update
This commit is contained in:
baiobelfer
parent
4c2536250b
commit
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\documentclass{report}
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% Pakiety do ustawienia marginesów
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\usepackage{geometry}
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\geometry{
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a4paper,
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left=2.6cm,
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right=2.6cm,
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top=2.6cm,
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bottom=2.6cm
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}
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\usepackage[
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sortcites,
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backend=biber,
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hyperref=true,
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firstinits=true,
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maxbibnames=99,
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]{biblatex}
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\addbibresource{references.bib}
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% Kodowanie i język
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\usepackage[utf8]{inputenc} % Dla pdfLaTeX
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\usepackage[T1]{fontenc}
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\usepackage[polish]{babel}
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\usepackage{listings}
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% Pakiety do stylizacji
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\usepackage{titlesec}
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\usepackage{tocloft}
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\usepackage{enumitem}
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% \setlist[longenum,1]{label=\arabic*., nosep}
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% \setlist[longenum,2]{label=\arabic*), nosep}
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% \setlist[longenum,3]{label=\alph*., nosep}
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\newlist{longenum}{enumerate}{5}
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\setlist[longenum,1]{label=\arabic*.}
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\setlist[longenum,2]{label=\arabic*)}
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\setlist[longenum,3]{label=\alph*.}
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\setlist[longenum,4]{label=\alph*)}
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\setlist[longenum,5]{label=--}
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% Pakiet do nagłówków i stopek
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\usepackage{fancyhdr}
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\pagestyle{fancy}
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\fancyhf{} % Czyszczenie domyślnych nagłówków i stopek
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\fancyhead[L]{Biotech, PCz}
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\fancyhead[R]{M. Pabiszczak} % Lewy nagłówek
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\fancyfoot[L]{Commit UUID: \texttt{\commitUUID} \\ Commit Date: \texttt{\commitDate}} % Lewa stopka - informacje linia po linii
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\fancyfoot[R]{\thepage} % Prawa stopka - Numer strony
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% Pakiety do dodawania znaków wodnych
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\usepackage{eso-pic} % Pakiet do wstawiania znaków wodnych
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\usepackage{graphicx} % Pakiet do wstawiania obrazów
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\usepackage{transparent} % Pakiet do przezroczystości obrazów
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% Pakiety dodatkowe
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\usepackage{datetime2} % Pakiet do obsługi daty i godziny
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\usepackage{ulem} % Pakiet do przekreślania tekstu
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% Definicje kolorów
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\usepackage{xcolor}
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\definecolor{wzo}{rgb}{0.000, 0.502, 0.000} % intensywny zielony
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\definecolor{szo}{rgb}{0.196, 0.803, 0.196} % limonkowy
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\definecolor{pzo}{rgb}{0.235, 0.702, 0.443} % średni zielony
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\definecolor{zoz}{rgb}{0.235, 0.702, 0.700} % średni zielony
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\definecolor{stat}{rgb}{0.541, 0.169, 0.886} % fioletowy
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\definecolor{kN}{rgb}{1.000, 0.647, 0.000} % pomarańczowy
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\definecolor{uO}{rgb}{0.275, 0.514, 0.706} % niebieski
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\definecolor{rO}{rgb}{0.0, 0.0, 0.5} % ciemno granatowy
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\definecolor{uRODO}{rgb}{0.000, 0.502, 0.502} % teal
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\definecolor{rRODO}{rgb}{0.125, 0.698, 0.667} % jasny teal
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\definecolor{kor}{rgb}{1.0, 0.0, 0.0} % czerwony
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\definecolor{zs}{rgb}{1.0, 0.0, 0.0} % Kolor Teal (lub dowolny wybrany kolor)
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\definecolor{lightgray}{rgb}{0.70, 0.70, 0.70}
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% Definicja kolorów
