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A fragment comprising the last third of bovine serum albumin which accounts for almost all the antigenic reactivity of the native protein.

The fragmentation of native bovine serum albumin by trypsin has been studied in aqueous solution under various conditions with regard to the yield and size of the fragments obtained. From a partial tryptic hydrolysate at pH 8.2 (40 degrees, 1 hour), a homogeneous fragment was isolated in high yield by gel filtration on Sephadex G-100, followed by chromatography on DEAE-cellulose. The molecular weight of the fragment by gel filtration on calibrated Sephadex G-100 columns and by sodium dodecyl sulfate electrophoresis was 22,500. After reduction of the disulfide bonds followed by alkylation of the resultant thiol groups with iodoacetamide, the fragment retained homogeneity by disc electrophoresis and its molecular weight remained unchanged, indicating that it was composed of a single polypeptide chain. From its amino acid composition, sequence of the first 20 residues, and actions of carboxypeptidases A or B, it was unequivocally assigned to positions 377-571 in albumin. The inhibitory activity of the fragment was 90 to 93% towards the immune reaction of the protein with the IgG fraction of the antisera. The IgGfraction accounted for 96% of the total antibody activity in the antisera. An immunoabsorbent of fragment 377-571 removed 89 to 95% of the antibody to albumin. A fluorescent derivative of the fragment, which retained full immunochemical activity, was found to bind 2 mol of antibody/mol of peptide. The disulfides in peptide 377-571 were essential for its immunochemical reaction because the latter was entirely abolished upon reduction and S-alkylation of the disulfides. Since this fragment comprised only a third of the albumin molecule, but accounted for 90 to 95% of its antigenic reactivity, the results indicated that native albumin carries identical repeating antigenic reactive sites.

Amino Acid Sequence↗

Fragment C of tetanus toxin antagonizes the neuromuscular blocking properties of native tetanus toxin.

Tetanus toxin, fragment B and fragment C were assayed for toxicity on the mouse phrenic nerve-hemidiaphragm preparation. The native toxin was a potent blocker of neuromuscular transmission; fragment B possessed little toxicity and fragment C was atoxic. Pretreatment of tissues with fragment C antagonized the neuromuscular blocking properties of tetanus toxin, but not those of type A botulinum toxin or beta-bungarotoxin. Agents that antagonize cholera toxin (B subunit) and diphtheria toxin (CRM197) did not antagonize tetanus toxin and did not alter the ability of fragment C to antagonize tetanus toxin. Fragment C exerted its effect by competing with unbound toxin for receptor sites on the nerve membrane. The fragment did not: 1) displace bound toxin; 2) inhibit internalization of toxin; or 3) inhibit intracellular expression of toxicity. In assays on intact cells, under conditions in which toxin binding was not dissociable, fragment C binding to phrenic nerves had an apparent KD of approximately 1.4 X 10(-7) M. Homogenates of mouse cerebral cortex adsorbed tetanus toxin and these homogenates competed with phrenic nerves for unbound toxin. Homogenized cortex did not displace or promote desorption of toxin already bound to phrenic nerves. Homogenates of eel and torpedo electric organ were not very effective in adsorbing toxin.

Adsorption↗

Fragments of rabbit striated muscle alpha-tropomyosin. II. Binding to troponin-T.

