Assignment G - Hypotheses: Comment & Insight

Chagas disease, known as a neglected tropical disease by the World Health Organization (WHO), is caused by the parasite Trypanosoma cruzi, and is most commonly transmitted to humans via triatomine bugs. Before 2025, much of the research looking at occurrences of triatomine bugs for vector surveillance was focused on American triatomine bugs, usually found in the Americas. However, in 2025, Ceccarelli et al. published a comprehensive review study focused on occurrences of non-American triatomine bugs, usually found in Oceania and Asia. Their research included survey data from 1926 to 2022, with 95.3% of all occurrences on non-American triatomine bugs being collected in the past 10 years. This is important research because it provides a comprehensive dataset for surveillance tracking and prevention efforts on a global scale.

One of the main difficulties with disease prevention efforts is that insects are not stationary creatures. The bugs can become unintentional hitchhikers, hitching rides across borders on trains, cars, or hikers. As global trade continues, the distribution of American triatomine and non-American triatomine bugs will continue to shift. Chagas disease is a widespread condition that has immense impact on human health and is not limited to isolated areas. Understanding this complexity is vitally important to the prevention and elimination efforts by the WHO.

While only 34 countries have recorded occurrences of triatomine bugs, 44 countries have seen cases of the disease. This discrepancy in disease vectors and cases highlights the importance of continuous vector surveillance efforts. Continuous funding for additional surveys are necessary to identify local population changes and ensure no vector hotspots are missed. Cross-collaboration with other countries is necessary to identify global population changes and facilitate disease prevention efforts on a global scale.

Final Exam Review

Lecture 1: Origins

• Life likely began in water, then evolved/diversified to move onto land ...
  • when did the very 1st, most primitive life - cells - arise on Earth?
  • Likely what type of cells were they: prokaryotic v. eukaryotic ... extremophiles or not?
• In what type of cells did photosynthesis arise?
• Coal deposits in rock, are from the remains of what?
  • Fossil fuels are evidence of what type of event.
  • How many mass extinctions occurred in Earth history?
  • How do we know that?
• How does oxygen in the atmosphere affect organisms body size (insects, plants)?
  • How do can we correlate the two - what evidence?

Lecture 2: Phylogeny

• Organisms: For organisms, what is extinct vs. extant?
• What are the three domains of life, what is LUCA?
• Phylogeny: lineages split when a new synapomorphy arises.
  • What is a synapomorphy? What is a node, internal vs. terminal?
  • What is a clade, sister species, outgroup, the root?
• Which of the three types of groups above is useful to classify organisms:
  • Monophyletic group
  • Polyphyletic group
  • Paraphyletic group
• What is the difference between homology and analogous traits?
  • If two different animal species have similar traits, what are the two ways that may have occurred?
• What are some types of data we use to construct Phylogeny (skim original lecture 2, slides 21-27, titles!

Lecture 3: Prokaryotes

• What are SIX the kingdoms of life?
  • Which PROKARYOTIC kingdom is most closely related to us?
• Name characteristic differences between prokaryotes and eukaryote cells.
  • What are plasmids?
  • Why are they important?
• The horizontal lines crisscrossing the phylogenetic tree between the three domains of life?
  • What two processes could cause this?
  • Know the endosymbiont theory, transformation, transduction, conjugation?
• What is carbon (or nitrogen) 'fixation'?
• what does 'fixing' an element mean?
  • What type of Prokarote fixes carbon (via photosynthesis)?
• What is an 'extremophile' what does that mean and which Prokaryotes are this?
  • What is a pathogen and which Prokaryotes are sometimes that?
• How do Prokaryote cells move? Contrast with how Eukaryotic cells move.

Lecture 4: Eukaryotes

• The "MICROBIAL EUKARYOTES" (formerly Protists) are mixed-bag of traits. Some traits are similar to those seen in prokaryotes, many are new traits arising in more complex cells, and seen in 'higher' (multicellular) organisms!
• Know these organisms:
  • Dinoflagellates vs. Diatoms,
  • Plasmodium vs. Paramecium,
  • Rhizaria,
  • N.fowleri,
  • Trypanosomes,
  • Euglena,
  • True Amoebas:
  • For each organism, know the interesting, unique traits or behaviors, how it interacts/lives its niche.
  • Notice that Amoebas are this 1st with new/different *motility, actin-based pseudopods and phagocytosis.
• Compare and contrast Actin vs Tubulin-based cytoskeletal structures in cells.