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\definecolor{backcolour}{rgb}{0.95,0.95,0.92} % jasny szary
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\definecolor{codegreen}{rgb}{0,0.6,0} % zielony
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\definecolor{codegray}{rgb}{0.5,0.5,0.5} % szary
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\definecolor{codepurple}{rgb}{0.58,0,0.82} % fioletowy
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\definecolor{magentacolor}{rgb}{1.0, 0.0, 1.0} % magenta
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% Styl dla kodu
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\lstdefinestyle{mystyle}{
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backgroundcolor=\color{backcolour},
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commentstyle=\color{codegreen},
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keywordstyle=\color{magentacolor},
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numberstyle=\tiny\color{codegray},
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stringstyle=\color{codepurple},
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basicstyle=\ttfamily\footnotesize,
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breaklines=true,
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captionpos=b,
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numbers=left,
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numbersep=5pt,
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showspaces=false,
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showstringspaces=false,
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showtabs=false,
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tabsize=2,
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extendedchars=true, % Umożliwia polskie znaki
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literate={ą}{{\k{a}}}1 {ć}{{\'c}}1 {ę}{{\k{e}}}1 {ł}{{\l{}}}1 {ń}{{\'n}}1 {ó}{{\'o}}1 {ś}{{\'s}}1 {ż}{{\.z}}1 {ź}{{\'z}}1
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}
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% Ustawienie stylu jako domyślnego
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\lstset{style=mystyle}
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% Definicja nowej komendy \zs
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\newcommand{\zs}{\textcolor{zs}{Zespół Szkół }}
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% Wczytanie pliku z informacjami o commit
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\input{commit.tex}
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% Globalne ustawienie list
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\setlist{leftmargin=*} % Usunięcie dodatkowego wcięcia dla wszystkich list
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% Wyłączenie wcięcia akapitu
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\setlength{\parindent}{0pt}
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% % Definicja znaku wodnego
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% \newcommand\BackgroundPic{
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% \AtPageCenter{
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% \makebox(0,0){
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% \transparent{0.15} % Ustawienie przezroczystości na 10%
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% \includegraphics[width=0.9\textwidth, keepaspectratio]{png/logo.png}
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% }
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% }
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% }
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\begin{document}
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% Dodanie znaku wodnego do tła każdej strony
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\AddToShipoutPictureBG*{\BackgroundPic}
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% \begin{enumerate}[leftmargin=*]
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\newpage
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\input{modules/crispr}
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\label{sec:crispr}
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\newpage
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\input{modules/bio}
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\label{sec:bio}
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% \newpage
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% \input{modules/wymagania_edukacyjne} % Wczytaj zawartość pliku
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% \label{sec:wymagania_edukacyjne}
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% \end{enumerate}
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\newpage
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\printbibliography
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\end{document}
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@ -0,0 +1,23 @@
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# Pobranie pełnego UUID commita
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full_uuid=`git log -1 --format="%H"`
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# Pobranie daty commita
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commit_date=`git log -1 --format="%cd" --date=iso`
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# Pobranie komentarza z commita
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commit_message=`git log -1 --format="%s"`
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# Pobranie tagu z commita, jeśli istnieje
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commit_tag=`git describe --tags --exact-match 2>/dev/null`
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# Generowanie pliku commit.tex z UUID, datą, komentarzem i tagiem (jeśli istnieje)
