Published multiple files

Author: Quartz Syncer

content/T/EGB/Lecture01.md

@@ -2,7 +2,7 @@
 
 At a glance:
 
-- Presentation 
+- Presentation
 - Why Gene Cloning and DNA Analysis are Important (Brown Ch01)
 - The circular Bio economy
 - Exciting examples of the application of molecular genetics
@@ -17,25 +17,25 @@ Course Structure:
 - **PL (Laboratory)** classes — **mandatory**
 
 This course introduces and integrates **molecular biology** and
-**molecular biotechnology** with a 
-practical introduction to **bioinformatics**. 
+**molecular biotechnology** with a
+practical introduction to **bioinformatics**.
 
-The goal is to understand how and why DNA is manipulated in the lab and how 
+The goal is to understand how and why DNA is manipulated in the lab and how
 biological data are analysed and interpreted using bioinformatics tools.
 
 The TP classes focus on searching for, comparing and interpreting sequences
 from databases and *in-silico* simulation of widely used cloning methods.
 
 The laboratory class is a plasmid construction project that demonstrate both
- molecular biology techniques as well as the strategy needed for the construction 
-of a new plasmid vector. The laboratory course is divided into nine sessions of 
+ molecular biology techniques as well as the strategy needed for the construction
+of a new plasmid vector. The laboratory course is divided into nine sessions of
 which each student takes part in three.
 
 👉 The course emphasizes **why and when** to use techniques, not just **how**.
 
 A **personal laptop** is required for TP work.
 
-## Assessment
+## Assessmen
 
 Final grade comprises:
 
@@ -67,10 +67,10 @@ By the end of the course, you should be able to:
 - Integrate lab results with computational analysis
 
 
-# Why Gene Cloning and DNA Analysis Are Important
+# Why Gene Cloning and DNA Analysis Are Importan
 
-Brown chapter 01 explains why gene cloning and DNA analysis are central to modern biology, 
-medicine, and biotechnology. Seminal experiments in genetics. The advent of restriction enzymes 
+Brown chapter 01 explains why gene cloning and DNA analysis are central to modern biology,
+medicine, and biotechnology. Seminal experiments in genetics. The advent of restriction enzymes
 and gene cloning. DNA topology, sequence file formats. Primary vs secondary databases.
 
 ## Core Ideas
@@ -93,8 +93,8 @@ Understanding biology at the molecular level requires the ability to clone and a
 
 # The circular bio economy
 
-A **circular bioeconomy** is an economic model that uses **renewable biological resources** (plants, algae, microbes, organic residues, 
-food waste, manure, forestry/agri by-products) to produce **food, materials, chemicals, and energy**, while keeping resources in use 
+A **circular bioeconomy** is an economic model that uses **renewable biological resources** (plants, algae, microbes, organic residues,
+food waste, manure, forestry/agri by-products) to produce **food, materials, chemicals, and energy**, while keeping resources in use
 for as long as possible through **reuse, cascading use, and recycling** to minimize waste and fossil fuel inputs.
 
 ### Key ideas
@@ -123,5 +123,5 @@ How we can use checksums to keep track of sequences.
 ## Literature
 
 ### Brown T. Gene Cloning and DNA Analysis - An Introduction 8ed (2020)
-- Chapter 01 Why Gene Cloning and DNA Analysis are Important
+- Chapter 01 Why Gene Cloning and DNA Analysis are Importan
 

content/T/EGB/Lecture02.md

@@ -21,6 +21,3 @@ DNA manipulation relies on enzyme specificity and molecular complementarity.
 
 ### Brown T. Gene Cloning and DNA Analysis - An Introduction 8ed (2020)
 - Chapter 04 Manipulation of Purified DNA
-
-
-

content/T/EGB/Lecture03.md

@@ -1,7 +1,7 @@
 # Polymerase Chain Reaction (PCR)
 
 ## What is PCR?
-PCR is a technique that amplifies a specific DNA sequence exponentially in vitro. This class will cover 
+PCR is a technique that amplifies a specific DNA sequence exponentially in vitro. This class will cover
 exactly how and why PCR works in detail. Primer design. Engineering DNA fragments with PCR, overlap extension PCR.
 
 ## Core Components

content/T/EGB/Lecture04.md

@@ -8,13 +8,13 @@ This class focuses on how DNA fragments are maintained, replicated, and selected
 - Common vectors include plasmids, bacteriophages, and yeast artificial chromosomes.
 
