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It will be recreated by -% biber as required. -% -\begingroup -\makeatletter -\@ifundefined{ver@biblatex.sty} - {\@latex@error - {Missing 'biblatex' package} - {The bibliography requires the 'biblatex' package.} - \aftergroup\endinput} - {} -\endgroup - - -\refsection{0} - \datalist[entry]{nty/global//global/global} - \entry{doudnaNewFrontierGenome2014}{article}{} - \name{author}{2}{}{% - {{hash=db6ee88c2505c20e204e8ea38dc1a7ed}{% - family={Doudna}, - familyi={D\bibinitperiod}, - given={Jennifer\bibnamedelima A.}, - giveni={J\bibinitperiod\bibinitdelim A\bibinitperiod}}}% - {{hash=147cdad451a06b98a827e8850511922a}{% - family={Charpentier}, - familyi={C\bibinitperiod}, - given={Emmanuelle}, - giveni={E\bibinitperiod}}}% - } - \strng{namehash}{ac39f49ff392a08abaa0153e03e063c9} - \strng{fullhash}{ac39f49ff392a08abaa0153e03e063c9} - \strng{bibnamehash}{ac39f49ff392a08abaa0153e03e063c9} - \strng{authorbibnamehash}{ac39f49ff392a08abaa0153e03e063c9} - \strng{authornamehash}{ac39f49ff392a08abaa0153e03e063c9} - \strng{authorfullhash}{ac39f49ff392a08abaa0153e03e063c9} - \field{sortinit}{D} - \field{sortinithash}{6f385f66841fb5e82009dc833c761848} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \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} - \field{day}{28} - \field{issn}{0036-8075, 1095-9203} - \field{journaltitle}{Science} - \field{langid}{english} - \field{month}{11} - \field{number}{6213} - \field{shortjournal}{Science} - \field{title}{The New Frontier of Genome Engineering with {{CRISPR-Cas9}}} - \field{urlday}{22} - \field{urlmonth}{10} - \field{urlyear}{2024} - \field{volume}{346} - \field{year}{2014} - \field{dateera}{ce} - \field{urldateera}{ce} - \field{pages}{1258096} - \range{pages}{1} - \verb{doi} - \verb 10.1126/science.1258096 - \endverb - \verb{urlraw} - \verb https://www.science.org/doi/10.1126/science.1258096 - \endverb - \verb{url} - \verb https://www.science.org/doi/10.1126/science.1258096 - \endverb - \endentry - \entry{jinekProgrammableDualRNAGuidedDNA2012}{article}{} - \name{author}{6}{}{% - {{hash=3aa57e081fa07841f82a2722cbf3fce1}{% - family={Jinek}, - familyi={J\bibinitperiod}, - given={Martin}, - giveni={M\bibinitperiod}}}% - {{hash=33bbdf41a18c108757feb6e3e9135dbe}{% - family={Chylinski}, - familyi={C\bibinitperiod}, - given={Krzysztof}, - giveni={K\bibinitperiod}}}% - {{hash=6354fb90208c2bc8c428afa3c4a7502b}{% - family={Fonfara}, - familyi={F\bibinitperiod}, - given={Ines}, - giveni={I\bibinitperiod}}}% - {{hash=30d432e9ac0b22aa65c70baacd7b3d81}{% - family={Hauer}, - familyi={H\bibinitperiod}, - given={Michael}, - giveni={M\bibinitperiod}}}% - {{hash=db6ee88c2505c20e204e8ea38dc1a7ed}{% - family={Doudna}, - familyi={D\bibinitperiod}, - given={Jennifer\bibnamedelima A.}, - giveni={J\bibinitperiod\bibinitdelim A\bibinitperiod}}}% - {{hash=147cdad451a06b98a827e8850511922a}{% - family={Charpentier}, - familyi={C\bibinitperiod}, - given={Emmanuelle}, - giveni={E\bibinitperiod}}}% - } - \strng{namehash}{37e33dd0cf7e17cf0a3fb2fb26848a11} - \strng{fullhash}{6b32f7927e60c50bc32a624f451e2060} - \strng{bibnamehash}{6b32f7927e60c50bc32a624f451e2060} - \strng{authorbibnamehash}{6b32f7927e60c50bc32a624f451e2060} - \strng{authornamehash}{37e33dd0cf7e17cf0a3fb2fb26848a11} - \strng{authorfullhash}{6b32f7927e60c50bc32a624f451e2060} - \field{sortinit}{J} - \field{sortinithash}{b2f54a9081ace9966a7cb9413811edb4} - \field{labelnamesource}{author} - \field{labeltitlesource}{title} - \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.