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echo "\\newcommand{\\commitUUID}{${full_uuid}}" > commit.tex
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echo "\\newcommand{\\commitDate}{${commit_date}}" >> commit.tex
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echo "\\newcommand{\\commitComment}{${commit_message}}" >> commit.tex
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# Sprawdzenie, czy istnieje tag
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if [ -n "$commit_tag" ]; then
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echo "\\newcommand{\\commitTag}{${commit_tag}}" >> commit.tex
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else
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echo "\\newcommand{\\commitTag}{}" >> commit.tex
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fi
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@ -0,0 +1,4 @@
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\newcommand{\commitUUID}{98463cfa7bc8b50867b6481bc63a28b9eb0d4478}
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\newcommand{\commitDate}{2024-10-22 10:31:59 +0200}
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\newcommand{\commitComment}{start}
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\newcommand{\commitTag}{}
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@ -0,0 +1,17 @@
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\relax
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\providecommand{\transparent@use}[1]{}
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\abx@aux@refcontext{nty/global//global/global}
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\providecommand\babel@aux[2]{}
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\@nameuse{bbl@beforestart}
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\catcode `"\active
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\abx@aux@cite{0}{doudnaNewFrontierGenome2014}
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\abx@aux@segm{0}{0}{doudnaNewFrontierGenome2014}
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\babel@aux{polish}{}
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\newlabel{sec:crispr}{{}{1}}
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\newlabel{sec:bio}{{}{3}}
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\abx@aux@read@bbl@mdfivesum{nohash}
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\abx@aux@read@bblrerun
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\abx@aux@defaultrefcontext{0}{doudnaNewFrontierGenome2014}{nty/global//global/global}
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\abx@aux@defaultrefcontext{0}{jinekProgrammableDualRNAGuidedDNA2012}{nty/global//global/global}
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\abx@aux@defaultrefcontext{0}{montecilloCRISPRCas9SystemPlant2020}{nty/global//global/global}
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\gdef \@abspage@last{4}
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@ -0,0 +1,210 @@
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% $ biblatex auxiliary file $
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% $ biblatex bbl format version 3.2 $
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% Do not modify the above lines!
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%
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% This is an auxiliary file used by the 'biblatex' package.
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% This file may safely be deleted. It will be recreated by
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% biber as required.
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%
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\begingroup
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\makeatletter
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\@ifundefined{ver@biblatex.sty}
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{\@latex@error
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{Missing 'biblatex' package}
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{The bibliography requires the 'biblatex' package.}
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\aftergroup\endinput}
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{}
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\endgroup
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\refsection{0}
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\datalist[entry]{nty/global//global/global}
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\entry{doudnaNewFrontierGenome2014}{article}{}
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\name{author}{2}{}{%
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{{hash=db6ee88c2505c20e204e8ea38dc1a7ed}{%
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family={Doudna},
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familyi={D\bibinitperiod},
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given={Jennifer\bibnamedelima A.},
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giveni={J\bibinitperiod\bibinitdelim A\bibinitperiod}}}%
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{{hash=147cdad451a06b98a827e8850511922a}{%
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family={Charpentier},
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familyi={C\bibinitperiod},
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given={Emmanuelle},
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giveni={E\bibinitperiod}}}%
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}
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\strng{namehash}{ac39f49ff392a08abaa0153e03e063c9}
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\strng{fullhash}{ac39f49ff392a08abaa0153e03e063c9}
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\strng{bibnamehash}{ac39f49ff392a08abaa0153e03e063c9}
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\strng{authorbibnamehash}{ac39f49ff392a08abaa0153e03e063c9}