The interactions of a variety of large fragments of rabbit skeletal muscle alpha-tropomyosin, prepared as previously described, with troponin-T and a soluble tropomyosin-binding fragment of troponin-T (CB1) have been investigated by affinity chromatography and gel filtration. No specific interactions between NH2-terminal fragments encompassing residues 1-189 with troponin, troponin-T, or CB1 immobilized on a Sephadex 4B column could be demonstrated. Similarly, there was no interaction between these fragments and CB1 on a gel filtration column operated in 0.1 M KCl, 10 mM imidazole pH 7.0 buffer. On the other hand, all fragments encompassing residues 190-284 showed interaction with troponin-T on the affinity column and with CB1 by gel filtration. When mixtures of two fragments, one of which had the intact NH2-terminal sequence of the original tropomyosin structure and the other the intact COOH-terminal sequence, were applied to the gel filtration column, there was no indication of interaction between them. However, when CB1 was included in the mixture, a ternary complex of the three components was demonstrable. Fragments in which 10 or 12 residues at the NH2-terminal end of the alpha-tropomyosin sequence were absent showed no evidence of forming a ternary complex with CB1 and the COOH-terminal fragments. We conclude that the binding of the troponin-T fragment, CB1, to the COOH-terminal third of the alpha-tropomyosin molecule enhances head-to-tail aggregation of tropomyosin molecules either indirectly by the transmission of conformational changes to the head-to-tail overlap region or more directly by binding close to or at this region.

Animals↗

Diagnostic accuracy and tumor-targeting kinetics of complete versus fragmented 99mTc-labeled anti-carcinoembryonic antigen antibodies: an intraindividual comparison.

The goal of this study was to intraindividually compare a complete versus a fragmented, directly 99mTc-labeled, monoclonal anti-carcinoembryonic antigen (CEA) antibody, with respect to their antigen-targeting kinetics, sensitivity, and diagnostic accuracy in patients with CEA-expressing tumors. Twenty-five patients were investigated with the 99mTc-labeled anti-CEA IgG1 BW 431/26 and the F(ab')2/Fab' fragment mixture F023C5 within 7 days. For quantitative analysis, the region of interest technique was applied to planar scans, whole-body scans, and single photon emission computed tomography slices 10 min to 48 h postinjection (PI). Final correlations were performed according to the histopathology after surgery or biopsy. Earliest tumor detection was possible with complete IgG1 4 h PI (52% of finally positive lesions). Twenty-four- or even 48-h scans were necessary in 48% of finally positive lesions; tumor detection with fragments was possible in 17% at 1 h PI and in 94% at 4 h PI. With both monoclonal antibodies, in 35%, single photon emission computed tomography was necessary for tumor detection. Absolute antibody uptake in tumor lesions was higher with complete monoclonal antibodies than with fragments. The sensitivity of fragments was higher in detecting primary tumors, local recurrences, and lymph node metastases. For detection of liver metastases, sensitivity was also higher for fragments than for IgG (87 versus 73%), but in scintigraphically positive lesions, tumor:background ratios were significantly lower with fragments (1.26 +/- 0.12 versus 1.70 +/- 0.32; P < 0.01). Therefore, fragments seem to be more suitable for earlier detection of lesions known for their good vascularization, vascular permeability, and antigen accessibility, such as local recurrences, lymph node metastases, and peritoneal carcinomatoses. In liver metastases (high interstitial pressure, low vascular leakage), sensitivity of fragments is higher, but their rapid serum and whole-body clearance lead to a lower absolute antibody uptake, with the consequence of significantly lower tumor:background ratios than with IgG.

Adenocarcinoma↗

Cytokeratin 19 fragment CYFRA 21-1 compared with carcinoembryonic antigen, squamous cell carcinoma antigen and neuron-specific enolase in lung cancer. Results of an international multicentre study.

