Glossary of BIO 112 Study Guide 3

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What is systematics?
The branch of biology that studies the diversity of life
What does systematics encompass?
It encompasses taxonomy and helps reconstruct the phylogenetic history
What is taxonomy?
The study of naming and classifying the diverse forms of life
What is phylogeny?
The evolutionary history of a species or group of related species
What are the three steps to classification?
1. Name each level.
2. Describe in detail each category.
3. Eliminate characteristics that are least alike.
What is a problem that arises when classifying?
Opinions differ among taxonomists, i.e. where some protists would best fit is debatable
What should each subsequent division in the hierarchy of classification represent?
A closer phylogenetic history
When does classifying become most difficult?
It increases towards classifying the last two organisms
What does the hierarchy of classification reflect?
The degree of relatedness
What are the seven worldwide recognized levels of the hierarchy of classification?
Kingdom, Phylum, Class, Order, Family, Genus, Species
What are the three prefixes signifying more refined classification within the hierarchy of classification?
sub-, supra-, infra-
Which scientist created the binomial nomenclature and hierarchy of classification? When?
Carlus Linneaus in the 1700s
What is binomial nomenclature?
It is the two-part Latin name of a species
What does the name of a species include?
It includes the genus and specific epithet
What is the proper format utilized when indicating a species?
Genus is upper-case, specific epithet is lower-case, and whole species name is underlined or italicized
Why is binomial nomenclature such a gift to science?
It avoids cumbersome names, i.e. the European honeybee example (the lo~ong name versus the binomial nomenclature)
Why is Latin the language used in classification?
It is a dead language, thus it does not change
What is phenetics?
It is an approach to taxonomy that classifies organisms based on the similarities and differences in phenotypic characters; It does not consider evolution (homology, phylogeny, or analogy)
What is cladistics?
It is an approach to taxonomy that classifies organisms based on their position on the phylogenetic tree; It does not consider the degree of morphological divergence
What is a clade?
An evolutionary branch
What is an outgroup?
A species or group of species that is closely related to the group of species being studied
What is synapomorphy?
Similarity is based on derived characteristics (homologies), such as characteristics that evolved in a common ancestor on that fork of the tree, but not common to all species found on that branch
What is a dichotomous key?
It is a species key that compares two forms of a feature
How does a dichotomous key work?
After each conclusion of a feature, it progresses to another pair of features
What is a dichotomous key used for?
It is used to distinguish between closely related species, i.e. the frog handout
What percentage of viruses causes cancer?
Besides cancer, what other illnesses do viruses cause?
Flus (such as the Spanish flu that caused 22 million deaths in 1912) and autoimmune diseases (such as multiple sclerosis)
What does the outer coating of a virus consist of?
Depends on the type of virus; It may consist of lipids, proteins, or glycoproteins
What type of nucleic acid does a virus have?
Depends on the type of virus; It may have RNA or DNA strand(s)
List an example of a virus with double-stranded DNA and its symptoms.
Papovavirus causes papilloma (human warts and cervical cancer) and polyoma (tumors in certain animals);
Adenovirus causes respiratory diseases and tumors in certain animals;
Herpesvirus causes herpes simplex I (cold sores), herpes simplex II (genital sores), varicella zoster (chicken pox and shingles), and Epstein-Barr virus (mononucleosis and Burkett's lymphoma);
Poxvirus causes smallpox, vaccinia, and cowpox
List an example of a virus with single-stranded DNA and its symptoms.
Parvovirus causes roseola, though most parvoviruses depend on co-infection with adenoviruses for growth
List an example of a virus with double-stranded RNA and its symptoms.
Reovirus causes diarrhea and mild respiratory diseases
List an example of a virus with single-stranded RNA that serves as mRNA and its symptoms.
Picornavirus causes poliovirus, rhinovirus (common cold), and enteric (intestinal) viruses;
Togavirus causes rubella virus, yellow fever virus, and encephalitis virus
List an example of a virus with single-stranded RNA used as a template for mRNA and its symptoms.
Rhabdovirus causes rabies;
Paramyxovirus causes measles and mumps;
Orthomyxovirus causes influenza
List an example of a virus with single-stranded RNA used as a template for DNA synthesis and its symptoms.