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\strng{authornamehash}{ac39f49ff392a08abaa0153e03e063c9}
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\strng{authorfullhash}{ac39f49ff392a08abaa0153e03e063c9}
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\field{sortinit}{D}
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\field{sortinithash}{6f385f66841fb5e82009dc833c761848}
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\field{labelnamesource}{author}
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\field{labeltitlesource}{title}
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\field{abstract}{The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics. , CRISPR-cas: A revolution in genome engineering The ability to engineer genomic DNA in cells and organisms easily and precisely will have major implications for basic biology research, medicine, and biotechnology. Doudna and Charpentier review the history of genome editing technologies, including oligonucleotide coupled to genome cleaving agents that rely on endogenous repair and recombination systems to complete the targeted changes, self-splicing introns, and zinc-finger nucleases and TAL effector nucleases. They then describe how clustered regularly interspaced palindromic repeats (CRISPRs), and their associated (Cas) nucleases, were discovered to constitute an adaptive immune system in bacteria. They document development of the CRISPR-Cas system into a facile genome engineering tool that is revolutionizing all areas of molecular biology. Science , this issue 10.1126/science.1258096}
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\field{day}{28}
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\field{issn}{0036-8075, 1095-9203}
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\field{journaltitle}{Science}
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\field{langid}{english}
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\field{month}{11}
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\field{number}{6213}
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\field{shortjournal}{Science}
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\field{title}{The New Frontier of Genome Engineering with {{CRISPR-Cas9}}}
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\field{urlday}{22}
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\field{urlmonth}{10}
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\field{urlyear}{2024}
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\field{volume}{346}
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\field{year}{2014}
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\field{dateera}{ce}
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\field{urldateera}{ce}
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\field{pages}{1258096}
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\range{pages}{1}
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\verb{doi}
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\verb 10.1126/science.1258096
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\endverb
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\verb{urlraw}
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\verb https://www.science.org/doi/10.1126/science.1258096
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\endverb
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\verb{url}
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\verb https://www.science.org/doi/10.1126/science.1258096
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\endverb
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\endentry
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\entry{jinekProgrammableDualRNAGuidedDNA2012}{article}{}
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\name{author}{6}{}{%
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{{hash=3aa57e081fa07841f82a2722cbf3fce1}{%
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family={Jinek},
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familyi={J\bibinitperiod},
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given={Martin},
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giveni={M\bibinitperiod}}}%
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{{hash=33bbdf41a18c108757feb6e3e9135dbe}{%
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family={Chylinski},
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familyi={C\bibinitperiod},
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given={Krzysztof},
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giveni={K\bibinitperiod}}}%
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{{hash=6354fb90208c2bc8c428afa3c4a7502b}{%
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family={Fonfara},
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familyi={F\bibinitperiod},
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given={Ines},
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giveni={I\bibinitperiod}}}%
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{{hash=30d432e9ac0b22aa65c70baacd7b3d81}{%
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family={Hauer},
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familyi={H\bibinitperiod},
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given={Michael},
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giveni={M\bibinitperiod}}}%
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{{hash=db6ee88c2505c20e204e8ea38dc1a7ed}{%
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family={Doudna},
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familyi={D\bibinitperiod},
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given={Jennifer\bibnamedelima A.},
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giveni={J\bibinitperiod\bibinitdelim A\bibinitperiod}}}%
