Molecular cloning of cholecystokinin (CCK) and CCK-A receptor and mechanism of CCK-induced gastrointestinal motility in Suncus murinus.

Cholecystokinin (CCK) is a peptide hormone mainly secreted by small intestinal endocrine I-cells and functions as a regulator of gallbladder contraction, gastric emptying, gastrointestinal (GI) motility, and satiety. The cellular effects of CCK in these peripheral tissues are predominantly mediated via CCK-A receptors which are found in smooth muscles, enteric neurons, and vagal afferent neurons in humans and animal models. Although various functions of CCK have been reported to be neurally mediated, it can also stimulate contraction via the CCK receptor on the smooth muscle. However, the entire underlying neural and cellular mechanisms involved in CCK-induced GI contractions are not clearly understood. Here, we first determined the cDNA and amino acid sequences of CCK and CCK-A receptor along with the distributions of cck mRNA and CCK-producing cells in house musk shrew (Suncus murinus, the laboratory strain named as suncus) and examined the mechanism of CCK-induced contraction in the GI tract. Mature suncus CCK-8 was identical to other mammalian species tested here, and suncus CCK-A receptor presented high nucleotide and amino acid homology with that of human, dog, mouse, and rat, respectively. Suncus CCK mRNA and CCK-producing cells were found mainly in small intestine and colon. In the organ bath study, CCK-8 induced dose-dependent contractions in the suncus stomach, duodenum, and jejunum, and these contractions were inhibited by atropine and CCK-A receptor antagonist. These results suggest that CCK-8-induced contraction is mediated in the myenteric cholinergic neural network and that CCK-A receptor is partly responsible for CCK-8-induced contractions. This study indicates that suncus is a useful animal model to study the functions of CCK involved in GI motility.

Molecular Structure of Gardenia Blue Pigments by Reaction of Genipin with Benzylamine and Amino Acids.

Genipin was reacted with benzylamine and several amino acids to prepare gardenia blue (GB). The time-course of GB formation with benzylamine was monitored by high-performance liquid chromatography (HPLC), liquid chromatography time-of-flight mass spectrometry (LC-TOFMS), and 1H and 13C NMR measurements. In this experiment, we determined the molecular structures of some intermediates using accurate masses and additional NMR techniques such as heteronuclear multiple bond correlation (HMBC). GBs with amino acids (GB-AAs) were characterized by both liquid and solid-state NMR measurements. Interestingly, many significant peaks appeared in the solid-state NMR spectra, although the 13C NMR spectra from solution samples did not show any distinct peaks. Therefore, we determined that GB-AAs had an alternating copolymer structure composed of methyne and 5H-2-pyrindine, which was substituted by amino acids at N atom and linked with methyne at 5 and 7 positions. To confirm this molecular structure, the pyrolysis gas chromatography-mass spectrometry (GC-MS) measurement of GB-AAs was carried out, and 5H-2-pyrindine and its methyl derivatives were formed as main pyrolysis products from the polymer chains.

Spatiotemporal variation of roadkills show mass mortality events for amphibians in a highly trafficked road adjacent to a national park, Costa Rica / Variación espacio-temporal de atropellos de vertebrados muestra eventos de mortalidad masiva de anfibios en una carretera altamente transitada adyacente a un parque nacional, Costa Rica

Abstract Roads have detrimental impacts on wildlife populations around the world. Specifically, roads pose direct and indirect threats to wildlife by limiting dispersal movements or through vehicle-related mortality. The rate of wildlife mortality varies both in time and space depending on the landscape composition and the type and use of road infrastructure. The objective of this study was to investigate spatiotemporal variation of vertebrate mortality in a 4 km segment of the 34 national road, adjacent to Carara National Park, Costa Rica. We conducted 81 roadkill surveys by car and bicycle from June 2010 to May 2011, georeferenced the locations of the kills and identified them to the lowest possible taxonomic level. We recorded a total of 4 709 road-killed animals of at least 58 species of vertebrates during the whole study. Amphibians accounted for 93.5 % of all the vertebrate losses and showed strong spatiotemporal variation of mass mortality events. Reptiles, especially snakes, were the second most affected taxon followed by mammals and birds. Relative mortality per day in the 4 km segment was 125.4 amphibians, 4.6 reptiles, 2.7 mammals, 1 bird and 0.46 undetermined. Road proximity to the border of the park, traffic volumes and lack of enforcement of speed limits may influence the high rate of roadkills found. We suggest the reinforcement of speed limits, wildlife crossing signage and the retrofitting of the existing culverts as under passes for animals to minimize vertebrate mortality at the road adjacent to Carara National Park.