The diagnostic value of the water-soluble cytokeratin 19 fragment CYFRA 21-1 in lung cancer was assessed in comparison with carcinoembryonic antigen, squamous cell carcinoma antigen, and neuron-specific enolase. The cut-off value, defined as 95% specificity versus a group of 526 patients suffering from benign chest diseases, was set at 3.3 micrograms/l for cytokeratin 19 fragment CYFRA 21-1 (carcinoembryonic antigen: 7.8 micrograms/l, squamous cell carcinoma antigen: 1.9 micrograms/l, neuron-specific enolase: 13.7 micrograms/l). Elevated pretreatment cytokeratin 19 fragment CYFRA 21-1 concentrations were recorded: in 112 of 244 (46%) patients with all histological types of lung cancer (carcinoembryonic antigen: 32%, squamous cell carcinoma antigen: 25%, neuron-specific enolase: 28%), in 89 of 177 (50%) patients with non-small cell lung cancer (carcinoembryonic antigen: 33%, squamous cell carcinoma antigen: 24%, neuron-specific enolase: 12%), in 47 of 81 (58%) patients with squamous cell carcinoma (carcinoembryonic antigen: 23%, squamous cell carcinoma antigen: 32%, neuron-specific enolase: 14%), in 27 of 63 (42%) patients with adenocarcinoma (carcinoembryonic antigen: 44%, squamous cell carcinoma antigen: 14%, neuron-specific enolase: 9%), in 15 of 33 (45%) patients with other non-small cell lung cancer (carcinoembryonic antigen: 36%, squamous cell carcinoma antigen: 24%, neuron-specific enolase: 14%), and in 20 of 55 (36%) patients with small cell lung cancer (carcinoembryonic antigen: 32%, neuron-specific enolase: 77%). Three of 12 patients with undefined histological type showed cytokeratin 19 fragment CYFRA 21-1 elevations. The best performance in terms of sensitivity and diagnostic accuracy was attained with the cytokeratin 19 fragment CYFRA 21-1 test in squamous cell carcinoma. In small cell lung cancer neuron-specific enolase was confirmed to be superior to the other markers. Cytokeratin 19 fragment CYFRA 21-1 concentrations increased with the extent of the malignant disease in non-small cell lung cancer. The positivity rate of cytokeratin 19 fragment CYFRA 21-1 in tumour stage TNM I was only 23% (carcinoembryonic antigen: 23%, squamous cell carcinoma antigen: 14%), i.e. the markers under study cannot be used for the diagnosis of early stage disease. Cytokeratin 19 fragment CYFRA 21-1 differentiated significantly between squamous cell carcinoma and the other histological types (p < 0.01). In addition, cytokeratin 19 fragment CYFRA 21-1 distinguished significantly the operable group TNM I-IIIa from inoperable TNM IIIb-IV (p < 0.05), but not TNM IIIa from IIIb. Out of 177 patients with non-small cell lung cancer, 90 individuals were monitored after surgery.(ABSTRACT TRUNCATED AT 400 WORDS)

Adenocarcinoma↗

Proteolytic fragments of phosphoinositide-specific phospholipase C-delta 1. Catalytic and membrane binding properties.

Active proteolytic fragments of phosphoinositide-specific phospholipase C-delta 1 (PLC-delta 1) were generated by trypsin digestion of the native protein. Brief proteolysis produced a 77-kDa fragment that contained the highly conserved X and Y regions but lacked the amino-terminal domain (amino acids 1-60). Prolonged digestion of PLC-delta 1 produced two fragments, one of 45 kDa that contained the entire X region and another of 32 kDa that consisted of the entire Y region and COOH-terminal domain. The 45- and 32-kDa fragments were isolated as an active heterodimeric complex. The 77-kDa fragment and the complex catalyzed calcium-dependent hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) in detergent/phospholipid mixed micelles. When compared with the native enzyme, both the 77-kDa fragment and the complex exhibited a reduced capacity to processively hydrolyze PIP2; increasing the mole fraction of PIP2 in the mixed micelle surface greatly increased the rate of PIP2 hydrolysis catalyzed by the native enzyme but not the fragments. Both fragments also exhibited a reduced affinity for substrate; the native enzyme bound to bilayer vesicles consisting of phosphatidylcholine and PIP2 with high affinity (Ka approximately 10(6) M-1), whereas the fragments bound weakly (Ka < 10(4) M-1). These results demonstrate that the X, Y, and COOH-terminal regions form a calcium-dependent catalytic core that is resistant to proteolysis. The amino-terminal domain appears to be essential for high affinity binding to PIP2 but not catalysis. These observations are consistent with the idea that the amino-terminal domain forms part of a PIP2 binding site, which anchors PLC-delta 1 to the membrane surface during processive hydrolysis of its substrate.

