was measured in cats, pumas and foxes. It differed in animals occupying both niches. SL: cat 29.3 torr, puma 36.3 torr, fox 26.2 torr; HA: cat 22.5 torr, puma 31.1 torr, fox 18.5 torr. Heme and globins were fractionated by HPLC. Puma and fox hemoglobins also showed structural differences. P₅₀ is lower in genotypically HA-adapted species studied and can differentiate SL and HA populations of the same species.     

Analysis of the discrete structure of antibodies by affinity and antigen-binding capacity

Immune sera are a mixture of different groups of antibodies belonging to the same class of immunoglobulins, but differing in their affinity. The graphic analysis and numerical methods permit the determination of the size and affinity of each group of antibodies. Differences in affinity are manifested as differences in antigen-binding capacity. The antigen-binding capacity index, calculated as the product of the association constant multiplied by the concentration of the active centers of antibodies, is proposed.     

Correlating structure and affinity for PEX5:PTS1 complexes

Many proteins that are destined to reside within the lumen of the peroxisome contain the peroxisomal targeting signal-1 (PTS1), a C-terminal tripeptide approximating the consensus sequence -Ser-Lys-Leu-COO(-). The PTS1 is recognized by the tetratricopeptide repeat (TPR) domains of PEX5, a cytosolic receptor that cycles between the cytoplasm and the peroxisome. To gain insight into the energetics of PTS1 binding specificity and to correlate these with features from the recently determined structure of a PEX5:PTS1 complex, we used a fluorescence-based binding assay that enables the quantitation of the dissociation constants for PTS1-containing peptide complexes with the TPR region of human PEX5. Through application of this assay to a collection of pentapeptides containing different C-terminal tripeptide sequences, including both natural and unnatural amino acids, the thermodynamic effects of sequence variation were examined. PTS1 variants that correspond to known functional targeting signals bind to the PEX5 fragment with a change in the standard binding free energy within 1.8 kcal mol(-1) of that corresponding to the peptide ending with -Ser-Lys-Leu-COO(-). The results suggest that a binding energy threshold may determine the functionality of PTS1 sequences.     

Subunit structure of the high and low affinity human interleukin-15 receptors

Radio-iodinated cytokines and monoclonal antibodies directed at the IL-2R beta- and gamma-chains were used to analyze the structure of the cell-surface IL-15 and IL-2 receptors expressed by the human lymphoma cell clone YT-2C2. YT-2C2 cells are IL-2R alpha negative and express IL-2R gamma (15,000 molecules/cell) in excess of IL-2R beta (11,000 molecules/cell). Accordingly, they display a number of beta/gamma complexes of intermediate affinity for IL-2 and IL-15 which is equivalent to the number of beta-chains. Both cytokines compete for binding to this beta/gamma complex. There are about 800 high affinity IL-15 receptors, suggesting the presence of a similar number of IL-15R alpha-chains. Within the common intermediate affinity beta/gamma-complex, the anti-beta-chain A41 mAb defines an epitope which is similarly engaged in IL-2 and IL-15 binding, whereas the anti-beta-chain 284 mAb defines an epitope which does not display similar interaction with either cytokines. Thus, although IL-2 and IL-15 compete for binding to this beta/gamma-complex, they do not use similar binding areas. Cross-linking and immunoprecipitation experiments have shown that the high affinity IL-15 receptors comprises IL-2R beta/gamma, in association with IL-15R alpha and that the three chains can be efficiently cross-linked to IL-15 and co-immunoprecipitated. Contrary to the intermediate affinity situation, high affinity IL-15 binding and subunit cross-linking were not affected by excess amounts of IL-2, A41 or 284 mAb, suggesting that when engaged in the IL-15 high affinity complex, the beta- and gamma-chains adopt different conformations, at least with respect to IL-15 binding. Finally, we provide evidence for the participation of a novel 35 kDa component within the high affinity structure. This component is immunoprecipitated with anti-IL-2R gamma mAb but not with anti-IL-2R beta mAb and might correspond to a truncated form of IL-2R gamma-chain.     

Quantitative structure/retention relationships in affinity chromatography.

Affinity chromatography (AC) followed by quantitative structure/retention relationships (QSRR) analysis provides information on both the analytes and the macromolecules forming the stationary phases. QSRR equations derived for test series of analytes (often drugs) are interpreted in terms of structural requirements of the specific binding sites on macromolecules. Chromatographically demonstrated differences in analyte/macromolecule interactions may be relevant to molecular pharmacology and rational drug design. Multiple regression analysis of appropriately designed sets of affinity-chromatographic data may help increase the speed and efficiency of search as for new drugs and reduce the need for in vivo screening. Specific high-performance affinity-chromatographic separations can be optimized by rational selection of chiral columns, the characteristics of which are provided by QSRR.     

Shell structure in Difflugia Lobostoma observed by scanning and transmission electron microscopy

Observations by scanning and transmission electron microscopy provide information about shells of Difflugia lobostoma which suggests a complex activity in shell construction. As observed by scanning microscopy, the shell consists of a single layer of sand grains which are organized into rosettes. The sand grains of the rosettes are different in size from those of flat areas between rosettes suggesting that the organism sorts these stones and places them according to size. Hydrofluoric acid treatment dissolves the sand but leaves a web of cement material intact. Examination of such acid treated specimens by transmission microscopy shows structure in the cement material of the shell, and granules of similar structure in the cell body. The rosette pattern observed differs from shell patterns in other species of Difflugia, and this suggests that shell structure may be species specific.     

