doc/1

@@ -0,0 +1,164 @@
+\documentclass{report}
+
+% Pakiety do ustawienia marginesów
+\usepackage{geometry}
+\geometry{
+    a4paper,
+    left=2.6cm,
+    right=2.6cm,
+    top=2.6cm,
+    bottom=2.6cm
+}
+
+\usepackage[
+    sortcites,
+    backend=biber,
+    hyperref=true,
+    firstinits=true,
+    maxbibnames=99,
+    ]{biblatex}
+\addbibresource{references.bib}
+
+% Kodowanie i język
+\usepackage[utf8]{inputenc}   % Dla pdfLaTeX
+\usepackage[T1]{fontenc}
+\usepackage[polish]{babel}
+
+
+\usepackage{listings}
+
+
+% Pakiety do stylizacji
+\usepackage{titlesec}
+\usepackage{tocloft}
+\usepackage{enumitem}
+
+% \setlist[longenum,1]{label=\arabic*., nosep}
+% \setlist[longenum,2]{label=\arabic*), nosep}
+% \setlist[longenum,3]{label=\alph*., nosep}
+
+\newlist{longenum}{enumerate}{5}
+\setlist[longenum,1]{label=\arabic*.}
+\setlist[longenum,2]{label=\arabic*)}
+\setlist[longenum,3]{label=\alph*.}
+\setlist[longenum,4]{label=\alph*)}
+\setlist[longenum,5]{label=--}
+
+% Pakiet do nagłówków i stopek
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{}  % Czyszczenie domyślnych nagłówków i stopek
+\fancyhead[L]{Biotech, PCz}
+\fancyhead[R]{M. Pabiszczak}  % 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
+
+% Pakiety do dodawania znaków wodnych
+\usepackage{eso-pic}      % Pakiet do wstawiania znaków wodnych
+\usepackage{graphicx}     % Pakiet do wstawiania obrazów
+\usepackage{transparent}  % Pakiet do przezroczystości obrazów
+
+% Pakiety dodatkowe
+\usepackage{datetime2}    % Pakiet do obsługi daty i godziny
+\usepackage{ulem}         % Pakiet do przekreślania tekstu
+
+% Definicje kolorów
+\usepackage{xcolor}
+\definecolor{wzo}{rgb}{0.000, 0.502, 0.000}      % intensywny zielony
+\definecolor{szo}{rgb}{0.196, 0.803, 0.196}      % limonkowy
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+% Definicja kolorów
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+\definecolor{magentacolor}{rgb}{1.0, 0.0, 1.0} % magenta
+
+% Styl dla kodu
+\lstdefinestyle{mystyle}{
+    backgroundcolor=\color{backcolour},   
+    commentstyle=\color{codegreen},
+    keywordstyle=\color{magentacolor},
+    numberstyle=\tiny\color{codegray},
+    stringstyle=\color{codepurple},
+    basicstyle=\ttfamily\footnotesize,
+    breaklines=true,
+    captionpos=b,
+    numbers=left,
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+    showspaces=false,
+    showstringspaces=false,
+    showtabs=false,
+    tabsize=2,
+    extendedchars=true,    % Umożliwia polskie znaki
+    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
+}
+
+% Ustawienie stylu jako domyślnego
+\lstset{style=mystyle}
+
+% Definicja nowej komendy \zs
+\newcommand{\zs}{\textcolor{zs}{Zespół Szkół }}
+
+% Wczytanie pliku z informacjami o commit
+\input{commit.tex}
+
+% Globalne ustawienie list
+\setlist{leftmargin=*}  % Usunięcie dodatkowego wcięcia dla wszystkich list
+
+% Wyłączenie wcięcia akapitu
+\setlength{\parindent}{0pt}
+
+% % Definicja znaku wodnego
+% \newcommand\BackgroundPic{
+%     \AtPageCenter{
+%         \makebox(0,0){
+%             \transparent{0.15} % Ustawienie przezroczystości na 10%
+%             \includegraphics[width=0.9\textwidth, keepaspectratio]{png/logo.png}
+%         }
+%     }
+% }
+
+
+
+\begin{document}
+
+% Dodanie znaku wodnego do tła każdej strony
+\AddToShipoutPictureBG*{\BackgroundPic}
+
+% \begin{enumerate}[leftmargin=*]
+
+    \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}
+
+% \end{enumerate}
+\newpage
+
+\printbibliography
+
+
+\end{document}

doc/commit.tex

@@ -1,4 +1,4 @@
-\newcommand{\commitUUID}{a933aa76f247eff8d178a6293628be451baecdf0}
+\newcommand{\commitUUID}{98463cfa7bc8b50867b6481bc63a28b9eb0d4478}
-\newcommand{\commitDate}{2024-10-23 18:30:31 +0200}
+\newcommand{\commitDate}{2024-10-22 10:31:59 +0200}
-\newcommand{\commitComment}{init}
+\newcommand{\commitComment}{start}
 \newcommand{\commitTag}{}