Retrovirus causes RNA tumor viruses (i.e. leukemia viruses), and HIV (AIDS virus)
Which scientist removed sap from a diseased plant and sprayed a healthy plant with it? When?
A. Mayer in 1883
When the healthy plant that was sprayed with diseased plant sap became sick, what did A. Mayer conclude?
Something in the sap caused the disease; bacteria was the suspected culprit
Which scientist filtered diseased sap then sprayed a healthy plant with it? When?
D. Ivanowsky in the late 1880s
When the healthy plant that was sprayed with filtered diseased plant sap became sick, what did D. Ivanowsky conclude?
Bacterial toxin passed through the filter to cause the disease
Which scientist filtered the diseased sap, sprayed the healthy plant, continued the process with ten plants down the line, and tried to culture the disease in a petri dish? When?
M. Beijerinck in 1897
When the disease could not be cultured in a petri dish, what did M. Beijerinck conclude?
The disease-causing organism was reproducing within the plant
In the virus researches, which plant and disease were used?
Tobacco plant; tobacco mosaic disease
Which scientist precipitated crystals out of a pathogenic solution and then used them to infect the host plant? When?
W. Stanley in 1935
When the precipitated crystals infected the plant, what did W. Stanley conclude?
The pathogen acts like a chemical, not a living organism
What is the lytic (virulent) cycle?
A viral mode of reproduction in which the virus uses host machinery (mRNA, DNA, etc) to replicate its components
What is the lysogenic (temperate) cycle?
A viral mode of reproduction in which the virus injects its DNA or RNA directly into the host genome
What are the four steps of the lytic (virulent) cycle?
1. DNA/RNA is uncoated as it enters the host cell.
2. DNA/RNA is replicated using host nucleotides.
3. Protein capsid is replicated using host ribosomes.
4. Virus re-assembles and exits cell en masse.
What are the four steps of the lysogenic (temperate)cycle?
1. Phage DNA is integrated into host genome.
2. Host copies viral DNA when it copies its own.
3. Viral DNA is passed on to host cell during host cell replication.
4. Replication. (In bacteria the replication is exponential.)
What are bacteriophages?
"Bacteria eaters" are viruses that infect bacteria
What reproduction cycle do phages use?
Phages can use either cycle, but T-phages specifically use the lytic cycle
Which scientist based his experiment on the observation that milkmaids exposed to cow pox were resistant to small pox? When?
E. Jenner in the late 1800s
When the farm boy who was pricked with a needle covered in cowpox pus was resistant to small pox, what did the scientist conclude?
A harmless derivative of pathogenic microbes can be used to stimulate the immune system (vaccinations)
What are prions?
Infectious misfolded form of a protein normally present in brain cells
Which scientist came up with the prion hypothesis?
Stanley Prusiner
What is the prion hypothesis?
When prions get into a cell they convert the normal protein form to the prion version
What kind of sicknesses do prions cause?
Degenerative brain diseases such as scrapie, bovine encephalitis "mad cow disease", Creutzfeldt-Jakob disease, and chronic wasting disease, all of which can cross between species
Which kingdom and domains do prokaryotes fall into?
Kingdom: Monera
Domains: Bacteria and Archaea
What are some characteristics of prokaryotes?
They're widespread (cosmopolitan), abundant, tiny (about 1 micron in diameter), can be disease-causing or benevolent, and they have no nucleus or other membrane-bound organelles
What are proteobacteria?
A large and diverse clade of gram-negative bacteria including aerobic and anaerobic species, autotrophs, heterotrophs, and chemoautotrophs. There are five subgroups.
What are alpha proteobacteria?
Many species of this group are closely associated with eukaryotic hosts, as either mutual symbionts or parasites.
Examples of this group: Rhizobium, which converts atmospheric nitrogen into useable form in nodules;
Agrobacterium, which causes plant tumors used by crop engineers;
Rickettsias, responsible for Rocky Mountain spotted fever
What are beta proteobacteria?
This subgroup contains Nitrosomonas, which converts ammonium to nitrite
What are gamma proteobacteria?
This subgroup contains:
Chromatium, a photosynthesizing sulfur bacteria;
Legionella, a heterotroph causing Legionnaire's disease;
Vibrio cholerae, a pathogen that causes cholera;
Salmonella, a microbe that causes food poisoning;
Escherichia coli, a species that lives in the intestine
What are epsilon proteobacteria?
