BIOL 1030 Lectures 1-6

Unifying principles of life

Life is organized through conserved genetic and cellular mechanisms. Genes control development, development involves differential gene expression, cells interact through induction, and many developmental mechanisms are evolutionarily conserved.

Developmental Biology

The study of how organisms change in space and time, beginning with a relatively simple starting state and producing a more complex organism with specialized cells, tissues, organs, and body axes.

Life cycle

The sequence of developmental stages through which an organism passes. A typical animal life cycle includes fertilization, cleavage, gastrulation, organogenesis, birth or hatching, growth, adulthood, reproduction, and the next generation.

Fertilization

The union of sperm and egg that produces a single-celled zygote. It is often used as the starting point of the animal life cycle, although a life cycle can technically begin at any stage.

Cleavage

A series of rapid cell divisions after fertilization. Cleavage converts one zygote into a ball of cells without greatly increasing the embryo’s overall size.

Blastula

A hollow ball of cells produced by cleavage.

Blastocyst

The mammalian form of a blastula. It contains an outer layer of cells and an inner cell mass.

Gastrulation

The developmental process in which the ball of cells rearranges into an embryo with three germ layers and established body axes.

Body axes

The major spatial directions of an organism, including the anterior-posterior or front-back axis, dorsal-ventral or top-bottom axis, and left-right axis.

Organogenesis

The process through which organs and organ systems begin to form after the basic germ layers and body plan have been established.

Birth

The point at which an organism exits the embryonic or fetal environment and begins postembryonic life.

Growth into adulthood

The developmental period in which an organism increases in size, continues specializing, reaches sexual maturity, and develops adult structures.

Observation

A method of studying development by directly examining organisms, cells, tissues, or developmental changes.

Microscopy

The use of microscopes to observe cells, tissues, embryos, structures, or gene-expression patterns that cannot be seen with the unaided eye.

Staining

A technique that uses dyes or other substances to make cells, tissues, molecules, or metabolic processes easier to visualize.

New technologies

Modern methods that allow researchers to observe development, measure gene expression, compare genomes, and analyze cells at increasingly precise levels.

Physical perturbation

A developmental experiment that changes an organism physically in order to determine how a tissue, cell, or structure contributes to development.

Transplantation

The movement of one tissue or group of cells to a different location or organism to determine what fate it adopts and whether its behavior depends on its original or new environment.

Ablation

The deliberate removal or destruction of a tissue or group of cells. Researchers study the resulting consequences to determine what the removed cells were required for.

Genetic perturbation

An experiment that alters a gene or its activity and examines the resulting effect on development.

Genetics

The study of genes and hereditary processes.

Genome

The complete set of DNA in a cell or organism. Nearly all cells in a multicellular organism generally contain the same genome.

DNA

The molecule that stores and transmits hereditary information from parent cells to daughter cells. DNA is double-stranded and is made from repeating nucleotide subunits.

Nucleotides

The repeating building blocks of DNA. Their sequence stores genetic information.

Gene

A specific segment of DNA containing information for producing a functional product, usually a protein or functional RNA. Genes also control developmental processes.

Protein

A functional molecule made from an amino-acid sequence encoded by a gene. Proteins can act as enzymes, receptors, structural components, signaling molecules, or transcription factors.

Mutations

Permanent alterations in the nucleotide sequence of DNA. Mutations can change the resulting RNA, protein sequence, or activity of a gene.

Mutagen

An environmental agent or laboratory treatment that increases the frequency of mutations, such as UV light, chemical agents, or CRISPR-based genome editing.

Amino-acid sequence

The order of amino acids in a protein. Mutations can alter this sequence and therefore change the protein’s structure or function.

Start codon

A codon in mRNA, usually AUG, that signals where translation begins and establishes the reading frame of the protein.

Stop codon

A codon that signals the end of translation. It does not encode an amino acid.

