molecular bio test 3 (key words)

Agrobacterium tumefaciens

strategy to genetically modify plants, this bacterium naturally transfers DNA into plant cells and is widely used as a gene-delivery vector

AquaBounty

developed AquAdvantage salmon, this salmon contains a growth-hormone transgene allowing faster growth and earlier market size.

Arctic Apple

is a genetically engineered apple designed to resist browning after cutting or bruising.

It produces RNA molecules that suppress expression of polyphenol oxidase (PPO),

BT toxin

derived from the bacterium Bacillus thuringiensis, damage the digestive tract of susceptible insects, leading to insect death

highly specific toward certain insect groups

are considered substantially less toxic to humans than many conventional insecticides.

Biolistics

(“gene gun”) strategy to gentically modify plants

DNA-coated particles are physically shot into plant cells

De novo domestication

the intentional transformation of wild species into domesticated forms—typically through selective breeding or modern genetic methods—to create new crops or animals suited for human use.

EPA

The Environmental Protection Agency, responsible for protecting human health and the environment by developing and enforcing national environmental regulations.

EPSPS

5-enolpyruvylshikimate-3-phosphate synthase), an enzyme required for synthesis of aromatic amino acids in plants and many microorganisms.

FDA

the Food and Drug Administration, a U.S. federal agency responsible for protecting public health by regulating food, drugs, medical devices, cosmetics, and related products.

Glyphosate

the active ingredient in Roundup herbicide, inhibits EPSPS,

Innate Potato

It is designed to resist blackspot bruising, browning and to contain less of the amino acid asparagine that turns into acrylamide during the frying of potatoes (Acrylamide is a probable human carcinogen). it is NOT transgenic

Polyploidy

the condition of having more than two complete sets of chromosomes in a cell or organism

Protoplast fusion

a type of genetic modification in plants by which two distinct species of plants are fused together to form a new hybrid plant with the characteristics of both

Roundup Ready crops

engineered to tolerate glyphosate, the active ingredient in Roundup herbicide, express a glyphosate-resistant bacterial EPSPS enzyme, allowing crops to survive herbicide treatment.

USDA

United States Department of Agriculture, responsible for food, agriculture, natural resources, rural development, and nutrition programs

GMOs can be generated by:

introducing mutations,

modifying endogenous genes,

silencing genes,

introducing foreign DNA

transgenic organism.

When a GMO contains DNA originating from a different species

CaMV 35S promoter

viral promoters, which became extremely widespread in plant biotechnology

Modern GM and gene-edited crops are increasingly engineered for:

drought tolerance,

salt tolerance,

disease resistance,

improved nutritional value,

longer shelf life,

climate resilience

How can GM ingredients be detected in food?

using PCR (polymerase chain reaction).

Many GM crops contain shared engineered regulatory sequences

PCR primers targeting these regions can amplify GM-specific DNA fragments

Which countries produce the largest amounts of GM crops?

the United States,

Brazil,

Argentina,

Polyploidy induction

Chemicals such as colchicine can disrupt microtubules and chromosome segregation, sometimes producing larger polyploid plants.

Agrobacterium tumefaciens

This bacterium naturally transfers DNA into plant cells and is widely used as a gene-delivery vector.

RNA interference

Plants can be engineered to produce siRNAs that silence target genes

Cas9

associated with the guide RNA, which recognize and cleave matching foreign DNA (generates a double-strand break in the DNA)

CCR5

a receptor commonly used by HIV,

CRISPR

Clustered Regularly Interspaced Short Palindromic Repeats, natural defense mechanisms found in bacteria, and archaea, functions as an adaptive immune system

Cystic fibrosis

inherited condition impacting the respiratory system and digestive tract marked by the secretion of dense and viscous mucus

DNA repair mechanisms

molecular processes through which a cell detects and repairs damages within its genomic DNA

Editing by homology-directed repair

uses a homologous DNA template to repair the break, Researchers can supply engineered donor DNA to insert sequences, or correct mutations, more precise but less efficient

Editing by non-homologous end joining

directly rejoins DNA ends but is error-prone, useful for gene knockout experiments

Endonuclease

enzyme that cleaves phosphodiester bonds in DNA and RNA

Gene knockout

intentional genome modification that results in the inactivation of a specific gene