doc/main.aux

@@ -6,17 +6,12 @@
 \catcode `"\active 
 \abx@aux@cite{0}{doudnaNewFrontierGenome2014}
 \abx@aux@segm{0}{0}{doudnaNewFrontierGenome2014}
-\abx@aux@cite{0}{jinekProgrammableDualRNAGuidedDNA2012}
-\abx@aux@segm{0}{0}{jinekProgrammableDualRNAGuidedDNA2012}
-\abx@aux@cite{0}{jinekProgrammableDualRNAGuidedDNA2012}
-\abx@aux@segm{0}{0}{jinekProgrammableDualRNAGuidedDNA2012}
-\abx@aux@cite{0}{montecilloCRISPRCas9SystemPlant2020}
-\abx@aux@segm{0}{0}{montecilloCRISPRCas9SystemPlant2020}
-\abx@aux@cite{0}{doudnaNewFrontierGenome2014}
-\abx@aux@segm{0}{0}{doudnaNewFrontierGenome2014}
 \babel@aux{polish}{}
 \newlabel{sec:crispr}{{}{1}}
 \newlabel{sec:bio}{{}{3}}
-\abx@aux@read@bbl@mdfivesum{nobblfile}
+\abx@aux@read@bbl@mdfivesum{nohash}
 \abx@aux@read@bblrerun
-\gdef \@abspage@last{3}
+\abx@aux@defaultrefcontext{0}{doudnaNewFrontierGenome2014}{nty/global//global/global}
+\abx@aux@defaultrefcontext{0}{jinekProgrammableDualRNAGuidedDNA2012}{nty/global//global/global}
+\abx@aux@defaultrefcontext{0}{montecilloCRISPRCas9SystemPlant2020}{nty/global//global/global}
+\gdef \@abspage@last{4}

doc/main.bbl

@@ -0,0 +1,210 @@
+% $ biblatex auxiliary file $
+% $ biblatex bbl format version 3.2 $
+% Do not modify the above lines!
+%
+% This is an auxiliary file used by the 'biblatex' package.
+% This file may safely be deleted. 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
+      \endverb
+      \verb{urlraw}
+      \verb https://www.mdpi.com/2073-4395/10/7/1033
+      \endverb
+      \verb{url}
+      \verb https://www.mdpi.com/2073-4395/10/7/1033
+      \endverb
+    \endentry
+  \enddatalist
+\endrefsection
+\endinput
+

doc/main.bcf

@@ -2350,10 +2350,6 @@
   </bcf:bibdata>
   <bcf:section number="0">
     <bcf:citekey order="1" intorder="1">doudnaNewFrontierGenome2014</bcf:citekey>
-    <bcf:citekey order="2" intorder="1">jinekProgrammableDualRNAGuidedDNA2012</bcf:citekey>
-    <bcf:citekey order="3" intorder="1">jinekProgrammableDualRNAGuidedDNA2012</bcf:citekey>
-    <bcf:citekey order="4" intorder="1">montecilloCRISPRCas9SystemPlant2020</bcf:citekey>
-    <bcf:citekey order="5" intorder="1">doudnaNewFrontierGenome2014</bcf:citekey>
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doc/main.blg

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doc/main.log

@@ -1,4 +1,4 @@
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+LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 132.
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-LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 139.
+LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 132.
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-LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 139.
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-LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 139.
+LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 132.
-LaTeX Font Info:    ... okay on input line 139.
+LaTeX Font Info:    ... okay on input line 132.
 
 *geometry* driver: auto-detecting
 *geometry* detected driver: pdftex
@@ -629,12 +629,12 @@ Package biblatex Info: Automatic encoding selection.
 \openout3 = `main.bcf'.
 
 Package biblatex Info: Trying to load bibliographic data...
-Package biblatex Info: ... file 'main.bbl' not found.
+Package biblatex Info: ... file 'main.bbl' found.
-
+ (./main.bbl)
-No file main.bbl.
+Package biblatex Info: Reference section=0 on input line 132.
-Package biblatex Info: Reference section=0 on input line 139.
+Package biblatex Info: Reference segment=0 on input line 132.
-Package biblatex Info: Reference segment=0 on input line 139.
 \c@lstlisting=\count415
+
 (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
 [Loading MPS to PDF converter (version 2006.09.02).]
 \scratchcounter=\count416
@@ -673,40 +673,20 @@ Underfull \hbox (badness 10000) detected at line 2
 [][]
  []
 
-
-LaTeX Warning: Citation 'doudnaNewFrontierGenome2014' on page 1 undefined on in
-put line 7.
-
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-
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-ined on input line 17.
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-ined on input line 23.
-
-
-LaTeX Warning: Citation 'montecilloCRISPRCas9SystemPlant2020' on page 1 undefin
-ed on input line 41.
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-
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+43.
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-l.150     \newpage
+l.143     \newpage
                   
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@@ -736,14 +716,16 @@ File: lstlang1.sty 2020/03/24 1.8d listings language file
 (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty
 File: lstlang1.sty 2020/03/24 1.8d listings language file
 ) [2]) [3]
+[4
 
-LaTeX Warning: Empty bibliography on input line 161.
+] (./main.aux)
-
-(./main.aux)
 
 LaTeX Warning: There were undefined references.
 
