viral titre =
the concentration of virions 

  dominant   sporophyte

    "Viruses are naturally responsive to a number of biological stimuli, including pH, redox, and proteases. The viruses undergo physiochemical changes when exposed to these endogenous stimuli that allow behavior such as more efficient cargo delivery, increased stability, or modified intracellular trafficking." from Stimulus-responsive viral vectors for controlled delivery   https://www.ncbi.nlm.nih.gov

   As of 2020, approx. 148,000 species of fungi, mostly terrestrial, have been identified but the global biodiversity of fungi is still a mystery. Over 1.5 million living animal species have been described including 1 million insects. Estimations suggest there are more than 7 million animal species in total. There are an estimated 320,000 plant species in the world. 

RNA virus

                                               evidence to support the endosymbiotic theory:
1. chloroplasts & mitochondria contain DNA that is unlike nuclear DNA but similar to plasmid DNA in bacteria
2. mitochondria & chloroplasts are surrounded by membranes similar to bacterial membranes
3. mitochondria & chloroplasts are produced via a process similar to binary fission (bacterial reproduction)
4. the structure/molecular chemistry of chloroplasts parallels cyanobacteria.

 evolutionary adaptation #2:
​              vascular tissue

   trypanosomiasis
 (sleeping sickness):
      trympanosum

1. virus first hypothesis: viruses evolved along side cells from basic polymers.
2. regression hypothesis: viruses evolved from free-living cells.
3. escapist/progressive hypothesis says that viruses originated from RNA/DNA molecules that escaped from a host cell.
Why aren't we sure?

Viruses leave no fossil record...

 Is a virus different than a virion?
​           I've heard both words...

   giardia

 evolutionary adaptation #3:
            pollen and seeds

birdsfoot
​ trefoil

viruses have different nucleic acids,
different shapes and sizes of their capsids, and they may or may not have 
a lipid envelope, obtained from its host cell, surrounding the capsid.

and what about bacteria and eukaryotic cells?

Our gut contains > 100 trillion symbiotic microbes

  When/how were viruses discovered?

the Omicron variant spreads more easily than the original SARS-CoV-2 virus and the Delta variant.

   malaria:
​plasmodium

 Antigenic drift = the accumulation of a series of genetic mutations
Antigenic shift = “mixing” of genes from influenza viruses from different species

Viruses like SARS-CoV-2 continuously evolve via genetic mutations during replication of the genome. 

           plant

   structure

Archaea are resistant antimicrobial agents. Why? It has to do with the composition of their cells walls...

 budding

strep

Mosses, the simplest of plants, evolved from a filamentous green algae (protist) over 500 million years ago. As a primitive moss
consumed atmospheric carbon, oxygen concentration in the atmosphere increased permitting the evolution of modern life.

ESBL
Extended Spectrum Beta-Lactamase is an enzyme made by some bacteria. The enzyme prevents certain antibiotics from being able to kill the bacteria. The bacteria then become resistant to the antibiotics.

   DNA analyses showed in 1998 that fungi and animals last common ancestor was 1.538 billion years ago while plants and fungi last common ancestor was 1.547 billion years ago proving that fungi split from animals 9 million years after plants did. Fungi are more closely related to animals than to plants.

 plant 

​tissue

 omicron variant = B.1.1.529  : delta variant =B.1.617.2
using Greek nomenclature (Omicron) avoids the stigma and xenophobia that occurs when a virus is named after the location where it was first discovered. The letter/numbers is the scientific classification for this variant. The first letter in the sequence identifies the virus’ root lineage or its closest-known “ancestor” virus in the wild. The first lineage B viruses were sampled on Dec. 24, 2019, in humans which resembled the A virus found in bats. Viruses descending from these lineages get categorized into A.1 or B.1. The category B.1 refers to a variant traced back to the covid-19 outbreak in northern Italy in early 2020. Variants have at least one key difference in nucleotides from its ancestor. As the sequence is extended, B.1.1 lineage, for instance, descends from its B.1 ancestor using the same rules. From there on it gets a bit more complicated, but ultimately the number/letter sequence permits scientists to identify the variant's ancestry and potential threat. 

  host cell/receptor specificity:
​ligand of virus and receptor of host must be compatible

   moss

next up...
modifications of
​flowers stems roots leaves

 and then there's pathogenic fungi...:(

   The Alternation of Generations  
  describes the life cycle of plants. A haploid      (1n) multicellular gametophyte alternates  with a diploid (2n) multicellular sporophyte. 