Lecture 5: Viruses

• What types of cells can be infected by viruses?
  • All cells can be infected by viruses.
• What are the differences in viral coatings, how does that affect infection biology?
• Why is it difficult to create a viral phylogenetic tree?
  • Because there's so much genetic variation due to how fast they replicate and mutate.
• Why may one vaccination not perfectly protect against different strains of a virus:
  • why do we need boosters,
  • ex: why do we need a new flu vaccine every year?
• Name some viruses that affect human health, animal health, plant health? Know the biology the THREE we studied, that can be sexually transmitted.
• What are some enzymes encoded in virus genomes that are virus-special: NOT FOUND IN REGULAR CELLS?
  • What is RT,
  • what is RdRp?
• Influenza: What influenza (ABCD) causes most season flu (and global pandemics) -
  • what are its hosts?
  • How many strands of RNA make up its genome?
  • How is diversity generated in these viruses - how do new strains get new combinations of H and N genes.
  • What do H and N stand for?
  • What does the H protein do?
  • what does the N protein do?
• What are bacteriophages (phage)?
  • What do they infect?
  • why could they be better than pharmaceuticals to fight animal/plant infections?
• What type of virus is HIV and why are these types of viruses so difficult to rid from the cell/body?

Lecture 6: Photosynthesis

• When did photosynthesis first evolve and in what type of cells?
  • Photosynthesis first evolved in cyanobacteria, bacterial cells, and then got engulfed into red algae as early chloroplasts.
• Which major groups of animals photosynthesize, which do not?
  • bacteria/eubacteria (ex: cyanobacteria)
  • archaebacteria (none)
  • microbial eukaryotes (euglena, diatoms, dinoflagellates, volvox)
  • fungi (none, but lichen symbioses exist +algae or cyanobacteria)
  • note: algae are photosynthetic microbial eukaryotes
  • plants (yes)
  • animals (none, but coral symbioses exist +dinoflagellates)
  • note: the dinoflagellates are zooxanthellae, did not study
  • note: sea slugs & some salamanders eat/harbor chloroplasts
• Photosynthesis:
  • What is the energy input?
  • Final products?
  • Anabolic or catabolic?
  • Where within the chloroplast does photophosphorylation happen?
  • What is the energy-carrier name that shuttles electrons?
• Cellular Respiration?
  • What is the energy input?
  • Final products?
  • Catabolic or anabolic?
  • Where within the mitochondria does oxidative phosphorylation happen?
  • What is the energy-carrier name that shuttles electrons?
• What are the two phases of photosynthesis called?
  • Where in the chloroplast do they take place?
  • How are the two phases connected (what two molecules)?
  • Which phase creates oxygen?
  • Which phase creates sugar?
• What molecules absorb light to release an electron into the 'electron transport chain?
  • What molecule splits to give up an electron to regenerate the pigment back to its normal function?
• What type of energy gradient is harnessed to create ATP, in chloroplasts?
  • In mitochondria?
  • What are the reactions called that transfer electrons between members, to create the energy gradient

Lecture 7: Plants

• What is the unique hallmark of each group of Aquatic Plants that distinguishes them from each other:
  • Glaucophytes (outgroup)
  • Red Algae
  • Green Plants
• Remember photosynthesis requires absorption of certain wavelength of light that correspond to different energies of light.
  • If red is a long-wavelength, low-energy color, why are Red Algae are found in deeper water?
• What is the basic building block of starch?
  • Where are starch granules stored in the plant cell?
  • What is the difference between amylose and pectin?

...LAND plants ...

