├── .gitignore ├── API-1.0.0 ├── API-1.1.0 ├── API-2.0.0 ├── COPYING-MIT.txt ├── CREDITS ├── Makefile ├── README ├── README.mdown ├── RELEASE-1.0.0 ├── RELEASE-1.1.0 ├── RELEASE-2.0.0 ├── RELEASE-2.0.1 ├── RELEASE-2.0.2 ├── build.xml ├── composer.json ├── doc └── RecordFormat.mdown ├── package.xml ├── package_compatible.xml ├── src └── LibRIS │ ├── ParseException.php │ ├── RISReader.php │ ├── RISTags.php │ └── RISWriter.php └── tests ├── Banyuls.ris ├── derik-test.ris ├── short.ris ├── simple_test.php └── test1.ris /.gitignore: -------------------------------------------------------------------------------- 1 | bin/build/ 2 | -------------------------------------------------------------------------------- /API-1.0.0: -------------------------------------------------------------------------------- 1 | Basic usage of LibRIS: 2 | 3 | require 'LibRIS.php'; 4 | 5 | // Parse and print 6 | $ris = new LibRIS(); 7 | $ris->parseFile('./data.ris'); 8 | $ris->printRecords(); 9 | 10 | // Clone the above and write records. 11 | $records = $ris->getRecords(); 12 | $rw = new RISWriter(); 13 | print $rw->writeRecords($records); 14 | 15 | -------------------------------------------------------------------------------- /API-1.1.0: -------------------------------------------------------------------------------- 1 | Basic usage of LibRIS: 2 | 3 | require 'LibRIS.php'; 4 | 5 | // Parse and print 6 | $ris = new LibRIS(); 7 | $ris->parseFile('./data.ris'); 8 | $ris->printRecords(); 9 | 10 | // Clone the above and write records. 11 | $records = $ris->getRecords(); 12 | $rw = new RISWriter(); 13 | print $rw->writeRecords($records); 14 | 15 | New in 1.1.0: Regex expanded to cover EndNote cases. 16 | 17 | -------------------------------------------------------------------------------- /API-2.0.0: -------------------------------------------------------------------------------- 1 | LibRIS has been refactored to contain the following classes: 2 | 3 | - \LibRIS\RISReader: Read RIS files. 4 | - \LibRIS\RISWriter: Write RIS files. 5 | - \LibRIS\RISTags: Tags and labels for RIS files. 6 | - \LibRIS\ParseException: Thrown when parsing RIS fails. 7 | -------------------------------------------------------------------------------- /COPYING-MIT.txt: -------------------------------------------------------------------------------- 1 | LibRIS 2 | Matt Butcher 3 | Copyright (C) 2010 Matt Butcher 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in 13 | all copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 21 | THE SOFTWARE. -------------------------------------------------------------------------------- /CREDITS: -------------------------------------------------------------------------------- 1 | Matt Butcher [technosophos] (lead) 2 | Karl-Philipp Wulfert [animungo] (contributor) 3 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | 2 | test : 3 | php tests/simple_test.php 4 | 5 | pear : 6 | php ../pyrus.phar mk && php ../pyrus.phar package 7 | 8 | .PHONY: test pear 9 | -------------------------------------------------------------------------------- /README: -------------------------------------------------------------------------------- 1 | LibRIS is a tool for parsing RIS data and data files. -------------------------------------------------------------------------------- /README.mdown: -------------------------------------------------------------------------------- 1 | # LibRIS: An RIS parser for PHP 2 | 3 | * Author: Matt Butcher , 2010-02-06 4 | * License: An MIT-like license (COPYING-MIT.txt) 5 | 6 | This library provides basic marshaling and unmarshaling support for 7 | the RIS format. 8 | 9 | RIS is used to encode metadata about references. The normative 10 | reference for the format can be found here: 11 | 12 | [http://www.refman.com/support/risformat_intro.asp](http://www.refman.com/support/risformat_intro.asp) 13 | 14 | # Installation 15 | 16 | **Method 1:** Install using Packagist. 17 | 18 | 1. Follow the instructions at http://packagist.org 19 | 2. In your new project, create a `composer.json` file which requires 20 | LibRIS: 21 | 22 | ```javascript 23 | { 24 | "require": { 25 | "technosophos/LibRIS": ">=1.0.0" 26 | } 27 | } 28 | ``` 29 | 30 | When you next run `php composer.phar install` it will automatically 31 | fetch and install LibRIS. 32 | 33 | Note that as of LibRIS 2.0.0, the Composer autoloader can load 34 | LibRIS: 35 | 36 | ```php 37 | 46 | ``` 47 | 48 | **Method 2:** Install LibRIS using Pear 49 | 50 | Use your `pear` client to install LibRIS: 51 | 52 | pear channel-discover pear.querypath.org 53 | pear install querypath/LibRIS 54 | 55 | For more, see [pear.querypath.org](http://pear.querypath.org). 56 | 57 | Use it in your scripts like this: 58 | 59 | 62 | 63 | If you have already installed LibRIS using Pear, you can upgrade your library to the latest stable release by doing `pear upgrade LibRIS`. 64 | 65 | **Method 3:** Download LibRIS 66 | 67 | 1. Get LibRIS from [the downloads page](http://github.com/technosophos/LibRIS/downloads) 68 | 2. Uncompress the files (`tar -zxvf LibRIS-1.0.0.tgz`) 69 | 3. Put the files where you want them to go. 70 | 71 | Use it in your scripts like this: 72 | 73 | 76 | 77 | # Using LibRIS 78 | 79 | General usage for this class is simple: 80 | 81 | - The LibRIS class is used to parse RIS. 82 | - The RISWriter class is used for writing RIS data into a string. 83 | 84 | Here's an example (from test/simple_test.php): 85 | 86 | ```php 87 | parseFile('./test1.ris'); 93 | 94 | $ris->printRecords(); 95 | 96 | $records = $ris->getRecords(); 97 | 98 | $rw = new \LibRIS\RISWriter(); 99 | print $rw->writeRecords($records); 100 | ?> 101 | ``` 102 | 103 | Here's a line-by-line explanation of the code above: 104 | 105 | 1. Include the libraries. 106 | 2. You don't need this if you use an autoloader. 107 | 3. 108 | 4. Create a new LibRIS reader 109 | 5. Parse a file 110 | 6. 111 | 7. Pretty-print the parsed records 112 | 8. 113 | 9. Create a new writer 114 | 10. Turn our parsed record back into a valid RIS record. 115 | 116 | The format of the records is documented in `doc/RecordFormat.mdown`. 117 | 118 | # I Found a Bug! 119 | 120 | If you found a bug, *please* let me know. The best way is to file a report at 121 | [http://github.com/technosophos/LibRIS/issues](http://github.com/technosophos/LibRIS/issues). 122 | 123 | You can also find me on Freenode's IRC in #querypath. 124 | 125 | ## The Phing Script 126 | 127 | This file includes a Phing `build.xml` script. However, it is rarely used. 128 | 129 | If you are interested in using this as part of a build toolchain, see [phing.info](http://phing.info) 130 | 131 | ## Why is there a README file and a README.mdown file? 132 | 133 | * README is a required file for the Pear packaging system. 134 | * README.mdown is the GitHub-friendly README file for this project. 135 | -------------------------------------------------------------------------------- /RELEASE-1.0.0: -------------------------------------------------------------------------------- 1 | This is the initial release of LibRIS. 2 | 3 | LibRIS is a tool for parsing or generating LibRIS data. It is 4 | intended as a development library. 5 | -------------------------------------------------------------------------------- /RELEASE-1.1.0: -------------------------------------------------------------------------------- 1 | 1.1.0: 2 | 3 | Updates for better EndNote export support. 4 | 5 | Thanks to Jean-Luc Aucouturier for contributions. 6 | -------------------------------------------------------------------------------- /RELEASE-2.0.0: -------------------------------------------------------------------------------- 1 | LibRIS 2.0. 2 | 3 | The 2.0.x branch is reorganized and now requires PHP 5.3 to properly 4 | function. 5 | 6 | It supports the following new features: 7 | 8 | - Refactored library 9 | - PSR-0 support for autoloading 10 | - Packagist/Composer support. 11 | -------------------------------------------------------------------------------- /RELEASE-2.0.1: -------------------------------------------------------------------------------- 1 | Updated composer package ONLY. No other changes. 2 | -------------------------------------------------------------------------------- /RELEASE-2.0.2: -------------------------------------------------------------------------------- 1 | - Issue #4 fixed by animungo. 2 | -------------------------------------------------------------------------------- /build.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 16 | 17 | 18 | To build LibRIS, run: 19 | 20 | phing build 21 | 22 | This will create a generic dev release of LibRIS and copy the releasable files to the dist/ directory. All documentation will be generated, and both a minimal and full version of the code will be generated. The non-compressed files will be available for inspection in bin/build/. 23 | 24 | A numbered release can be built with: 25 | 26 | phing build -Dversion=2.0-Alpha1 27 | 28 | These are the basic tasks we anticipate performing with phing. However, the build script supports the running of several other tasks which may help you when debugging or developing LibRIS. Important ones are listed below. A complete list can be obtained by running 'phing -l' in this directory. 29 | 30 | To generate docs, do: 31 | 32 | phing doc 33 | 34 | Documentation will be stored in docs/. You can start with docs/index.html. 35 | 36 | To run unit tests, do: 37 | 38 | phing test 39 | 40 | The above will generate HTML test results which will be placed in test/reports/. If you wish to run the test and print the results directly the the command line, you should run 'phing ftest' instead. 41 | 42 | To run coverage analysis, do: 43 | 44 | phing coverage 45 | 46 | This will create HTML pages describing code coverage. The coverage analysis will be available in test/coverage 47 | 48 | To print this message, do: 49 | 50 | phing info 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 110 | 111 | ${releasedir} 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 | 206 | 215 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 265 | 266 | 267 | 268 | 269 | 270 | 271 | 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | 304 | 305 | 306 | 308 | 309 | 310 | 311 | 312 | 313 | 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | -------------------------------------------------------------------------------- /composer.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "technosophos/LibRIS", 3 | "description": "An RIS parser. RIS is a format for reference metadata.", 4 | "type": "library", 5 | "keywords": ["RIS", "File parser", "Reference", "Bibliography"], 6 | "license": "MIT or GPLv2", 7 | "homepage": "https://github.com/technosophos/LibRIS", 8 | "authors": [ 9 | { 10 | "name" : "M Butcher", 11 | "homepage" : "http://technosophos.com" 12 | } 13 | ], 14 | 15 | "autoload": { 16 | "psr-0": {"LibRIS": "src/"} 17 | }, 18 | 19 | "require": { 20 | "php": ">=5.3.0" 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /doc/RecordFormat.mdown: -------------------------------------------------------------------------------- 1 | This document describes the format of parsed data returned by LibRIS->parseFile(). 2 | 3 | Consider a record like this: 4 | 5 | TY - JOUR 6 | JF - Ethics and Information Technology 7 | T1 - At the foundations of information justice 8 | VL - 11 9 | IS - 1 10 | SP - 57 11 | EP - 69 12 | PY - 2009/03/01/ 13 | UR - http://dx.doi.org/10.1007/s10676-009-9181-2 14 | M3 - 10.1007/s10676-009-9181-2 15 | AU - Butcher, Matthew 16 | N2 - Abstract goes here.... 17 | ER - 18 | 19 | We will run this code: 20 | 21 | parseFile('./short.ris'); 26 | print_r($ris->getRecords()); 27 | ?> 28 | 29 | The output of the above will be this: 30 | 31 | Array 32 | ( 33 | [0] => Array 34 | ( 35 | [TY] => Array 36 | ( 37 | [0] => JOUR 38 | ) 39 | 40 | [JF] => Array 41 | ( 42 | [0] => Ethics and Information Technology 43 | ) 44 | 45 | [T1] => Array 46 | ( 47 | [0] => At the foundations of information justice 48 | ) 49 | 50 | [VL] => Array 51 | ( 52 | [0] => 11 53 | ) 54 | 55 | [IS] => Array 56 | ( 57 | [0] => 1 58 | ) 59 | 60 | [SP] => Array 61 | ( 62 | [0] => 57 63 | ) 64 | 65 | [EP] => Array 66 | ( 67 | [0] => 69 68 | ) 69 | 70 | [PY] => Array 71 | ( 72 | [0] => 2009/03/01/ 73 | ) 74 | 75 | [UR] => Array 76 | ( 77 | [0] => http://dx.doi.org/10.1007/s10676-009-9181-2 78 | ) 79 | 80 | [M3] => Array 81 | ( 82 | [0] => 10.1007/s10676-009-9181-2 83 | ) 84 | 85 | [AU] => Array 86 | ( 87 | [0] => Butcher, Matthew 88 | ) 89 | 90 | [N2] => Array 91 | ( 92 | [0] => Abstract goes here.... 93 | ) 94 | 95 | ) 96 | 97 | ); 98 | 99 | Thus, to get the title of the first record, you would use syntax like this: 100 | 101 | $results[0]['T1'][0]; 102 | 103 | .end 104 | -------------------------------------------------------------------------------- /package.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | LibRIS 4 | pear.querypath.org 5 | LibRIS is a tool for parsing RIS data and data files. 