Nonsense mutation

A mutation that changes a codon into a stop codon, usually producing a shortened and nonfunctional protein.

Missense mutation

A mutation that changes a codon so that a different amino acid is incorporated into the protein. It does not create a stop codon.

Frameshift mutation

A mutation caused by an insertion or deletion of nucleotides that shifts the reading frame. Because codons are read in groups of three, the downstream amino-acid sequence is usually extensively changed.

Silent mutation

A mutation that changes the DNA sequence without changing the amino acid encoded by the codon.

Differentiated

Describes a cell that has acquired specialized structures, gene-expression patterns, and functions.

Tissues

Groups of similar cells that work together to perform a particular function.

Organs

Structures made from multiple tissues that work together to perform a specific function.

Organ systems

Groups of organs with interrelated functions, such as the digestive, nervous, or circulatory systems.

Evolution

The process through which populations change over time through differential survival and reproduction. Evolution has produced the diversity of past and present life.

Common ancestor

An ancestral organism from which two or more descendant species evolved. All life on Earth is connected through common ancestry.

Fossil record

The preserved physical evidence of past organisms and their traits. It can be used to study evolutionary relationships.

Genetic record

The information contained in DNA sequences that can be compared among organisms to infer evolutionary relationships.

Phylogenetic tree

A branching diagram showing when populations split and how organisms or sequences are evolutionarily related. Phylogenetic trees can be based on anatomy, fossils, or molecular evidence.

Model systems

Species selected for laboratory research because they are easy to grow, manipulate, observe, or reproduce. Information from a model system can reveal conserved biological mechanisms in other organisms.

Evolutionary conservation

The preservation of genes, structures, or developmental mechanisms across different species because those features originated in a common ancestor and remain useful.

Yeast

A simple, single-celled model organism that can reproduce by budding and is useful for studying cell division and genetics.

Caenorhabditis elegans (C. elegans)

A nematode worm commonly used as a model system for genetics, development, cell death, and cell signaling.

Drosophila

A fruit fly model organism widely used to study genetics, embryonic development, segmentation, and homeotic genes.

Thale cress

A small flowering plant used as a model system for plant development and genetics.

Clonal population

A population of genetically identical organisms or cells. Clonal populations help researchers control genetic variation in experiments.

Homologous genes

Genes in different species that evolved from a common ancestral gene. Homologous genes may retain related functions.

Necessary

A factor is necessary when the process cannot occur normally without it. Loss of that factor disrupts the process.

Sufficient

A factor is sufficient when its presence or activity alone can produce a particular process or outcome.

Scientific method

A process in which researchers make observations, ask questions, form testable hypotheses, make predictions, conduct experiments using quantifiable data, and revise conclusions based on reproducible evidence.

Testable hypothesis

A proposed explanation that can be examined through an experiment or observation.

Reproducible evidence

Evidence that can be obtained again when the same experiment or analysis is repeated.

Differential gene expression

The process by which different cells express different sets or amounts of genes, producing different proteins and cellular functions.

Nuclear equivalence

The principle that differentiated somatic cells retain essentially all the genetic information that was present in the original fertilized egg.

Cytoplasmic inequivalence

The unequal distribution of cytoplasmic components, such as mRNAs and proteins, among cells or daughter cells. These differences can influence cell fate.

Developmental cascade

A sequence in which one developmental change triggers another, producing a chain of coordinated events.

Induction

A process in which one group of cells sends a signal that changes the gene expression, behavior, or fate of neighboring cells.

Loss of function (LOF)

A mutation or condition that reduces or eliminates the normal activity of a gene product. LOF describes what happens to the action of the gene, not whether a structure is gained or lost.

Gain of function (GOF)

A mutation or condition that gives a gene product increased, new, misplaced, mistimed, or otherwise altered activity.

BMP7

A developmental gene whose normal function is required for the formation of structures such as eyes, kidneys, and adrenal glands in the mouse examples discussed.