• What adaptations were required by plants to migrate onto land, survive in non-aquatic habitats: wet/moist vs. fully dry land?
• In what tissues are sugars made?
• Compare and contrast: non-vascular (=avascular) vs. vascular plants, regarding which type has each trait:
  • cell walls,
  • stomata (what 3 things move in/out), cuticle
  • cellulose, lignin
  • rhizoids vs. true roots
  • rhizomes vs. stolons
  • hydroid/leptoid vs. xylem/phloem
  • xylem/phloem do what; dead v. live, passive v. active transport
  • transpiration:
    • occurs in which plants?
    • what energy drives it?
    • what is the positive-pressure?
    • what is the negative pressure?
    • which way does water move through a plant?
  • mycorrhizae: associates with which plants? to what advantage?
    • Associate with plant roots to increase surface area for absorption and share nutrients.
• Mosses vs. Ferns (snapshot in evolution) how transport water, how anchored, haploid vs. diploid greenery, how do they reproduce/spread?
• Gymnosperms vs. Angiosperms reproduction:
  • structures cones v. flowers,
  • fruiting or not,
  • what drives pollination,
  • how does each avoid self-pollination,
  • seed dispersal mechanisms.

Lecture 8: Fungi

• What does saprophyte or saprophytic mean?
  • On what organisms can fungi thrive: live, dead, or both?
• Most fungi are multicellular. Name two single-celled fungi: one we eat and one that makes us sick.
• What makes the cell walls of fungal cells different from plant cell walls?
  • What is cellulose v. chitin, starch v. glycogen?
  • What are the building blocks?
  • What is ergosterol, where is it found, what does it do, what animal molecule is v. similar to it?
  • Name at one cellular trait shared by fungal & animal cells that makes them closely related (vs. plants), hints: autotrophic vs. heterotrophic, structural sugars/proteins, energy storage.
• What are mycelia? What is the biological purpose of hyphae (there are at least three, know at least one)?
  • Describe the two different types of hyphae structure based on how the cells are organized.
  • What are haustoria; why are they different than hyphae?
• Note: most mycelial hyphae are usually haploid, only transiently do they mate/fuse to be diploid.
  • Are spores haploid or diploid?
  • what is karyogamy?
  • what does 'dikaryon' vs. diploid mean?
• Name a distinguishing trait and an example organism of each group:
  • Microsporidia
  • Basidiomycetes
  • Ascomycetes
  • Zygomycetes
  • Glomeromycetes
  • Chytrids.
  • Which are the mycorrhizae in assoc. with plant roots?
  • which group include amphibian pathogens vs. human pathogens, vs. insect pathogens?
  • which group makes medicine vs which make hallucinogens?
  • which include edible versions?
  • which includes baker/brewer yeast?
• Why are fungi critical to the carbon cycle?
  • What do they breakdown, what do they produce/create?
  • What would happen to global carbon sources without fungi?

Lecture 9-10: Animals 1-2

• Of six kingdoms, which ONE harbors ALL multicellular organisms: Archaea, Eubacteria, Microbial Eukaryotes (Protista), Fungi, Plantae, Animalia.
• Animal cells have TIGHT JUNCTIONS, DESMOSOMES, GAP JUNCTIONS; know what each does and an example tissue/function for each.
• What is meant by monoblast, diploblast, triploblast?
  • Which group has symmetry that is: ill-defined vs. radial vs. bilateral?
  • Name an organism in each group.
• Name two cnidarian animals;
  • how many tissue layers;
  • what symmetry;
  • sessile or motile, or both,
  • name body forms
  • how do they hunt food - what cell type and what harpoon-like weapon do they possess,
  • what digestive organ do they use?
• What are corals;
  • what organism(s) are involved
  • what light-generating mechanisms do they have?
  • what is "bleaching?"
• Corals have beautiful pigments, but can also “glow”. It that glowing achieved through fluorescence or through bioluminescence?
  • What is the difference: Which “glowing” is luciferase enzyme-based, requiring a substrate and ATP energy?
  • Which “glowing” is via absorption of a high-energy uv light, and emission at a different (lower energy) wavelength (color)?
• Triploblastic animal early embryonic development: difference between protostomes, and deuterostomes?
• What are the three internal body plans for simple animals with bilateral symmetry?
• Be able to compare/contrast these groups:
  • Mollusks vs. Arthropods.
  • Among the Arthropods: Crustacea v. Hexapod v. Arachnid.
  • Traits: habitats/environments, circulatory systems, gas exchange, feeding structures, mantle, jointed appendages, exoskeletons, molting (ecdysis) or not, motility,
  • From what structures did wings evolve?
• What are HOX genes?
  • what do they encode?
  • where are they located/expressed?
  • How are they related to metamorphosis (complete v. incomplete). Give an example for each.
• Arthropods - of the Hexapods:
  • Odonata are dragon & damsel flies, aerial hunters with superb eyesight;
  • Coleoptera are beetles with hard thickened elytra outer wings;
  • Hemiptera include ‘kissing bugs’ with piercing/sucking mouthparts;
  • Hymenoptera are thin-waisted and often stinging bees, wasps, ants;
  • Diptera are two-winged insects like flies, mosquitoes;
  • Lepidoptera are butterflies & moths;
  • flightless ... Psocodea are lice;
  • flightless ... Siphonaptera are fleas.
  • Arachnids: scorpions, ticks, mites, spiders, harvestmen (one body segment, 2 eyes, no silk spinnerets, no venom)