6 | 7 | 8 | Matt Butcher 9 | technosophos 10 | matt@aleph-null.tv 11 | yes 12 | 13 | 2012-02-03 14 | 15 | 16 | 2.0.0 17 | 2.0.0 18 | 19 | 20 | stable 21 | stable 22 | 23 | New BSD License 24 | LibRIS 2.0. 25 | 26 | The 2.0.x branch is reorganized and now requires PHP 5.3 to properly 27 | function. 28 | 29 | It supports the following new features: 30 | 31 | - Refactored library 32 | - PSR-0 support for autoloading 33 | - Packagist/Composer support. 34 | 35 | 36 | LibRIS has been refactored to contain the following classes: 37 | 38 | - \LibRIS\RISReader: Read RIS files. 39 | - \LibRIS\RISWriter: Write RIS files. 40 | - \LibRIS\RISTags: Tags and labels for RIS files. 41 | - \LibRIS\ParseException: Thrown when parsing RIS fails. 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 5.3.0 66 | 67 | 68 | 2.0.0a1 69 | 70 | 71 | 72 | 73 | 74 | -------------------------------------------------------------------------------- /package_compatible.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | LibRIS 4 | pear.querypath.org 5 | LibRIS is a tool for parsing RIS data and data files. 6 | 7 | 8 | Matt Butcher 9 | technosophos 10 | matt@aleph-null.tv 11 | yes 12 | 13 | 2012-02-03 14 | 15 | 16 | 2.0.0 17 | 2.0.0 18 | 19 | 20 | stable 21 | stable 22 | 23 | New BSD License 24 | LibRIS 2.0. 25 | 26 | The 2.0.x branch is reorganized and now requires PHP 5.3 to properly 27 | function. 28 | 29 | It supports the following new features: 30 | 31 | - Refactored library 32 | - PSR-0 support for autoloading 33 | - Packagist/Composer support. 34 | 35 | 36 | LibRIS has been refactored to contain the following classes: 37 | 38 | - \LibRIS\RISReader: Read RIS files. 39 | - \LibRIS\RISWriter: Write RIS files. 40 | - \LibRIS\RISTags: Tags and labels for RIS files. 41 | - \LibRIS\ParseException: Thrown when parsing RIS fails. 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 5.2.0 60 | 61 | 62 | 1.4.8 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | -------------------------------------------------------------------------------- /src/LibRIS/ParseException.php: -------------------------------------------------------------------------------- 1 | parseFile('path/to/file.ris'); 27 | * 28 | * // Parse a string containing RIS data. 29 | * $reader->parseString($someRisString); 30 | * 31 | * // Parse an array of lines. 32 | * $reader->parseArray($arrayOfRISDirectives); 33 | * 34 | * // Get an associative array of records. 35 | * $array = $reader->getRecords(); 36 | * 37 | * // Dump the records to STDOUT 38 | * $reader->printRecords(); 39 | * 40 | * ?> 41 | * @endcode 42 | * 43 | * The data structure generated by this class is of the form 44 | * @code 45 | * array( 48 | * 'T1' => array('title one', 'title 2'), 49 | * 'TY' => array('JOUR'), 50 | * // Other tags and their values. 51 | * ), 52 | * [1] => array( 53 | * 'T1' => array('another entry'), 54 | * 'TY' => array('JOUR'), 55 | * ), 56 | * ); 57 | * ?> 58 | * @endcode 59 | */ 60 | class RISReader { 61 | 62 | const RIS_EOL = "\r\n"; 63 | const LINE_REGEX = '/^(([A-Z1-9]{2})\s+-(.*))|(.*)$/'; 64 | 65 | protected $data = NULL; 66 | 67 | public function __construct($options = array()) { 68 | 69 | } 70 | 71 | /** 72 | * Parse an RIS file. 73 | * 74 | * This will parse the file and return a data structure representing the 75 | * record. 76 | * 77 | * @param string $filename 78 | * The full path to the file to parse. 79 | * @param StreamContext $context 80 | * The stream context (in desired) for handling the file. 81 | * @retval array 82 | * An indexed array of individual sources, each of which is an 83 | * associative array of entry details. (See LibRIS) 84 | */ 85 | public function parseFile($filename, $context = NULL) { 86 | if (!is_file($filename)) { 87 | throw new ParseException(sprintf('File %s not found.', htmlentities($filename))); 88 | } 89 | $flags = FILE_SKIP_EMPTY_LINES | FILE_TEXT; 90 | $contents = file($filename, $flags, $context); 91 | 92 | $this->parseArray($contents); 93 | } 94 | 95 | /** 96 | * Parse a string of RIS data. 97 | * 98 | * This will parse an RIS record into a representative data structure. 99 | * 100 | * @param string $string 101 | * RIS-formatted data in a string. 102 | * @param StreamContext $context 103 | * The stream context (in desired) for handling the file. 104 | * @retval array 105 | * An indexed array of individual sources, each of which is an 106 | * associative array of entry details. (See {@link LibRIS}) 107 | */ 108 | public function parseString($string) { 109 | $contents = explode (RISReader::RIS_EOL, $string); 110 | $this->parseArray($contents); 111 | } 112 | 113 | /** 114 | * Take an array of lines and parse them into an RIS record. 115 | */ 116 | protected function parseArray($lines) { 117 | $recordset = array(); 118 | 119 | // Do any cleaning and normalizing. 120 | $this->cleanData($lines); 121 | 122 | $record = array(); 123 | $lastTag = NULL; 124 | foreach ($lines as $line) { 125 | $line = trim($line); 126 | $matches = array(); 127 | 128 | preg_match(self::LINE_REGEX, $line, $matches); 129 | if (!empty($matches[3])) { 130 | $lastTag = $matches[2]; 131 | $record[$matches[2]][] = trim($matches[3]); 132 | } 133 | // End record and prep a new one. 134 | elseif (!empty($matches[2]) && $matches[2] == 'ER') { 135 | $lastTag = NULL; 136 | $recordset[] = $record; 137 | $record = array(); 138 | } 139 | elseif (!empty($matches[4])) { 140 | // Append to the last one. 141 | // We skip leading info (like BOMs). 142 | if (!empty($lastTag)) { 143 | $lastEntry = count($record[$lastTag]) - 1; 144 | // We trim because some encoders add tabs or multiple spaces. 145 | // Standard is silent on how this should be handled. 146 | $record[$lastTag][$lastEntry] .= ' ' . trim($matches[4]); 147 | } 148 | } 149 | } 150 | if (!empty($record)) $recordset[] = $record; 151 | 152 | $this->data = $recordset; 153 | } 154 | 155 | public function getRecords() { 156 | return $this->data; 157 | } 158 | 159 | public function printRecords() { 160 | $format = "%s:\n\t%s\n"; 161 | foreach ($this->data as $record) { 162 | foreach ($record as $key => $values) { 163 | foreach ($values as $value) { 164 | printf($format, RISTags::describeTag($key), $value); 165 | } 166 | } 167 | 168 | print PHP_EOL; 169 | } 170 | } 171 | 172 | /** 173 | * Clean up the data before processing. 174 | * 175 | * @param array $lines 176 | * Indexed array of lines of data. 177 | */ 178 | protected function cleanData(&$lines) { 179 | 180 | if (empty($lines)) return; 181 | 182 | // Currently, we only need to strip a BOM if it exists. 183 | // Thanks to Derik Badman (http://madinkbeard.com/) for finding the 184 | // bug and suggesting this fix: 185 | // http://blog.philipp-michels.de/?p=32 186 | $first = $lines[0]; 187 | if (substr($first, 0, 3) == pack('CCC', 0xef, 0xbb, 0xbf)) { 188 | $lines[0] = substr($first, 3); 189 | } 190 | } 191 | 192 | } 193 | -------------------------------------------------------------------------------- /src/LibRIS/RISTags.php: -------------------------------------------------------------------------------- 1 | 'Type', 31 | 'ID' => 'Reference ID', 32 | 'T1' => 'Title', 33 | 'TI' => 'Book title', 34 | 'CT' => 'Title of unpublished reference', 35 | 'A1' => 'Primary author', 36 | 'A2' => 'Secondary author', 37 | 'AU' => 'Author', 38 | 'Y1' => 'Primary date', 39 | 'PY' => 'Publication year', 40 | 'N1' => 'Notes', 41 | 'KW' => 'Keywords', 42 | 'RP' => 'Reprint status', 43 | 'SP' => 'Start page', 44 | 'EP' => 'Ending page', 45 | 'JF' => 'Periodical full name', 46 | 'JO' => 'Periodical standard abbreviation', 47 | 'JA' => 'Periodical in which article was published', 48 | 'J1' => 'Periodical name - User abbreviation 1', 49 | 'J2' => 'Periodical name - User abbreviation 2', 50 | 'VL' => 'Volume', 51 | 'IS' => 'Issue', 52 | 'T2' => 'Title secondary', 53 | 'CY' => 'City of Publication', 54 | 'PB' => 'Publisher', 55 | 'U1' => 'User 1', 56 | 'U2' => 'User 2', 57 | 'U3' => 'User 3', 58 | 'U4' => 'User 4', 59 | 'U5' => 'User 5', 60 | 'T3' => 'Title series', 61 | 'N2' => 'Abstract', 62 | 'SN' => 'ISSN/ISBN/ASIN', 63 | 'AV' => 'Availability', 64 | 'M1' => 'Misc. 1', 65 | 'M2' => 'Misc. 2', 66 | 'M3' => 'Misc. 3', 67 | 'AD' => 'Address', 68 | 'UR' => 'URL', 69 | 'L1' => 'Link to PDF', 70 | 'L2' => 'Link to Full-text', 71 | 'L3' => 'Related records', 72 | 'L4' => 'Images', 73 | 'ER' => 'End of Reference', 74 | 75 | // Unsure about the origin of these 76 | 'Y2' => 'Primary date 2', 77 | 'BT' => 'Institution [?]', 78 | ); 79 | 80 | public static $tagDescriptions = array( 81 | 'TY' => 'Type of reference (must be the first tag)', 82 | 'ID' => 'Reference ID (not imported to reference software)', 83 | 'T1' => 'Primary title', 84 | 'TI' => 'Book title', 85 | 'CT' => 'Title of unpublished reference', 86 | 'A1' => 'Primary author', 87 | 'A2' => 'Secondary author (each name on separate line)', 88 | 'AU' => 'Author (syntax. Last name, First name, Suffix)', 89 | 'Y1' => 'Primary date', 90 | 'PY' => 'Publication year (YYYY/MM/DD)', 91 | 'N1' => 'Notes ', 92 | 'KW' => 'Keywords (each keyword must be on separate line preceded KW -)', 93 | 'RP' => 'Reprint status (IN FILE, NOT IN FILE, ON REQUEST (MM/DD/YY))', 94 | 'SP' => 'Start page number', 95 | 'EP' => 'Ending page number', 96 | 'JF' => 'Periodical full name', 97 | 'JO' => 'Periodical standard abbreviation', 98 | 'JA' => 'Periodical in which article was published', 99 | 'J1' => 'Periodical name - User abbreviation 1', 100 | 'J2' => 'Periodical name - User abbreviation 2', 101 | 'VL' => 'Volume number', 102 | 'IS' => 'Issue number', 103 | 'T2' => 'Title secondary', 104 | 'CY' => 'City of Publication', 105 | 'PB' => 'Publisher', 106 | 'U1' => 'User definable 1', 107 | 'U2' => 'User definable 2', 108 | 'U3' => 'User definable 3', 109 | 'U4' => 'User definable 4', 110 | 'U5' => 'User definable 5', 111 | 'T3' => 'Title series', 112 | 'N2' => 'Abstract', 113 | 'SN' => 'ISSN/ISBN (e.g. ISSN XXXX-XXXX)', 114 | 'AV' => 'Availability', 115 | 'M1' => 'Misc. 1', 116 | 'M2' => 'Misc. 2', 117 | 'M3' => 'Misc. 3', 118 | 'AD' => 'Address', 119 | 'UR' => 'Web/URL', 120 | 'L1' => 'Link to PDF', 121 | 'L2' => 'Link to Full-text', 122 | 'L3' => 'Related records', 123 | 'L4' => 'Images', 124 | 'ER' => 'End of Reference (must be the last tag)', 125 | ); 126 | 127 | /** 128 | * Map of all types (tag TY) defined for RIS. 129 | * @var array 130 | * @see http://en.wikipedia.org/wiki/RIS_%28file_format%29 131 | * @see http://www.refman.com/support/risformat_intro.asp 132 | */ 133 | public static $typeMap = array( 134 | 'ABST' => 'Abstract', 135 | 'ADVS' => 'Audiovisual material', 136 | 'ART' => 'Art Work', 137 | 'BOOK' => 'Whole book', 138 | 'CASE' => 'Case', 139 | 'CHAP' => 'Book chapter', 140 | 'COMP' => 'Computer program', 141 | 'CONF' => 'Conference proceeding', 142 | 'CTLG' => 'Catalog', 143 | 'DATA' => 'Data file', 144 | 'ELEC' => 'Electronic Citation', 145 | 'GEN' => 'Generic', 146 | 'HEAR' => 'Hearing', 147 | 'ICOMM' => 'Internet Communication', 148 | 'INPR' => 'In Press', 149 | 'JFULL' => 'Journal (full)', 150 | 'JOUR' => 'Journal', 151 | 'MAP' => 'Map', 152 | 'MGZN' => 'Magazine article', 153 | 'MPCT' => 'Motion picture', 154 | 'MUSIC' => 'Music score', 155 | 'NEWS' => 'Newspaper', 156 | 'PAMP' => 'Pamphlet', 157 | 'PAT' => 'Patent', 158 | 'PCOMM' => 'Personal communication', 159 | 'RPRT' => 'Report', 160 | 'SER' => 'Serial publication', 161 | 'SLIDE' => 'Slide', 162 | 'SOUND' => 'Sound recording', 163 | 'STAT' => 'Statute', 164 | 'THES' => 'Thesis/Dissertation', 165 | 'UNPB' => 'Unpublished work', 166 | 'VIDEO' => 'Video recording', 167 | ); 168 | } 169 | -------------------------------------------------------------------------------- /src/LibRIS/RISWriter.php: -------------------------------------------------------------------------------- 1 | writeRecords($records); 16 | * ?> 17 | * @endcode 18 | */ 19 | class RISWriter { 20 | 21 | public function __construct() {} 22 | 23 | /** 24 | * Write a series of records to a single RIS string. 25 | * 26 | * @param array $records 27 | * An array in the format generated by RISReader::parseFile() 28 | * @retval string 29 | * The record as a string. 30 | */ 31 | public function writeRecords($records) { 32 | $buffer = array(); 33 | foreach ($records as $record) { 34 | $buffer[] = $this->writeRecord($record); 35 | } 36 | return implode(RISReader::RIS_EOL, $buffer); 37 | } 38 | 39 | /** 40 | * Write a single record as an RIS string. 41 | * 42 | * The record should be an associative array of tags to values. 43 | * 44 | * @param array $tags 45 | * An associative array of key => array(value1, value2,...). 46 | * @retval string 47 | * The record as a string. 