Amino Acid Sequence↗

[Cloning of DNA fragments containing promoter activity from Streptomyces mycarofaciens 1748].

A DNA fragment containing promoter activity has been cloned from midecamycin producing strain (S. mycarofaciens 1748)., using promoter-probe plasmid vector pIJ486. The molecular size of this fragment was 2.3kb as shown by restriction analysis. A HindIII-HindIII 2.08KB DNA fragment obtained from the original fragment has been analysed by subcloning it into polylinker of vector pIJ486/7 which have opposite direction. The result showed that HindIII-HindIII 2.08kb DNA fragment has promoter activity in both direction. Transformants of plasmid containing this fragment in vector pIJ487 in S. lividans TK24 were resistant to Km in the level of 20mg/ml, but in vector pIJ 486 were resistant to the level of 3mg/ml. It indicated that a rather strong promoter activity region was in the HindIII/XbaI-HindIII direction. BamHI fragments (A-0.79kg, B-0.67kb, C-0.62kb) in 2.08kb DNA fragment have been studied in regards of their promoter activity. The result suggested that A-0.79kb region has the same promoter activity as in HindIII-HindIII 2.08kb DNA fragment.

Cloning, Molecular↗

[Certain features of monoclonal rheumatoid immunoglobulin M fragmentation by "hot" trypsin].

Using analytical ultracentrifugation and affinity chromatography, it has been shown that "hot" trypsin (hydrolysis at 58-60 degrees C) releases two types of fragments from the monoclonal (Waldenstrom disease) immunoglobulin M possessing a rheumatoid activity (IgM-RF). The first fragment corresponds to a normal Fab-fragment as can be judged from its molecular weight. The other fragment designated as a (Fc)*5-fragment has a much higher molecular weight as compared with typical (Fc)*5-fragment released from non-rheumatoid IgM. According to calculations, the (Fc)*5-fragment retains two uncleaved Fab-regions and displays a rheumatoid activity. The Fab-fragments pool cleaved from IgM-RF consists of non-rheumatoid and rheumatoid components at an approximate ratio of 3:1. It seems, therefore, likely, that ten Fab-regions of IgM-RF are nonidentical with regard to their functional and structural properties. Most of those do not possess a rheumatoid activity and are more readily cleaved from IgM-RF by "hot" trypsin in comparison with rheumatoid active fragments.

Antibodies, Monoclonal↗

Chemical design of radiolabeled antibody fragments for low renal radioactivity levels.

The renal uptake of radiolabeled antibody fragments presents a problem in targeted imaging and therapy. We hypothesized that the renal radioactivity levels of radiolabeled antibody fragments could be reduced if radiolabeled compounds of urinary excretion were released from glomerularly filtered antibody fragments before they were incorporated into renal cells by the action of brush border enzymes, present on the lumen of renal tubules. 3'-[131I]Iodohippuryl N(epsilon)-maleoyl-L-lysine ([131I]HML) was conjugated with a thiolated Fab fragment because the glycyl-lysine sequence in HML is a substrate for a brush border enzyme and metaiodohippuric acid is released by cleavage of the linkage. Fab fragments were also radiolabeled by direct radioiodination (125I-Fab) or by conjugation with meta-[125I]-iodohippuric acid via an amide bond [N-(5-maleimidopentyl) 3'-iodohippuric acid amide ([125I]MPH-Fab)] or an ester bond [maleimidoethy 3'-iodohippurate ([125I]MIH-Fab)] by procedures similar to those used for [131I]HML-Fab. In biodistribution experiments in mice, [131I]HML-Fab demonstrated markedly low renal radioactivity levels with kidney:blood ratios of radioactivity of 1 from 10 min to 1 h due to rapid release of meta-[131I]iodohippuric acid. [125]MIH-Fab and 1251-Fab reached their peak ratios of 3.8 and 7.3 at 1 h, respectively, and [125I]MPH-Fab showed the maximum ratio of 16.8 at 6 h. In subcellular distribution studies, both [125I]MIH-Fab and 125I-Fab showed migration of radioactivity from the membrane to the lysosomal fraction of the renal cells from 10 to 30 min postinjection, whereas the majority of the radioactivity was detected only in the membrane fraction after administration of [131I]HML-Fab at both time points. In nude mice, [131I]HML-Fab showed one-quarter of the renal radioactivity of simultaneously administered 125I-Fab without impairing the target radioactivity levels 3 h after injection. These findings indicated that HML is a useful reagent for targeted imaging and therapy using antibody fragments as vehicles. These findings also suggested that the radiochemical design of radiolabeled antibody fragments that liberate radiometabolites of urinary excretion from antibody fragments by the action of brush border enzymes may constitute a new strategy for reducing the renal radioactivity levels of antibody fragments.