 
+LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
+
+
 Package biblatex Warning: Please (re)run Biber on the file:
 (biblatex)                main
 (biblatex)                and rerun LaTeX afterwards.
@@ -753,24 +735,26 @@ Package logreq Info: Writing requests to 'main.run.xml'.
 
  ) 
 Here is how much of TeX's memory you used:
- 17843 strings out of 476091
+ 17887 strings out of 476091
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+ 38078 multiletter control sequences out of 15000+600000
- 518652 words of font info for 43 fonts, out of 8000000 for 9000
+ 520871 words of font info for 46 fonts, out of 8000000 for 9000
  1141 hyphenation exceptions out of 8191
- 63i,11n,102p,673b,1626s stack positions out of 10000i,1000n,20000p,200000b,200000s
+ 63i,11n,102p,1948b,1634s stack positions out of 10000i,1000n,20000p,200000b,200000s
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-b></usr/share/texmf/fonts/type1/public/cm-super/sfrm0500.pfb></usr/share/texmf/
+b></usr/share/texmf/fonts/type1/public/cm-super/sfbx2488.pfb></usr/share/texmf/
-fonts/type1/public/cm-super/sfrm1000.pfb></usr/share/texmf/fonts/type1/public/c
+fonts/type1/public/cm-super/sfcc1000.pfb></usr/share/texmf/fonts/type1/public/c
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+m-super/sfrm0500.pfb></usr/share/texmf/fonts/type1/public/cm-super/sfrm1000.pfb
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+></usr/share/texmf/fonts/type1/public/cm-super/sfti1000.pfb></usr/share/texmf/f
-Output written on main.pdf (3 pages, 193796 bytes).
+onts/type1/public/cm-super/sftt0800.pfb></usr/share/texmf/fonts/type1/public/cm
+-super/sftt1000.pfb>
+Output written on main.pdf (4 pages, 218035 bytes).
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+ 67 PDF objects out of 1000 (max. 8388607)
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doc/main.tex

@@ -37,19 +37,28 @@
 % \setlist[longenum,2]{label=\arabic*), nosep}
 % \setlist[longenum,3]{label=\alph*., nosep}
 
+% \newlist{longenum}{enumerate}{5}
+% \setlist[longenum,1]{label=\arabic*.}
+% \setlist[longenum,2]{label=\arabic*)}
+% \setlist[longenum,3]{label=\alph*.}
+% \setlist[longenum,4]{label=\alph*)}
+% \setlist[longenum,5]{label=--}
+
+
+% Definiowanie nowego typu listy 'longenum' z pięcioma poziomami numeracji
 \newlist{longenum}{enumerate}{5}
-\setlist[longenum,1]{label=\arabic*., nosep}
+\setlist[longenum,1]{label=\arabic*., left=.5em}
-\setlist[longenum,2]{label=\arabic*)}
+\setlist[longenum,2]{label=\arabic*), left=1.em}
-\setlist[longenum,3]{label=\alph*.}
+\setlist[longenum,3]{label=\alph*., left=1.5em}
-\setlist[longenum,4]{label=\alph*)}
+\setlist[longenum,4]{label=\alph*), left=2em}
-\setlist[longenum,5]{label=--}
+\setlist[longenum,5]{label=--, left=3.5em}
 
 % Pakiet do nagłówków i stopek
 \usepackage{fancyhdr}
 \pagestyle{fancy}
 \fancyhf{}  % Czyszczenie domyślnych nagłówków i stopek
 \fancyhead[L]{Biotech, PCz}
-\fancyhead[R]{M. Pab.}  % Lewy nagłówek
+\fancyhead[R]{M. Pabiszczak}  % 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
@@ -65,20 +74,6 @@
 