} - \field{day}{17} - \field{issn}{0036-8075, 1095-9203} - \field{journaltitle}{Science} - \field{langid}{english} - \field{month}{8} - \field{number}{6096} - \field{shortjournal}{Science} - \field{title}{A {{Programmable Dual-RNA}}–{{Guided DNA Endonuclease}} in {{Adaptive Bacterial Immunity}}} - \field{urlday}{22} - \field{urlmonth}{10} - \field{urlyear}{2024} - \field{volume}{337} - \field{year}{2012} - \field{dateera}{ce} - \field{urldateera}{ce} - \field{pages}{816\bibrangedash 821} - \range{pages}{6} - \verb{doi} - \verb 10.1126/science.1225829 - \endverb - \verb{file} - \verb /home/user/Zotero/storage/7LCA9MTW/Jinek et al. - 2012 - A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity.pdf - \endverb - \verb{urlraw} - \verb https://www.science.org/doi/10.1126/science.1225829 - \endverb - \verb{url} - \verb https://www.science.org/doi/10.1126/science.1225829 - \endverb - \endentry - \entry{montecilloCRISPRCas9SystemPlant2020}{article}{} - \name{author}{3}{}{% - {{hash=88e54511e65b4b9c405a3a373ffdd902}{% - family={Montecillo}, - familyi={M\bibinitperiod}, - given={Jake\bibnamedelimb Adolf\bibnamedelima V.}, - giveni={J\bibinitperiod\bibinitdelim A\bibinitperiod\bibinitdelim V\bibinitperiod}}}% - {{hash=7c9f7c3643e6518c34fca0f8e364adc9}{% - family={Chu}, - familyi={C\bibinitperiod}, - given={Luan\bibnamedelima Luong}, - giveni={L\bibinitperiod\bibinitdelim L\bibinitperiod}}}% - {{hash=cf54ec41494a92c77b00877f12d16ddf}{% - family={Bae}, - familyi={B\bibinitperiod}, - given={Hanhong}, - giveni={H\bibinitperiod}}}% - } - \strng{namehash}{524ef06d09073b2142e7302333a0d952} - \strng{fullhash}{524ef06d09073b2142e7302333a0d952} - \strng{bibnamehash}{524ef06d09073b2142e7302333a0d952} - \strng{authorbibnamehash}{524ef06d09073b2142e7302333a0d952} - \strng{authornamehash}{524ef06d09073b2142e7302333a0d952} - \strng{authorfullhash}{524ef06d09073b2142e7302333a0d952} - \field{sortinit}{M} - \field{sortinithash}{4625c616857f13d17ce56f7d4f97d451} - \field{labelnamesource}{author} - \field{labeltitlesource}{shorttitle} - \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.} - \field{day}{17} - \field{issn}{2073-4395} - \field{journaltitle}{Agronomy} - \field{langid}{english} - \field{month}{7} - \field{number}{7} - \field{shortjournal}{Agronomy} - \field{shorttitle}{{{CRISPR-Cas9 System}} for {{Plant Genome Editing}}} - \field{title}{{{CRISPR-Cas9 System}} for {{Plant Genome Editing}}: {{Current Approaches}} and {{Emerging Developments}}} - \field{urlday}{22} - \field{urlmonth}{10} - \field{urlyear}{2024} - \field{volume}{10} - \field{year}{2020} - \field{dateera}{ce} - \field{urldateera}{ce} - \field{pages}{1033} - \range{pages}{1} - \verb{doi} - \verb 10.3390/agronomy10071033 - \endverb - \verb{file} - \verb /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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Pabiszczak} % Lewy nagłówek +\fancyhead[R]{M. Pab.} % Lewy nagłówek \fancyfoot[L]{Commit UUID: \texttt{\commitUUID} \\ Commit Date: \texttt{\commitDate}} % Lewa stopka - informacje linia po linii \fancyfoot[R]{\thepage} % Prawa stopka - Numer strony @@ -140,6 +140,10 @@ \input{modules/crispr} \label{sec:crispr} + \newpage + \input{modules/arabidopsis} + \label{sec:bio} + \newpage \input{modules/bio} \label{sec:bio} diff --git a/doc/modules/arabidopsis.tex b/doc/modules/arabidopsis.tex new file mode 100644 index 0000000..4d0ac80 --- /dev/null +++ b/doc/modules/arabidopsis.tex @@ -0,0 +1,65 @@ +\item +\begin{center} + \fbox{ + \begin{minipage}{0.9\textwidth} + \textbf{Arabidopsis jako roślina modelowa} + \end{minipage} + } +\end{center} +\section* + +\begin{longenum} + \item Dlaczego Arabidopsis