          How do viruses replicate?

50-85% death rate

and what about bacteria and viruses?
both can be pathogenic...but only one is alive

      vascular tissue

   Kingdom Fungi

         leaves

there are some multicellular protists. giant kelp is a species of brown algae that grows to be over 200 feet long! there are also seaweeds that are green and red algae.

amoeba invade the wall of the intestine causing ulcers, bleeding, and diarrhea

     evolutionary adaptation #4:
                flowers and fruit

   fern

         stems

 flowers assist plant reproduction. A flowers color, scent and shape facilitates pollination, seed growth and seed dispersal. 

RSV =

Currently, the dominant variant nationwide is BQ.1.1, with 34% of cases, followed by XBB.1.5, with 28% of cases. the original omicron variant is no longer dominant. subvariants of omicron are circulating, including BQ.1.1, XBB.1.5, and BQ.1."

and pathogenic...

lichens are symbiotic composites of algae or cyanobacteria and fungi

Penicillin was discovered by Alexander Fleming after an uncovered
Petri dish in his lab became contaminated with mold. He saw that the bacteria near the mold had died. Fleming identified the mold as belonging to the Penicillium genus. 

transposons

what is herd immunity and why does it matter...
​why did vaccination (and while we are at it...masks) become a polarizing political issue??

         woody stems

In monocots, the vascular bundles are both distributed throughout the pith of the stem so they are unable to produce the concentric rings of xylem we call wood. Still, some may be "woody" like palms and bamboo. And not all dicots have woody stems. Tomato, carrot, and potato plants don’t have woody stems.

There is a sequence to viral replication:
​1. attachment: virus bonds to specific host cell                via ligand/receptor match
2. import: virus enters host cell or injects                          genome into the host cell.
3. biosynthesis: new viral components are                        synthesized using host cell machinery 
​4. assembly: components are assembled into                  new virus
5. release: virus exit host cell via budding or                    lysis

​so remembering that while only about 5% of bacterial species are pathogenic, bacteria have been the cause of much human suffering

Bats carry a lot of pollen in their fur compared to other pollinators and can fly long distances which benefits plants living in low densities habitats. They're attracted to flowers with a musty, rotten odor due to sulphur compounds. Bat flowers may be light-colored to be seen at night or a dull color if they only open at night. 

    How are viruses classified?

Cells in the vascular cambium divide toward the outside of the tree making bark and toward the center of the tree making wood. Wood is deposited each year in rings of growth.

  zika

virus are released from the host cell by either:
1. lysis: host cell destroyed
​2. budding: cell continues to produce virus

how are bacteria and archaea
different? ​ or similar?

     pathogenicity of       a  few known viruses

95% of bacteria is 

  sars-cov-2 spike
  protein specifically
  binds to ACE2
  receptor

some viruses are able remain dormant until reactivated = latency
A latent viral infection is a persistent infection...

 routine vaccines

  what about Dr. Dorothy Hodgkin?

  evolutionary adaptation #1:           sporophyte dominance

and a marvel of adaptation...

A vascular bundle is the transport system in vascular plants:
xylem moves water and mineral solutes
 up from the roots to the leaves while phloem carries photosynthetic products (glucose) down from the leaves to other parts of the plant. 

   Domain Eukarya

         roots

above are examples of RNA and DNA viruses

  yearly flu vaccines

ACE-2 = Angiotensin-converting enzyme 2 is an enzyme of the renin–angiotensin–aldosterone system (RAAS)
AND
is a receptor on cell surfaces through which SARS-CoV-2 enters the host cells.
ACE-2 is found in heart, kidneys, and lungs cells. 
What does ACE-2 normally do? ---------->

​flowers 

cell walls are composed of polysaccharides.  The composition of their cell walls also differs from the eukaryotic cell walls found in plants (cellulose) or fungi (chitin).

peptidoglycan cell wall

stems

 disease causing protists

Archaea are not generally found in the human gut and are not pathogenic. 

   What is the general ​structure of a virus?

 virus = poison

identifying bacteria

 angiosperm

antibiotic
​resistance 

A virus consists of genetic material covered by a protein capsid. 
Virion is the extracellular, vector stage of an intracellular virus, which allows the transmission of a virus from an infected, host cell to another host cell. 