Wild type (WT)

The usual or reference form of an organism, gene, or phenotype in a population.

Bithorax mutation

A mutation affecting Drosophila development in which the normal gene prevents formation of a second pair of wings. Loss of that gene’s function can produce an extra pair of wings.

Antp

A Drosophila homeotic gene. Gain of Antp function in the wrong location can cause legs to develop where antennae normally form.

let-60

The C. elegans homolog of RAS. Loss of let-60 function can eliminate vulva formation, while gain of function can produce multiple vulvas.

Necessary gene function

If loss of a gene prevents a developmental process, the gene is necessary for that process.

Genotype

The exact genetic constitution of an individual, including the alleles present at particular genes.

Phenotype

The observable properties of an organism resulting from genetic and environmental factors. A phenotype is what can be observed and does not have to be caused entirely by genetics.

Haploid

A cell or organism with one copy of each chromosome and one copy of each gene. Human sperm and eggs are haploid.

Diploid

A cell or organism with two copies of each chromosome and generally two copies of each gene.

Allele

A specific sequence variant of a gene. The two copies of a gene in a diploid organism may have identical or different alleles.

Homozygous

Having two identical alleles of a gene, such as +/+ or -/-.

Heterozygous

Having two different alleles of a gene, such as +/-.

Dominant

An allele or mutation that produces a phenotype when only one copy is present.

Recessive

An allele or mutation that produces a phenotype primarily when both copies are mutant or affected.

Semi-dominant

Describes a mutation whose heterozygous phenotype is different from wild type and whose homozygous phenotype is often more severe or lethal.

Haploinsufficiency

A condition in which one normal copy of a gene does not produce enough gene product for normal function.

Brachyury (T)

A gene involved in establishing the anterior-posterior body axis. Certain T mutations are nonsense loss-of-function mutations with semi-dominant effects and can be embryonic lethal in homozygotes.

Functional conservation

The preservation of a gene’s ability to perform a related function in different organisms.

RAS

A small GTPase involved in signaling pathways that regulate cell division and cell morphology. RAS is conserved from yeast to humans.

Kras

A mouse RAS gene. Loss-of-function or altered RAS activity can affect cell division and cancer-related phenotypes.

Forward genetics

A largely unbiased approach in which mutations are generated randomly and the resulting phenotype is used to identify the responsible gene.

Reverse genetics

An approach in which a specific gene is deliberately altered and the resulting phenotype is examined.

Genetic screen

A procedure used to generate or identify mutations that affect a process or phenotype.

Catch it / Show it

An experiment that detects where, when, or how strongly a gene product or gene activity is present.

Break it

An experiment that disrupts a gene and asks whether the developmental process still occurs. It tests whether the gene is necessary.

Rescue it

An experiment that replaces a missing gene function to determine whether the normal phenotype or process can be restored.

Move it

An experiment that expresses a gene in a new or ectopic location to determine whether the gene is sufficient to produce a function there.

Ectopic expression

Expression of a gene in a location, cell type, or developmental time where it is not normally expressed.

Staining

A method that uses dyes or other substances to visualize cells, tissues, metabolic processes, or living and dead cells.

In situ hybridization (ISH)

A technique that uses a labeled complementary nucleic-acid probe to detect where a particular RNA transcript is located in a tissue.

Immunolocalization

A method that uses antibodies to detect where a particular protein is located in a cell or tissue.

Immunohistochemistry

Another name for immunolocalization, especially when antibody detection is visualized through an enzyme-generated color reaction.

Immunofluorescence

An antibody-based method in which a fluorescent molecule is used to visualize a target protein.

Reporter gene fusion

A genetic construct that attaches an easily detected reporter gene to the regulatory region or coding region of a gene of interest.

Transcriptional fusion

A construct in which a reporter gene, such as GFP, is placed under the control of another gene’s promoter and regulatory sequences. It reports where and when transcription is activated but does not necessarily show where the original protein is located.