Animals↗

Regulation of neutrophil functions by elastase-generated IgG fragments.

IgG is split by neutrophil elastase into Fc and Fab fragments. These IgG fragments influence the functions of stimulated neutrophils such as chemotaxis, oxidative burst, and enzyme release. FMLP stimulated leukocyte chemotaxis is specifically inhibited by the elastase generated Fc fragments. Seven nmol Fc/10(6) PMN totally inhibit the chemotaxis stimulated by 16 to 125 nM FMLP. Native IgG and Fab fragments show no effect. FMLP-stimulated superoxide anion generation is specifically inhibited by Fc fragments with half maximal inhibition by 1.2 nmol/10(6) PMN. The generation of hydrogen peroxide is concomitantly stimulated, resulting in a superoxide dismutase-like effect. FMLP-stimulated elastase and myeloperoxidase release are enhanced by Fab fragments (10 nmol/10(6) PMN) to 206 and 155%, respectively, of reference values by 25 nM FMLP, while Fc and native IgG stimulate to a less extent. Consequently, elastase-generated Fc fragments have an inhibitory effect on inflammation by reducing chemotaxis and oxidative burst of stimulated neutrophils. The release stimulating activity of Fab fragments results in an up-regulation of elastase induced IgG degradation.

Chemotaxis, Leukocyte↗

In vitro sonographic evaluation of common bile duct stones and fragments with a high-frequency microprobe.

PURPOSE: This study was conducted to evaluate the sonographic characteristics of common bile duct (CBD) stones and stone fragments scanned in vitro with a high-frequency (20-MHz) microprobe. METHODS: We sonographically examined 4 whole CBD stones (1 cholesterol stone with radiant cross section, 1 cholesterol stone with lamellar cross section, 1 black pigment stone, and 1 brown pigment stone), 44 fragments of a cholesterol stone (diameter range, 1.1-3.0 mm; mean diameter, 2.0 mm), and 75 fragments of a black pigment stone (diameter range, 1.1-3.0 mm; mean diameter, 2.0 mm). The chemical composition of all stones was analyzed by infrared absorption spectroscopy. All stones and fragments were placed in a plastic box filled with physiologic saline solution for scanning with a 20-MHz microprobe and a 5-MHz probe. Echogenic foci and acoustic shadows revealed at each frequency were compared. RESULTS: At 5 MHz, the 4 CBD stones showed different sonographic characteristics. The cholesterol stone with radiant cross section showed an echogenic focus but no definite acoustic shadow, whereas the cholesterol stone with lamellar cross section showed an echogenic line, several echogenic spots, and a definite acoustic shadow. The black pigment stone showed an echogenic line with a vague acoustic shadow, and the brown pigment stone showed echogenicity of the whole stone and a definite acoustic shadow. At 20 MHz, the 4 stones showed an echogenic line with a definite acoustic shadow. All fragments appeared as echogenic foci at 20 and 5 MHz. Seventy-seven percent (34) and 5% (2) of 44 cholesterol stone fragments cast a definite acoustic shadow at 20 and 5 MHz, respectively. Sixty-nine percent (52) and 15% (11) of 75 black pigment stone fragments cast a definite acoustic shadow at 20 and 5 MHz, respectively. Among fragments 1.5 mm in diameter and smaller, only 45% (5 of 11) from a cholesterol stone and 30% (6 of 20) from a black pigment stone showed a definite acoustic shadow at 20 MHz. CONCLUSIONS: High-frequency (20-MHz) sonography demonstrates a definite acoustic shadow more frequently among CBD stones and fragments 1.6 mm in diameter or larger than does low-frequency (5-MHz) sonography, but it does not discriminate the chemical composition.