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{{hash=147cdad451a06b98a827e8850511922a}{%
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family={Charpentier},
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familyi={C\bibinitperiod},
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||||||
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given={Emmanuelle},
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giveni={E\bibinitperiod}}}%
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}
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\strng{namehash}{37e33dd0cf7e17cf0a3fb2fb26848a11}
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\strng{fullhash}{6b32f7927e60c50bc32a624f451e2060}
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\strng{bibnamehash}{6b32f7927e60c50bc32a624f451e2060}
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\strng{authorbibnamehash}{6b32f7927e60c50bc32a624f451e2060}
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\strng{authornamehash}{37e33dd0cf7e17cf0a3fb2fb26848a11}
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\strng{authorfullhash}{6b32f7927e60c50bc32a624f451e2060}
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\field{sortinit}{J}
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\field{abstract}{Ditching Invading DNA Bacteria and archaea protect themselves from invasive foreign nucleic acids through an RNA-mediated adaptive immune system called CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated (Cas). Jinek et al. (p. 816 , published online 28 June; see the Perspective by Brouns ) found that for the type II CRISPR/Cas system, the CRISPR RNA (crRNA) as well as the trans-activating crRNA—which is known to be involved in the pre-crRNA processing—were both required to direct the Cas9 endonuclease to cleave the invading target DNA. Furthermore, engineered RNA molecules were able to program the Cas9 endonuclease to cleave specific DNA sequences to generate double-stranded DNA breaks. , A prokaryotic RNA–directed targeting system can be designed to cleave any DNA sequence. , Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.}
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\field{abstract}{Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.}
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\field{shorttitle}{{{CRISPR-Cas9 System}} for {{Plant Genome Editing}}}
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\field{title}{{{CRISPR-Cas9 System}} for {{Plant Genome Editing}}: {{Current Approaches}} and {{Emerging Developments}}}
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\fancyhf{} % Czyszczenie domyślnych nagłówków i stopek
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\fancyhead[L]{Biotech, PCz}
|
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\fancyhead[R]{M. Pabiszczak} % Lewy nagłówek
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\fancyfoot[L]{Commit UUID: \texttt{\commitUUID} \\ Commit Date: \texttt{\commitDate}} % Lewa stopka - informacje linia po linii
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|
||||||
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literate={ą}{{\k{a}}}1 {ć}{{\'c}}1 {ę}{{\k{e}}}1 {ł}{{\l{}}}1 {ń}{{\'n}}1 {ó}{{\'o}}1 {ś}{{\'s}}1 {ż}{{\.z}}1 {ź}{{\'z}}1
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\setlist{leftmargin=*} % Usunięcie dodatkowego wcięcia dla wszystkich list
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\begin{document}
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% Dodanie znaku wodnego do tła każdej strony
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% \begin{enumerate}[leftmargin=*]
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||||||
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||||||
|
\newpage
|
||||||
|
\input{modules/crispr}
|
||||||
|
\label{sec:crispr}
|
||||||
|
|
||||||
|
\newpage
|
||||||
|
\input{modules/bio}
|
||||||
|
\label{sec:bio}
|
||||||
|
|
||||||
|
% \newpage
|
||||||
|
% \input{modules/wymagania_edukacyjne} % Wczytaj zawartość pliku
|
||||||
|
% \label{sec:wymagania_edukacyjne}
|
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% \end{enumerate}
|
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||||||
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|
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\end{document}
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|
@ -0,0 +1,110 @@
|
||||||
|
|
||||||
|
\item
|
||||||
|
\begin{center}
|
||||||
|
\fbox{
|
||||||
|
\begin{minipage}{0.9\textwidth}
|
||||||
|
\textbf{Projektowanie systemu CRISPR do edycji genów Arabidopsis z użyciem Biopythona}
|
||||||
|
\end{minipage}
|
||||||
|
}
|
||||||
|
\end{center}
|
||||||
|
|
||||||
|
\vspace{1cm}
|
||||||
|
\textbf{Cel:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Nauczenie projektowania sekwencji gRNA do edycji genów.
|
||||||
|
\item Wykorzystanie Biopython do edycji genów odporności na suszę w \textit{Arabidopsis thaliana}.
|
||||||
|
\item Zaprojektowanie gRNA do wyciszenia lub modyfikacji genu.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\textbf{Wprowadzenie:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item \textit{Arabidopsis thaliana} to modelowy organizm w badaniach roślinnych.
|
||||||
|
\item CRISPR umożliwia modyfikację genów związanych z odpornością na suszę.
|
||||||
|
\item W ćwiczeniu zaprojektujesz sekwencje gRNA do modyfikacji genów.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\section*{Krok 1: Przygotowanie środowiska}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Zainstaluj Biopython:
|
||||||
|
\begin{lstlisting}[language=bash]
|
||||||
|
pip install biopython
|
||||||
|
\end{lstlisting}
|
||||||
|
\item Załaduj sekwencje genów \textit{Arabidopsis} do pliku \texttt{arabidopsis\_genes.fasta}.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\section*{Krok 2: Analiza sekwencji genów}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Użyj Biopython do załadowania sekwencji genów.