Resumen Las carreteras tienen impactos perjudiciales en las poblaciones de vida silvestre en todo el mundo. Específicamente, los caminos representan amenazas directas e indirectas a la vida silvestre limitando los movimientos de dispersión, o debido a la mortalidad por atropellos por vehículos. La tasa de mortalidad de la fauna varía tanto en el tiempo como en el espacio, dependiendo de la composición del paisaje y del tipo y uso de la infraestructura vial. El objetivo de este estudio fue investigar la variación espaciotemporal de la mortalidad de vertebrados en un tramo de 4 km de la carretera nacional 34, adyacente al Parque Nacional Carara, Costa Rica. Llevamos a cabo 81 censos de vertebrados atropellados utilizando un vehículo y una bicicleta entre junio 2010 y mayo 2011, georreferenciamos las ubicaciones de los cuerpos y los identificamos al nivel taxonómico más bajo posible. Registramos un total de 4 709 animales muertos por carretera de al menos 58 especies de vertebrados durante todo el estudio. Los anfibios representaron el 93.5 % de todos los vertebrados y mostraron una fuerte variación espaciotemporal en eventos de mortalidad masiva. Los reptiles, especialmente las serpientes, fueron el segundo taxón más afectado seguido por los mamíferos y las aves. La mortalidad relativa por día en el segmento de 4 km fue de 125.4 anfibios, 4.6 reptiles, 2.7 mamíferos, 1 ave y 0.46 indeterminado. La proximidad de la carretera al límite del parque, los volúmenes de tránsito y la falta de cumplimiento de los límites de velocidad pueden influir en la alta tasa de mortalidad registrada. Sugerimos la reducción en los límites de velocidad, la señalización de cruce de vida silvestre y la readecuación de las alcantarillas existentes como pasos para los animales para minimizar la mortalidad de los vertebrados en la carretera adyacente al Parque Nacional Carara.

Printed multifunctional flexible device with an integrated motion sensor for health care monitoring.

Real-time health care monitoring may enable prediction and prevention of disease or improve treatment by diagnosing illnesses in the early stages. Wearable, comfortable, sensing devices are required to allow continuous monitoring of a person's health; other important considerations for this technology are device flexibility, low-cost components and processing, and multifunctionality. To address these criteria, we present a flexible, multifunctional printed health care sensor equipped with a three-axis acceleration sensor to monitor physical movement and motion. Because the device is designed to be attached directly onto the skin, it has a modular design with two detachable components: One device component is nondisposable, whereas the other one is disposable and designed to be worn in contact with the skin. The design of this disposable sensing sheet takes into account hygiene concerns and low-cost materials and fabrication methods as well as features integrated, printed sensors to monitor for temperature, acceleration, electrocardiograms, and a kirigami structure, which allows for stretching on skin. The reusable component of the device contains more expensive device components, features an ultraviolet light sensor that is controlled by carbon nanotube thin-film transistors, and has a mechanically flexible and stable liquid metal contact for connection to the disposable sensing sheet. After characterizing the electrical properties of the transistors and flexible sensors, we demonstrate a proof-of-concept device that is capable of health care monitoring combined with detection of physical activity, showing that this device provides an excellent platform for the development of commercially viable, wearable health care monitors.

Mechanically Flexible and High-Performance CMOS Logic Circuits.

Low-power flexible logic circuits are key components required by the next generation of flexible electronic devices. For stable device operation, such components require a high degree of mechanical flexibility and reliability. Here, the mechanical properties of low-power flexible complementary metal-oxide-semiconductor (CMOS) logic circuits including inverter, NAND, and NOR are investigated. To fabricate CMOS circuits on flexible polyimide substrates, carbon nanotube (CNT) network films are used for p-type transistors, whereas amorphous InGaZnO films are used for the n-type transistors. The power consumption and voltage gain of CMOS inverters are <500 pW/mm at Vin = 0 V (<7.5 nW/mm at Vin = 5 V) and >45, respectively. Importantly, bending of the substrate is not found to cause significant changes in the device characteristics. This is also observed to be the case for more complex flexible NAND and NOR logic circuits for bending states with a curvature radius of 2.6 mm. The mechanical stability of these CMOS logic circuits makes them ideal candidates for use in flexible integrated devices.