48 | */ 49 | public function writeRecord($tags) { 50 | $buffer = array(); 51 | $fmt = '%s - %s'; 52 | 53 | $buffer[] = sprintf($fmt, 'TY', $tags['TY'][0]); 54 | unset($tags['TY']); 55 | 56 | foreach ($tags as $tag => $values) { 57 | foreach ($values as $value) { 58 | $buffer[] = sprintf($fmt, $tag, $value); 59 | } 60 | } 61 | $buffer[] = 'ER - '; 62 | 63 | return implode(RISReader::RIS_EOL, $buffer); 64 | } 65 | 66 | } 67 | -------------------------------------------------------------------------------- /tests/Banyuls.ris: -------------------------------------------------------------------------------- 1 | TY - JOUR 2 | AU - Alonso-Gómez, A.L. 3 | AU - Alonso-Bedate, M. 4 | AU - Delgado, M.J. 5 | PY - 1993 6 | TI - The inhibition by indoleamines (tryptamine and serotonin) of ocular serotonin-N-acetyltransferase from Rana perezi is temperature-dependent 7 | SP - 33-36 8 | JF - Neuroscience Letters 9 | VL - 155 10 | IS - 1 11 | N1 - AANAT T°C 12 | N1 - Abstr 13 | N2 - Temperature effects on ocular serotonin N-acetyltransferase (NAT) kinetics characteristics from Rana perezi have been studied with respect to tryptamine and serotonin as substrates. Monoamine oxidase (MAO) activity does not interfere in NAT assay at acceptoramine concentrations used in NAT kinetics characterization from R. perezi retina. NAT shows an inhibition by high substrate (serotonin) concentration, which is temperature-dependent. NAT follows the Michaelis-Menten equation at low temperature, whereas at high temperatures (>10°C) an inhibition by serotonin is observed. This inhibition of NAT activity by serotonin could act as an amplification mechanism to increase daily melatonin rhythm amplitude in the retina of ectotherms. 14 | ID - 109 15 | ER - 16 | 17 | TY - JOUR 18 | AU - Bahri-Sfar, L. 19 | AU - Lemaire, C. 20 | AU - Ben Hassine, O.K. 21 | AU - Bonhomme, F. 22 | PY - 2000 23 | TI - Fragmentation of sea bass populations in the 24 | western and eastern Mediterranean as revealed by 25 | microsatellite polymorphism 26 | SP - 929^935 27 | JF - Proceedings of the Royal Society of London Series B Biological Sciences 28 | VL - 267 29 | IS - 1446 30 | N1 - labrax Genet 31 | N1 - pdf 32 | N2 - We studied the genetic structure at six microsatellite loci of the Mediterranean sea bass (Dicentrarchus labrax) on 19 samples collected from different localities in the western and eastern Mediterranean basins. Significant divergence was found between the two basins. The distance tree showed two separate clusters of populations which matched well with geography, with the noticeable exception of one Egyptian sample which grouped within the western clade, a fact attributable to the introduction of aquaculture broodstock. No heterogeneity was observed within the western basin (theta = 0.0014 and n.s.). However, a significant level of differentiation was found among samples of the eastern Mediterranean (theta = 0.026 and p < 0.001). These results match with water currents but probably not with the dispersal abilities of this fish species. We thus hypothesize that selective forces are at play which limit long-range dispersal, a fact to be taken into account in the debate about speciation processes in the marine environment. 33 | ID - 125 34 | ER - 35 | 36 | TY - JOUR 37 | AU - Bahri-Sfar, L. 38 | AU - Lemaire, C. 39 | AU - Chatain, B. 40 | AU - Divanach, P. 41 | AU - Ben Hassine, O.K. 42 | AU - Bonhomme, F. 43 | PY - 2005 44 | TI - Impact of aquaculture on the genetic structure of Mediterranean populations of Dicentrarchus 45 | SP - 71-76 46 | JF - Aquatic Living Resources 47 | VL - 16 48 | IS - 1 49 | N1 - labrax Genet 50 | N1 - pdf 51 | N2 - A phylogeographic analysis based on 6 polymorphic microsatellites was performed on 15 sea bass samples. five from Western Mediterranean, seven from Eastern Mediterranean and three coming from French aquaculture stocks. Among the eastern samples, three did not cluster according to their geographic origin but rather with the occidental group. Furthermore. a somewhat lower allelic diversity was observed within these particular samples, indicating that they originated from a limited number of progenitors of foreign origin. Among the aquaculture stocks, only one revealed a significant reduction of genetic variability, indicating that these stocks are largely outbred and open to wild fishes. The fact that the use of occidental fingerlings to seed broodstocks in the eastern basin facilities dates back to the early 80s at the latest poses the question of the biological mechanisms explaining the maintainance of fish from occidental origin within an oriental context for two or three generations. 52 | ID - 133 53 | ER - 54 | 55 | TY - JOUR 56 | AU - Benyassi, A. 57 | AU - Schwartz, C. 58 | AU - Coon, S.L. 59 | AU - Klein, D.C. 60 | AU - Falcon, J. 61 | PY - 2000 62 | TI - Melatonin synthesis: arylalkylamine N-acetyltransferases in trout retina and pineal organ are different 63 | SP - 255-8 64 | JF - Neuroreport 65 | VL - 11 66 | IS - 2 67 | Y2 - Feb 7 68 | N1 - 10674465 69 | N1 - AANAT T°C 70 | N1 - pdf 71 | KW - Acetyl Coenzyme A/metabolism/pharmacology 72 | Animals 73 | Arylamine N-Acetyltransferase/*metabolism/pharmacology 74 | Buffers 75 | Dose-Response Relationship, Drug 76 | Enzyme Activation/drug effects/physiology 77 | Female 78 | Hydrogen-Ion Concentration 79 | Melatonin/*biosynthesis 80 | Oncorhynchus mykiss/*metabolism 81 | Phenethylamines/metabolism/pharmacology 82 | Pineal Gland/*enzymology 83 | Proteins/metabolism 84 | Retina/*enzymology 85 | Temperature 86 | N2 - Serotonin N-acetyltransferase (AANAT) is the first enzyme in the conversion of serotonin to melatonin. Changes in AANAT activity determine the daily rhythm in melatonin secretion. Two AANAT genes have been identified in the pike, pAANAT-1 and pAANAT-2, expressed in the retina and in the pineal, respectively. The genes preferentially expressed in these tissues encode proteins with distinctly different kinetic characteristics. Like the pike, trout retina primarily expresses the AANAT-1 gene and trout pineal primarily expresses the AANAT-2 gene. Here we show that the kinetic characteristics of AANAT in these tissues differ as in pike. These differences include optimal temperature for activity (pineal: 12 degrees C; retina: 25 degrees C) and relative affinity for indoleethylamines compared to phenylethylamines. In addition, retinal AANAT exhibited substrate inhibition, which was not seen with pineal AANAT. The kinetic differences between AANAT-1 and AANAT-2 appear to be defining characteristics of these gene subfamilies, and are not species specific. 87 | AD - Laboratoire de Neurobiologie Cellulaire et Neuroendocrinologie, CNRS UMR 6558, Universite de Poitiers, France. 88 | ID - 99 89 | ER - 90 | 91 | TY - JOUR 92 | AU - Besseau, L. 93 | AU - Benyassi, A. 94 | AU - Moller, M. 95 | AU - Coon, S.L. 96 | AU - Weller, J.L. 97 | AU - Boeuf, G. 98 | AU - Klein, D.C. 99 | AU - Falcon, J. 100 | PY - 2006 101 | TI - Melatonin pathway: breaking the 'high-at-night' rule in trout retina 102 | SP - 620-7 103 | JF - Exp Eye Res 104 | VL - 82 105 | IS - 4 106 | Y2 - Apr 107 | N1 - 16289161 108 | N1 - AANAT 109 | N1 - pdf 110 | KW - Acetylserotonin O-Methyltransferase/metabolism 111 | Animals 112 | Arylalkylamine N-Acetyltransferase/metabolism 113 | Circadian Rhythm/physiology 114 | Dark Adaptation/physiology 115 | Female 116 | Melatonin/*metabolism 117 | Oncorhynchus mykiss/*metabolism 118 | Photic Stimulation/methods 119 | Pineal Gland/metabolism 120 | RNA, Messenger/analysis 121 | Retina/*metabolism 122 | N2 - Pineal melatonin synthesis increases at night in all vertebrates, due to an increase in the activity of arylalkylamine N-acetyltransferase (AANAT). Melatonin is also synthesized in the retina of some vertebrates and it is generally assumed that patterns of pineal and retinal AANAT activity and melatonin production are similar, i.e. they exhibit a high-at-night pattern. However, the situation in fish is atypical because in some cases retinal melatonin increases during the day, not the night. Consistent with this, we now report that light increases the activity and abundance of the AANAT expressed in trout retina, AANAT1, at a time when the activity and abundance of pineal AANAT, AANAT2, decreases. Likewise, exposure to darkness causes retinal AANAT protein and activity to decrease coincident with increases in the pineal gland. Rhythmic changes in retinal AANAT protein and activity are 180 degrees out of phase with those of retinal AANAT1 mRNA; all appear to be driven by environmental lighting, not by a circadian oscillator. The atypical high-during-the-day pattern of retinal AANAT1 activity may reflect an evolutionary adaptation that optimizes an autocrine/paracrine signaling role of melatonin in photoadaptation and phototransduction; alternatively, it might reflect an adaptation that broadens and enhances aromatic amine detoxification in the retina. 123 | AD - Laboratoire Arago, Universite P&M Curie (UPMC) and CNRS, UMR 7628, BP44, 66651 Banyuls/Mer-Cedex, France. 124 | ID - 97 125 | ER - 126 | 127 | TY - CONF 128 | AU - Boeuf, G. 129 | AU - Lasserre, P. 130 | PY - 1978 131 | TI - Aspects de la régulation osmotique chez le bar juvénile (Dicentrarchus labrax) en élevage et introduit dans les lagunes amenagées de Certes bassin d'Arcachon (Gitonde) 132 | BT - Colloque National Ecotron 133 | CY - Brest 134 | PB - Publ. Sci. Tech. CNEXO 135 | VL - 7 136 | SP - 673-688 137 | N1 - Aspects de la régulation osmotique chez le bar juvénile (Dicentrarchus labrax) en élevage et introduit dans les lagunes amenagées de Certes bassin d'Arcachon (Gitonde) 138 | N1 - labrax salt 139 | N1 - paper 140 | ID - 137 141 | ER - 142 | 143 | TY - JOUR 144 | AU - Bonhomme, F. 145 | AU - Naciri, M. 146 | AU - Bahri-Sfar, L. 147 | AU - Lemaire, C. 148 | PY - 2002 149 | TI - Comparative analysis of genetic structure of two closely related sympatric marine fish species Dicentrarchus labrax and Dicentrarchus punctatus 150 | SP - 213-220 151 | JF - Comptes Rendus Biologies 152 | VL - 325 153 | IS - 3 154 | N1 - labrax Genet 155 | N1 - pdf 156 | N2 - We present here the genetic structure existing among five samples of the spotted sea bass Dicentrarchus punctatus, and we compare it to what prevails in the common sea bass D. labrax, a congeneric species sampled on almost the same geographical range. A genetic distance tree inferred from the polymorphism at six microsatellite loci shows a distinct pattern for the two species. D. labrax samples appears to be genetically more homogeneous with a global Fst of 3% as compared to the 10% observed at D. punctatus, indicating a lesser level of gene flow in the latter species. While appearing more differentiated, D. punctatus presents no clear geographical organisation of its genetic variability in opposition to D. labrax samples. This allows us to propose this pair of closely relative species as a good candidate for the study by comparative analysis of the biological and/or historical factors affecting genetic differentiation in marine environment. 157 | 158 | ID - 132 159 | ER - 160 | 161 | TY - JOUR 162 | AU - Breton, G. 163 | AU - Kay, S.A. 164 | PY - 2007 165 | TI - Plant biology: time for growth 166 | SP - 265-6 167 | JF - Nature 168 | VL - 448 169 | IS - 7151 170 | Y2 - Jul 19 171 | N1 - 17637650 172 | N1 - Clock plant 173 | N1 - pdf 174 | KW - Arabidopsis/genetics/*growth & development/*radiation effects 175 | Arabidopsis Proteins/genetics/metabolism 176 | Biological Clocks/*physiology/radiation effects 177 | Circadian Rhythm/*physiology/radiation effects 178 | Gene Expression Regulation, Plant 179 | Hypocotyl/genetics/growth & development/radiation effects 180 | *Light 181 | Seedling/genetics/growth & development/radiation effects 182 | Time Factors 183 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17637650 184 | ID - 214 185 | ER - 186 | 187 | TY - JOUR 188 | AU - Canosa, L.F. 189 | AU - Chang, J.P. 190 | AU - Peter, R.E. 191 | PY - 2007 192 | TI - Neuroendocrine control of growth hormone in fish 193 | SP - 1-26 194 | JF - Gen Comp Endocrinol 195 | VL - 151 196 | IS - 1 197 | N1 - Rev Hormones 198 | N1 - pdf 199 | N2 - The biological actions of growth hormone (GH) are pleiotropic, including growth 200 | promotion, energy mobilization, gonadal development, appetite, and social 201 | behavior. Accordingly, the regulatory network for GH is complex and includes many 202 | endocrine and environmental factors. In fish, the neuroendocrine control of GH is 203 | multifactorial with multiple inhibitors and stimulators of pituitary GH 204 | secretion. In fish, GH release is under a tonic negative control exerted mainly 205 | by somatostatin. Sex steroid hormones and nutritional status influence the level 206 | of brain expression and effectiveness of some of these GH neuroendocrine 207 | regulatory factors, suggesting that their relative importance differs under 208 | different physiological conditions. At the pituitary level, some, if not all, 209 | somatotropes can respond to multiple regulators. Therefore, ligand- and 210 | function-specificity, as well as the integrative responses to multiple signals 211 | must be achieved at the level of signal transduction mechanisms. Results from 212 | investigations on a limited number of stimulatory and inhibitory GH-release 213 | regulators indicate that activation of different but convergent intracellular 214 | pathways and the utilization of specific intracellular Ca(2+) stores are some of 215 | the strategies utilized. However, more work remains to be done in order to better 216 | understand the integrative mechanisms of signal transduction at the somatotrope 217 | level and the relevance of various GH regulators in different physiological 218 | circumstances. 