Lecture 11: Animals 3

• What is special about primitive chordates (4 characteristics)?
  • a dorsal, hollow nerve cord evolves in later species: CNS
  • a flexible rodlike notochord evolves in later species: vertebrae
  • pharyngeal slits in later species evolve into gills, which later in evolution contribute to forming jaws and even later, ear bones
  • a post-anal tail, in later species evolves into useful posterior appendages, though later lost/vetigial in great apes.
• Fishes:
  • when did vertebrae arise,
  • jaws (from what previous structure did jaws arise),
  • true bones (how different from cartilage),
  • lobed fins (what difference from ray-fins);
  • swim bladder (later as primitive lung).
  • How did the Tiktaalik fossil illustrate evolution from water to land?
  • Head structure,
  • eye placement,
  • rib development,
  • jointed thick-boned appendages,
  • gas exchange.
• Why are amphibians seen as a transitional species?
  • What three ways do they exchange gas?
  • For what function are they all still dependent on aquatic habitats.
  • Note: almost all amphibians are freshwater inhabitants.
• From what vertebrates did birds evolve?
  • Are birds a separate group of animals, or are they associated with amphibians, reptiles, or mammals?
  • What about flighted dinosaurs (extinct) - what group?
  • What are the differences in types of wings in vertebrates?
  • What are the similarities?
  • What is analogous between them, what is homologous among them?
• Both reptiles and mammals have amniotic eggs. What is the importance of these eggs?
  • What are the similarities between internally and externally incubated anmiotic eggs?
  • Other adaptations for reptiles: thick external keratinized epidermis to resist dehydration, strong jaws and claws (also keratin-based).
• What differentiates the three groups of mammals?
  • Name each group … describe the specific hallmarks of each.
  • What do ALL mammals have in common?
  • How do we know what our human closest animal relatives are?
  • What are they?
  • On what data do we base our conclusions about humans related to other primates?

Lecture 12: Animals 4 - Energy

• What is the definition of a ‘heterotroph.’
  • Name three broad categories of food molecules.
  • Where is the energy physically found in a food molecule?
  • What does it mean to ‘burn’ food, what are the products created when burning energy, in animal bodies
• How is metabolic rate measured?
  • What does BMR stand for (the units).
  • Why do we say that mice need more food than elephants?
• What animals regulate internal body temperature, and which ones are conformers?
  • Which are homeotherms?
  • which are poikilotherms?
  • Name some. Reptiles - diverse!
    • Which are homeotherms, which poikilotherms?
• Exceptions: how might poikilotherms regulate body temperature? (lizards, bees ... other?).
  • When might homeotherms conform their body temperature? (ground hog, bears... other?)
• What is the TNZ?
  • Must it be the same temp range for all homeotherms?
  • Why does metabolic rate rise at environmental temps cooler than the TNZ and at temps hotter than the TNZ?
  • Do poikilotherms show this type of metabolism?
• What is the difference between brown fat and white fat in mammals?
  • What is shivering thermogenesis, and in what tissue?
  • What is non-shivering thermogenesis and in what tissue?
  • Which type of thermogenesis is ATP-dependent (burns ATP) and which one is not (directly creates heat)?
• In arctic animals – why are arteries and veins close together and not far apart?
  • What is the advantage of closely juxtaposed arteries & veins, and countercurrent flow?
  • What are some other temp control systems in animals?