High-performance, mechanically flexible, and vertically integrated 3D carbon nanotube and InGaZnO complementary circuits with a temperature sensor.

A vertically integrated inorganic-based flexible complementary metal-oxide-semiconductor (CMOS) inverter with a temperature sensor with a high inverter gain of ≈50 and a low power consumption of <7 nW mm(-1) is demonstrated using a layer-by-layer assembly process. In addition, the negligible influence of the mechanical flexibility on the performance of the CMOS inverter and the temperature dependence of the CMOS inverter characteristics are discussed.

Toward flexible and wearable human-interactive health-monitoring devices.

This Progress Report introduces flexible wearable health-monitoring devices that interact with a person by detecting from and stimulating the body. Interactive health-monitoring devices should be highly flexible and attach to the body without awareness like a bandage. This type of wearable health-monitoring device will realize a new class of electronics, which will be applicable not only to health monitoring, but also to other electrical devices. However, to realize wearable health-monitoring devices, many obstacles must be overcome to economically form the active electrical components on a flexible substrate using macroscale fabrication processes. In particular, health-monitoring sensors and curing functions need to be integrated. Here recent developments and advancements toward flexible health-monitoring devices are presented, including conceptual designs of human-interactive devices.

Fully printed, highly sensitive multifunctional artificial electronic whisker arrays integrated with strain and temperature sensors.

Mammalian-mimicking functional electrical devices have tremendous potential in robotics, wearable and health monitoring systems, and human interfaces. The keys to achieve these devices are (1) highly sensitive sensors, (2) economically fabricated macroscale devices on flexible substrates, and (3) multifunctions beyond mammalian functions. Although highly sensitive artificial electronic devices have been reported, none have been fabricated using cost-effective macroscale printing methods and demonstrate multifunctionalities of artificial electronics. Herein we report fully printed high-sensitivity multifunctional artificial electronic whiskers (e-whisker) integrated with strain and temperature sensors using printable nanocomposite inks. Importantly, changing the composition ratio tunes the sensitivity of strain. Additionally, the printed temperature sensor array can be incorporated with the strain sensor array beyond mammalian whisker functionalities. The sensitivity for the strain sensor is impressively high (∼59%/Pa), which is the best sensitivity reported to date (>7× improvement). As the proof-of-concept for a truly printable multifunctional artificial e-whisker array, two- and three-dimensional space and temperature distribution mapping are demonstrated. This fully printable flexible sensor array should be applicable to a wide range of low-cost macroscale electrical applications.

Enteroscopic and radiologic diagnoses, treatment, and prognoses of small-bowel tumors.

BACKGROUND: Small-bowel tumors (SBTs) represent a diagnostic challenge. OBJECTIVE: To evaluate the usefulness of contrast-enhanced CT (CECT), fluoroscopic enteroclysis (FE), videocapsule endoscopy (VCE), and double-balloon endoscopy (DBE) and the outcome after treatment. DESIGN: Single-center, retrospective study. SETTING: Tertiary-care referral hospital. PATIENTS: Between June 2003 and May 2011, 159 consecutive patients with SBTs (93 malignant and 66 benign) were enrolled. MAIN OUTCOME MEASUREMENTS: Comparison of diagnostic yields among CECT, FE, VCE, and DBE and the prognosis. RESULTS: CECT and FE had significantly lower diagnostic yields of SBTs ≤ 10 mm, but VCE and DBE had high yields of SBTs regardless of size. CECT had a significantly lower diagnostic yield of epithelial tumors compared with subepithelial tumors. When stratified by the site, the diagnostic yield of VCE for SBTs located only in the distal duodenum/the proximal jejunum (73%) was significantly lower than that for SBTs located in other areas (90%). Comparisons among the 4 methods revealed that VCE and DBE had significantly higher diagnostic yields than CECT, and DBE had significantly higher diagnostic yields than VCE, but a combination of CECT and VCE had a diagnostic yield similar to that of DBE. The histologic diagnostic yield of SBTs by DBE was 92%, and 25% of SBTs were enteroscopically treated. Metastatic tumors had the poorest overall survival, followed by adenocarcinomas and malignant lymphomas. LIMITATIONS: Retrospective comparative study. CONCLUSION: For the detection of SBTs, a combination screening method by using VCE and CECT is recommended. DBE is useful for histologic diagnosis and endoscopic treatment.