219 | AD - Department of Biological Sciences, University of Alberta, Edmonton, Alta., Canada 220 | ID - 108 221 | ER - 222 | 223 | TY - JOUR 224 | AU - Coon, S.L. 225 | AU - Begay, V. 226 | AU - Deurloo, D. 227 | AU - Falcon, J. 228 | AU - Klein, D.C. 229 | PY - 1999 230 | TI - Two arylalkylamine N-acetyltransferase genes mediate melatonin synthesis in fish 231 | SP - 9076-82 232 | JF - J Biol Chem 233 | VL - 274 234 | IS - 13 235 | Y2 - Mar 26 236 | N1 - 10085157 237 | N1 - AANAT 238 | N1 - pdf 239 | KW - Amino Acid Sequence 240 | Animals 241 | Arylamine N-Acetyltransferase/chemistry/*genetics 242 | Circadian Rhythm/genetics 243 | Cloning, Molecular 244 | Evolution, Molecular 245 | Fishes/*genetics/metabolism 246 | Gene Expression Regulation/genetics 247 | Kinetics 248 | Melatonin/*biosynthesis 249 | Molecular Sequence Data 250 | Pineal Gland/enzymology 251 | RNA, Messenger/metabolism 252 | Recombinant Proteins/genetics 253 | Retina/enzymology 254 | Sequence Alignment 255 | Sequence Analysis, DNA 256 | Serotonin/metabolism 257 | N2 - Serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase, AANAT, EC 2.3.1.87) is the first enzyme in the conversion of serotonin to melatonin. Large changes in AANAT activity play an important role in the daily rhythms in melatonin production. Although a single AANAT gene has been found in mammals and the chicken, we have now identified two AANAT genes in fish. These genes are designated AANAT-1 and AANAT-2; all known AANATs belong to the AANAT-1 subfamily. Pike AANAT-1 is nearly exclusively expressed in the retina and AANAT-2 in the pineal gland. The abundance of each mRNA changes on a circadian basis, with retinal AANAT-1 mRNA peaking in late afternoon and pineal AANAT-2 mRNA peaking 6 h later. The pike AANAT-1 and AANAT-2 enzymes (66% identical amino acids) exhibit marked differences in their affinity for serotonin, relative affinity for indoleethylamines versus phenylethylamines and temperature-activity relationships. Two AANAT genes also exist in another fish, the trout. The evolution of two AANATs may represent a strategy to optimally meet tissue-related requirements for synthesis of melatonin: pineal melatonin serves an endocrine role and retinal melatonin plays a paracrine role. 258 | AD - Section on Neuroendocrinology, Laboratory of Developmental Neurobiology, NICHD, National Institutes of Health, Bethesda, Maryland 20892-4480, USA. 259 | ID - 86 260 | ER - 261 | 262 | TY - JOUR 263 | AU - Coon, S.L. 264 | AU - Klein, D.C. 265 | PY - 2006 266 | TI - Evolution of arylalkylamine N-acetyltransferase: emergence and divergence 267 | SP - 2-10 268 | JF - Mol Cell Endocrinol 269 | VL - 252 270 | IS - 1-2 271 | N1 - AANAT evol 272 | N1 - pdf 273 | N2 - The melatonin rhythm-generating enzyme, arylalkylamine N-acetyltransferase (AANAT) is known to have recognizable ancient homologs in bacteria and fungi, but not in other eukaryotes. Analysis of new cDNA and genomic sequences has identified several additional homologs in other groupings. First, an AANAT homolog has been found in the genome of the cephalochordate amphioxus, representing the oldest homolog in chordates. Second, two AANAT homologs have been identified in unicellular green algae. The homologs in amphioxus, unicellular green algae, fungi and bacteria are similarly primitive in that they lack sequences found in vertebrate AANATs that are involved in regulation and that facilitate binding and catalysis. In addition, all these sequences are intronless. These features are consistent with horizontal transfer of the AANAT ancestor from bacteria to green algae, fungi and chordates. Lastly, a third AANAT gene has been found in teleost fish, suggesting that AANAT genes serve multiple functions in addition to melatonin synthesis. 274 | AD - Section on Neuroendocrinology, Office of the Scientific Director, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20894, USA. coons@mail.nih.gov 275 | ID - 113 276 | ER - 277 | 278 | TY - JOUR 279 | AU - Davis, A.J. 280 | AU - Jenkinson, L.S. 281 | AU - Lawton, J.H. 282 | AU - Shorrocks, B. 283 | AU - Wood, S. 284 | PY - 1998 285 | TI - Making mistakes when predicting shifts in species range in response to global warming 286 | JF - Nature 287 | IS - 783-786 288 | N1 - AANAT T°C 289 | N1 - pdf 290 | N2 - Many attempts to predict the biotic responses to climate change rely on the |[lsquo]|climate envelope|[rsquo]| approach1, 2, 3, in which the current distribution of a species is mapped in climate-space and then, if the position of that climate-space changes, the distribution of the species is predicted to shift accordingly4, 5, 6. The flaw in this approach is that distributions of species also reflect the influence of interactions with other species7, 8, 9, 10, so predictions based on climate envelopes may be very misleading if the interactions between species are altered by climate change11. An additional problem is that current distributions may be the result of sources and sinks12, in which species appear to thrive in places where they really persist only because individuals disperse into them from elsewhere13,14. Here we use microcosm experiments on simple but realistic assemblages to show how misleading the climate envelope approach can be. We show that dispersal and interactions, which are important elements of population dynamics15, must be included in predictions of biotic responses to climate change 291 | ID - 205 292 | ER - 293 | 294 | TY - JOUR 295 | AU - Delarbre, C. 296 | AU - Spruytb, N. 297 | AU - Delmarreb, C. 298 | AU - Gallutc, C. 299 | AU - Barrielc, V. 300 | AU - Janvierd, P. 301 | AU - Laudetb, V. 302 | AU - Gachelina, G. 303 | PY - 1998 304 | TI - The Complete Nucleotide Sequence of the Mitochondrial DNA 305 | of the Dogfish, Scyliorhinus canicula 306 | SP - 331-344 307 | JF - Genetics 308 | VL - 150 309 | N1 - Phylogeny 310 | N1 - pdf 311 | N2 - We have determined the complete nucleotide sequence of the mitochondrial DNA (mtDNA) of the dogfish, Scyliorhinus canicula. The 16,697-bp-long mtDNA possesses a gene organization identical to that of the Osteichthyes, but different from that of the sea lamprey Petromyzon marinus. The main features of the mtDNA of osteichthyans were thus established in the common ancestor to chondrichthyans and osteichthyans. The phylogenetic analysis confirms that the Chondrichthyes are the sister group of the Osteichthyes. 312 | ID - 119 313 | ER - 314 | 315 | TY - JOUR 316 | AU - Dijk, D.J. 317 | AU - Archer, S.N. 318 | PY - 2009 319 | TI - Light, Sleep, and Circadian Rhythms: Together Again 320 | SP - e1000145 321 | JF - PLoS Biology 322 | VL - 7 323 | IS - 6 324 | N1 - Rhythm 325 | N1 - pdf 326 | N2 - This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 327 | Funding: The authors' research on light, sleep, and circadian rhythms is supported by the BBSRC, AFOSR, Wellcome Trust, and Philips Lighting. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 328 | Competing interests: The authors have declared that no competing interests exist. 329 | ID - 207 330 | ER - 331 | 332 | TY - JOUR 333 | AU - Falcón, J. 334 | PY - 1999 335 | TI - Cellular circadian clocks in the pineal 336 | SP - 121-62 337 | JF - Prog Neurobiol 338 | VL - 58 339 | IS - 2 340 | Y2 - Jun 341 | N1 - 10338357 342 | N1 - AANAT pineal 343 | N1 - pdf 344 | KW - Animals 345 | Biological Clocks/*physiology 346 | *Circadian Rhythm 347 | Melatonin/biosynthesis/metabolism 348 | Photoreceptors, Vertebrate/physiology 349 | Phototransduction/physiology 350 | Pineal Gland/anatomy & histology/cytology/innervation/*physiology 351 | N2 - Daily rhythms are a fundamental feature of all living organisms; most are synchronized by the 24 hr light/dark (LD) cycle. In most species, these rhythms are generated by a circadian system, and free run under constant conditions with a period close to 24 hr. To function properly the system needs a pacemaker or clock, an entrainment pathway to the clock, and one or more output signals. In vertebrates, the pineal hormone melatonin is one of these signals which functions as an internal time-keeping molecule. Its production is high at night and low during day. Evidence indicates that each melatonin producing cell of the pineal constitutes a circadian system per se in non-mammalian vertebrates. In addition to the melatonin generating system, they contain the clock as well as the photoreceptive unit. This is despite the fact that these cells have been profoundly modified from fish to birds. Modifications include a regression of the photoreceptive capacities, and of the ability to transmit a nervous message to the brain. The ultimate stage of this evolutionary process leads to the definitive loss of both the direct photosensitivity and the clock, as observed in the pineal of mammals. This review focuses on the functional properties of the cellular circadian clocks of non-mammalian vertebrates. How functions the clock? How is the photoreceptive unit linked to it and how is the clock linked to its output signal? These questions are addressed in light of past and recent data obtained in vertebrates, as well as invertebrates and unicellulars. 352 | AD - CNRS UMR 6558, Departement des Neurosciences, Universite de Poitiers, France. Jack.Falcon@campus.univ-poitiers.fr 353 | ID - 79 354 | ER - 355 | 356 | TY - JOUR 357 | AU - Falcón, J. 358 | AU - Besseau, L. 359 | AU - Fuentès, M. 360 | AU - Sauzet, S. 361 | AU - Magnanou, E. 362 | AU - Boeuf, G. 363 | PY - 2009 364 | TI - Structural and functional evolution of the pineal melatonin system in vertebrates. 365 | SP - 101-111 366 | JF - Trends in Comparative Endocrinology and Neurobiology: Ann N Y Acad Sci 367 | VL - 1163 368 | N1 - Clock Review 369 | N1 - pdf 370 | N2 - In most species daily rhythms are synchronized by the photoperiodic cycle. They are generated by the circadian system, which is made of a pacemaker, an entrainment pathway to this clock, and one or more output signals. In 371 | vertebrates, melatonin produced by the pineal organ is one of these outputs. The production of this time-keeping hormone is high at night and low during the day. Despite the fact that this is a well-preserved pattern, the pathways through which the photoperiodic information controls the rhythm have been profoundly modified from early vertebrates to mammals. The photoperiodic control is direct in fish and frogs and indirect in mammals. In the former, full circadian systems are found in photoreceptor cells of the pineal organ, retina, and possibly brain, thus forming a network where melatonin could be a hormonal synchronizer. In the latter, the three elements of a circadian system are scattered: the photoreceptive units are in the eyes, the clocks are in the suprachiasmatic nuclei of the hypothalamus, and the melatonin-producing units are in the pineal cells. Intermediate situations are observed in sauropsids. Differences are also seen at the level of the arylalkylamine N-acetyltransferase (AANAT), the enzyme responsible for the daily variations in melatonin production. In contrast to tetrapods, teleost fish AANATs are duplicated and display tissue-specific expression; also, pineal AANAT is special--it responds to temperature in a species-specific manner, which reflects the fish ecophysiological preferences. This review summarizes anatomical, structural, and molecular aspects of the evolution of the melatonin-producing system in vertebrates. 372 | ID - 136 373 | ER - 374 | 375 | TY - JOUR 376 | AU - Falcón, J. 377 | AU - Besseau, L. 378 | AU - Sauzet, S. 379 | AU - Boeuf, G. 380 | PY - 2007 381 | TI - Melatonin effects on the hypothalamo-pituitary axis in fish 382 | SP - 81-8 383 | JF - Trends in Endocrinolology and Metabolism 384 | VL - 18 385 | IS - 2 386 | Y2 - Mar 387 | N1 - 17267239 388 | N1 - Clock Review 389 | N1 - pdf 390 | KW - Animals 391 | Evolution, Molecular 392 | Fishes/genetics/growth & development/*physiology 393 | Hypothalamo-Hypophyseal System/*drug effects/physiology 394 | Melatonin/*pharmacology 395 | Models, Biological 396 | Pineal Gland/physiology 397 | Pituitary-Adrenal System/*drug effects/physiology 398 | Receptors, Melatonin/genetics/physiology 399 | Reproduction/physiology 400 | N2 - Melatonin, a hormonal output signal of vertebrate circadian clocks, contributes to synchronizing behaviors and neuroendocrine regulations with the daily and annual variations of the photoperiod. Conservation and diversity characterize the melatonin system: conservation because its pattern of production and synchronizing properties are a constant among vertebrates; and diversity because regulation of both its synthesis and modes of action have been profoundly modified during vertebrate evolution. Studies of the targets and modes of action of melatonin in fish, and their parallels in mammals, are of interest to our understanding of time-related neuroendocrine regulation and its evolution from fish to mammals, as well as for aquacultural purposes. 