Genome editing

the targeted modification of the DNA sequence of a cell or organism. can therefore:

remove,

modify,

or introduce genetic functions

Germ line

Edits affect:

sperm,

eggs,

or embryos,

Guide RNA

cell fragments of the invading DNA that are integrated into the CRISPR locus and transcribed, associated with Cas proteins, base pairs with a complementary DNA target sequence

Huntington disease

hereditary disorder marked by the degeneration of nerve cells in the brain, arising from the elongation of glutamine codons within a specific gene

IVF

in vitro fertilization, a process in which an egg is fertilized by sperm outside the body—typically in a laboratory dish—to create an embryo for later transfer into the uterus

Meganuclease, TALEN and ZFN

predate CRISPR-based systems and were widely used before the mid-2010s. function as programmable molecular scissors, contain a DNA-recognition component, DNA recognition depends on engineered proteins

Mitochondrial donation/replacement

the replacement of mitochondria in one or more cells to prevent or ameliorate disease. used to prevent the transmission of mitochondrial diseases from mother to child

Mosaicism

some cells are edited, while others remain unedited, resulting phenotype may become unpredictable

Off-target editing

occurs when CRISPR cuts unintended genomic sites. This can potentially:

disrupt normal genes,

activate oncogenes,

or generate harmful mutations

PAM

short DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system

Pre-implantation genetic diagnosis

the genetic profiling of embryos prior to implantation

how does CRISPR function as an adaptive immune system

1. When foreign DNA enters a prokaryotic cell fragments of the invading DNA can be integrated into the CRISPR locus.

2. These fragments are later transcribed into guide RNAs.

3. Guide RNAs associate with Cas proteins, which recognize and cleave matching foreign DNA during future infections.

Diseases caused by ______ mutations are currently the most tractable targets.

single-gene

what cells can be edited

circulating blood cells,

somatic tissues,

stem cells,

embryos,

or germline cells

Somatic editing

Edits affect only the treated individual.

This approach is increasingly accepted clinically.

How is CRISPR delivered into cells?

Viral vectors (AAV, and lentiviruses) or Lipid nanoparticles

Ex vivo editing

Cells are removed, edited outside the body, and reinfused.

Local in vivo delivery

CRISPR components are injected directly into a tissue, or organ.

The eye is an attractive target because local delivery is relatively straightforward, and immune responses are reduced.

Systemic in vivo delivery

Components are delivered through bloodstream infusion.

This remains technically challenging

Safe-harbor loci

genomic regions where insertion of foreign DNA is less likely to disrupt essential genes.

CRISPR babies

Chinese researcher He Jiankui announced embryos were edited to disrupt CCR5 in 2018, The announcement triggered massive international criticism

addgene

a nonprofit plasmid repository that enables global laboratories to share genetic materials more effectively

ABE

Adenine base editors, convert A•T base pairs into G•C base pairs.

Acr proteins

Anti-CRISPR proteins, natural inhibitors of CRISPR systems. systems by:

preventing DNA binding,

blocking guide-RNA recognition,

inhibiting DNA cleavage,

or disrupting Cas-protein assembly.

Cas13

an RNA-targeting CRISPR enzyme, a complex with a guide RNA designed to recognize a specific target RNA sequence. Upon target recognition it becomes activated and cleaves nearby reporter RNAs.

Cas9 nickase

introduces a single-strand DNA nick that improves editing efficiency while still avoiding the double-strand breaks associated with conventional CRISPR-Cas9. in prime and base editors

CBE

Cytosine base editors, convert C•G base pairs into T•A base pairs, contains APOBEC1, a cytidine deaminase that converts cytosine (C) into uracil (U).(converts the resulting U-G mismatch into a T-A )

David Liu

No naturally occurring enzyme converts adenine into guanine in DNA. he engineered TadA, a bacterial enzyme that normally edits RNA, into an enzyme capable of modifying DNA.