 VOCs have a large number of mutations, some of which are concerning. omicron expresses 50 mutations in its genome. 30 of these mutations are in the gene which codes for the spike (CoV-2 surface protein) which binds to our ACE2 receptors to gain entry to our cells.   

replicase ORF1ab, spike (S), envelope (E), membrane (M) and nucleocapsid (N) in 5′ to 3′ direction of the viral genome micron

 bacterial  morphology

  fungi naturally produce antibiotics to kill or inhibit the growth of bacteria, limiting their competition in the natural environment.

2023: It is estimated that about 667 million people were infected with COVID-19  with 6.7 million deaths (underreported?)

   flower evolution

  examples of antibiotic       resistance bacteria
1. MRSA     2. VRE    3. ESBL

 lysis

            herpes

Coronaviruses = enveloped positive-sense RNA 

Viruses were first discovered by 
scientists in the late 19th century
experimenting with tobacco plants afflicted with

tobacco mosaic disease.
​It was found this disease could be transmitted by a liquid filtrate from one plant to another even after all bacteria from the extract had been removed. For years, scientists theorized these remaining infectious agents were just very small bacteria. It wasn't until electron microscopy came on the science in the mid 20th century that these infectious agents were proved to be novel parasites = viruses!  

   how did plants evolve?

anthrax

 gymnosperm

 Archaeans evolved separately from eubacteria and eukaryotes.

let's explore living organisms....

  timeline for RNA vaccine research...
      ...it did NOT happen overnight
​1971: mRNA is transferred between rabbit and                 frog cells. frog cells produce rabbit                         proteins using rabbit mRNA.
​1990 - 2005: vaccine research using the transfer               technology begins, addressing several 
             problems:
   a. free inserted mRNA broken down in host             cell by RNAnucleases. mRNA stability                   increased with the addition of cap/tail                   sequences. mRNA nucleotides chemically
       modified to be recognized as self.
2010: delivery to whole organism vs in vitro                    cells. Lipid nanoparticle (LPN) research                begun in 1978 is adapted for delivery.                    Their charge permits endocytosis of                        mRNA encased within LPN vacuole.  
2018: LPNs approved by FDA after 40 years of                 research and improvement.   
2020: NIH/viral genome sequenced and mRNA           sequence identified. Clinical trials begin. 

Domain Archae

unlike bacteria, a viral growth curve in a host cell is not exponential

Roots absorb water and minerals and transport them up to the stem. Roots also support a plant, anchor a plant and store food.

  The first vascular plants evolved 420 million years ago. Vascular tissue permitted plants to grow up not just out, increasing their photosynthetic capabilities and range. 

 omicron...delta...what is a variant of concern (VOC) vs a variant of interest (VOI)?

        Ebola

Domain archaea include:
 halophiles (salty lovers),
 methanogens (methane producers),
 thermophiles (hot temp lovers). 

DNA viruses generate mRNA while RNA viruses have to synthesize both viral RNA and mRNA. The viral RNA is generated through a replication intermediate, referred to as the “antigenome” or “minus” (−) strand, which serves as a template for viral RNA synthesis. Single-stranded RNA genomes may be either: 
1. sense or the “plus” (+) strand
2. nonsense or “minus” (−) strand.
ssRNA(+) genomes act as mRNA, are infectious upon entry into host cells, and are immediately translated into protein, including the enzymes required for viral reproduction.
(−) ssRNA, which is not mRNA, requires a virus-encoded RNA-replicating enzyme that is carried within the virion to copy (−) RNA to (+) RNA that is recognized by the host cell translation machinery. The enzyme also synthesizes more viral RNA using the (+) RNA as template. The other class of (+) RNA viruses is the retroviruses. Here, the virion carries an enzyme that converts the ssRNA(+) into dsDNA upon infection. 

flowers and their pollinators have develpped a mutualistic relationship. flowers benefit by having their pollen distributed to other flowers and
pollinators benefit by feeding on the nectar that flowers produce. 

   Kingdom Plantae

leaves

plasmids

       rabies

  fungi use enzymes to digest organic matter then they absorb the organic compounds to be used as a food source.  As natural recyclers, they return nutrients from dead organisms back into the soil.

mRNA vaccines
 mRNA vaccines rely on the insertion of viral mRNA into host cells. the host cells then translates the viral mRNA, producing the protein antigen 

Domain Bacteria includes the eubacteria we're familiar with. Most bacteria are heterotrophic and these heterotrophs are mostly saprobic (absorb decaying organic matter). Some bacteria
are parasitic/pathogenic while still others are autotrophic. 