|
||||||
|
\item Identyfikuj miejsca docelowe CRISPR w sekwencjach genów.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\textbf{Przykładowy kod:}
|
||||||
|
\begin{lstlisting}[language=Python]
|
||||||
|
from Bio import SeqIO
|
||||||
|
from Bio.Seq import Seq
|
||||||
|
|
||||||
|
# Załaduj sekwencje genów z pliku FASTA
|
||||||
|
def load_sequences(file_path):
|
||||||
|
return list(SeqIO.parse(file_path, "fasta"))
|
||||||
|
|
||||||
|
# Znajdź potencjalne sekwencje gRNA (20 nukleotydów + PAM "NGG")
|
||||||
|
def find_crispr_sites(sequence):
|
||||||
|
pam = "NGG"
|
||||||
|
sites = []
|
||||||
|
for i in range(len(sequence) - 23):
|
||||||
|
target = sequence[i:i+20]
|
||||||
|
pam_site = sequence[i+20:i+23]
|
||||||
|
if pam_site.endswith("GG"):
|
||||||
|
sites.append(target + pam_site)
|
||||||
|
return sites
|
||||||
|
|
||||||
|
# Przykład użycia
|
||||||
|
genes = load_sequences("arabidopsis_genes.fasta")
|
||||||
|
for gene in genes:
|
||||||
|
print(f"Gene ID: {gene.id}")
|
||||||
|
crispr_sites = find_crispr_sites(str(gene.seq))
|
||||||
|
print(f"Potential CRISPR sites: {crispr_sites[:5]}") # wyświetl tylko 5 pierwszych
|
||||||
|
\end{lstlisting}
|
||||||
|
|
||||||
|
\section*{Krok 3: Projektowanie sekwencji gRNA}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Wyszukaj potencjalne sekwencje gRNA w sekwencjach genów.
|
||||||
|
\item Zidentyfikuj najbardziej odpowiednie miejsca do modyfikacji.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\section*{Krok 4: Analiza wydajności i specyficzności gRNA}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Upewnij się, że gRNA nie ma niepożądanych miejsc docelowych w genomie.
|
||||||
|
\item Użyj dodatkowych algorytmów do oceny specyficzności.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\section*{Zadanie:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Znajdź potencjalne miejsca CRISPR w jednym z wybranych genów.
|
||||||
|
\item Wybierz najlepsze gRNA do edycji genu.
|
||||||
|
\item Zapisz wyniki w pliku \texttt{selected\_grnas.txt}.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\textbf{Przykład formatu pliku wynikowego:}
|
||||||
|
\begin{verbatim}
|
||||||
|
Gene ID: AT3G02990
|
||||||
|
Selected gRNA: ACTGACTGACTGACTGACTGGG (pos: 150-170)
|
||||||
|
\end{verbatim}
|
||||||
|
|
||||||
|
\section*{Dodatkowe wyzwania:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Zintegruj narzędzia Biopythona do analizy specyficzności gRNA w całym genomie \textit{Arabidopsis}.
|
||||||
|
\item Zaprojektuj gRNA do edycji wielu genów jednocześnie.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\section*{Podsumowanie:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Poznasz, jak używać narzędzi bioinformatycznych do projektowania gRNA.
|
||||||
|
\item Nauczysz się, jak zwiększać odporność roślin na stresy środowiskowe.
|
||||||
|
\end{itemize}
|
||||||
|
|
||||||
|
\section*{Referencje:}
|
||||||
|
\begin{itemize}
|
||||||
|
\item Biopython Tutorial and Cookbook
|
||||||
|
\item Zhang, H. et al. (2019). \textit{Genome editing in plants using CRISPR-Cas9}. Nature Reviews Genetics, 20(12), 769-788.
|
||||||
|
\end{itemize}
|
||||||
|
|
@ -0,0 +1,40 @@
|
||||||
|
\item
|
||||||
|
\begin{center}
|
||||||
|
\fbox{
|
||||||
|
\begin{minipage}{0.9\textwidth}
|
||||||
|
\textbf{CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)} to narzędzie do edycji genów. Umożliwia precyzyjne modyfikacje DNA. Zostało odkryte jako część systemu odpornościowego bakterii \cite{doudnaNewFrontierGenome2014}.