Electroporation

technique that uses an electrical field to introduce nucleic acids into cells

fluorophores

a fluorescent chemical compound that can re-emit light upon light excitation

Indel

insertion and deletion

Micro-injection

microscope-guided method used to introduce DNA or other substances directly into a selected cell using a fine glass micropipette

pegRNA

prime-editing guide RNA, in prime editors, it guides the complex to the target site, and it contains the sequence that will be written into the genome

Prime editing

CRISPR-derived tools capable of introducing:

precise substitutions,

small insertions,

and small deletions

without generating double-strand DNA breaks.

contain:

a Cas9 nickase,

a reverse transcriptase,

a pegRNA

Progeria

genetic disorder leading to accelerated aging in a child, not due to inheritance

Rapid directed evolution

an accelerated form of protein engineering that combines traditional directed evolution cycles with advanced computational and synthetic biology

Transfection

process of artificially introducing nucleic acids into cells, utilizing means other than viral infection or micro-injection

base editors

CRISPR-derived tools designed to change one DNA base into another without generating a double-strand DNA break. can generate both missense and nonsense mutations, require a PAM sequence

SHERLOCK and CARMEN

CRISPR systems used for diagnostics, uses Cas13

allele

Different versions of the same locus, individuals can have 2 different ones max

Capillary electrophoresis

Amplified DNA fragments are separated according to size, used to generate DNA profile

Chain of custody

the documented record of the collection, transfer, storage, and analysis of physical evidence from the crime scene to the courtroom.

Consumer genealogy database

an online platform that stores genetic data from individuals who have voluntarily taken direct‑to‑consumer DNA tests

CODIS

Combined DNA Index System, the FBI software platform used to manage and compare forensic DNA profiles.

Investigative genetic genealogy (IGG)

combines:

forensic DNA analysis,

consumer genealogy databases,

and family-tree reconstruction

to identify potential suspects or unidentified remains

Microsatellite

a tract of repetitive DNA that consists of a particular sequence of base pairs repeated a large number of times

NDIS

National DNA Index System, the national-level DNA database operating within CODIS.

STR

Short tandem repeats, microsatellites consisting of short DNA sequences repeated consecutively at a specific genomic location.

Individuals frequently differ in the number of repeat units (useful for human identification)

Locus

the physical location of a DNA sequence on a chromosome

Lukis Anderson

Publicized person who was unjustly convicted due to indirect DNA transfer

The Innocence Project

is a nonprofit organization dedicated to:

exonerating wrongfully convicted individuals through DNA testing

Touch DNA

DNA recovered from skin cells left behind after handling or contacting an object, often contains DNA from multiple individuals, making interpretation more difficult.

Secondary DNA transfer

occurs when DNA is transferred indirectly through an intermediate person or object

The Golden State Killer

Mediatized case that demonstrated that criminals don't necessarily have to be profiled in the NDIS to be identified based on the DNA they leave on crime scenes

Antigenic drift

evolving through gradual accumulation of mutations over time (because influenza RNA polymerase lacks proofreading activity, resulting in a relatively high mutation rate.).

Antigenic shift

a sudden major change in influenza A viruses.

Shift occurs when two influenza A viruses infect the same cell, and exchange RNA segments through reassortment.

B/Victoria

common influenza B lineage

B/Yamagata

extremely rare influenza B lineage and may have disappeared from circulation

Cap snatching

Influenza mRNAs require a 5’ cap for efficient translation.

To obtain these caps, the viral polymerase:

o host RNAs are cleaved,

o short capped RNA fragments are stolen,

o and these fragments are used as primers for viral mRNA synthesis

GeneXpert Xpress

Rapid molecular tests detect viral RNA using RT-PCR, or isothermal amplification, more accurate

Hemagglutinin

the viral attachment and fusion protein.

HA:

o binds sialic-acid receptors on host cells,

o mediates fusion between viral and cellular membranes,

o and initiates infection.

HA contains a head region(classifies Flu A), and a stalk region

Human challenge trial

trials in which participants are intentionally challenged (whether or not they have been vaccinated) with an infectious disease organism

ID Now

Rapid influenza diagnostic tests (RIDTs) detect viral antigens, are inexpensive, and provide results within minutes.

However, RIDTs are less sensitive than molecular tests and may produce false-negative results.

Influenza A

o infects humans and numerous animal species,

o causes seasonal epidemics,

o and is responsible for all known influenza pandemics

Influenza B

o primarily infects humans,

o causes seasonal epidemics,

o but does not cause pandemics

Influenza C

o infects humans,

o generally causes mild disease,

o and is not associated with major epidemics

Influenza D

o primarily infects cattle,

o can infect pigs and other livestock,

o and is not currently known to cause significant disease in humans