Organisms and groups · Species
Ageratina adenophora
Ageratina adenophora, commonly called crofton weed, is a perennial shrub in the daisy family, Asteraceae.
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EcoGenesis · Encyclopedia
Library of the living world
Organisms, anatomy, processes and learning journeys. Read the explanations and follow their links to data and sources.
A
Organisms and groups · Species
Amanita muscaria
Fly agaric is a mushroom-forming fungus associated with tree roots. Its familiar red cap is only the visible part of this partnership.
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Organisms and groups · Kingdom
Animalia
Animals are multicellular eukaryotes obtaining organic nutrition from other organisms or their remains. Their cells lack cell walls. Most animals have specialized tissues, but sponges show why a familiar arrangement of organs cannot be assumed for every animal. Mobility often changes during life; a larva and an adult can differ substantially.
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Organisms and groups · Species
Arabidopsis thaliana
Arabidopsis thaliana is a small annual flowering plant in the mustard family, Brassicaceae.
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Organisms and groups · Domain
Archaea
Like bacteria, archaea lack a membrane-enclosed nucleus. Their cell envelopes differ, however: characteristic membrane lipids have branched chains with ether linkages, and their walls lack bacterial peptidoglycan. Cells that look similar can therefore differ substantially at the molecular level.
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Organisms and groups · Phylum
Arthropoda
Arthropods combine a segmented body, jointed appendages and an external covering containing chitin. They replace this covering through moulting as they grow. Appendages can support movement, sensing or food handling. Insects, spiders, crustaceans and myriapods illustrate different combinations of these features; their bodies are not all divided into the same regions.
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B
Organisms and groups · Species
Bacillus subtilis
Bacillus subtilis is a Gram-positive bacterium associated with soil and the region around plant roots.
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Organisms and groups · Species
Bacillus subtilis
Bacillus subtilis is a rod-shaped bacterium studied for cell development, protein production and endospore formation.
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Organisms and groups · Domain
Bacteria
Bacterial DNA occupies a region called the nucleoid, without a surrounding nuclear envelope. A cell membrane separates the cell contents from the environment, while ribosomes assemble proteins. Most bacteria have a wall containing peptidoglycan. These features help explain cell organization, but a flagellum or capsule should not be added to every representative.
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Proteins
BRCA2 · P51587
BRCA2 is UniProt protein record P51587 for Homo sapiens (NCBI 9606). The retained sequence contains 3418 amino acids.
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C
Organisms and groups · Species
Caenorhabditis elegans
Caenorhabditis elegans is a nematode: a small, free-living roundworm with a transparent body.
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Proteins
CDC28 · P00546
CDC28 is UniProt protein record P00546 for Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (NCBI 559292). The retained sequence contains 298 amino acids.
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Modules
Cell differentiation: reading an image and its source
First locate a structure and determine whether the material actually shows it. Selecting a label should highlight the relevant area; an invisible detail needs a separate diagram. Before explaining why cells differ, record which cells were observed and how.
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Organisms and groups · Species
Chlamydomonas reinhardtii
Chlamydomonas reinhardtii is a single-celled green alga, not a small animal or a miniature leafy plant.
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Structure
Chloroplast
A chloroplast is a photosynthetic organelle of plants and algae. Its thylakoid membranes and surrounding stroma perform complementary tasks: light-driven electron transport helps produce ATP and NADPH, while carbon-fixation reactions use them to build organic compounds. Different compartments bring these reactions together in one organelle.
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Guides
Classification and evolutionary trees: what is the difference?
A classification branch tells you where a source places a taxon. A phylogenetic tree represents a hypothesis about relationships among the lineages studied. These views are related, but drawing them with similar lines does not make them the same data. First check whether the view shows classification, a species phylogeny or a gene-family tree.
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Guides
Comparing spruces using traits and genome data
Begin with identity. Open *Picea abies* and *Picea glauca* and check scientific names, source and rank. If another catalogue accepts a different name, preserve its treatment separately with a citation. A similar common name or a shared genus does not make records interchangeable.