jest rośliną modelową? + \begin{longenum} + \item \textbf{Genom mały i dobrze poznany}: Arabidopsis thaliana była pierwszą rośliną, której pełny genom został zsekwencjonowany. Dzięki niewielkiemu genomowi (około 135 Mb) oraz dużej liczbie dostępnych narzędzi genetycznych, jest idealnym modelem do badań nad genetyką roślin. + \item \textbf{Krótki cykl życiowy}: Arabidopsis ma szybki cykl życiowy (około 6 tygodni od nasion do nasion), co pozwala na szybkie prowadzenie badań i eksperymentów. + \item \textbf{Łatwość manipulacji genetycznych}: Dzięki liczbie dostępnych mutantów, linii transgenicznych oraz technik takich jak CRISPR, Arabidopsis jest świetnym systemem modelowym do badania funkcji genów. + \end{longenum} + + \item Bazy danych do analizy genów Arabidopsis + \begin{longenum} + \item \textbf{TAIR (The Arabidopsis Information Resource)}: + \begin{longenum} + \item Największa baza danych zawierająca informacje o genomie Arabidopsis, sekwencjach genów, mutantach oraz ich funkcjach. + \item Można wyszukiwać specyficzne geny oraz przeglądać informacje dotyczące ekspresji genów, fenotypów oraz publikacji. + \end{longenum} + \item \textbf{ATTED-II}: + \begin{longenum} + \item Baza danych powiązań genetycznych oparta na współekspresji genów w różnych warunkach. + \item Może być używana do identyfikacji genów związanych z odpowiedzią na stresy środowiskowe, takie jak susza. + \end{longenum} + \item \textbf{ARaport}: + \begin{longenum} + \item Narzędzie do analizowania i wizualizowania profili ekspresji genów Arabidopsis. + \item Umożliwia analizę genów aktywowanych w odpowiedzi na różne czynniki stresowe. + \end{longenum} + \item \textbf{Gene Ontology (GO)}: + \begin{longenum} + \item Baza danych klasyfikacji funkcji genów, która pomaga w identyfikacji i analizie genów odpowiedzialnych za określone procesy biologiczne, takie jak odporność na stresy abiotyczne. + \end{longenum} + \end{longenum} + + \item Geny Arabidopsis związane z odpornością na suszę + \begin{longenum} + \item \textbf{DREB1A (Dehydration-Responsive Element-Binding Protein 1A)}: + \begin{longenum} + \item Gen kodujący czynnik transkrypcyjny, który reguluje ekspresję wielu genów odpowiedzi na stres, w tym suszę. + \item Wzmacnia odporność na suszę poprzez aktywowanie ścieżek sygnałowych odpowiedzi na niedobór wody. + \end{longenum} + \item \textbf{RD29A (Response to Dehydration 29A)}: + \begin{longenum} + \item Jeden z głównych genów markerowych dla stresu suszy, regulowany przez DREB1A. + \item Jego ekspresja jest indukowana przez stres związany z odwodnieniem oraz niską temperaturą. + \end{longenum} + \item \textbf{NHX1 (Sodium/Hydrogen Exchanger 1)}: + \begin{longenum} + \item Gen kodujący białko transportujące jonów, które pomaga w utrzymaniu homeostazy jonowej w warunkach suszy. + \item Jego nadekspresja poprawia zdolność rośliny do przetrwania suszy poprzez zwiększenie magazynowania jonów i regulację ciśnienia osmotycznego. + \end{longenum} + \item \textbf{P5CS1 (Δ1-Pyrroline-5-Carboxylate Synthetase 1)}: + \begin{longenum} + \item Kluczowy enzym w syntezie proliny, aminokwasu pełniącego rolę osmolitu, który pomaga roślinom przetrwać stres związany z odwodnieniem. + \item Wyższy poziom proliny w komórkach poprawia tolerancję na suszę. + \end{longenum} + \end{longenum} +\end{longenum} \ No newline at end of file diff --git a/doc/modules/crispr.tex b/doc/modules/crispr.tex index 7712f3f..b5b579e 100644 --- a/doc/modules/crispr.tex +++ b/doc/modules/crispr.tex @@ -37,4 +37,5 @@ \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} \ No newline at end of file +\end{longenum} +