Adult↗

Population of the black howler monkey (Alouatta pigra) in a fragmented landscape in Palenque, Chiapas, Mexico.

Little is known about the population characteristics of Alouatta pigra under conditions of forest fragmentation-information that is important to understanding its tolerance to habitat loss. In this work we present data on forest loss and on troop size, age, and sex composition for a population of black howler monkeys existing in the fragmented landscape surrounding the Mayan site of Palenque, Chiapas, Mexico. Two aerial photos (1:70,000) of the study area (261 km(2)) taken in 1984 and 2001 were examined to assess forest loss. Between June and December 2001 and January and March 2002 we surveyed 44 forest fragments for the presence of howler monkeys. Examination of aerial photos showed that 33% of the forest present in 1984 had disappeared by 2001, and detected an increment in the number of forest fragments present in the landscape. We discovered a total of 115 howler monkeys living in 22 of the 44 forest fragments studied, of which 107 were members of 18 troops. The rest were solitary males or small groups of males living in isolated forest fragments. Troop size ranged from two to 15 individuals (mean 5.9+3.0 ind). 31% and 15% of individuals in the troops were juveniles and infants, respectively, suggesting continued reproductive activity. Howler monkey troops in the forest fragments were on average smaller (5.9+/-3.0 ind) than troops in the nearby protected forest of the Mayan site (7.0+/-2.8 ind). The mean density of howlers in the forest fragments was 119+/-82.9 ind/km(2). The establishment of corridors is suggested as a possible conservation scenario for the fragmented howler population investigated, and as a conservation measure to connect this population with the howler population found in the protected forest of the Mayan site.

Age Distribution↗

Analysis of streptonigrin-induced incomplete chromosome elements and interstitial fragments in Chinese hamster cells using a telomeric PNA probe.

We investigated the induction of incomplete chromosome elements (ICEs; i.e., elements with a telomeric signal at only one terminal end) and interstitial fragments induced by the antibiotic streptonigrin (SN) in a Chinese hamster embryo (CHE) cell line using FISH with a telomeric peptide nucleic acid probe. CHE cells were treated with 0-250 ng/ml SN and chromosomal aberrations were analyzed in the first mitosis after treatment using the telomeric probe. Exposure of CHE cells to SN resulted in a linear concentration-related increase in all of the aberration types analyzed (P < 0.05) except ring chromosomes. Depending on the SN concentration employed, 33-68% of the metaphases contained one or more pairs of ICEs (an incomplete chromosome accompanied by a terminal fragment or two incomplete chromosomes accompanied by a compound fragment). Pooled data from all SN concentrations revealed that 77.8% of the acentric fragments were terminal fragments, 18.8% interstitial fragments, and 3.4% compound fragments. Furthermore, it was estimated that about 80% of excess acentric fragments induced by SN originated from incomplete exchanges or terminal deletions and 20% from complete exchanges (interstitial deletions). These results show that incomplete chromosomes and terminal fragments are the most frequent asymmetrical chromosomal aberrations induced by SN and indicate that true incompleteness is a very common event following exposure to SN.

Animals↗

Nuclear DNA fragmentation and expression of Bcl-2 in primary biliary cirrhosis.