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D
Proteins
D1 protein · PsbA
D1 is one of the central proteins of photosystem II. Together with D2 it provides a framework for light-driven electron transfer. The retained Arabidopsis UniProt entry links D1 to psbA and AtCg00020. This page connects that biological role with an exact 353-amino-acid sequence and its model-based annotation.
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Organisms and groups · Species
Danio rerio
The zebrafish, Danio rerio, is a small freshwater fish from South Asia, recognizable by dark horizontal stripes along its body.
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Proteins
DnaA · P03004
DnaA is UniProt protein record P03004 for Escherichia coli (strain K12) (NCBI 83333). The retained sequence contains 467 amino acids.
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Organisms and groups · Species
Drosophila melanogaster
Drosophila melanogaster is a small fly in the family Drosophilidae, familiar both as a laboratory animal and as an inhabitant of fermenting food.
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Organisms and groups · Species
Escherichia coli
Escherichia coli occurs in the intestines of people and other animals, but it is also found in water, food and other environmental settings.
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Organisms and groups · Domain
Eukaryota
Eukaryotic cells characteristically have an enclosed nucleus and internal membrane compartments with different functions. This organization lets us study a cell as interacting parts. The parts present depend on the cell type: a diagram containing a chloroplast does not describe every eukaryotic cell.
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F
Proteins
FLC · Q9S7Q7
FLC is UniProt protein record Q9S7Q7 for Arabidopsis thaliana (NCBI 3702). The retained sequence contains 196 amino acids.
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Learning journeys
FLC: how a molecular repressor connects winter to flowering
Working vocabulary: a gene locus identifies a region of DNA; a transcript is an RNA product of transcription; a protein is a different molecular product. Here, a perturbation means a deliberate change in a condition or gene activity, and phenotype means the measured organismal outcome, such as time to flowering.
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Modules
Flowering and FLC: from a record to an experiment
An FLC profile connects records; an experiment tests a particular question in particular material. Follow both paths: establish gene and protein identity, then examine the conditions and outcome of one study. State separately what the experiment did not test.
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Learning journeys
From a whole organism to a cell: what an anatomy image can tell you
Imagine three pictures: a whole plant, a thin view through a leaf, and a close view of a cell. Before asking which is most detailed, ask whether each picture answers the same question.
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Organisms and groups · Kingdom
Fungi
Fungi obtain organic compounds from their surroundings and absorb nutrients across cell surfaces. Their cell walls contain chitin and glucans; fungal cells have no chloroplasts of their own. Fungi include single-celled yeasts and forms that grow as threads called hyphae. A mass of hyphae forms a mycelium.
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Modules
Gene regulation: what is actually measured?
“Is this gene active?” is too broad for a precise investigation. Identify what was observed: a particular RNA, a protein, an interaction or a trait. Separate the measurement from the proposed mechanism in your notes, then find the conditions under which the result was obtained.
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Guides
Gene, transcript and protein: connecting the records
A molecular story can be represented by several records. A gene is described on a genomic sequence; a transcript represents an RNA product; a protein record describes an amino-acid sequence. RefSeq holds genomic, transcript and protein sequences as distinct connected objects. Begin by identifying which object you have opened.
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Courses
Genetics foundations: from inheritance to molecular records
Why do offspring resemble their parents without being identical to them? Begin with heredity and variation, then connect a genetics exercise to a genome, gene, transcript and protein. The route develops one habit: identify the material and assumptions before interpreting a result.
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H
Organisms and groups · Species
Halobacterium salinarum
Halobacterium salinarum is a salt-adapted archaeon, not a bacterium despite the word “bacterium” in its name.
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Organisms and groups · Family
Hominidae
Hominidae includes humans, orangutans, gorillas, chimpanzees and bonobos. Gibbons belong to the broader ape group but not this family. “Hominid” should therefore not be used as a synonym restricted to humans and their fossil relatives.
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Organisms and groups · Genus
Homo
Homo is a genus, while Homo sapiens is the species to which all living humans belong. The genus also includes fossil representatives. For example, early African fossils assigned to Homo erectus have relatively long legs and short arms, proportions associated with movement on the ground. Researchers continue to discuss species boundaries and the interpretation of particular…
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Organisms and groups · Species
Homo sapiens
Homo sapiens is the species to which all living humans belong.