401 | AD - Laboratoire Arago, UMR 7628/GDR2821, Universite Pierre et Marie Curie (UPMC) and CNRS, B.P. 44, Avenue du Fontaule, F-66651, Banyuls-sur-Mer Cedex, France. falcon@obs-banyuls.fr 402 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17267239 403 | ID - 206 404 | ER - 405 | 406 | TY - JOUR 407 | AU - Falcón, J. 408 | AU - Bolliet, V. 409 | AU - Collin, J.P. 410 | PY - 1996 411 | TI - Partial characterization of serotonin N - acetyltransferases from northern pike (Esox lucius, L.) pineal organ and retina: effects of temperature 412 | SP - 386-93 413 | JF - Pflugers Arch 414 | VL - 432 415 | IS - 3 416 | Y2 - Jul 417 | N1 - 8765997 418 | N1 - AANAT T°C 419 | N1 - Abstr 420 | KW - Acetyl Coenzyme A/metabolism 421 | Animals 422 | Arylamine N-Acetyltransferase/*metabolism 423 | Esocidae/*metabolism 424 | Female 425 | Hydrogen-Ion Concentration 426 | Kinetics 427 | Male 428 | Melatonin/metabolism 429 | Pineal Gland/*enzymology 430 | Proteins/metabolism 431 | Retina/*enzymology 432 | Temperature 433 | Tryptamines/metabolism 434 | N2 - In vertebrates, the nocturnal rise in pineal organ and retinal melatonin synthesis results from the increase in the activity of the serotonin N-acetyltransferase (NAT), a cAMP-dependent enzyme. In the fish pineal organ in culture, light and temperature act in a similar manner on cAMP content and NAT activity. It is not known whether the effects of temperature are mediated through cAMP or through modifications of NAT kinetics. The present study was designed: (1) to find out whether NAT activity from pineal organ homogenates is similar to NAT activity from pineal organs in culture, with regard to variations in temperature, and (2) to compare NAT activity from the pineal organ and the retina. Pineal organ and retinal NAT activity increased linearly with protein concentrations. Higher activities were obtained with 0.2 mol/l of phosphate buffer, pH 6. Higher molarity or a higher pH induced a decrease in retinal and pineal organ NAT activity: retinal NAT was more sensitive than pineal organ NAT to changes in molarity, whereas the opposite held true as far as pH was concerned. Pineal organ and retinal NAT obeyed the Michaelis-Menten equation with respect to increasing concentrations of acetyl-coenzyme A. With increasing concentrations of tryptamine: (1) pineal organ NAT activity increased in a manner suggesting positive co-operativity, (2) retinal NAT displayed, after an initial increase, inhibition by substrate. The kinetics of the reactions were temperature dependent. Maximal activities were reached at 18/20 degrees C in the pineal organ and at 37 degrees C in the retina. The present study is the first to describe the optimum conditions for the assay of NAT activity in homogenates from the retina of fish and from the pineal organ of poikilotherms, and also the first to compare some characteristics of NAT activity from these two analogous organs. Our results suggest that the effects of temperature on melatonin production are mediated, at least in part, through modifications of NAT kinetics. Future studies will aim to clarify whether the activities measured in the pineal organ and retinal homogenates reflect the presence of one or of several enzymes. 435 | AD - Laboratoire de Neurobiologie et Neuroendocrinologie Cellulaires, URA CNRS 1869 436 | ID - 70 437 | ER - 438 | 439 | TY - JOUR 440 | AU - Fields, P.A. 441 | AU - Somero, G.N. 442 | PY - 1998 443 | TI - Hot spots in cold adaptation: Localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes 444 | SP - 11476-11481 445 | JF - PNAS 446 | VL - 95 447 | IS - 19 448 | N1 - AANAT T°C 449 | N1 - pdf 450 | N2 - To elucidate mechanisms of enzymatic adaptation to extreme cold, we determined kinetic properties, thermal stabilities, and deduced amino acid sequences of lactate dehydrogenase A4 (A4-LDH) from nine Antarctic ( 1.86 to 1°C) and three South American (4 to 10°C) notothenioid teleosts. Higher Michaelis-Menten constants (Km) and catalytic rate constants (kcat) distinguish orthologs of Antarctic from those of South American species, but no relationship exists between adaptation temperature and the rate at which activity is lost because of heat denaturation. In all species, active site residues are conserved fully, and differences in kcat and Km are caused by substitutions elsewhere in the molecule. Within geographic groups, identical kinetic properties are generated by different substitutions. By combining our data with A4-LDH sequences for other vertebrates and information on roles played by localized conformational changes in setting kcat, we conclude that notothenioid A4-LDHs have adapted to cold temperatures by increases in flexibility in small areas of the molecule that affect the mobility of adjacent active-site structures. Using these findings, we propose a model that explains linked temperature-adaptive variation in Km and kcat. Changes in sequence that increase flexibility of regions of the enzyme involved in catalytic conformational changes may reduce energy (enthalpy) barriers to these rate-governing shifts in conformation and, thereby, increase kcat. However, at a common temperature of measurement, the higher configurational entropy of a cold-adapted enzyme may foster conformations that bind ligands poorly, leading to high Km values relative to warm-adapted orthologs. 451 | AD - Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950-3094 452 | ID - 110 453 | ER - 454 | 455 | TY - JOUR 456 | AU - Isorna, E. 457 | AU - Besseau, L. 458 | AU - Boeuf, G. 459 | AU - Desdevises, Y. 460 | AU - Vuilleumier, R. 461 | AU - Alonso-Gomez, A.L. 462 | AU - Delgado, M.J. 463 | AU - Falcon, J. 464 | PY - 2006 465 | TI - Retinal, pineal and diencephalic expression of frog arylalkylamine N-acetyltransferase-1 466 | SP - 11-8 467 | JF - Mol Cell Endocrinol 468 | VL - 252 469 | IS - 1-2 470 | Y2 - Jun 27 471 | N1 - AANAT evol 472 | N1 - pdf 473 | KW - Amino Acid Sequence 474 | Animals 475 | Arylalkylamine N-Acetyltransferase/*genetics 476 | Base Sequence 477 | Cloning, Molecular 478 | Diencephalon/*enzymology 479 | Epididymis/enzymology 480 | Evolution, Molecular 481 | Humans 482 | Male 483 | Phylogeny 484 | Pineal Gland/*enzymology 485 | RNA, Messenger/genetics 486 | Ranidae/classification/*genetics 487 | Retina/*enzymology 488 | N2 - The arylalkylamine N-acetyltransferase (AANAT) is a key enzyme in the rhythmic production of melatonin. Two Aanats are expressed in Teleost fish (Aanat1 in the retina and Aanat2 in the pineal organ) but only Aanat1 is found in tetrapods. This study reports the cloning of Aanat1 from R. perezi. Transcripts were mainly expressed in the retina, diencephalon, intestine and testis. In the retina and pineal organ, Aanat1 expression was in the photoreceptor cells. Expression was also seen in ependymal cells of the 3rd ventricle and discrete cells of the suprachiasmatic area. The expression of Aanat1 in both the retina and pineal organ, and the absence of Aanat2 suggests that green frog resembles more to birds and mammals than to Teleost fish, as far as Aanat is concerned. The significance of Aanat1 in extra-pineal and extra-retinal tissues remains to be elucidated; in the diencephalon, it might be associated to the so-called deep brain photoreceptor cells. 489 | AD - Laboratoire Arago, Universite Pierre et Marie Curie and CNRS, UMR 7628, B.P. 44, Avenue du Fontaule, F-66651 Banyuls/Mer-Cedex, France. 490 | ID - 22 491 | ER - 492 | 493 | TY - JOUR 494 | AU - Johns, J.C. 495 | AU - Somero, G.N. 496 | PY - 2004 497 | TI - Evolutionary Convergence in Adaptation of Proteins to Temperature: A4-Lactate Dehydrogenases of Pacific Damselfishes (Chromis spp.) 498 | SP - 314-320 499 | JF - Molecular Biology and Evolution 500 | VL - 21 501 | IS - 2 502 | N1 - AANAT T°C 503 | N1 - pdf 504 | N2 - We have compared the kinetic properties (Michaelis-Menten constant [Km] and catalytic rate constant [kcat]) and amino acid sequences of orthologs of lactate dehydrogenase-A (A4-LDH) from congeners of Pacific damselfishes (genus Chromis) native to cold-temperate and tropical habitats to elucidate mechanisms of enzymatic adaptation to temperature. Specifically, we determined whether the sites of adaptive variation and the types of amino acids involved in substitutions at these sites were similar in the Chromis orthologs and other orthologs of warm-adapted and cold-adapted A4-LDH previously studied. We report striking evolutionary convergence in temperature adaptation of this protein and present further support for the hypothesis that enzyme adaptation to temperature involves subtle amino acid changes at a few sites that affect the mobility of the portions of the enzyme that are involved in rate-determining catalytic conformational changes. We tested the predicted effects of differences in sequence using site-directed mutagenesis. A single amino acid substitution in a key hinge region of the A4-LDH molecule is sufficient to change the kinetic characteristics of a temperate A4-LDH to that of a tropical ortholog. This substitution is at the same location that was identified in previous studies of adaptive variation in A4-LDH and was hypothesized to be important in adjusting Km and kcat. Our results suggest that certain sites within an enzyme, notably those that establish the energy changes associated with rate-limiting movements of protein structure during catalysis, are "hot spots" of adaptation and that common types of amino acid substitutions occur at these sites to adapt structural "flexibility" and kinetic properties. Thus, despite the wide array of options that proteins have to adjust their structural stabilities in the face of thermal stress, the adaptive changes that couple "flexibility" to alterations of function may be limited in their diversity. 505 | Key Words: temperature adaptation • A4-LDH • enzyme kinetics • ldh-a gene • ortholog evolution • Chromis 506 | AD - Hopkins Marine Station, Stanford University, Pacific Grove, California 1 507 | E-mail: somero@stanford.edu. 508 | ID - 112 509 | ER - 510 | 511 | TY - JOUR 512 | AU - Kawauchi, H. 513 | AU - Sower, S.A. 514 | PY - 2006 515 | TI - The dawn and evolution of hormones in the adenohypophysis 516 | SP - 3-14 517 | JF - Gen Comp Endocrinol 518 | VL - 148 519 | IS - 1 520 | Y2 - Aug 521 | N1 - 16356498 522 | N1 - Rev Hormones 523 | N1 - pdf 524 | KW - Animals 525 | *Evolution, Molecular 526 | Models, Biological 527 | Petromyzon/*genetics 528 | Phylogeny 529 | Pituitary Gland/secretion 530 | Pituitary Gland, Anterior/*secretion 531 | Pituitary Hormones/metabolism 532 | Pituitary Hormones, Anterior/*genetics 533 | N2 - The adenohypophysial hormones have been believed to have evolved from several ancestral genes by duplication followed by evolutionary divergence. To understand the origin and evolution of the endocrine systems in vertebrates, we have characterized adenohypophysial hormones in an agnathan, the sea lamprey Petromyzon marinus. In gnathostomes, adrenocorticotropin (ACTH) and melanotropin (MSH) together with beta-endorphins (beta-END) are encoded in a single gene, designated as proopiomelanocortin (POMC), however in sea lamprey, ACTH and MSH are encoded in two distinct genes, proopoicortin (POC) gene and proopiomelanotropin (POM) gene, respectively. The POC and POM genes are expressed specifically in the rostral pars distalis (RPD) and the pars intermedia (PI), respectively. Consequently, the final products from both tissues are the same in all vertebrates, i.e., ACTH from the PD and MSH from the PI. The POMC gene might have been established in the early stages of invertebrate evolution by internal gene duplication of the MSH domains. The ancestral gene might be then inherited in lobe-finned fish and tetrapods, while internal duplication and deletion of MSH domains as well as duplication of whole POMC gene took place in lamprey and gnathostome fish. Sea lamprey growth hormone (GH) is expressed in the cells of the dorsal half of the proximal pars distalis (PPD) and stimulates the expression of an insulin-like growth factor (IGF) gene in the liver as in other vertebrates. Its gene consists of 5 exons and 4 introns spanning 13.6 kb, which is the largest gene among known GH genes. GH appears to be the only member of the GH family in the sea lamprey, which suggests that GH is the ancestral hormone of the GH family that originated first in the molecular evolution of the GH family in vertebrates and later, probably during the early evolution of gnathostomes. The other member of the gene family, PRL and SL, appeared by gene duplication. A beta-chain cDNA belonging to the gonadotropin (GTH) and thyrotropin (TSH) family was cloned. It is expressed in cells of the ventral half of PPD. Since the expression of this gene is stimulated by lamprey gonadotropin-releasing hormone, it was assigned to be a GTHbeta. This GTHbeta is far removed from beta-subunits of LH, FSH, and TSH in an unrooted tree derived from phylogenetic analysis, and takes a position as an out group, suggesting that lampreys have a single GTH gene, which duplicated after the agnathans and prior to the evolution of gnathostomes to give rise to LH and FSH. 534 | AD - Laboratory of Molecular Endocrinology, School of Fisheries Sciences, Kitasato University, Sanriku, Iwate 022-0101, Japan. hiroshi@kitasato-u.ac.jp 535 | ID - 106 536 | ER - 537 | 538 | TY - JOUR 539 | AU - Klein, D.C. 540 | PY - 2007 541 | TI - Arylalkylamine N-Acetyltransferase: "the Timezyme" 542 | SP - 4233-4237 543 | JF - J Biol Chem 544 | VL - 282 545 | IS - 7 546 | N1 - AANAT 547 | N1 - pdf 548 | N2 - Arylalkylamine N-acetyltransferase controls daily changes in melatonin production by the pineal gland and thereby plays a unique role in biological timing in vertebrates. Arylalkylamine N-acetyltransferase is also expressed in the retina, where it may play other roles in addition to signaling, including neurotransmission and detoxification. Large changes in activity reflect cyclic 3',5'-adenosine monophosphate-dependent phosphorylation of arylalkylamine N-acetyltransferase, leading to formation of a regulatory complex with 14-3-3 proteins. This activates the enzyme and prevents proteosomal proteolysis. The conserved features of regulatory systems that control arylalkylamine N-acetyltransferase are a circadian clock and environmental lighting. 