This subgroup contains Helicobacter pylori, the bacteria responsible for some stomach ulcers
What are chlamydias?
This parasitic clade requires hosts. They are unusual in that their gram-negative cell walls do not contain peptidoglycan. One example is Chlamydia trachomatis, a common cause of blindness and the most common STD.
What are spirochetes?
These heterotrophs can be free-living or parasitic. They are too thin to be visible without a microscope. They use rotations of internal flagellum-like filaments to move in a corkscrew pattern. This group includes:
Treponema pallidum, which causes the STD syphilis;
Borrelia burgdorferi, the pathogen that causes Lyme disease
What are gram-positive bacteria?
A clade rivaling proteobacteria in diversity, it includes all gram-positive bacteria and some closely related gram-negative ones. Some subgroups include: Actinomyces, responsible for tuberculosis and leprosy; Streptomyces, a source of many antibiotics and streptomycin; Bacillus anthraccis, a pathogen that causes anthrax; Clostridum botulinum, which produces the toxin that is potentially fatal and is used in anti-wrinkle treatments
What are cyanobacteria?
These autotrophic blue-green algae are the only prokaryotes with plantlike, oxygenic photosynthesis. They are abundant wherever there is water and can be found solitary or in colonies in fresh and salt water.
What are methanogens, and where are they found?
Most of them are in the archaea domain and are anaerobic. They are actually poisoned by oxygen. These are usually found in swamps, marshes, and the guts.
What are some important functions of methanogens?
They digest cellulose and are decomposers in sewage treatment plants, converting garbage and dung into methane fuel.
What are halophiles, and where are they found?
They are "salt lovers," living in places such as the Great Salt Lake and the Dead Sea. While some tolerate salinity, others require an environment ten times saltier than seawater.
What is bacteriorhodopsin?
It is a photosynthetic pigment very similar to the visual pigments in the retinas of our eyes.
What are thermophiles and where are they found?
They are "heat lovers," thriving in hot environments, such as in Yellowstone Park. Optimal conditions for most of these archaea are 60-80 degrees C. They are typically sulfur-metabolizing organisms.
What are the six major components of bacteria's structure?
Outer lipopolysaccharide coat (some species have), cell wall of peptidoglycan, plasma membrane, circular DNA attached to the plasma membrane, plasmids (fragments of DNA), and ribosomes (site of protein synthesis)
What does cocci bacteria look like?
What does spirilli bacteria look like?
What does bacilli bacteria look like?
What does sarcina bacteria look like?
What does strepto bacteria look like?
What does staphylo bacteria look like?
Grape-like clusters
What are obligate aerobes?
Organisms that need oxygen
What are facultative organisms?
Prefers either oxygen or no oxygen, but can survive in either environment
What are obligate anaerobes?
Oxygen will kill the organism
What is the energy source and carbon source for photoautotrophs?
Light is the energy source and CO₂ is the carbon source
What is the energy source and carbon source for photoheterotrophs?
Light is the energy source and organic compounds are the carbon source
What is the energy source and carbon source for chemoautotrophs?
Inorganic compounds are the energy source and CO₂ is the carbon source
What is the energy source and carbon source for chemoheterotophs?
Organic compounds are both the energy source and carbon source
What are flagella?
They are rotating extensions providing forward movement
What are filaments?
They are extensions around the entire cell providing corkscrew-like movements
What is gliding?
It is a movement allowed by the slime secretions
What is taxis?
It is movement oriented towards or away from a stimulus
What are exotoxins?
They are protein secretions, producing symptoms without the organism being present
What are the symptoms of exotoxins?
They are species specific, such as botulism where 1 gram of toxin = 1 million deaths
What are endotoxins?
They are protein secretions, producing symptoms when the organism is present
What are the symptoms of endotoxins?
They are generally flu-like, such as that which salmonella causes
What is the goal of Koch's Postulate?
To establish that a specific pathogen is the cause of a disease
Describe the four step process of Koch's Postulate.
1. Find the same pathogen in each diseased individual.
2. Isolate the pathogen from diseased subject and grow in pure culture.
3. Induce disease in experimental animals.
4. Isolate the same pathogen from animal after disease develops.
What is binary fission?