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Guides
How to read a biological classification
Classification helps you understand which group an organism belongs to and which groups are contained within it. Species, genus and family are ranks. *Arabidopsis thaliana*, *Arabidopsis* and Brassicaceae are examples of named groups, or taxa. A rank tells you the level in a classification; a name identifies the group being discussed. Begin a record by checking its scientific…
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I
Modules
Inheritance foundations: the assumptions of a simple model
Begin with the illustrative cross Aa × Aa. Assume a single diploid locus, equal transmission probabilities for A and a from each parent, independent combination of gametes and no selection changing the proportions between the stated stages. A table gives expected genotypes. Translating them into phenotypes requires an additional dominance assumption.
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L
Structure
Leaf
A leaf brings together light capture, gas exchange and transport. In a typical green leaf, chloroplasts in the mesophyll use light energy to build organic compounds from carbon dioxide. Water reaches the leaf through vascular tissue, while sugars can move to other parts of the plant. A leaf is therefore a working organ, not merely a flat surface.
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Modules
Leaf development: shape, size and specimen
Two leaves can be compared by length, but first identify how the measurement was made and which specimens it describes. Open the image and model, check the scale and the provenance of each variant. An altered teaching shape can help explore geometry when clearly distinguished from the measured leaf.
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M
Organisms and groups · Class
Mammalia
Hair and mammary glands that nourish young characterize mammals. Hair can be inconspicuous, as in whales. Their skeletal features include three middle-ear bones. Living mammals include monotremes, marsupials and placentals, so live birth is not a feature of every representative. A platypus lays eggs while still feeding its offspring milk.
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Proteins
MCM2 · P49736
MCM2 is UniProt protein record P49736 for Homo sapiens (NCBI 9606). The retained sequence contains 904 amino acids.
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Organisms and groups · Species
Methanocaldococcus jannaschii
Methanocaldococcus jannaschii is an archaeon: it belongs to Archaea, a different domain of cellular life from Bacteria.
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Modules
Model organisms and genomes
Start with identification before comparing data. Find the organism, open a particular assembly and follow a molecular record. Species, sample, assembly and gene are different objects. Save a separate identifier for each and note anything the source does not provide.
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Organisms and groups · Species
Mus musculus
The house mouse, Mus musculus, is a rodent in the family Muridae.
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Organisms and groups · Species
Mycobacterium tuberculosis
Mycobacterium tuberculosis is the bacterium best known for causing tuberculosis, a disease that usually affects the lungs but can also involve other organs.
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O
Guides
Orthologues, paralogues and gene families
A name search helps locate a record, but does not establish an evolutionary relationship. Homology means shared ancestry. Orthologues diverged through speciation; paralogues through gene duplication. Orthology can be one-to-one, one-to-many or many-to-many. Simply finding genes in different species is therefore insufficient to identify their relationship.
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P
Structure
Palisade mesophyll cell
Palisade mesophyll cells belong to a leaf’s internal photosynthetic tissue. In a typical eudicot leaf they are relatively closely packed beneath the upper epidermis and contain chloroplasts. Nearby spongy mesophyll is more loosely arranged, with air spaces supporting gas exchange. Cell, tissue and organ remain distinct structural levels.
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Organisms and groups · Species
Panthera leo
The lion is a large social cat. Its groups, called prides, defend territories and share the care of young.
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Processes
Photosynthesis
Photosynthesis couples energy capture with synthesis of organic compounds. In oxygenic photosynthesis, light-driven electron transfer uses water and releases oxygen; ATP and NADPH support carbon fixation. The carbon of new organic compounds comes from carbon dioxide. These are connected reactions rather than an instant conversion of light into a sugar molecule.
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Complexes
Photosystem II
Photosystem II is a membrane protein complex that starts electron transfer from water in oxygenic photosynthesis. Antenna pigments collect light energy and pass excitation to a reaction centre. Water oxidation supplies electrons and releases oxygen. Transfer onward to plastoquinone connects the complex to the rest of the pathway.