It is uncertain whether or not apoptosis is involved in the pathogenesis of primary biliary cirrhosis (PBC). The aims of this study were to assess the nuclear DNA fragmentation and expression of Bcl-2 in the biliary epithelial cells (BECs) and in the hepatocytes of PBC. Additionally, the effects of ursodeoxycholic acid (UDCA) on DNA fragmentation and Bcl-2 expression in PBC were evaluated. Liver tissue specimens from 35 PBC patients were examined by in situ nick-end labeling to detect any nuclear DNA fragments, and by immunohistochemistry for Bcl-2. Ten of these patients underwent a second liver biopsy after the treatment with UDCA. Sixteen histologically normal liver tissues and 17 chronic viral hepatitis C (CVHC) samples were chosen as controls. DNA fragmentation in BECs was more frequently found in PBC than in CVHC and more frequently than in the normal controls (both P < .05), and fragmentation in the hepatocytes of PBC more frequently than in normal controls (P < .01). Bcl-2 expression was more frequently found in both the BECs and hepatocytes of PBC than in the controls. UDCA significantly decreased the DNA fragmentation in BECs (P < .05) and the positivity for Bcl-2 in BECs (P < .01), although no significant decrease was found in hepatocytes. In conclusion, de novo Bcl-2 expression in hepatocytes of PBC was shown, and the increased nuclear DNA fragmentation and the Bcl-2 expression both in BECs and in hepatocytes may reflect apoptotic stress, although nuclear DNA fragmentation in BECs did not necessarily represent apoptosis. UDCA showed a potential effect of reducing nuclear DNA fragmentation in BECs.

Apoptosis↗

Navigation by fragment fitting: a theory of hippocampal function.

This paper describes a computational theory of spatial learning and navigation and its possible realization in the hippocampus. In the theory, mammals store memories of their geographical environment as a large number of independent fragments. A typical fragment denotes a few prominent landmarks in some region, their geometric relations, and their nongeometric properties, such as smells and visual cues. Navigation involves piecing together current sense data and relevant fragments to form a local map of the animal's surroundings; this is like solving a jigsaw puzzle. This computational model has been implemented in a computer program, whose performance is broadly consistent with observed levels of animal performance, and laboratory results, in spatial learning. Possible realizations of the model in animal brains are discussed. Unlike some neural net models of spatial learning, the model is strongly geometric, and uses special neural structures to store and manipulate two-dimensional vectors and bearings. A possible neural architecture is described in which the hippocampus performs the geometric operations; this has a long-term memory for fragments (somewhere in the neocortex), which can associatively recall fragments into a number of parallel fragment fitters, in the dentate gyrus and CA3 regions. These vary the positions and orientations of their fragments, to optimize the fit of the fragments to each other and to the animal's recent sense data. A local map of the animal's surroundings is stored in CA1 and subicular regions, where matching of fragment positions and attributes takes place. Mismatches are passed back via the entorhinal cortex to improve the fit during the next hippocampal theta cycle. The model offers the potential for understanding current data on spatial learning, on the neuroanatomy of the hippocampus and on place cells in a coherent framework, as well as understanding the role of the hippocampus in nonpositional memory tasks. Comparisons with experimental data are given.

Animals↗

CD44 stimulation by fragmented hyaluronic acid induces upregulation of urokinase-type plasminogen activator and its receptor and subsequently facilitates invasion of human chondrosarcoma cells.

It has been established that fragmented hyaluronic acid (HA), but not native high molecular weight HA, can induce angiogenesis, cell proliferation and migration. We have studied the outside-in signal transduction pathways responsible for fragmented HA-mediated cancer cell invasion. In our study, we have studied the effects of CD44 stimulation by ligation with HA upon the expression of matrix metalloproteinases (MMPs)-2 and -9 as well as urokinase-type plasminogen activator (uPA), its receptor (uPAR) and its inhibitor (PAI-1) and the subsequent induction of invasion of human chondrosarcoma cell line HCS-2/8. Our study indicates that (i) CD44 stimulation by fragmented HA upregulates expression of uPA and uPAR mRNA and protein but does not affect MMPs secretion or PAI-1 mRNA expression; (ii) the effects of HA fragments are critically HA size dependent: high molecular weight HA is inactive, but lower molecular weight fragmented HA (Mr 3.5 kDa) is active; (iii) cells can bind avidly Mr 3.5 kDa fragmented HA through a CD44 molecule, whereas cells do not effectively bind higher Mr HA; (iv) a fragmented HA induces phosphorylation of MAP kinase proteins (MEK1/2, ERK1/2 and c-Jun) within 30 min; (v) CD44 is critical for the response (activation of MAP kinase and upregulation of uPA and uPAR expression); and (vi) cell invasion induced by CD44 stimulation with a fragmented HA is inhibited by anti-CD44 mAb, MAP kinase inhibitors, neutralizing anti-uPAR pAb, anti-catalytic anti-uPA mAb or amiloride. Therefore, our study represents the first report that CD44 stimulation induced by a fragmented HA results in activation of MAP kinase and, subsequently, enhances uPA and uPAR expression and facilitates invasion of human chondrosarcoma cells.