Cell replication that produces clone organisms, a process that can be as quick as every 20 minutes
What is a colony?
Many individual cells are formed, often representing a single genome
List the four stages in a colony lifecycle.
1. Cells undergo binary fission.
2. Exponential growth occurs.
3. Colony reaches carrying capacity.
4. Decline in population size.
What is the goal of reproduction (at least with bacteria)?
To exchange genetic material
What is transformation?
The uptake of genes from the environment
What is conjugation?
The exchange of genes using pili (the extensions between cells)
What is transduction?
The transfer of genes via a virus; When the virus copies its own DNA, using either the lytic or lysogenic cycle, it also copies a tiny piece of bacteria DNA
What are the best methods of bacteria reproduction, as well as the cause of bacterial evolution?
Conjugation and transformation
What is an antibiotic?
A chemical that kills or limits the growth of bacteria
What is one way in which antibiotics work to destroy bacteria?
It inhibits the formation of the peptidoglycan cell wall (penicillin)
What is an endospore?
It is a thick, resistant coat surrounding bacterial chromosome when it is exposed to harsh conditions, such as the bacteria found in an 11,000 yr old Mastodon intestine that was alive and well due to the protective endospore
What are some characteristics of eukaryotes?
About 100 times the size of the prokaryotes, they have a nucleus as well as other membrane-bound organelles, and also have autosomal organelles (that have their own DNA)
What is a hypothesis for how autosomes came to be a part of other organisms?
Lynn Margulis' endosymbiosis hypothesis
How many clades are currently in the eukaryote domain?
Eleven, including fungi, animalia, planta, and eight protista
What is the difference between a spore and a gamete?
A gamete is a haploid cell that must fuse with another cell to produce a multicellular individual whereas a spore is a haploid cell that does not need to fuse with another cell to produce a multicellular individual
What is a sporophyte?
This is the multicellular diploid stage following the zygote resulting from fertilization and will lead to the creation of spores
What is a gametophyte?
This is the multicellular haploid stage that follows the spores resulting from meiosis and will lead to the creation of gametes
What is syngamy?
The union of two gametes aka conjugation or fertilization ("sny" = to come together; "gamy" = gametes)
What part of the reproductive cycle is haploid?
Meiosis occurs, resulting in haploid cells called spores. The spores develop into multicellular haploid cells called gametophytes. The gametophytes undergo mitosis to create gametes ready for fertilization.
What part of the reproductive cycle is diploid?
Fertilization occurs, resulting in a diploid cell called a zygote. The zygote develops into a diploid multicellular organism called a sporophyte. The sporophyte undergoes meiosis, leading to the haploid stages.
Which allows for more genetic variation: asexual or sexual?
Asexual has no genetic variation since it produces only clones, whereas sexual reproduction forces genetic variation
What is the baseline of eukaryote phylogeny?
Small ribosomal subunits (SSU-rRNA) unites all forms of life since there is no variation between species
What are some examples concerning autosomes that demonstrate eukaryote phylogeny?
Some transitions include alpha proteobacteria that have mitochondria and cyanobacteria that have plastids (organelles responsible for photosynthesis)
What modes of acquiring nutrition are protist known to use?
Photosynthesis, absorption, and ingestion of organic matter
What modes of transportation are protists known to use?
None (such as in endosymbiosis), flagella (one or many), pseudopodia, podia, or cilia
What modes of reproduction are protists known to use?
Asexual (no need to add genetic variation since the way of life works fine), sexual (environmental pressures causes a need for change), or both
What ways of life are protists known to live?
Free living, parasitic (one host or two may be needed), and symbiosis
This clade of protista lack mitochondria, have multiple flagella, and two nuclei.
This clade of protista lack mitochondria, have two flagella, and an undulating membrane.
This is a clade of protista which includes euglenoids and kinetoplastids.
They have two flagella rising from an anterior chamber, a contractile vacuole (to maintain water balance), an eyespot (light detector for phototaxis), paramylon (glucose polymer functioning as a storage molecule), protein bands (for support), and pyrenoi
What is strange about the euglenoids' feeding habits?
They are mixotrophic. Despite the pyrenoid, chloroplast, and paramylon, enabling them to feed autotrophically, they also eat their neighbors.
They are symbiotic, have one large mitochondrion, and a kinetoplast (which stores extra-nuclear DNA).