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Organisms and groups · Species
Physcomitrium patens
Physcomitrium patens is a moss whose older name, Physcomitrella patens, remains common in research titles.
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Organisms and groups · Species
Picea abies
Norway spruce, Picea abies, is an evergreen conifer in the pine family, Pinaceae.
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Organisms and groups · Species
Picea glauca
White spruce, widely known as Picea glauca, is a North American conifer in the pine family, Pinaceae.
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Courses
Plant development: from observation to a gene
How do you turn a growing plant into a question that can be tested? Start with Arabidopsis, examine a leaf at several levels of organization and follow an example of flowering regulation involving FLC. You will build a small investigation: an object, an image or record, a question and a source.
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Organisms and groups · Kingdom
Plantae
Mosses, ferns, conifers and flowering plants illustrate the diversity of land plants. Their life cycles alternate between a spore-producing generation, the sporophyte, and a gamete-producing generation, the gametophyte. The developing embryo receives protection and nourishment from the maternal gametophyte. The size and prominence of these generations differ among groups.
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Organisms and groups · Species
Plasmodium falciparum
Plasmodium falciparum is an apicomplexan parasite that causes malaria in humans.
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Organisms and groups · Order
Primates
Primates include lemurs, tarsiers, monkeys, apes and humans. Grasping adaptations and visual perception of space characterize the group: overlapping visual fields help assess depth. Hand and foot structure, posture and locomotion vary; a human foot is not organized like the grasping foot of a tree-dwelling primate.
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Organisms and groups · Species
Pseudomonas aeruginosa
Pseudomonas aeruginosa is a bacterium found in environmental settings, including soil, water and wet surfaces, as well as in association with plants and animals.
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R
Guides
Reading protein structures and assessing predictions
Before rotating a model, identify what it represents. An experimental structure is based on measurements; a computed model predicts atomic positions. For the former, check the experimental method and its relevant quality measures. For the latter, check the modelling method and confidence estimates. RCSB presents these categories separately. An attractive three-dimensional view…
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S
Organisms and groups · Species
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a single-celled fungus best known as baker’s and brewer’s yeast.
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Organisms and groups · Species
Schizosaccharomyces pombe
Schizosaccharomyces pombe is an ascomycete fungus known as fission yeast.
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Organisms and groups · No rank
Severe acute respiratory syndrome coronavirus 2
SARS-CoV-2 is the virus that causes COVID-19, a disease that can range from an infection without symptoms to serious illness.
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Structure
Spruce needles
A spruce needle is a leaf. Its narrow form changes how the organ presents a surface to light and air. Conifer needles illustrate a leaf form with reduced exposed surface and sunken stomata, features that help limit water loss. The needle dimensions below belong to Picea abies rather than every conifer.
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Organisms and groups · Species
Trypanosoma brucei
Trypanosoma brucei is a eukaryotic parasite classified among the kinetoplastids.
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Learning journeys
Two spruces, many kinds of evidence: from a cone to a genome
Norway spruce is Picea abies in the Oregon State University reference, whereas the US Forest Service white-spruce review treats Picea glauca. These are the two subjects of this comparison.
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W
Guides
What a GBIF occurrence map shows
A GBIF occurrence map displays published records of organisms, such as specimens and field observations. A point tells you that a source reported an organism at a place and time; it does not count every individual there. First check which taxon, place, dates and record types the query includes.
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Learning journeys
Which tree answers your question?
First read the legend, not the silhouette. A branching shape is a way of arranging information; it does not specify whether the information is classification, ancestry, similarity or a set of body parts.
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Guides
Why study plant development with Arabidopsis?
*Arabidopsis thaliana* connects observable plant development with genes and their activity. A model organism's value also comes from accumulated data and the ability to compare studies. The genome publication in 2000 provided a major foundation for investigating gene functions. Its numbers describe that historical assembly and annotation, not automatically the latest…
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Organisms and groups · Species
Wollemia nobilis
Wollemia nobilis, the Wollemi pine, is a conifer of the Araucariaceae family that came to scientific attention in 1994.
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