Chromogenic labeling of milk oligosaccharides: purification by affinity chromatography and structure determination

Oligosaccharides from human milk were derivatized with 4'-N,N-dimethylamino-4-amino-azobenzene (DAAB) by reductive amination and purified by affinity chromatography on immobilized antibodies followed by resolution of the retained antigenic molecules by adsorption chromatography on HPLC. The visibility to the naked eye and the favorable handling properties of the DAAB-oligosaccharides (desalting, quantification) offered distinctive advantages over underivatized oligosaccharides. Analysis by MS and NMR identified the two major antigens as the Lewis a active pentasaccharide and the Lewis b active hexasaccharide, respectively. Further derivation of DAAB-oligosaccharides by palmitoylamidoacetaldehyde generated glycolipid-like compounds suitable for immunological detection by in situ overlay techniques after separation by thin-layer chromatography.     

Cell number and cellular composition in vermiform larvae of dicyemid mesozoans

Cell numbers and cellular composition were examined in vermiform larvae of 44 species of dicyemid mesozoans phylum Dicyemida belonging to six genera: Conocyema , Dicyema , Dicyemennea , Dicyemodeca , Microcyema and Pseudicyema . In addition, the literature on vermiform larvae of another 59 species was reviewed. Vermiform larvae typically have a constant number of peripheral cells that are species specific. Interspecific variations in the total number of peripheral cells range from 10 to 39. The most frequent number is either 22 or 23. Differences in the total number of peripheral cells are mostly due to differences in the number of trunk peripheral cells, such as parapolar cells, diapolar cells and uropolar cells. The body length of vermiform larvae is positively correlated with the number of trunk peripheral cells. Interspecific variations in the total number of trunk peripheral cells range from 2 to 31. The most frequent number is 14. In species with 14 trunk peripheral cells, individual variations of cell numbers were minimal. In species with more trunk peripheral cells, some individual variations appeared. Increase and decrease of trunk cell number might cause diversity of dicyemids, which is possibly related to speciation in these simple multicellular animals.     

Characterization of rat Leydig cell gonadotropin receptor structure by affinity cross-linking

The present study was intended to examine the structure of the rat Leydig cell gonadotropin receptor. Leydig cell suspensions were prepared by either collagenase digestion or mechanical disruption of the testes. The cells were incubated with 125I-human chorionic gonadotropin (hCG) following which the bound 125I-hCG was covalently cross-linked to the cell surface receptor using a cleavable (dithiobis(succinimidyl propionate] and a noncleavable (disuccinimidyl suberate) cross-linking reagent. The extracted cross-linked membrane proteins were resolved on sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing and nonreducing conditions and subjected to autoradiographic analysis. Under nonreducing conditions, three radiolabeled bands, in addition to intact hCG and its alpha-subunit, were detected with apparent molecular weights of 184,000, 136,000, and 103,000. However, under reducing conditions, three radiolabeled bands migrated on the gel corresponding to molecular weights of 144,000, 106,000, and 75,000. The binding of 125I-hCG to the receptor was inhibited by hCG and luteinizing hormone, but not by a number of other peptides or proteins. The radiolabeled bands were not detectable in hCG down-regulated Leydig cells. Furthermore, a similar autoradiographic pattern of 125I-hCG-linked complexes was seen when the 125I-linked receptor complex was subjected to immunoprecipitation with anti-hCG antibodies followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In addition, evidence was obtained indicating that these three labeled bands were derived from the same molecular species. The data suggests that the hCG receptor in Leydig cell is probably an oligomeric complex with a molecular weight of about 250,000, which is composed of three polypeptide chains of molecular weights 121,000, 83,000, and 52,000 held together through noncovalent forces. Additionally, collagenase treatment of Leydig cells does not appear to alter the autoradiographic pattern of the 125I-hCG-linked receptor.     

Attached vermiform gastropods in Carboniferous marginal marine stromatolites and biostromes

Tubiform fossils conventionally referred to Serpula cf. advena Salter and species of Spirorbis Lamarck from the British Lower Limestone Shales and Border Group (Lower Carboniferous) are re-examined. They occur in peritidal carbonate environments of schizohaline aspect. These fossils superficially resemble calcareous polychaete tubes but have skeletal characters, including molluscan wall structure, numerous internal septa, and protoconch, which indicate that they represent a new group of substrate-attached, disjunctly coiled gastropods. They resemble archaeogastropods in internal morphology of the skeleton but show parallels in external form and occurrence with the extant Vermetidae. There are two principal modes of occurrence: (1) erect tubes forming intertidal biostromes associated with non-skeletal algal laminites, and (2) prostrate discoidal tubes encrusting subtidal skeletal stromatolites or occasionally forming larger irregular bioherms. These biostromes and bioherms are comparable in structure to Recent vermetid reef developments.     

Histology of vermiform appendix-like organ in slow loris.

The vermiform appendix-like organ (VALO) of the slow loris was investigated for its histology and immunohistochemical characteristics. The VALO has a much thinner wall with flat folded mucosa and shallower crypts than the cecal mucosa, while cellular components and population of the mucosa were similar to those of the cecum. No coalescent lymph nodules were seen in the submucosa. Immunohistochemically 5-HT-positive cells in the crypts and CD3- and CD8-positive lymphocytes in the lymph nodules were shown in the VALO as well as in the cecum. These findings suggest that the VALO is a low-differentiated vermiform appendix of the slow loris.