genetics for natural resources

DNA can be found in two main locations: the nucleus and mitochondria.
Amplification methods:
- PCR (Polymerase Chain Reaction): A technique to create copies of DNA segments.
- Gel electrophoresis: Used to separate DNA fragments by size after amplification.
- Genome-wide sequencing: Screens the entire genome to analyze variations across sequences.

Genetic sequence variations occur in various forms and locations within the genome.
Genetic engineering explores these variations for several applications.

Gene splicing: Involves altering a gene to influence function.
Transcription process includes the need for a promoter (start) and terminator (end).
Example:
- A gene with two specific nucleotide sequences (e.g., two T's) can make a protein that glows green; variations like AT or AA do not result in fluorescence.

Genes can be inserted into different organisms to study their functions.
Example of application:
- Transgenic salmon: Growth hormones from one species are introduced into another.
Some fish possess unique genes that can be used for research and application in genetic modification.

Although less common, genetic engineering practices are present in conservation genetics.
Aquaculture: Selective breeding aims to create new lineages for sustainable fish populations.
Gene therapies in medicine involve adding DNA to a patient’s cells, often using
- Adeno-associated viral vectors to deliver the genetic material.

Expression vectors facilitate the expression of genetic traits.
Example uses include yeast fermentation in cheese production and insulin production.
Green Fluorescent Protein (GFP): Commonly utilized as a marker to indicate gene expression across various organisms such as mice and fish.

Genetic variation in plants is exploited for agricultural benefits, such as:
- Pesticide resistance: Altered sequences in crop plants that resist pest attacks.
- Herbicide tolerance: Creating crops resilient to herbicides.
An extension of traditional selective breeding practices aimed at improving crop quality and yield.

Importance of understanding advancements in DNA sequencing technology.
Sanger Sequencing:
- Procedure established in the early 2000s for reading nucleotide sequences.
- Capable of sequencing 600-800 base pairs at a time.
- Used in the first human genome sequences, noted for lower data throughput compared to newer methods.

Also termed high-throughput sequencing.
Utilizes massively parallel processing for data generation.
- Example:
- Recent project outputting 1.5 billion sequences from fish research in under two weeks at a cost of $1,500.
Sequencing by synthesis: No need for electrophoresis; uses fluorescence to monitor sequences.
Key process:
- Utilize a flow cell where DNA folds and primers create complementary strands.
- Automated imaging captures the fluorescence to generate data.

Statistical models are required to manage errors in sequencing.
Common error rates are around 1-2% across sequences, which can have significant implications concerning data quality.

Bioinformatics combines genetics, computational science, and statistical modeling.
New technologies such as Nanopore sequencing enable field-based sequencing without the need to transport biological samples.
- Useful in remote conservation genetics applications.
Allowing for end-to-end molecular reads enhances data quality and precision.

Gene expression studies examine which genes are active in certain environmental conditions.
RNA sequencing (RNA-seq) and microarrays are two methods for analyzing gene expression:
- RNA-seq measures gene expression levels across the genome.
- Microarrays provide a visual representation of gene on-off scenarios via fluorescence.

Shifts in methodologies over time indicate a move towards sequencing rather than traditional SNP panels.
Comparative analysis: Genetics across populations can reveal genetic diversity metrics, which provide insights into species adaptation and conservation needs.

Assigned reading: Open Genetics Chapter 5.
Course readings are made available online, strengthening the understanding of genetic concepts relevant to the material discussed.