Adjuvants, Immunologic↗

Thermodynamics of the reconstitution of tuna cytochrome c from two peptide fragments.

Two peptide fragments from tuna cytochrome c (cyt c), N-fragment (residues 1-44 containing the heme) and C-fragment (residues 45-103), combine to form a 1:1 fragment complex. This was clearly proved by ion-spray mass spectrometry. It was found from CD and NMR spectra that the structure of the fragment complex formed is similar to that of an intact cyt c, although each isolated fragment itself is unstructured. Binding constants and enthalpies upon the complex formation were directly observed by isothermal titration calorimetry. Thermodynamic parameters (deltaG(o)b, deltaHb, deltaS(o)b, and deltaC(b)p)) associated with the complex formation were determined at various pHs and temperatures. DeltaHb was found to be almost independent of pH values. The change in heat capacity accompanying the complex formation (deltaC(b)p) was directly determined from the temperature dependence of deltaHb. In addition, the change in heat capacity and enthalpy upon tuna cyt c unfolding were determined by differential scanning calorimetry. Thermodynamic parameters for the unfolding/dissociation process of the fragment complex were compared with those for cyt c unfolding at pH 3.9 and 303 K. In a comparison of two unfolding processes, the heat capacity change of each was very close to the other, while both the unfolding enthalpy and entropy of the fragment complex were larger than those of tuna cyt c. These thermodynamic data suggest that the internal interactions between polar groups (hydrogen bonding) and nonpolar groups (van der Waals interactions) are preserved in the fragment complex as well as in the native state of cyt c.

Animals↗

CHOP proteins into structural domain-like fragments.

We developed a method CHOP dissecting proteins into domain-like fragments. The basic idea was to cut proteins beginning from very reliable experimental information (PDB), proceeding to expert annotations of domain-like regions (Pfam-A), and completing through cuts based on termini of known proteins. In this way, CHOP dissected more than two thirds of all proteins from 62 proteomes. Analysis of our structural domain-like fragments revealed four surprising results. First, >70% of all dissected proteins contained more than one fragment. Second, most domains spanned on average over approximately 100 residues. This average was similar for eukaryotic and prokaryotic proteins, and it is also valid-although previously not described-for all proteins in the PDB. Third, single-domain proteins were significant longer than most domains in multidomain proteins. Fourth, three fourths of all domains appeared shorter than 210 residues. We believe that our CHOP fragments constituted an important resource for functional and structural genomics. Nevertheless, our main motivation to develop CHOP was that the single-linkage clustering method failed to adequately group full-length proteins. In contrast, CLUP-the simple clustering scheme CLUP introduced here-succeeded largely to group the CHOP fragments from 62 proteomes such that all members of one cluster shared a basic structural core. CLUP found >63,000 multi- and >118,000 single-member clusters. Although most fragments were restricted to a particular cluster, approximately 24% of the fragments were duplicated in at least two clusters. Our thresholds for grouping two fragments into the same cluster were rather conservative. Nevertheless, our results suggested that structural genomics initiatives have to target >30,000 fragments to at least cover the multimember clusters in 62 proteomes.

Amino Acids↗