549 | ID - 114 550 | ER - 551 | 552 | TY - JOUR 553 | AU - Klein, D.C. 554 | AU - Coon, S.L. 555 | AU - Roseboom, P.H. 556 | AU - Weller, J.L. 557 | AU - Bernard, M. 558 | AU - Gastel, J.A. 559 | AU - Zatz, M. 560 | AU - Iuvone, P.M. 561 | AU - Rodriguez, I.R. 562 | AU - Begay, V. 563 | AU - Falcon, J. 564 | AU - Cahill, G.M. 565 | AU - Cassone, V.M. 566 | AU - Baler, R. 567 | PY - 1997 568 | TI - The melatonin rhythm-generating enzyme: molecular regulation of serotonin N-acetyltransferase in the pineal gland 569 | SP - 307-57; discussion 357-8 570 | JF - Recent Progress Hormone Research 571 | VL - 52 572 | N1 - 9238858 573 | N1 - Mel age 574 | N1 - Abs 575 | KW - Amino Acid Sequence 576 | Animals 577 | Arylamine N-Acetyltransferase/chemistry/genetics/*metabolism 578 | Base Sequence 579 | Evolution 580 | Humans 581 | Melatonin/*blood 582 | Molecular Sequence Data 583 | Pineal Gland/*enzymology 584 | RNA, Messenger/metabolism 585 | Species Specificity 586 | N2 - A remarkably constant feature of vertebrate physiology is a daily rhythm of melatonin in the circulation, which serves as the hormonal signal of the daily light/dark cycle: melatonin levels are always elevated at night. The biochemical basis of this hormonal rhythm is one of the enzymes involved in melatonin synthesis in the pineal gland-the melatonin rhythm-generating enzyme-serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase, AA-NAT, E.C. 2.3.1.87). In all vertebrates, enzyme activity is high at night. This reflects the influences of internal circadian clocks and of light. The dynamics of this enzyme are remarkable. The magnitude of the nocturnal increase in enzyme activity ranges from 7- to 150-fold on a species-to-species basis among vertebrates. In all cases the nocturnal levels of AA-NAT activity decrease very rapidly following exposure to light. A major advance in the study of the molecular basis of these changes was the cloning of cDNA encoding the enzyme. This has resulted in rapid progress in our understanding of the biology and structure of AA-NAT and how it is regulated. Several constant features of this enzyme have become apparent, including structural features, tissue distribution, and a close association of enzyme activity and protein. However, some remarkable differences among species in the molecular mechanisms involved in regulating the enzyme have been discovered. In sheep, AA-NAT mRNA levels show relatively little change over a 24-hour period and changes in AA-NAT activity are primarily regulated at the protein level. In the rat, AA-NAT is also regulated at a protein level; however, in addition, AA-NAT mRNA levels exhibit a 150-fold rhythm, which reflects cyclic AMP-dependent regulation of expression of the AA-NAT gene. In the chicken, cyclic AMP acts primarily at the protein level and a rhythm in AA-NAT mRNA is driven by a noncyclic AMP-dependent mechanism linked to the clock within the pineal gland. Finally, in the trout, AA-NAT mRNA levels show little change and activity is regulated by light acting directly on the pineal gland. The variety of mechanisms that have evolved among vertebrates to achieve the same goal-a rhythm in melatonin-underlines the important role melatonin plays as the hormonal signal of environmental lighting in vertebrates. 587 | AD - Section on Neuroendocrinology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-4480, USA. 588 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9238858 589 | ID - 21 590 | ER - 591 | 592 | TY - JOUR 593 | AU - Lemaire, C. 594 | AU - Allegrucci, G. 595 | AU - Naciri, M. 596 | AU - Bahri-Sfar, L. 597 | AU - Kara, H. 598 | AU - Bonhomme, F. 599 | PY - 2000 600 | TI - Do discrepancies between microsatellite and allozyme variation reveal differential selection between sea and lagoon in the sea bass (Dicentrarchus labrax)? 601 | SP - 457-467 602 | JF - Molecular Ecology 603 | VL - 9 604 | IS - 4 605 | N1 - labrax Genet 606 | N1 - pdf 607 | N2 - In the present study the genetic structure of Dicentrarchus labrax (14 samples from the Mediterranean) was analysed at six microsatellite loci, in order to test the hypothesis that some enzymatic loci undergo selection between marine and lagoon habitat. Eight of the 14 samples were analysed at both microsatellite and allozyme markers. The analysis of the genetic variation among the Mediterranean samples showed that (i) &Fcirc;ST values obtained with the six microsatellite loci were much smaller than those obtained with the 28 allozymes and (ii) microsatellite loci seemed to reflect more the geographical proximity than an ecological one. Thirteen enzymatic loci exhibited moderate to high values compared with microsatellites. This was interpreted as evidence that these allozymes are non-neutral. However, only six loci seemed to be implicated in differentiation between marine and lagoon samples, the causes of selection being unknown for the others. A possible scenario of population dynamics of the sea bass between marine and lagoon habitat is suggested 608 | ID - 124 609 | ER - 610 | 611 | TY - JOUR 612 | AU - Magne Olufsenn, M. 613 | AU - Smalås, A.O. 614 | AU - Moe, E. 615 | AU - Brandsdal, B.O. 616 | PY - 2005 617 | TI - Increased Flexibility as a Strategy for Cold Adaptation A comparative Molecular Dynamics Study of Cold- and Warm-active Uracil DNA Glycosylase 618 | SP - 18042-18048 619 | JF - J Biol Chem 620 | VL - 280 621 | IS - 18 622 | N1 - AANAT T°C 623 | N1 - pdf 624 | N2 - From the Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway 625 | Uracil DNA glycosylase (UDG) is a DNA repair enzyme in the base excision repair pathway and removes uracil from the DNA strand. Atlantic cod UDG (cUDG), which is a cold-adapted enzyme, has been found to be up to 10 times more catalytically active in the temperature range 15-37 °C as compared with the warm-active human counterpart. The increased catalytic activity of cold-adapted enzymes as compared with their mesophilic homologues are partly believed to be caused by an increase in the structural flexibility. However, no direct experimental evidence supports the proposal of increased flexibility of cold-adapted enzymes. We have used molecular dynamics simulations to gain insight into the structural flexibility of UDG. The results from these simulations show that an important loop involved in DNA recognition (the Leu272 loop) is the most flexible part of the cUDG structure and that the human counterpart has much lower flexibility in the Leu272 loop. The flexibility in this loop correlates well with the experimental kcat/Km values. Thus, the data presented here add strong support to the idea that flexibility plays a central role in adaptation to cold environments. 626 | ID - 111 627 | ER - 628 | 629 | TY - JOUR 630 | AU - Myers, B.R. 631 | AU - Sigal, Y.M. 632 | AU - Julius, D. 633 | PY - 2009 634 | TI - Evolution of Thermal Response Properties in a Cold-Activated TRP Channel 635 | SP - e5741 636 | JF - PLoS ONE 637 | VL - 4 638 | IS - 5 639 | N1 - AANAT Temp 640 | N1 - pdf 641 | N2 - Animals sense changes in ambient temperature irrespective of whether core body temperature is internally maintained (homeotherms) or subject to environmental variation (poikilotherms). Here we show that a cold-sensitive ion channel, TRPM8, displays dramatically different thermal activation ranges in frogs versus mammals or birds, consistent with variations in these species' cutaneous and core body temperatures. Thus, somatosensory receptors are not static through evolution, but show functional diversity reflecting the characteristics of an organism's ecological niche. 642 | ID - 209 643 | ER - 644 | 645 | TY - JOUR 646 | AU - Naciri, M. 647 | AU - Lemaire, C. 648 | AU - Borsa, P. 649 | AU - Bonhomme, F. 650 | PY - 1999 651 | TI - Genetic study of the Atlantic/Mediterranean transition in sea bass (Dicentrarchus labrax) 652 | SP - 591-596 653 | JF - Journal of Heredity 654 | VL - 90 655 | IS - 6 656 | N1 - labrax Genet 657 | N1 - pdf 658 | N2 - We report on the genetic differentiation among populations of the common (or European) sea bass (Dicentrarchus labrax) from the North Sea, Britanny, Portugal, Morocco, the Alboran Sea, and the western Mediterranean. Based on allele-frequency variation at six microsatellite loci, a distance free inferred from Reynold's coancestry coefficient showed that sea bass populations clustered into two distinct groups of populations, an Atlantic group which includes the Alboran Sea east of Gibraltar Strait, and a western Mediterranean group. While no clear geographical pattern emerged within each of these two entities, the sharp transition led us to postulate that the divide may correspond to the Almeria-Oran oceanographic front. This divide was evidenced by a small but highly significant FST (0.018, P<.001), corresponding at equilibrium to an average effective number of migrants Nm on the order of 14 individuals per generation. We emphasize the idea that the passive retention of larvae on either side of the oceanographic front is not a sufficient explanation for the persistence of this divide. 659 | ID - 131 660 | ER - 661 | 662 | TY - JOUR 663 | AU - Nebel, C. 664 | AU - Romestand, B. 665 | AU - Nègre-Sadargues, G. 666 | AU - Grousset, E. 667 | AU - Aujoulat, F. 668 | AU - Bacal, J. 669 | AU - Bonhomme, F. 670 | AU - Charmantier, G. 671 | PY - 2005 672 | TI - Differential freshwater adaptation in juvenile sea-bass Dicentrarchus labrax: involvement of gills and urinary system 673 | JF - Journal of Experimental Biology 674 | N1 - labrax salt 675 | N1 - pdf 676 | KW - teleost, 677 | osmoregulation, 678 | gills, 679 | kidney, 680 | Na+/K+-ATPase, 681 | sea-bass, 682 | Dicentrarchus labrax 683 | N2 - The effects of long-term freshwater acclimatization were investigated in juvenile sea-bass Dicentrarchus labrax to determine whether all sea-bass juveniles are able to live in freshwater and to investigate the physiological basis of a successful adaptation to freshwater. This study particularly focused on the ability of sea-bass to maintain their hydromineral balance in freshwater and on their ion (re)absorbing abilities through the gills and kidneys. Two different responses were recorded after a long-term freshwater acclimatization. (1) Successfully adapted sea-bass displayed standard behavior; their blood osmolality was maintained almost constant after the freshwater challenge, attesting to their efficient hyperosmoregulation. Their branchial and renal Na+/K+-ATPase abundance and activity were high compared to seawater fish due to a high number of branchial ionocytes and to the involvement of the urinary system in active ion reabsorption, producing hypotonic urine. (2) Sea-bass that had not successfully adapted to freshwater were recognized by abnormal schooling behavior. Their blood osmolality was low (30% lower than in the successfully adapted sea-bass), which is a sign of acute osmoregulatory failure. High branchial Na+/K+-ATPase abundance and activity compared to successfully adapted fish were coupled to a proliferation of gill chloride cells, whose ultrastructure did not display pathological signs. The large surface used by the gill chloride cells might negatively interfere with respiratory gas exchanges. In their urinary system, enzyme abundance and activity were low, in accordance with the observed lower density of the kidney tubules. Urine was isotonic to blood in unsuccessfully adapted fish, ruling out any participation of the kidney in hyperosmoregulation. The kidney failure seems to generate a compensatory ion absorption through increased gill activity, but net ion loss through urine seems higher than ion absorption by the gills, leading to lower hyper-osmoregulatory performance and to death 684 | ID - 126 