 % Definicje kolorów
 \usepackage{xcolor}
-\definecolor{wzo}{rgb}{0.000, 0.502, 0.000}      % intensywny zielony
-\definecolor{szo}{rgb}{0.196, 0.803, 0.196}      % limonkowy
-\definecolor{pzo}{rgb}{0.235, 0.702, 0.443}      % średni zielony
-
-\definecolor{zoz}{rgb}{0.235, 0.702, 0.700}      % średni zielony
-
-\definecolor{stat}{rgb}{0.541, 0.169, 0.886}     % fioletowy
-\definecolor{kN}{rgb}{1.000, 0.647, 0.000}       % pomarańczowy
-\definecolor{uO}{rgb}{0.275, 0.514, 0.706}       % niebieski
-\definecolor{rO}{rgb}{0.0, 0.0, 0.5}             % ciemno granatowy
-\definecolor{uRODO}{rgb}{0.000, 0.502, 0.502}    % teal
-\definecolor{rRODO}{rgb}{0.125, 0.698, 0.667}    % jasny teal
-\definecolor{kor}{rgb}{1.0, 0.0, 0.0}            % czerwony
-\definecolor{zs}{rgb}{1.0, 0.0, 0.0}             % Kolor Teal (lub dowolny wybrany kolor)
 
 \definecolor{lightgray}{rgb}{0.70, 0.70, 0.70}
 
@@ -112,8 +107,6 @@
 % Ustawienie stylu jako domyślnego
 \lstset{style=mystyle}
 
-% Definicja nowej komendy \zs
-\newcommand{\zs}{\textcolor{zs}{Zespół Szkół }}
 
 % Wczytanie pliku z informacjami o commit
 \input{commit.tex}

doc/modules/crispr.tex

@@ -7,38 +7,34 @@
     }
 \end{center}
 
-\vspace{1cm}
+\vspace{.5cm}
-\textbf{Główne komponenty CRISPR:}
+\begin{longenum}
-\begin{itemize}
+    \item Jak działa CRISPR?
-    \item \textbf{Białko Cas9:}
+    \begin{longenum}
-    \begin{itemize}
+        \item CRISPR działa w połączeniu z enzymem Cas9, który działa jako "nożyczki" tnące DNA. System działa w kilku etapach:
-        \item Enzym, który przecina DNA.
+        \begin{longenum}
-        \item Rozpoznaje specyficzne miejsca w genomie.
+            \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 Działa jak molekularne nożyczki \cite{jinekProgrammableDualRNAGuidedDNA2012}.
+            \item \textbf{Cięcie DNA}: Po dotarciu do docelowej sekwencji, Cas9 przecina dwie nici DNA, tworząc przerwę.
-    \end{itemize}
+            \item \textbf{Naprawa DNA}: Komórki próbują naprawić uszkodzoną sekwencję DNA, co może skutkować wprowadzeniem mutacji lub dodaniem nowego genu.
-    \item \textbf{Przewodnik RNA (gRNA):}
+        \end{longenum}
-    \begin{itemize}
+    \end{longenum}
-        \item Krótki fragment RNA.
-        \item Prowadzi białko Cas9 do docelowego DNA.
-        \item Wiąże się z wybraną sekwencją DNA \cite{jinekProgrammableDualRNAGuidedDNA2012}.
-    \end{itemize}
-\end{itemize}
 
-\vspace{1cm}
+    \vspace{0.5cm}
-\textbf{Zastosowania CRISPR:}
+    \item Zastosowania CRISPR
-\begin{itemize}
+    \begin{longenum}
-    \item Modyfikacja genów:
+        \item CRISPR ma szerokie zastosowania w różnych dziedzinach:
-    \begin{itemize}
+        \begin{longenum}
-        \item Knock-out genów (wyłączenie funkcji genu).
+            \item \textbf{Biotechnologia}: Edycja genów roślin, aby poprawić ich odporność na choroby, suszę, czy zwiększyć plony.
-        \item Wprowadzenie mutacji.
+            \item \textbf{Medycyna}: Potencjalne terapie genowe do leczenia chorób dziedzicznych, takich jak mukowiscydoza czy anemia sierpowata.
-        \item Zmiana sekwencji DNA.
+            \item \textbf{Badania naukowe}: Badania nad funkcją genów i modelowanie chorób genetycznych.
-    \end{itemize}
+        \end{longenum}
-\end{itemize}
+    \end{longenum}
 
-\vspace{1cm}
+    \vspace{0.5cm}
-\textbf{Przykłady zastosowań:}
+    \item Przykład w kontekście Arabidopsis
-\begin{itemize}
+    \begin{longenum}
-    \item Zwiększenie odporności roślin na suszę \cite{montecilloCRISPRCas9SystemPlant2020}.
+        \item CRISPR może być użyty do wprowadzenia modyfikacji w genach Arabidopsis odpowiedzialnych za reakcje na stres suszy.
-    \item Poprawa cech rolniczych zwierząt.
+        \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 Terapia genowa u ludzi \cite{doudnaNewFrontierGenome2014}.
+        \item Dzięki CRISPR można tworzyć bardziej odporne odmiany roślin, co ma znaczący wpływ na rolnictwo, zwłaszcza w obliczu zmian klimatycznych.
-\end{itemize}
+    \end{longenum}
+\end{longenum}