Outcome after enteroscopy for patients with obscure GI bleeding: diagnostic comparison between double-balloon endoscopy and videocapsule endoscopy.

BACKGROUND: Double-balloon endoscopy (DBE) and videocapsule endoscopy (VCE) have been useful in managing obscure GI bleeding (OGIB). OBJECTIVE: This study compared diagnostic yields of OGIB between DBE and VCE, and evaluated the outcome after DBE. DESIGN: A single-center retrospective study. SETTING: A tertiary-referral hospital. PATIENTS: Between June 2003 and February 2007, 162 consecutive patients with OGIB were enrolled and treated. The diagnostic yield between VCE and DBE was compared in 74 patients. MAIN OUTCOME MEASUREMENTS: Comparison of diagnostic yields between DBE and VCE, and the prognosis after DBE. RESULTS: Of 162 patients, 95 (59%) were diagnosed with small-bowel diseases. They were treated by medical, enteroscopic, and surgical therapies (n = 35, 30, and 30, respectively). A comparison of the overall diagnostic yield between DBE (64%) and VCE (54%) was not significantly different. The 4 VCE-positive DBE-negative cases were because of inaccessibility of DBE. The 11 VCE-negative DBE-positive cases were because of a failure to detect lesions in the proximal small bowel and the Roux-en-Y loop, and because of diverticula. At a median follow-up of 555 days after DBE, 11 patients with small-bowel diseases developed rebleeding; all were treated by enteroscopic or medical therapies. Vascular diseases, comorbidities, especially portal hypertensive disease and chronic renal failure that required hemodialysis, and severe anemia (Hb

Small-bowel obstruction: diagnostic comparison between double-balloon endoscopy and fluoroscopic enteroclysis, and the outcome of enteroscopic treatment.

BACKGROUND: Small-bowel obstruction (SBO) sometimes remains undiagnosed and untreatable without surgery. OBJECTIVE: To evaluate the diagnostic yields of SBO between double-balloon endoscopy (DBE) and fluoroscopic enteroclysis (FE), and the outcome of enteroscopic treatment. DESIGN: Single-center, retrospective, and prospective study. SETTING: Tertiary-referral hospital. PATIENTS: Between June 2003 and July 2007, 66 consecutive patients with SBO were enrolled, investigated, and treated. MAIN OUTCOME MEASUREMENTS: A comparison of diagnostic yields between DBE and FE, and the prognosis after enteroscopic balloon dilation. RESULTS: The diagnostic yield of DBE for SBO (95%) was higher than that of FE (71%) in 59 patients who underwent both examinations (P= .004). The first treatment included 27 surgical, 25 enteroscopic, and 14 conservative therapies. Of 47 enteroscopic balloon dilation procedures in 22 patients, 45 (96%) were successful. Of 16 patients with Crohn's disease, 11 (69%) remained asymptomatic over the postdilation follow-up period but 5 relapsed: 2 recovered by repeated dilations, but 3 required surgery. Of 6 patients who had diseases other than Crohn's disease, 4 (67%) remained asymptomatic but 2 relapsed: one with remission of metastasis recovered by repeated dilations, and one with ischemic enteritis required surgery. Anastomotic stricture was an independent marker of the symptom-free outcome (hazard ratio 0.037-0.084, P= .037). Two acute pancreatitis, one perforation, and one exacerbation of SBO complications occurred. LIMITATIONS: Small sample size and participation bias. CONCLUSIONS: DBE was useful for the diagnosis of SBO. Balloon dilation is considered an alternative to surgery in patients with fibrotic strictures both related and unrelated to Crohn's disease.

varDB: a pathogen-specific sequence database of protein families involved in antigenic variation.