685 | ER - 686 | 687 | TY - JOUR 688 | AU - Nozue, K. 689 | AU - Covington, M.F. 690 | AU - Duek, P.D. 691 | AU - Lorrain, S. 692 | AU - Fankhauser, C. 693 | AU - Harmer, S.L. 694 | AU - Maloof, J.N. 695 | PY - 2007 696 | TI - Rhythmic growth explained by coincidence between internal and external cues 697 | SP - 358-361 698 | JF - Nature 699 | VL - 448 700 | N1 - Rhythm 701 | N1 - pdf 702 | N2 - Most organisms use circadian oscillators to coordinate physiological and developmental processes such as growth with predictable daily environmental changes like sunrise and sunset. The importance of such coordination is highlighted by studies showing that circadian dysfunction causes reduced fitness in bacteria1 and plants2, as well as sleep and psychological disorders in humans3. Plant cell growth requires energy and water—factors that oscillate owing to diurnal environmental changes. Indeed, two important factors controlling stem growth are the internal circadian oscillator4, 5, 6 and external light levels7. However, most circadian studies have been performed in constant conditions, precluding mechanistic study of interactions between the clock and diurnal variation in the environment. Studies of stem elongation in diurnal conditions have revealed complex growth patterns, but no mechanism has been described8, 9, 10. Here we show that the growth phase of Arabidopsis seedlings in diurnal light conditions is shifted 8–12 h relative to plants in continuous light, and we describe a mechanism underlying this environmental response. We find that the clock regulates transcript levels of two basic helix–loop–helix genes, phytochrome-interacting factor 4 (PIF4) and PIF5, whereas light regulates their protein abundance. These genes function as positive growth regulators; the coincidence of high transcript levels (by the clock) and protein accumulation (in the dark) allows them to promote plant growth at the end of the night. Thus, these two genes integrate clock and light signalling, and their coordinated regulation explains the observed diurnal growth rhythms. This interaction may serve as a paradigm for understanding how endogenous and environmental signals cooperate to control other processes 703 | ID - 208 704 | ER - 705 | 706 | TY - JOUR 707 | AU - Olufsen, M. 708 | AU - Smalås, A.O. 709 | AU - E., M. 710 | AU - Brandsdal, B.J. 711 | PY - 2005 712 | TI - Increased Flexibility as a Strategy for Cold Adaptation. A comparative Molecular Dynamics Study of Cold and Warm-active Uracil DNA Glycosylase 713 | SP - 18042-18048 714 | JF - The journal of Biological Chemistry 715 | VL - 280 716 | IS - 18 717 | N1 - AANAT Temp 718 | N1 - pdf 719 | N2 - Uracil DNA glycosylase (UDG) is a DNA repair enzyme in the base excision repair pathway and removes uracil from the DNA strand. Atlantic cod UDG (cUDG), which is a cold-adapted enzyme, has been found to be up to 10 times more catalytically active in the temperature range 15-37 °C as compared with the warm-active human counterpart. The increased catalytic activity of cold-adapted enzymes as compared with their mesophilic homologues are partly believed to be caused by an increase in the structural flexibility. However, no direct experimental evidence supports the proposal of increased flexibility of cold-adapted enzymes. We have used molecular dynamics simulations to gain insight into the structural flexibility of UDG. The results from these simulations show that an important loop involved in DNA recognition (the Leu272 loop) is the most flexible part of the cUDG structure and that the human counterpart has much lower flexibility in the Leu272 loop. The flexibility in this loop correlates well with the experimental kcat/Km values. Thus, the data presented here add strong support to the idea that flexibility plays a central role in adaptation to cold environments. 720 | ID - 202 721 | ER - 722 | 723 | TY - JOUR 724 | AU - Ortlund, E.A. 725 | AU - Bridgham, J.T. 726 | AU - Redinbo, M.R. 727 | AU - Thornton, J.W. 728 | PY - 2007 729 | TI - Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis 730 | SP - 1544 - 1548 731 | JF - Science 732 | VL - 317 733 | IS - 5844 734 | N1 - AANAT evol 735 | N1 - pdf 736 | N2 - The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein—the ~450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations—substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes—played a major role in determining GR's evolutionary trajectory 737 | ID - 203 738 | ER - 739 | 740 | TY - JOUR 741 | AU - Pörtner, H.O. 742 | AU - Peck, M.A. 743 | PY - 2010 744 | TI - Climate change effects on fishes and fisheries: towards a cause-and-effect understanding. 745 | JF - Journal of Fish Biology 746 | VL - no. doi: 10.1111/j.1095-8649.2010.02783 747 | N1 - Fish T°C 748 | N1 - pdf 749 | N2 - Ongoing climate change is predicted to affect individual organisms during all life stages, thereby affecting populations of a species, communities and the functioning of ecosystems. These effects of climate change can be direct, through changing water temperatures and associated phenologies, the lengths and frequency of hypoxia events, through ongoing ocean acidification trends or through shifts in hydrodynamics and in sea level. In some cases, climate interactions with a species will also, or mostly, be indirect and mediated through direct effects on key prey species which change the composition and dynamic coupling of food webs. Thus, the implications of climate change for marine fish populations can be seen to result from phenomena at four interlinked levels of biological organization: (1) organismal-level physiological changes will occur in response to changing environmental variables such as temperature, dissolved oxygen and ocean carbon dioxide levels. An integrated view of relevant effects, adaptation processes and tolerance limits is provided by the concept of oxygen and capacity-limited thermal tolerance (OCLT). (2) Individual-level behavioural changes may occur such as the avoidance of unfavourable conditions and, if possible, movement into suitable areas. (3) Population-level changes may be observed via changes in the balance between rates of mortality, growth and reproduction. This includes changes in the retention or dispersion of early life stages by ocean currents, which lead to the establishment of new populations in new areas or abandonment of traditional habitats. (4) Ecosystem-level changes in productivity and food web interactions will result from differing physiological responses by organisms at different levels of the food web. The shifts in biogeography and warming-induced biodiversity will affect species productivity and may, thus, explain changes in fisheries economies. This paper tries to establish links between various levels of biological organization by means of addressing the effective physiological principles at the cellular, tissue and whole organism levels. 750 | ID - 215 751 | ER - 752 | 753 | TY - JOUR 754 | AU - Ravi, V. 755 | AU - Venkatesh, B. 756 | PY - 2008 757 | TI - Rapidly evolving fish genomes and teleost diversity 758 | SP - 544-50 759 | JF - Current Opinion in Genetics & Development 760 | VL - 18 761 | IS - 6 762 | Y2 - Dec 763 | N1 - 19095434 764 | N1 - Phylogeny 765 | N1 - pdf 766 | KW - Animals 767 | *Biodiversity 768 | Conserved Sequence/genetics 769 | DNA, Intergenic/genetics 770 | *Evolution, Molecular 771 | Fishes/*genetics 772 | Genes, Duplicate/*genetics 773 | Genome/*genetics 774 | Models, Genetic 775 | Phylogeny 776 | N2 - Teleost fishes are the largest and most diverse group of vertebrates. The diversity of teleosts has been attributed to a whole-genome duplication (WGD) event in the ray-finned fish lineage. Recent comparative genomic studies have revealed that teleost genomes have experienced frequent gene-linkage disruptions compared to other vertebrates, and that protein-coding sequences in teleosts are evolving faster than in mammals, irrespective of their duplication status. A significant number of conserved noncoding elements (CNEs) shared between cartilaginous fishes and tetrapods have diverged beyond recognition in teleost fishes. The divergence of CNEs seems to have been initiated in basal ray-finned fishes before the WGD. The fast evolving singleton and duplicated genes as well as the divergent CNEs might have contributed to the diversity of teleost fishes. 777 | AD - Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore, Singapore. 778 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19095434 779 | ID - 201 780 | ER - 781 | 782 | TY - JOUR 783 | AU - Santini, F. 784 | AU - Harmon, L.J. 785 | AU - Carnevale, G. 786 | AU - Alfaro, M.E. 787 | PY - 2009 788 | TI - Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes 789 | SP - 194 790 | JF - BMC Evolutionary Biology 791 | VL - 9 792 | N1 - 19664233 793 | N1 - Phylogeny 794 | N1 - pdf 795 | KW - Animals 796 | *Evolution 797 | *Gene Duplication 798 | *Genome 799 | Phylogeny 800 | Skates (Fish)/*genetics 801 | N2 - BACKGROUND: One of the main explanations for the stunning diversity of teleost fishes (approximately 29,000 species, nearly half of all vertebrates) is that a fish-specific whole-genome duplication event (FSGD) in the ancestor to teleosts triggered their subsequent radiation. However, one critical assumption of this hypothesis, that diversification rates in teleosts increased soon after the acquisition of a duplicated genome, has never been tested. RESULTS: Here we show that one of three major diversification rate shifts within ray-finned fishes occurred at the base of the teleost radiation, as predicted by the FSGD hypothesis. We also find evidence for two rate increases that are much younger than the inferred age of the FSGD: one in the common ancestor of most ostariophysan fishes, and a second one in the common ancestor of percomorphs. The biodiversity contained within these two clades accounts for more than 88% of living fish species. CONCLUSION: Teleosts diversified explosively in their early history and this burst of diversification may have been caused by genome duplication. However, the FSGD itself may be responsible for a little over 10% of living teleost biodiversity. ~88% of species diversity is derived from two relatively recent radiations of freshwater and marine fishes where genome duplication is not suspected. Genome duplications are a common event on the tree of life and have been implicated in the diversification of major clades like flowering plants, vertebrates, and gnathostomes. However our results suggest that the causes of diversification in large clades are likely to be complex and not easily ascribed to a single event, even a dramatic one such as a whole genome duplication. 802 | AD - Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 651 Charles Young Dr, South, Los Angeles, CA 90095, USA. michaelalfaro@ucla.edu. 803 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19664233 804 | ID - 200 805 | ER - 806 | 807 | TY - JOUR 808 | AU - Sauzet, S. 809 | AU - Besseau, L. 810 | AU - Herrera Perez, P. 811 | AU - Coves, D. 812 | AU - Chatain, B. 813 | AU - Peyric, E. 814 | AU - Boeuf, G. 815 | AU - Munoz-Cueto, J.A. 816 | AU - Falcon, J. 817 | PY - 2008 818 | TI - Cloning and retinal expression of melatonin receptors in the European sea bass, Dicentrarchus labrax 819 | SP - 186-95 820 | JF - General and Comparative Endocrinology 821 | VL - 157 822 | IS - 2 823 | Y2 - Jun 824 | N1 - 18555069 825 | N1 - Mel receptors 826 | N1 - pdf 827 | KW - Amino Acid Sequence 828 | Animals 829 | Bass/*genetics 830 | Cloning, Molecular 831 | Fish Proteins/*genetics 832 | *Gene Expression Profiling 833 | In Situ Hybridization 834 | Molecular Sequence Data 835 | Receptor, Melatonin, MT1/genetics 836 | Receptor, Melatonin, MT2/genetics 837 | Receptors, Melatonin/*genetics 838 | Retina/*metabolism 839 | Sequence Homology, Amino Acid 840 | N2 - Melatonin contributes to synchronizing behaviors and physiological functions to daily and seasonal rhythm in fish. However, no coherent vision emerges because the effects vary with the species, sex, age, moment of the year or sexual cycle. And, scarce information is available concerning the melatonin receptors, which is crucial to our understanding of the role melatonin plays. We report here the full length cloning of three different melatonin receptor subtypes in the sea bass Dicentrarchus labrax, belonging, respectively, to the MT1, MT2 and Mel1c subtypes. MT1, the most abundantly expressed, was detected in the central nervous system, retina, and gills. MT2 was detected in the pituitary gland, blood cells and, to a lesser extend, in the optic tectum, diencephalon, liver and retina. Mel1c was mainly expressed in the skin; traces were found in the retina. The cellular sites of MT1 and MT2 expressions were investigated by in situ hybridization in the retina of pigmented and albino fish. The strongest signals were obtained with the MT1 riboprobes. Expression was seen in cells also known to express the enzymes of the melatonin biosynthesis, i.e., in the photoreceptor, inner nuclear and ganglion cell layers. MT1 receptor mRNAs were also abundant in the retinal pigment epithelium. The results are consistent with the idea that melatonin is an autocrine (neural retina) and paracrine (retinal pigment epithelium) regulator of retinal function. The molecular tools provided here will be of valuable interest to further investigate the targets and role of melatonin in nervous and peripheral tissues of fish. 841 | AD - Universite Pierre et Marie Curie-Paris6, UMR7628, Laboratoire Arago, Avenue Fontaule, BP44, F-66651 Banyuls-sur-Mer, Cedex, France. 