Исследование общих закономерностей эволюции генома человека при дупликации генов и точечном мутагенезе
Диссертация
Если внешние группы по каким-либо причинам не доступны, то можно использовать другие методы укоренения деревьев. Один такой метод использовать гипотезу о «молекулярных часах». При этом делается допущение,' что скорости мутационных изменений примерно постоянны во времени и между организмами (или последовательностями). Современной теоретической основой этого метода является нейтральная теория… Читать ещё >
Содержание
- Обзор литературы
- Актуальность исследуемой области
- Основные виды мутаций
- Влияние соматических и наследуемых мутаций
- Методы реконструкции мутационных и эволюционных событий
- Закономерности процессов мутагенеза и эволюции
- Глава 1. — Анализ загрязнений транскрипционных данных человека
- 1. 1. Введение
- 1. 2. Методы
- 1. 2. 1. Создание коллекции «мусорных «EST
- 1. 2. 2. Полимеразная цепная реакция (ПЦР)
- 1. 3. Результаты и обсуждение
- 1. 3. 1. Человеческие EST, не имеющие сходства с последовательностями из генома человека
- 1. 3. 2. Загрязнения в базе данных EST человека
- 1. 3. 3. Растительные EST в базе данных EST человека
- 1. 3. 4. Анализ загрязнений рибосомальными мРНК в базе данных EST человека
- 1. 3. 5. Экспериментальный поиск «пропущенных» генов человека
- 1. 4. Выводы
- Глава 2. — Сравнительных анализ частот нуклеотидных слов в геноме человека, а также в геномах других эукариот
- 2. 1. Введение
- 2. 2. Методы
- 2. 2. 1. Выборка анализируемых геномов
- 2. 2. 2. Разорванные слова
- 2. 2. 3. Частотность
- 2. 2. 4. Статистические методы для подсчета ожидаемых частот слов
- 2. 2. 5. Минимальная частотность
- 2. 3. Результаты и обсуждение
- 2. 3. 1. Сравнение методов для подсчета ожидаемых частот слов
- 2. 3. 2. Одно буквенные слова
- 2. 3. 3. Недопредставленные двухбуквенные слова
- 2. 3. 4. Перепредставленные двухбуквенные слова
- 2. 3. 5. Недопредставленные трехбуквенные и четырехбуквенные словабО
- 2. 3. 6. Перепредставленные трехбуквенные и четырехбуквенные слова
- 2. 3. 7. Пятибуквенные, шестибуквенные и семибуквенные слова
- 2. 3. 8. Сравнение с маскированными геномами
- 2. 3. 9. Сравнение с кодирующими последовательностями
- 2. 4. Выводы
- Глава 3. — Исследование мутационных контекстов в геноме человека
- 3. 1. Введение
- 3. 2. Методы
- 3. 2. 1. Критерии включения полиморфизмов
- 3. 2. 2. Мутационный контекст и подконтекст
- 3. 2. 3. Контраст
- 3. 2. 4. Минимальный контраст
- 3. 2. 5. Мутационное смещение
- 3. 2. 6. Статистическая значимость
- 3. 3. Результаты
- 3. 4. Обсуждение
- 3. 5. Выводы
- Глава 4. — Исследование эволюции недавно дуплицированных генов человека
- 4. 1. Введение
- 4. 2. Методы
- 4. 2. 1. Составление выборки семейств паралогичных генов человека
- 4. 2. 2. Подсчет dN и dS
- 4. 2. 3. Исследование асимметрии эволюции паралогов
- 4. 2. 4. Сравнение с ортологами
- 4. 2. 5. Анализ GOstat
- 4. 2. 6. Транскрипционные данные
- 4. 2. 7. Анализ PolyPhen
- 4. 3. Результаты
- 4. 3. 1. Оценка индивидуальных значений dN и dS
- 4. 3. 2. Индивидуальные значения dN и dS паралогичных генов
- 4. 3. 3. Асимметрия в несинонимичных сайтах
- 4. 3. 4. Асимметрия в синонимичных сайтах
- 4. 3. 5. Анализ программой PolyPhen
- 4. 3. 6. Анализ с помощью базы данных Pride
- 4. 4. Обсуждение
- 4. 5. Выводы
- Глава 5. — Исследование эволюции сайтов сплайсинга в семействах паралогичных генов человека
- 5. 1. Введение
- 5. 2. Методы
- 5. 2. 1. Составление выборки семейств паралогичных генов
- 5. 2. 2. Определение сайтов сплайсинга
- 5. 2. 3. Составление выравниваний окрестностей сайтов сплайсинга
- 5. 2. 4. Построение деревьев
- 5. 2. 5. Реконструкция предковых состояний
- 5. 2. 6. Вычисление веса сайта
- 5. 3. Результаты и обсуждение
- 5. 4. Выводы
- Глава 6. — Метилированные цитозины реже мутируют в СрО островах
- 6. 1. Введение
- 6. 2. Методы
- 6. 2. 1. Метилированные цитозины
- 6. 2. 2. Полиморфизмы
- 6. 2. 3. Направленные замены
- 6. 2. 4. СрО острова
- 6. 2. 5. Составление контрольных выборок Срв динуклеотидов
- 6. 2. 6. Оценка частоты мутаций 5тСрО>ТрО
- 6. 2. 7. Частоты аллелей
- 6. 2. 8. Частота рекомбинаций
- 6. 2. 9. Отрицательный отбор в генах
- 6. 3. Результаты
- 6. 3. 1. Частота направленных мутаций 5тСрО>ТрО понижена в Срв островах
- 6. 3. 2. Распределение частот аллелей в СрО островах смещено в сторону редких аллелей
- 6. 3. 3. Смещенная генная конверсия не объясняет снижение частоты мутаций 5тСрО>ТрО в СрО островах
- 6. 3. 4. Отрицательный отбор не может объяснить снижение частоты мутаций 5шСрО>ТрО в СрО островах
- 6. 3. 5. Данные по полиморфизмам подтверждают сниженную частоту 5шСрС>ТрО мутаций в СрО островах
- 6. 4. Обсуждение
- 6. 5. Выводы
- Выводы
- Благодарности
- Список публикаций по теме диссертации
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