Bioinformatics: BLAST, GenBank, and CLUSTALW2

• Computational tools utilized to manage and analyze biological data is considered bioinformatics.
• Bioinformatics is helpful when studying DNA sequences, gene function, protein structures, and evolutionary relationships.
• Bioinformatics is used across drug discovery, disease research, & biotechnology.

BLAST

• BLAST stands for basic local alignment search tool.
• An unknown DNA or protein sequence is compared against a database of known sequences using BLAST.
• BLAST can identify similar sequences & determine evolutionary relationships.
• BLAST is used to identify bacterial species from patient samples.

GenBank

• GenBank is a public database that stores genetic sequences including DNA, RNA, and protein sequences.
• Scientists worldwide use GenBank to share and retrieve genetic data.

CLUSTALW2

• CLUSTALW2 is a multiple sequence alignment tool which aligns multiple DNA or protein sequences to find conserved regions.
• CLUSTALW2 helps construct phylogenetic trees to show evolutionary relationships.

Bacterial Identification Using BLAST

• First, bacterial DNA is isolated from a sample, and then amplified via polymerase chain reaction (PCR).
• The DNA is sequenced then compared using BLAST to identify species.
• A phylogenetic tree is constructed using CLUSTALW2 to compare evolutionary relationships.

The Scientific Method

• The scientific method involves: making observations, asking questions, developing a hypothesis, designing an experiment, collecting and analyzing data, drawing conclusions, and communicating findings.
• To start, make observations and identifying a phenomenon of interest.
• Next formulate questions like "Why does this happen?"
• Then develop a hypothesis, which is a testable statement predicting an outcome.
• An experiment is designed to test the hypothesis in a controlled manner.
• Data is collected and analyzed using tools such as statistics to interpret results.
• Conclusions are drawn to support or reject the hypothesis.
• Findings are communicated by publishing or sharing results with the scientific community.

Phenotypic Plasticity

• An organism's ability to change its physical traits in response to the environment is phenotypic plasticity.
• Oak leaves changing their size, shape, and structure depending on sunlight exposure is an example of phenotypic plasticity.

Lab Techniques

• ImageJ Software measures leaf area and shape from digital images whereas Microsoft Excel creates graphs and analyzes statistical data.

Microscopy

• Light microscopy uses visible light to magnify specimens, includes compound and stereomicroscopes, but has limitations in resolution compared to electron microscopes.
• Electron microscopy uses electron beams instead of light and includes transmission electron microscopes (TEM) for high-resolution internal images and scanning electron microscopes (SEM) which scans the surface to create a 3D image.
• Electron microscopy offers higher resolution and the ability to see cell structures in detail.

Microscopy Concepts

• Magnification = Ocular lens × Objective lens, for example 10x eyepiece × 40× objective = 400x total magnification.
• Resolution is the ability to distinguish two close points as separate.
• The field of view is the visible area when looking through the microscope, decreasing as magnification increases.

Protist Diversity

• Protists are eukaryotic organisms unlike animals, plants, or fungi.
• Protists include Excavata, which includes Euglena that can photosynthesize and move using flagella, Chromalveolata which includes paramecia and diatoms, and Unikonta which includes amoebas, that move using pseudopodia.

Bilaterian Symmetry

• Bilateria refers to animals with a bilateral body plan, meaning they have left and right sides, dorsal (back) and ventral (front) surfaces, and anterior (head) and posterior (tail) ends.
• Bilaterian symmetry is associated with cephalization, the concentration of nerve tissue in the head.

Types of Body Cavities

• Acoelomates have no body cavity (e.g., flatworms).
• Pseudocoelomates have a body cavity partially lined with mesoderm (e.g., roundworms).
• Coelomates have a fully lined body cavity (e.g., annelids, mollusks, vertebrates).

Developmental Modes

• Protostomes develop a mouth first (e.g., mollusks, annelids, arthropods).
• Deuterostomes develop an anus first (e.g., echinoderms, chordates).

Major Animal Phyla

• Mollusca (clams, mussels, oysters) have a three-part body: muscular foot, visceral mass, mantle and an open circulatory system, using gills for respiration and filter-feeding.
• Annelida (earthworms, segmented worms) have a segmented body (metamerism) for flexibility and mobility, a closed circulatory system, and hermaphroditic reproduction requiring cross-fertilization.
• Arthropoda (crayfish, lobsters, insects, spiders) have an exoskeleton made of chitin, jointed appendages for movement, and an open circulatory system.
• Echinodermata (sea stars, sea urchins) have radial symmetry in adults, bilateral symmetry in larvae, a water vascular system for movement, and regeneration abilities.

Evolution of Land Plants

• Land plants evolved from algae (Chlorophyta & Charophyta).
• Plant adaptations for land include a cuticle (waxy layer to prevent water loss); spores with thick walls for protection; seeds to protect embryos; and UV-protective pigments.

Non-Vascular Plants (Bryophytes)

• These mosses are small in size due to lack of vascular tissue, they must live in moist environments for reproduction, and have a dominant gametophyte stage.
• Mosses (bryophyta) have rhizoids for root-like structures and spores in the sporangium via meiosis.
• Sphagnum moss absorbs up to 20x its weight in water.

Seedless Vascular Plants (Pterophytes – Ferns & Horsetails)

• Vascular tissue (xylem & phloem) allows for larger size with a dominant sporophyte stage and independent gametophyte, still requiring water for fertilization.
• Ferns are homosporous producing spores in bisexual gametophytes.

Vascular Seed Plants

• Gymnosperms ("Naked Seed" Plants – Conifers, Cycads, Ginkgo, Gnetophytes) are plants with a dominant sporophyte stage, seeds exposed on cones, and pollen carried by wind for fertilization, such as pine trees.
• Angiosperms are flowering plants with a dominant sporophyte stage as well as seeds enclosed in fruit which develops from the ovary via pollination by wind, water, or animals.
• Monocots (one cotyledon, parallel leaf veins) and eudicots (two cotyledons, branching leaf veins) are two groups of angiosperms.
• The seed structure includes a hypocotyl that becomes a lower stem, an epicotyl that becomes an upper stem & leaves, and a radicle which becomes the root.
• Coleoptile protects the young shoot in monocots.

Fungi

• Fungi are heterotrophic decomposers and have cell walls containing chitin, not cellulose.
• Fungi reproduce via spores (asexually or sexually) and their body structures include hyphae (filaments) and mycelium, a mass of hyphae which absorbs nutrients.
• Yeasts are unicellular fungi reproducing by budding, and basidiocarp is the reproductive structure of a mushroom.
• Lichens (symbiosis) are fungus + algae/cyanobacteria where the mycobiont (fungus) provides structure & water while the phycobiont provides food (photosynthesis).
• Lichens are indicators of air pollution because they are sensitive to toxins.