Lecture 13: Gas Exchange - Ventilation

• Name four tissues/interfaces where gas diffusion (exchange) can occur in animals -
  • are these liquid-liquid or liquid-air interfaces?
  • What gases are diffusing in/out of animals, and in which direction?
  • What determines if a gas will move across a membrane (concentration; diffusion follows chemical/physical laws).
  • What are some ways to maximize gas exchange in animals? Surface area, thin barrier, counter-current, etc...
• Why do animals perform gas exchange? Insects, amphibia, fish, reptiles, mammals.
  • What is the oxygen needed for; where does the carbon dioxide come from.
  • Are these gases ionic, polar, or not?
• Where are gases found in blood: liquid plasma or inside rbcs?
  • What does RBC stand for?
  • Hb protein carries both oxygen and carbon dioxide through vertebrate bodies, and where is Hb found: in the cells or in the plasma?
  • What does Hb stand for?
  • What are two ways birds adapt to high altitudes, and how do humans adapt?
• How do terrestrial insects breath?
  • Why is it important that fish gills have folds called lamellae?
  • What two motions pushes water through a fish, to get fresh gas exchange?
• What is “countercurrent” and how does is help with gas exchange (hint: oxygen concentrations)?
  • Can countercurrent happen in liquid (water) or gas (air) interfaces?
• Why are amphibians a snapshot in evolution regarding gas exchange?
• How do lungs maintain elasticity and structure – not collapse, what substance helps?
  • How do mucus and cilia function in the lung – what is critical for cilia to do their job?
• What is ‘tidal’ respiration of many amphibians, reptiles (not all) and mammals?
  • How is that different than Unidirectional airflow?
  • Which land organisms have unidirectional ventilation and how is that helpful?
  • How are bird lungs different than human lungs?
  • What is more efficient: tidal or unidirectional ventilation?

Lecture 14: Circulation - Blood Flow

• When did lungs arise;
  • which animals that have rudimentary lungs.?
• What protein carries oxygen in your blood?
  • What metal ion is required to carry oxygen?
  • How many proteins make a single hemoglobin molecule;
  • how many oxygen molecules (O2) are bound?
  • Where are O2 and CO2 found in the blood; how much in the plasma, how much carried in the RBCs; how much bound to Hb (see Module: pics/images).
• Why would the Red Blood Cell (rbc or RBC) evolve: what is the advantage of them, why do we need hemoglobin at all?
  • Which gases does Hemoglobin (Hb) bind & transport?
  • Carbonic anhydrase acidifies blood by using CO2 to generate H2CO3 (carbonic acid) which quickly converts to HCO3- (bicarbonate) and H+(protons)?
    • Where is this enzyme found in the blood: in rbcs or in plasma?
• Circulatory systems: what is 'open' and what is 'closed' circulatory systems?
  • What does “pulmonary” vs. "systemic" refer to?
  • Which animals have 1 vs. 2 'circuits'?
• Which animal groups have two chambered vs. three chambered vs. four chambered lungs?
  • At which evolutionary step does oxygenated blood stop mixed with the deoxygenated blood – when they are kept completely separate during circulation?
  • How are crocs and birds different than the other Reptiles?
• In 4-chambered hearts: which ventricle pumps blood to the lungs; which ventricle pumps blood out to the body?
  • Is blood flow unidirectional?
  • What is systole and diastole?
  • Why is high blood pressure bad, what causes it?
  • What is a heart attack, at the cellular/structural level?
  • Why might very low blood pressure bad?

Lecture 15: Behavior

• What are other names for "fixed action" behaviors?
  • Give an example.
  • Why are they tough to change?
  • What is "positive-associative learning" and what are some other common names for it?
• What is the difference between POSITIVE-associative and NEGATIVE-associative learning?
  • Give an examples of each.
• What is the difference between evolution and natural selection, which is the mechanism acting on individuals, and which is the overall, big picture phenomenon?
  • What is artificial selection?
• What is Epigenetics?
  • Is it reversible?
  • Is it caused by mutations?
  • What does it control?
  • Does it change over a lifetime?
  • What can influence it?
  • Does it refer to gene DNA sequence (wildtype vs. mutated) or to gene expression?
  • What is important for the phenotype or trait: gene DNA sequence, or gene expression?
• What is Biological Determinism (BD).
  • What are the assumptions of this idea.
  • What are the weaknesses of this idea (hint: think epigenetics).