Why is the African sleeping sickness protist difficult to destroy?
Trypanosoma has an undulating membrane and is able to change its coat to counter the host's defenses
This clade of protista includes dinoflagellates, apicomplexans, and ciliates
They have two flagella in grooves with a spinning movement, cellulose support, are bioluminescent, and are reef mutualists.
What causes "red tide"?
The blooms of Pfiesteria piscicida are a hunt for fish
These critters have complex lifecycles (two hosts needed) and are parasites.
This group has cilia, for movement and feeding, and two types of nuclei: macronucleus (controls everyday functions) and a micronucleus (used for sexual reproduction).
This clade consists of oomycota, diatoms, chrysophyta, and phaeophyta.
Water molds, white rust, and downy mildew belong to this group.
Phytophthroa infestans, which caused the potato blight in 1845-1847, killing more than 400,000 people and instigating the mass immigration to Ellis Island is an example of this group
They have two halves, are made of hydrated silica in an organic matrix, and store food molecules as lipids (instead of carbohydrates) in the form of laminarin. The cliffs of Dover are an example of their skeletons.
It belongs to the stramenopila clade, has two flagella, xanthophyll (yellow pigment), carotene (orange pigment), and is mixotrophic. One example is Dinobryon, a freshwater colonial species.
They are multicellular, belong to the stramenopila clade, and are "coldwater" algae, thus would be found in the Pacific for example.
Phaeophyta (brown algae)
This clade consists of red algae, which has phycoerythrin ( a reddish accessory pigment).
The name of the clade means green algae.
This clade consists of myxogastrida, plasmodial slime molds, and dictyostelida, cellular slime molds.
Physarum is an example.
Plasmodial slime molds
Describe the myxogastrid lifecycle.
1. Syngamy- Two cells unite to form a zygote.
2. Mitosis- Repeated divisions without cytoplasmic division.
3. Feeding- The multinucleate plasmodium feeds on organic refuse.
4. Maturation- Taking a web-like form, it prepares to fruit.
5. Fruiting- Plasmodium erects stalked fruiting bodies called sporangia.
6. Meiosis- Meiosis occurs in mature sporangium, creating spores which disperse and germinate.
What are the two main differences of a dictyostelid lifecycle compared to a myxogastrid lifecycle?
At the feeding stage, it is a solitary cell. It also has a short diploid stage.
Currently considered protists they are also in the animalia kingdom as they are found in porifera (sponges). They line the internal chambers of the sponges, contracting to trap food as weter is filtered through. For this reason they are known as collar c
Describe fungi's motility.
They don't move around. After putting down hyphae, they stay there.
Fungi is typically multi-cellular. What is the exception?
Yeast and chitridomycota, which are unicellular
What are the cell walls of fungus composed of?
Chitin, same as that of insects
What type of feeders are fungi?
What are saprobes?
Absorption feeders
What kind of lifestyle do fungi have?
They can be symbiotic or free living
What effect does fungi have on humans?
They can be both beneficial or deleterious
What are the four main structures of fungi?
Hypha, mycelium, septa (or aseptate), and haustorium
What are hyphae?
Filamentous fungal cells
What is a mycelium?
A group of hyphae tightly packed together
What is a septa?
The plasma membrane between individual cells
What is septate fungus?
A fungus with septa
What does coenocytic mean?
It means aseptate (without a plasma membrane between individual cells)
What is the haustorium?
The nutrient-absorbing hyphal tip of parastic fungi
What is the heterokaryon?
This is fused mycelium of two genetically different nuclei
What is plasmogamy?
The fusion of the cytoplasm between fungi cells
What is karyogamy?
The fusion of two genetically different nuclei in fungi
What is dikaryotic?
The resulting hybrid heterokaryon mycelium, aka the heterokaryon stage
What are the five phyla (divisions) of fungi?
Chitridomycota, zygomycota, ascomycota (yeast fits here), basidiomycota, and deuteromycota
What habitat is chitridomycota found?
It needs a water habitat
Which fungi is considered the most primitive?
Which fungus is unicellular, coenocytic,has flagellated zoospores, and is in a monophyletic clade?
What habitat is zygomycota found?
It lives in a terrestial habitat
Which fungus has coenocytic hyphae (septate during reproduction) and resistant zygosporangium at the sexual stage
Which type of fungus is pilobilus (dung fungus)?