842 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18555069 843 | ID - 212 844 | ER - 845 | 846 | TY - JOUR 847 | AU - Sower, S.A. 848 | AU - Freamat, M. 849 | AU - Kavanaugh, S.I. 850 | PY - 2009 851 | TI - The origins of the vertebrate hypothalamic–pituitary–gonadal (HPG) and hypothalamic–pituitary–thyroid (HPT) endocrine systems: New insights from lampreys 852 | SP - 20-29 853 | JF - General and Comparative Endocrinology 854 | VL - 161 855 | IS - 1 856 | N1 - Endocr Evol 857 | N1 - pdf 858 | N2 - The acquisition of a hypothalamic–pituitary axis was a seminal event in vertebrate evolution leading to the neuroendocrine control of many complex functions including growth, reproduction, osmoregulation, stress and metabolism. Lampreys as basal vertebrates are the earliest evolved vertebrates for which there are demonstrated functional roles for two gonadotropin-releasing hormones (GnRHs) that act via the hypothalamic–pituitary–gonadal axis controlling reproductive processes. With the availability of the lamprey genome, we have identified a novel GnRH form (lamprey GnRH-II) and a novel glycoprotein hormone receptor, lGpH-R II (thyroid-stimulating hormone-like receptor). Based on functional studies, in situ hybridization and phylogenetic analysis, we hypothesize that the newly identified lamprey GnRH-II is an ancestral GnRH to the vertebrate GnRHs. This finding opens a new understanding of the GnRH family and can help to delineate the evolution of the complex neuro/endocrine axis of reproduction. A second glycoprotein hormone receptor (lGpH-R II) was also identified in the sea lamprey. The existing data suggest the existence of a primitive, overlapping yet functional HPG and HPT endocrine systems in this organism, involving one possibly two pituitary glycoprotein hormones and two glycoprotein hormone receptors as opposed to three or four glycoprotein hormones interacting specifically with three receptors in gnathostomes. We hypothesize that the glycoprotein hormone/glycoprotein hormone receptor systems emerged as a link between the neuro-hormonal and peripheral control levels during the early stages of gnathostome divergence. The significance of the results obtained by analysis of the HPG/T axes in sea lamprey may transcend the limited scope of the corresponding physiological compartments by providing important clues in respect to the interplay between genome-wide events (duplications), coding sequence (mutation) and expression control level evolutionary mechanisms in definition of the chemical control pathways in vertebrates. 859 | ID - 210 860 | ER - 861 | 862 | TY - JOUR 863 | AU - Wang, T. 864 | AU - Overgaard, J. 865 | PY - 2007 866 | TI - The Heartbreak of Adapting to Global Warming 867 | SP - 49-50 868 | JF - Science 869 | VL - 315 870 | IS - 5808 871 | N1 - AANAT Temp 872 | N1 - pdf 873 | ID - 199 874 | ER - 875 | 876 | TY - JOUR 877 | AU - Wilkinson, C.W. 878 | PY - 2006 879 | TI - Roles of acetylation and other post-translational modifications in melanocortin function and interactions with endorphins 880 | SP - 453-71 881 | JF - Peptides 882 | VL - 27 883 | IS - 2 884 | Y2 - Feb 885 | N1 - 16280185 886 | N1 - Rev Hormones 887 | N1 - pdf 888 | KW - Acetylation 889 | Animals 890 | Endorphins/*metabolism 891 | Neurotransmitter Agents/physiology 892 | Pro-Opiomelanocortin/metabolism/*physiology 893 | *Protein Processing, Post-Translational 894 | Rats 895 | alpha-MSH/*metabolism 896 | N2 - Phylogenetic, developmental, anatomic, and stimulus-specific variations in post-translational processing of POMC are well established. For melanocortins, the role of alpha-N-acetylation and the selective activities of alpha, beta, and gamma forms are of special interest. Acetylation may shift the predominant activity of POMC products between endorphinergic and melanocortinergic actions-which are often in opposition. This review addresses: (1) variations in POMC processing; (2) the influence of acetylation on the functional activity of alpha-MSH; (3) state- and stimulus-dependent effects on the proportional distribution of forms of melanocortins and endorphins; (4) divergent effects of alpha-MSH and beta-endorphin administration; (5) potential roles of beta- and gamma-MSH. 897 | AD - Geriatric Research, Education and Clinical Center, VA Puget Sound Health Care System, Seattle, WA 98108, USA. wilkinso@u.washington.edu 898 | ID - 107 899 | ER - 900 | 901 | TY - JOUR 902 | AU - Zilberman-Peled, B. 903 | AU - Benhar, I. 904 | AU - Coon, S.L. 905 | AU - Ron, B. 906 | AU - Gothilf, Y. 907 | PY - 2004 908 | TI - Duality of serotonin-N-acetyltransferase in the gilthead seabream (Sparus aurata): molecular cloning and characterization of recombinant enzymes 909 | SP - 139-147 910 | JF - General and Comparative Endocrinology 911 | VL - 138 912 | IS - 2 913 | N1 - AANAT 914 | N1 - pdf 915 | KW - Melatonin; Serotonin; Indoleethylamine; Arylalkylamine-N-acetyltransferase; Pineal gland; Retina; Seabream 916 | N2 - Serotonin-N-acetyltransferase (arylalkylamine-N-acetyltransferase, AANAT) is the key enzyme in the biosynthesis of melatonin in the pineal gland and retinal photoreceptors. Rhythmic AANAT activity drives rhythmic melatonin production in these tissues. The presence of two AANATs, AANAT1 and AANAT2, has been previously demonstrated in three fresh water teleosts. This duality, the result of early gene duplication, is unique to teleost species. In this study, the cDNAs encoding for AANAT1 and AANAT2 were cloned from a marine fish, the gilthead seabream (sb, Sparus aurata). Northern blot hybridization analysis indicates that sbAANAT1 and sbAANAT2 are exclusively expressed in the retina and pineal gland, respectively. Bacterially expressed recombinant sbAANATs exhibit differential enzyme kinetics. Recombinant retinal sbAANAT1 has relatively high substrate affinity and low activity rate; it is inhibited by high substrate and product concentrations. In contrast, recombinant pineal sbAANAT2 exhibits low substrate affinity and high activity rate and is not inhibited by substrates or products. The two recombinant enzymes also exhibit differential substrate preference. Retinal sbAANAT1 acetylates a range of arylalkylamines while pineal sbAANAT2 preferentially acetylates indoleethylamines, especially serotonin. The different spatial expression patterns, enzyme kinetics, and substrate preferences of the two sbAANATs support the hypothesis that, as a consequence of gene duplication, teleosts have acquired two AANATs with different functions. Pineal AANAT2 specializes in the production of large amounts of melatonin that is released into the circulation and exerts an endocrine role. Retinal AANAT1, on the other hand, is involved in producing low levels of melatonin that execute a paracrine function. In addition, retinal AANAT1 may carry out an as yet unknown function that involves acetylation of arylalkylamines other than serotonin. 917 | ID - 115 918 | ER - 919 | 920 | TY - JOUR 921 | AU - Ziv, L. 922 | AU - Gothilf, Y. 923 | PY - 2006 924 | TI - Circadian time-keeping during early stages of development 925 | SP - 4146-51 926 | JF - Proc Natl Acad Sci U S A 927 | VL - 103 928 | IS - 11 929 | Y2 - Mar 14 930 | N1 - Clock Devel 931 | N1 - pdf 932 | KW - Animals 933 | Arylalkylamine N-Acetyltransferase/genetics 934 | Base Sequence 935 | Circadian Rhythm/*physiology/radiation effects 936 | Eye Proteins/antagonists & inhibitors/genetics 937 | Gene Expression Regulation, Developmental/radiation effects 938 | Larva/physiology/radiation effects 939 | Light 940 | Oligonucleotides, Antisense/genetics 941 | Period Circadian Proteins 942 | Pineal Gland/embryology/growth & development/physiology/radiation effects 943 | RNA, Messenger/genetics/metabolism 944 | Zebrafish/*embryology/genetics/growth & development/physiology 945 | Zebrafish Proteins/antagonists & inhibitors/genetics 946 | N2 - The zebrafish pineal gland is a photoreceptive organ containing an intrinsic central circadian oscillator, which drives daily rhythms of gene expression and the melatonin hormonal signal. Here we investigated the effect of light, given at early developmental stages before pineal gland formation, on the pineal circadian oscillator. Embryos that were exposed to light at 0-6, 10-13, or 10-16 h after fertilization exhibited clock-controlled rhythms of arylalkylamine-N-acetyltransferase (zfaanat2) mRNA in the pineal gland during the third and fourth day of development. This rhythm was absent in embryos that were placed in continuous dark within 2 h after fertilization (before blastula stage). Differences in the phases of these rhythms indicate that they are determined by the time of illumination. Light treatments at these stages also caused a transient increase in period2 mRNA levels, and the development of zfaanat2 mRNA rhythm was abolished by PERIOD2 knock-down. These results indicate that light exposure at early developmental stages, and light-induced expression of period2, are both required for setting the phase of the circadian clock. The 24-h rhythm is then maintained throughout rapid proliferation and, remarkably, differentiation. 947 | AD - Departments of Zoology and Neurobiochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel. 948 | UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16537499 949 | ID - 213 950 | ER - 951 | 952 | -------------------------------------------------------------------------------- /tests/derik-test.ris: -------------------------------------------------------------------------------- 1 | TY - BOOK 2 | ID - 394 3 | T1 - Narratology: Introduction to the Theory of Narrative 4 | A1 - Bal,Mieke 5 | PB - University of Toronto Press 6 | PY - 1997/12/31/ 7 | SN - 0802078060, 9780802078063 8 | ER - 9 | 10 | -------------------------------------------------------------------------------- /tests/short.ris: -------------------------------------------------------------------------------- 1 | TY - JOUR 2 | JF - Ethics and Information Technology 3 | T1 - At the foundations of information justice 4 | VL - 11 5 | IS - 1 6 | SP - 57 7 | EP - 69 8 | PY - 2009/03/01/ 9 | UR - http://dx.doi.org/10.1007/s10676-009-9181-2 10 | M3 - 10.1007/s10676-009-9181-2 11 | AU - Butcher, Matthew 12 | N2 - Abstract goes here.... 13 | ER - -------------------------------------------------------------------------------- /tests/simple_test.php: -------------------------------------------------------------------------------- 1 | parseFile($testdir . '/derik-test.ris'); 19 | 20 | $ris->printRecords(); 21 | 22 | $records = $ris->getRecords(); 23 | 24 | $rw = new \LibRIS\RISWriter(); 25 | print $rw->writeRecords($records); 26 | 27 | // Regression against Banyuls.ris 28 | $ris = new RISReader(); 29 | $ris->parseFile($testdir . '/Banyuls.ris'); 30 | 31 | $ris->printRecords(); 32 | 33 | $records = $ris->getRecords(); 34 | 35 | $rw = new \LibRIS\RISWriter(); 36 | print $rw->writeRecords($records); 37 | -------------------------------------------------------------------------------- /tests/test1.ris: -------------------------------------------------------------------------------- 1 |  2 | TY - JOUR 3 | JF - Ethics and Information Technology 4 | T1 - At the foundations of information justice 5 | VL - 11 6 | IS - 1 7 | SP - 57 8 | EP - 69 9 | PY - 2009/03/01/ 10 | UR - http://dx.doi.org/10.1007/s10676-009-9181-2 11 | M3 - 10.1007/s10676-009-9181-2 12 | AU - Butcher, Matthew 13 | N2 - Abstract  Is there such a thing as information justice? In this paper, I argue that the current state of the information economy, particularly 14 | as it regards information and computing technology (ICT), is unjust, conferring power disproportionately on the information-wealthy 15 | at great expense to the information-poor. As ICT becomes the primary method for accessing and manipulating information, it 16 | ought to be treated as a foundational layer of the information economy. I argue that by maximizing the liberties (freedom 17 | to use, freedom to distribute, freedom to modify, and so on) associated with certain computer software, an incentives-rich 18 | and stable environment can be established in ICT that will foster development of the information economy among the information 19 | poor. I suggest that the now-mature Free and Open Source Software paradigm, which has already produced widely-used enterprise-class 20 | applications, can be harnessed in support of these ends. 21 | 22 | ER - 23 | --------------------------------------------------------------------------------