 Pollen was first identified in the fossil record 140 million years ago. Pollen released plants from the requirement of water for fertilization.

                          hiv

viruses are obligate intracellular parasites.
Even though they contain DNA or RNA and they evolve via the mutation of their nucleic acids, they are not cellular, they rely on the

metabolic actions of their host, and they  replicate only by hijacking their host cell machinery. As far as a response to stimuli...

 all vaccines expose your immune system to the antigen of the pathogen. In this way, your immune system learns to recognize that antigen and circulate antibody producing memory cells.
vaccines are produced using:

a. live attenuated (weak) pathogens
b. killed pathogens
c. just the antigen
d. nucleic acids

  Kingdom Protista

staph infection 

    Viruses have been identified and classified by their phenotypes, the nucleic acids they carry, their host, how they replicate, and/or the disease they cause. 

A viruses replication strategy depends on its type of nucleic acid

antibiotics and bacterial infections

 cool fungi info...

   fruit evolution

Bees use scent to find flowers.  They only see the color of a flower when they get close to them and are attracted to blue, yellow, white, purple and violet flowers. Violet is their fave.

Now that we've explored (non-living) viruses...

  fungi can often reproduce by the formations of
spores which are able to withstand cold and draught, forming a new fungal body when the conditions are right. 

    Where did viruses come from?

To survive in the acidic stomach,
​ Helicobacter pylori secretes an enzyme called urease, converting urea to ammonia which neutralizes the acidity of the stomach. 

EBOV is transmitted via body fluids. It attacks the spleen and kidneys, killing cells that regulate
chemical/fluid balance and permit blood clotting.

antibiotic resistance can be transferred between bacterium by mobile genetic which carry antibiotic resistant genes. These elements are...

    What are viruses?

LUCA-->

       H = hemagglutinin   N = neuraminidase

            smallpox

  besides being a pizza                    topping...

roots

  Woody stems add height and girth           during every growing season.

1918: It is estimated that about 500 million people or one-third of the world's population became infected with H1N1. The number of deaths was estimated to be at least 50 million  

             cold

  Vaccines

   amoebic dysentery

The small intestine is less hospitable to microbial colonizers due to the release of bile in its lumen.
The large intestine with a pH near neutral, offers a neutral to mildly acidic pH which microbes find more welcoming. 

 ​ 45o million years ago, there was a supercontinent called
Pangaea
​ being formed by the shifting of the   Earth's plates. Life was mostly marine and the trilobites ruled the sea. Microbes clung to rocks, barely surviving in their semi aquatic habitat. From these protists, green mosses evolved, spreading from the   rocky edge of the water to dry land. The first true plants, mosses and their relations, spread and spread and over the next 40 million years, Pangaea was carpeted in moss. As carbon dioxide levels fell and O2 levels rose due to increased photosynthesis, the global temps dropped. Glaciers developed, weathering rocks into soil. 400 million years ago, the first vascular plants were able to take root, evolving into ferns. 

Antifungals target fungal cell wall/cell membranes.
When either is compromised, the fungal cell is degraded.
Azoles interfere the function of an enzyme required for  membrane function. Polyenes kill fungal cells by compromising the cell wall.

    Zika virus is a mosquito-borne flavivirus. It was identified in the mid 20th century first in monkeys and then in humans. Zika virus can be transmitted across the placenta resulting in microcephaly.
​​Zika destroys glial cells. Glial cells are responsible for producing all of the neurons in the brain. 

         flowers

even bacteria can be infected by a virus
                 its called a bacteriophage

Domain Bacteria

         coronavirus

The Gram Stain Technique:
assists in the identification of bacteria from an infection. 
When stained, if the bacteria stains purple, they are considered Gram-positive.

  As plants evolved, the sporophyte generation became dominant. In moss, the gametophyte (1n) generation is dominant. Starting with ferns, the sporophyte (2n) generation is dominant. higher plants have a microscopic gametophyte generation.

  Why do you think plants become
     2n dominant?
 What is the advantage?

 Athlete's foot (and ringworm etc) is caused by a type of fungi called dermatophyte that normally live on the skin and nails and hair but only grow out of control when
their environment gets moist  and warm. ew. 

  dominant   sporophyte

Flowering plants and their pollinators are amazing example of
co-evolution

The International Committee on Taxonomy of Viruses (ICTV) developed a  taxonomic classification for viruses. 

   what are fungi?

viruses can carry either RNA or DNA

 how did eukaryotic

         cells evolve?