UNLABELLED: Infectious diseases are a major threat to global public health and prosperity. The causative agents consist of a suite of pathogens, ranging from bacteria to viruses, including fungi, helminthes and protozoa. Although these organisms are extremely varied in their biological structure and interactions with the host, they share similar methods of evading the host immune system. Antigenic variation and drift are mechanisms by which pathogens change their exposed epitopes while maintaining protein function. Accordingly, these traits enable pathogens to establish chronic infections in the host. The varDB database was developed to serve as a central repository of protein and nucleotide sequences as well as associated features (e.g. field isolate data, clinical parameters, etc.) involved in antigenic variation. The data currently contained in varDB were mined from GenBank as well as multiple specialized data repositories (e.g. PlasmoDB, GiardiaDB). Family members and ortholog groups were identified using a hierarchical search strategy, including literature/author-based searches and HMM profiles. Included in the current release are>29,00 sequences from 39 gene families from 25 different pathogens. This resource will enable researchers to compare antigenic variation within and across taxa with the goal of identifying common mechanisms of pathogenicity to assist in the fight against a range of devastating diseases. AVAILABILITY: varDB is freely accessible at http://www.vardb.org/

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.

MOTIVATION: The identification of interactions between drugs and target proteins is a key area in genomic drug discovery. Therefore, there is a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently. RESULTS: In this article, we characterize four classes of drug-target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, and reveal significant correlations between drug structure similarity, target sequence similarity and the drug-target interaction network topology. We then develop new statistical methods to predict unknown drug-target interaction networks from chemical structure and genomic sequence information simultaneously on a large scale. The originality of the proposed method lies in the formalization of the drug-target interaction inference as a supervised learning problem for a bipartite graph, the lack of need for 3D structure information of the target proteins, and in the integration of chemical and genomic spaces into a unified space that we call 'pharmacological space'. In the results, we demonstrate the usefulness of our proposed method for the prediction of the four classes of drug-target interaction networks. Our comprehensively predicted drug-target interaction networks enable us to suggest many potential drug-target interactions and to increase research productivity toward genomic drug discovery. AVAILABILITY: Softwares are available upon request. SUPPLEMENTARY INFORMATION: Datasets and all prediction results are available at http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/drugtarget/.

[Meckel's diverticulum and duplication of the alimentary tract].

Meckel's diverticulum and duplication of the alimentary tract are very important as the congenital anomalies of ileum. As these two diseases have the common clinical characteristics such as sex, age, symptoms and complications, it is often difficult to diagnose before surgery. This report describes and compared the clinical aspects of Meckel's diverticulum and duplication of the alimentary tract, which were experienced at Nagoya University Hospital and Kariya Toyota General Hospital.

Diagnosis and treatment of obscure GI bleeding at double balloon endoscopy.

BACKGROUND: Double balloon endoscopy (DBE) and videocapsule endoscopy (VCE) have been useful in managing obscure GI bleeding (OGIB). OBJECTIVE: This study evaluated the usefulness of DBE for diagnosis, treatment, and prognosis of OGIB and compared diagnostic yield between DBE and VCE in Japan. METHODS: Detection rates of abnormalities and diagnostic yields between VCE and DBE were compared in 74 patients at 5 centers. Of 244 patients who underwent DBE at Nagoya University Hospital, 130 (53%) with OGIB were enrolled for investigation of therapeutic procedures. SETTING: Seven Japanese medical centers. PATIENTS: Of 1034 patients who underwent DBE between September 2000 and December 2005 at 7 medical centers, 479 (46%) with OGIB were enrolled. RESULTS: Overall diagnostic yield of DBE for OGIB was 277 of 479 (58%). In patients with overt-ongoing bleeding, overt-previous bleeding of sporadic type, overt-previous bleeding of first attack only, occult bleeding with continuous positive fecal occult blood test (FOBT), or occult bleeding with 1 positive FOBT with iron deficiency anemia, diagnostic yield was 24 of 31 (77%), 179 of 310 (58%), 34 of 72 (47%), 24 of 35 (71%), and 56 of 93 (60%), respectively. Regarding positive findings in 277 patients, ulcers or erosions (53%) were the most frequent, followed by angiodysplasia (23%), tumors or polyps (22%), and diverticula (4%). Diagnoses in these patients were as follows: chronic inflammatory diseases (24%), vascular diseases (24%), tumor or polyps (21%), drug or radiation injury (7%), other small-bowel diseases (7%), upper GI diseases (9%), colorectal diseases (9%), and biliary disease (0.4%). Small-bowel diseases were confirmed in 226 patients (47%). Comparison of overall detection rate of abnormalities in the small bowel between VCE (65%) and DBE (53%) was not significantly different, nor was that of overall diagnostic yield between VCE (50%) and DBE (53%). Eight acute pancreatitis and 4 perforation episodes occurred with no mortalities at DBE. Of 130 patients at Nagoya University Hospital, 78 (60%) were diagnosed with small-bowel diseases and underwent treatments as follows: medication or observation only (n = 30), enteroscopic therapies (electrocoagulation in 21, clipping in 4, and polypectomy in 3), and surgery (n = 22). Small-bowel vascular diseases were more prone to rebleeding than small-bowel nonvascular diseases in patients without surgical treatment at a median follow-up of 423 days. CONCLUSIONS: DBE was relatively safe and useful for diagnosis and treatment of OGIB. A spectrum of small-bowel diseases presenting with OGIB in Japan may be distinct from that in the Western world.