|
||||||
|
\end{minipage}
|
||||||
|
}
|
||||||
|
\end{center}
|
||||||
|
|
||||||
|
\vspace{.5cm}
|
||||||
|
\begin{longenum}
|
||||||
|
\item Jak działa CRISPR?
|
||||||
|
\begin{longenum}
|
||||||
|
\item CRISPR działa w połączeniu z enzymem Cas9, który działa jako "nożyczki" tnące DNA. System działa w kilku etapach:
|
||||||
|
\begin{longenum}
|
||||||
|
\item \textbf{Rozpoznanie celu}: CRISPR używa krótkiego odcinka RNA (gRNA - guide RNA), który jest komplementarny do docelowej sekwencji DNA. RNA prowadzi enzym Cas9 do odpowiedniego miejsca w genomie.
|
||||||
|
\item \textbf{Cięcie DNA}: Po dotarciu do docelowej sekwencji, Cas9 przecina dwie nici DNA, tworząc przerwę.
|
||||||
|
\item \textbf{Naprawa DNA}: Komórki próbują naprawić uszkodzoną sekwencję DNA, co może skutkować wprowadzeniem mutacji lub dodaniem nowego genu.
|
||||||
|
\end{longenum}
|
||||||
|
\end{longenum}
|
||||||
|
|
||||||
|
\vspace{0.5cm}
|
||||||
|
\item Zastosowania CRISPR
|
||||||
|
\begin{longenum}
|
||||||
|
\item CRISPR ma szerokie zastosowania w różnych dziedzinach:
|
||||||
|
\begin{longenum}
|
||||||
|
\item \textbf{Biotechnologia}: Edycja genów roślin, aby poprawić ich odporność na choroby, suszę, czy zwiększyć plony.
|
||||||
|
\item \textbf{Medycyna}: Potencjalne terapie genowe do leczenia chorób dziedzicznych, takich jak mukowiscydoza czy anemia sierpowata.
|
||||||
|
\item \textbf{Badania naukowe}: Badania nad funkcją genów i modelowanie chorób genetycznych.
|
||||||
|
\end{longenum}
|
||||||
|
\end{longenum}
|
||||||
|
|
||||||
|
\vspace{0.5cm}
|
||||||
|
\item Przykład w kontekście Arabidopsis
|
||||||
|
\begin{longenum}
|
||||||
|
\item CRISPR może być użyty do wprowadzenia modyfikacji w genach Arabidopsis odpowiedzialnych za reakcje na stres suszy.
|
||||||
|
\item Można zaprojektować gRNA, aby wycelować w specyficzne geny regulujące tolerancję na suszę, a następnie użyć CRISPR do knock-out lub zmodyfikowania tych genów w celu poprawienia adaptacji roślin do warunków niedoboru wody.
|
||||||
|
\item Dzięki CRISPR można tworzyć bardziej odporne odmiany roślin, co ma znaczący wpływ na rolnictwo, zwłaszcza w obliczu zmian klimatycznych.