Which type of fungus is rhizopus (bread mold)?
What habitat is ascomycota found?
Marine, freshwater, and terrestial habitats
What type of fungus is Tuber melanosporum (truffles)?
What type of fungus is Morchella escuelenta (morel)?
What are conida?
Naked spores (basically means they're not in caps)
What type of fungus has conida?
Which type of fungus is known as the sac fungi?
Which type of fungus has its sexual spores borne internally in asci?
What does "gonium" mean?
Structure that houses
What does "rhiz" mean?
What type of fungi are known as club fungi?
What type of fungus are mushrooms, shelf fungi, puffballs, rusts, and smuts?
Fairy rings are made up of which type of fungus?
What are basidia?
Club-like structures that sexual spores cling to
In what type of habitat are basidiomycota found?
Terrestial habitat
In what type of habitat are deuteromycota found?
Any habitat
Which type of fungi includes all phyla, has no known sexual stage, and is known as imperfect fungi?
Why is deuteromycota known as imperfect fungi?
Because no one has seen the sexual stage of it
Which fungus is a mold that rapidly grows and reproduces asexually?
In what type of habitat is yeast found?
Moist habitats
How does yeast reproduce?
It reproduces asexually by pinching off of the plasma membrane, aka "budding"
What type of fungus is Sacchromyces cervisae (brewer's yeast)?
List three examples of fungi associations.
Lichen, mycorrhizae, and deleterious fungi
What is mycosis?
Fungal infection
Which fungus produces lysergic acid (LSD)?
Puccinia gramis (wheat rust) and Claviceps purpurea (ergots)
What are the three types of lichen?
Crustose ("crusty"), foliose ("leafy"), and fruiticose ("branchy")
What is lichen?
The symbiotic association of millions of autotrophs in a fungal mesh of hyphae
What types of autotrophs are usually found in lichen?
Cyanobacteria or chlorophytes
What types of fungi are usually found in lichen?
Basidiomycota or ascomycota
What benefit do the autotrophs in lichen bring?
sugars and energy from photosynthesis
What benefit do the fungi in lichen bring?
uptake of nutrients and water as well as providing protection
What is soredia?
Alga + fungi, which reproduce asexually
In what habitat are lichen found?
Mountains and tundra
Why are lichens called pioneers?
They are usually the first life to come to a devastated area, such as land scraped by a glacier retreat or volcano eruption
How do lichens give indication of their environment?
Slow growth and rock substrate
What is mycorrhizae?
"fungus root" is a beneficial fungus that decomposes and recycles nutrients
What percentage of plants have mycorrhizae?
How do plants benefit by mycorrhizae?
There is increased surface area and absorption for nutrients and water
What is the relationship of mycorrizae?
Mutualism between vascular plant roots + fungi (all phyla)
What are deleterious fungi?
Giardia lamblia, a sickness caused by drinking water contaminated, is this type of protist
An example of this group is Trichomonas vaginalis, an STD.
Some examples of this group are ulva, volvox, and spirogyra.
They are symbiont with fungi to form lichen.
This clade consists of chlorophytes and charophyceans.
It is found in warm waters and does not have flagella.
They are parasites or saprobes (decomposers that absorb dead organic matter) and can be found in freshwater, saltwater, and soil.
Examples of this group are paramecium and stentor.
What is the macronucleus in ciliates used for?
Everyday functions
What is the micronucleus in ciliates used for?
Sexual reproduction
One example of this group is Plasmodium vivax (NOT to be confused with the slime molds), which causes malaria, contains plastids, and adapts its protein coat to host's defenses.
This group includes phytoplankton and zooplankton.
One example of this group is Trypanosoma, which causes African sleeping sickness.
What is the function of the kinetoplast in kinetoplastids?
It stores extra-nuclear DNA
This clade consists of both photosynthetic and heterotrophic flagellates.
One example of this group is euglena.
What is the contractile vacuole used for?
To maintain water balance
What is the eyespot used for?
It is a light detector for phototaxis
What is a paramylon?
A glucose polymer functioning as a storage molecule
What are protein bands in euglenoids used for?
What is the pyrenoid in euglenoids used for?
Found in the chloroplast, it is used for food production.

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