Small bowel tuberculosis diagnosed by the combination of video capsule endoscopy and double balloon enteroscopy.

Small bowel tuberculosis is sometimes encountered in oriental countries, and because its symptoms are vague and present a nonspecific pattern, confirmative diagnosis is difficult to achieve. In 2001, two new innovative endoscopic techniques for the small bowel, video capsule endoscopy and double balloon enteroscopy, were introduced, thus advancing the diagnostic technology for small bowel disorders. Our asymptomatic patient with small bowel tuberculosis was diagnosed definitively using the combination of video capsule endoscopy and double balloon enteroscopy. The number of such cases will increase when those procedures become more widely used. At present, the endoscopic view of small bowel tuberculosis is difficult to differentiate from Crohn's disease and drug-induced enteropathy, but from now on it will be possible to distinguish them utilizing endoscopic and fluoroscopic images. On the basis of the characteristics of small bowel tuberculosis with its endoscopic images, referring to our case report and previous literature, we report a topical diagnostic procedure, the combination of video capsule endoscopy and double balloon enteroscopy.

Predicting B cell epitope residues with network topology based amino acid indices.

We evaluate the performance of six amino acid indices in B cell epitope residue prediction using the classical sliding window method on five data sets. Four of the indices: i.e. relative connectivity, clustering coefficient, closeness and betweenness are newly derived from the topological parameters of residue networks. The other two are Parker's hydrophilicity and Levitt's index, known as the best indices so far for B cell epitope prediction. On four of the data sets, the performance of all the indices was comparable and poor in general. When applied to one well-annotated data set, the performances improved and the 4 network based indices showed better performance than that of Parker's hydrophilicity and Levitt's index. When using the relative connectivity index on this data set, the prediction accuracy, sensitivity and specificity reached 73.6%, 73.0% and 75.0% respectively, with an area under the curve about 0.796. Thus, we suggested that this index is a good choice for B cell epitope prediction. It also indicates that the low performance of B cell epitope prediction is not only due to the methods and amino acid indices used, but also the data set as well. Interestingly, on the well-annotated data set, the performance of B cell epitope residue prediction is very similar to that of protein surface residue prediction, especially at the 10 and 20 A2 cutoffs. It is suggested that the performance in surface residue prediction might form a theoretical upper limit for the performance of B cell epitope residue prediction methods.

MIMOX: a web tool for phage display based epitope mapping.

BACKGROUND: Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them. RESULTS: We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results. CONCLUSION: A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox.

CED: a conformational epitope database.

BACKGROUND: Antigen epitopes provide valuable information useful for disease prevention, diagnosis, and treatment. Recently, more and more databases focusing on different types of epitopes have become available. Conformational epitopes are an important form of epitope formed by residues that are sequentially discontinuous but close together in three-dimensional space. These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes. DESCRIPTION: We describe CED, a special database of well defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals. The database can be browsed or searched through a user-friendly web interface. Most epitopes in CED can also be viewed interactively in the context of their 3D structures. In addition, the entries are also hyperlinked to various databases such as Swiss-Prot, PDB, KEGG and PubMed, providing wide background information. CONCLUSION: A conformational epitope database called CED has been developed as an information resource for investigators involved in both theoretical and applied immunology research. It complements other existing specialised epitope databases. The database is freely available at http://web.kuicr.kyoto-u.ac.jp/~ced.