|
||||||
|
\end{longenum}
|
||||||
|
\end{longenum}
|
||||||
|
|
@ -0,0 +1,53 @@
|
||||||
|
@article{doudnaNewFrontierGenome2014,
|
||||||
|
title = {The New Frontier of Genome Engineering with {{CRISPR-Cas9}}},
|
||||||
|
author = {Doudna, Jennifer A. and Charpentier, Emmanuelle},
|
||||||
|
date = {2014-11-28},
|
||||||
|
journaltitle = {Science},
|
||||||
|
shortjournal = {Science},
|
||||||
|
volume = {346},
|
||||||
|
number = {6213},
|
||||||
|
pages = {1258096},
|
||||||
|
issn = {0036-8075, 1095-9203},
|
||||||
|
doi = {10.1126/science.1258096},
|
||||||
|
url = {https://www.science.org/doi/10.1126/science.1258096},
|
||||||
|
urldate = {2024-10-22},
|
||||||
|
abstract = {The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics. , CRISPR-cas: A revolution in genome engineering The ability to engineer genomic DNA in cells and organisms easily and precisely will have major implications for basic biology research, medicine, and biotechnology. Doudna and Charpentier review the history of genome editing technologies, including oligonucleotide coupled to genome cleaving agents that rely on endogenous repair and recombination systems to complete the targeted changes, self-splicing introns, and zinc-finger nucleases and TAL effector nucleases. They then describe how clustered regularly interspaced palindromic repeats (CRISPRs), and their associated (Cas) nucleases, were discovered to constitute an adaptive immune system in bacteria. They document development of the CRISPR-Cas system into a facile genome engineering tool that is revolutionizing all areas of molecular biology. Science , this issue 10.1126/science.1258096},
|
||||||
|
langid = {english}
|
||||||
|
}
|
||||||
|
|
||||||
|
@article{jinekProgrammableDualRNAGuidedDNA2012,
|
||||||
|
title = {A {{Programmable Dual-RNA}}–{{Guided DNA Endonuclease}} in {{Adaptive Bacterial Immunity}}},
|
||||||
|
author = {Jinek, Martin and Chylinski, Krzysztof and Fonfara, Ines and Hauer, Michael and Doudna, Jennifer A. and Charpentier, Emmanuelle},
|
||||||
|
date = {2012-08-17},
|
||||||
|
journaltitle = {Science},
|
||||||
|
shortjournal = {Science},
|
||||||
|
volume = {337},
|
||||||
|
number = {6096},
|
||||||
|
pages = {816--821},
|
||||||
|
issn = {0036-8075, 1095-9203},
|
||||||
|
doi = {10.1126/science.1225829},
|
||||||
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url = {https://www.science.org/doi/10.1126/science.1225829},
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urldate = {2024-10-22},
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abstract = {Ditching Invading DNA Bacteria and archaea protect themselves from invasive foreign nucleic acids through an RNA-mediated adaptive immune system called CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated (Cas). Jinek et al. (p. 816 , published online 28 June; see the Perspective by Brouns ) found that for the type II CRISPR/Cas system, the CRISPR RNA (crRNA) as well as the trans-activating crRNA—which is known to be involved in the pre-crRNA processing—were both required to direct the Cas9 endonuclease to cleave the invading target DNA. Furthermore, engineered RNA molecules were able to program the Cas9 endonuclease to cleave specific DNA sequences to generate double-stranded DNA breaks. , A prokaryotic RNA–directed targeting system can be designed to cleave any DNA sequence. , Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.},
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langid = {english},
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file = {/home/user/Zotero/storage/7LCA9MTW/Jinek et al. - 2012 - A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity.pdf}
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}
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@article{montecilloCRISPRCas9SystemPlant2020,
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title = {{{CRISPR-Cas9 System}} for {{Plant Genome Editing}}: {{Current Approaches}} and {{Emerging Developments}}},
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shorttitle = {{{CRISPR-Cas9 System}} for {{Plant Genome Editing}}},
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author = {Montecillo, Jake Adolf V. and Chu, Luan Luong and Bae, Hanhong},
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date = {2020-07-17},
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journaltitle = {Agronomy},
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shortjournal = {Agronomy},
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volume = {10},
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number = {7},
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pages = {1033},
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issn = {2073-4395},
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doi = {10.3390/agronomy10071033},
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url = {https://www.mdpi.com/2073-4395/10/7/1033},
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urldate = {2024-10-22},
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abstract = {Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.},
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langid = {english},
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file = {/home/user/Zotero/storage/JJPA5C9W/Montecillo et al. - 2020 - CRISPR-Cas9 System for Plant Genome Editing Current Approaches and Emerging Developments.pdf}
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}
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Reference in New Issue