 - Plasmids, Episomes
-- Selection markers 
+- Selection markers
 - Copy Number & Compatibility
 - Conjugation, mapping
 - pBR322 - cloning by insertional inactivation
 - pUC18 and 19 - blue/white screening
 - M13 - phage display & DNA origami
-- Phagemids 
+- Phagemids
 - Lambda - phage vector with high capacity
 - In-vitro packaging of Lambda / Cosmids
 - Yeast plasmids and Yeast Artificial Chromosomes
@@ -29,6 +29,3 @@ This class focuses on how DNA fragments are maintained, replicated, and selected
 - Chapter 05 Introduction of DNA into Living Cells
 - Chapter 06 Cloning Vectors for E. coli
 - Chapter 07 Cloning Vectors for Eukaryotes
-
-
-

content/T/EGB/Lecture05.md

@@ -1,7 +1,7 @@
 # Purification of DNA from Living Cells
 
-DNA purification is the foundation of all molecular biology workflows. This 
-class explains how to isolate DNA from cells different kinds of cells. 
+DNA purification is the foundation of all molecular biology workflows. This
+class explains how to isolate DNA from cells different kinds of cells.
 Alkaline lysis miniprep and chromatography. Quantity and quality assessment by
 spectrophotometer (A260/A280 ratio). Gel electrophoresis of DNA.
 

content/T/EGB/Lecture06.md

@@ -1,7 +1,7 @@
 # How to clone a new gene
 
 This lecture focuses on strategies to isolate a specific gene from a complex genome.
-A comprehensive overview of common strategies is presented and how the strategy must 
+A comprehensive overview of common strategies is presented and how the strategy mus
 be selected based on what is known about the gene beforehand.
 
 ## Approaches
@@ -18,6 +18,6 @@ be selected based on what is known about the gene beforehand.
 ## Literature
 
 ### Brown T. Gene Cloning and DNA Analysis - An Introduction 8ed (2020)
-- Chapter 08 How to Obtain a Clone of a Specific Gene 
+- Chapter 08 How to Obtain a Clone of a Specific Gene
 - Optional [video](https://youtu.be/Mwgi8LehP98?si=q601KvSBjUbjBKFX)
 

content/T/EGB/Lecture07.md

@@ -1,13 +1,13 @@
 # Studying Gene Expression and Function
 
-This lecture introduces the principal experimental approaches used to analyse gene expression and gene function. 
-It covers methods for studying RNA, including Northern hybridization and techniques for mapping transcript structure 
-such as S1 nuclease mapping, primer extension, and 5′ and 3′ RACE. The lecture also addresses the analysis of DNA–protein 
-interactions involved in transcriptional regulation, presenting methods such as gel retardation assays, DNase I footprinting, 
-modification interference assays, and functional analysis of regulatory regions using deletion analysis and reporter 
-genes. Approaches for identifying and characterizing the protein product of a cloned gene, including hybrid-arrest 
-and hybrid-release translation, are discussed. The lecture concludes with an introduction to protein engineering 
-and site-directed mutagenesis, including overlap extension PCR, whole-plasmid mutagenesis, and synthetic gene design, 
+This lecture introduces the principal experimental approaches used to analyse gene expression and gene function.
+It covers methods for studying RNA, including Northern hybridization and techniques for mapping transcript structure
+such as S1 nuclease mapping, primer extension, and 5′ and 3′ RACE. The lecture also addresses the analysis of DNA–protein
+interactions involved in transcriptional regulation, presenting methods such as gel retardation assays, DNase I footprinting,
+modification interference assays, and functional analysis of regulatory regions using deletion analysis and reporter
+genes. Approaches for identifying and characterizing the protein product of a cloned gene, including hybrid-arres
+and hybrid-release translation, are discussed. The lecture concludes with an introduction to protein engineering
+and site-directed mutagenesis, including overlap extension PCR, whole-plasmid mutagenesis, and synthetic gene design,
 highlighting their use in investigating protein structure–function relationships.
 
 

content/T/EGB/Lecture08.md

@@ -1,4 +1,4 @@
-# Sequencing Genes and Genomes, Studying Transcriptomes and Proteomes 
+# Sequencing Genes and Genomes, Studying Transcriptomes and Proteomes
 
 This lecture covers DNA sequencing
 strategies, from traditional Sanger sequencing to high-throughput next-

content/T/EGB/Lecture10.md

@@ -1,17 +1,17 @@
-# Sequence alignment
+# Sequence alignmen
 
 This lecture introduces the principles of sequence alignment as a fundamental
-tool in bioinformatics and molecular biology. 
+tool in bioinformatics and molecular biology.
 
 It explains the rationale for comparing DNA, RNA, and protein sequences to identify similarity, infer
-homology, and predict function and evolutionary relationships. 
+homology, and predict function and evolutionary relationships.
 
-The lecture covers pairwise sequence alignment, including global and local alignment
+The lecture covers pairwise sequence alignment, including global and local alignmen
 approaches, scoring schemes based on matches, mismatches, and gaps, and the
 use of substitution matrices for protein sequences. It also introduces
 heuristic alignment algorithms and database searching, with emphasis on tools
 such as BLAST, their underlying concepts, and their practical interpretation.
 Finally a note on the limitations of sequence alignment and the
-importance of biological context when drawing conclusions from alignment
+importance of biological context when drawing conclusions from alignmen
 results.
 

content/dscode.md

@@ -121,7 +121,7 @@ punctuation = ! # $ % & * + ( ) < = > @ /: ' , - . ; ? [ \ ] ^ _ ` { | } ~ "
 >format1 alphabet=dscode
 PEXIGULAOCQFZJ
 
->format2 two strings & space 
+>format2 two strings & space
 GATCGUAAAC
     CAUTUGCTAG