Virus Structure and Classification

Virus Components

• Viruses are noncellular particles that infect host cells to produce more virus particles
• Virions consist of a viral genome, either DNA or RNA, inside a protein capsid
• The capsid is made of repeating protein subunits that deliver the viral genome into a host cell
• Some viruses also contain an outer envelope composed of lipids derived from host cell membranes

Virus Categories and Tradeoffs

• Non-enveloped viruses are generally more resistant to physical stresses
• Non-enveloped viruses are more easily recognized by the immune system
• Non-enveloped viruses usually cause cell lysis.
• Enveloped viruses are more susceptible to physical stress
• Enveloped viruses can be more easily hidden from the immune system using the membrane from host cells
• Enveloped viruses do not immediately kill cells

Observing Viruses and Types of Virus Shapes

• Viruses can be observed in the lab using various methods
• Three common shapes include Icosahedral, Filamentous, and Tailed

Icosahedral Viruses

• These are polyhedral with 20 identical triangular faces, exhibiting rotational symmetry
• Some icosahedral viruses have a capsid enclosed in an envelope derived from the host cell membrane
• Glycoprotein spikes encoded by the virus are contained within the envelope

Filamentous Viruses

• Their capsid consists of a long protein tube, containing the coiled genome inside
• They vary in length based on genome size
• Filamentous viruses show helical symmetry

Tailed Viruses

• Tailed viruses possess complex multipart structures
• T4 bacteriophages are an example
• Tailed viruses have an icosahedral "head" and a helical "neck"

Viral Replication Strategies

• All animal viruses use host ribosomes to synthesize proteins for new virions
• Progeny viruses are released from the host cell
• DNA viruses use the host's DNA polymerase and replicate in the nucleus and cytoplasm
• RNA viruses employ RNA-dependent RNA polymerase for mRNA transcription in the cytoplasm
• Retroviruses use reverse transcriptase to convert their RNA genome into DNA for insertion into the host chromosome

Viral Tropism

• Viral tropism is the specificity of a virus for certain cells, tissues, or species
• Viral tropism is determined by receptors
• Most animal viruses enter the host as virions and release the genome from capsid
• Tropism dictates where and how efficiently a pathogen replicates, influencing virulence
• Viruses infecting a broad range of tissues or cells may be more likely to cause severe disease

Types of Tropism

• Cellular tropism is the ability of a pathogen to infect specific cell types
• Tissue tropism refers to the ability to infect specific tissues or organs
• Host tropism is the ability to infect specific host species

Plant Virus Replication Cycles

• Plant viruses use mechanisms differing from those of animal viruses and bacteriophages for cell infection
• Plant viruses infect cells via mechanical transmission
• Mechanical transmission can occur through contact with damaged tissues, animal vectors, or seeds
• Plasmodesmata, membrane channels connecting adjacent plant cells, transmit plant viruses to uninfected cells since the thick plant cell walls prevent the viruses from escaping via lysis/budding

Bacteriophage Replication Cycles: Lytic

• Bacteriophages enter the host cell, recognizing and attaching to it
• Bacteriophages hijack the host machinery to replicate their own DNA and proteins
• Bacteriophages assemble into new phage particles, ultimately causing the host cell to burst open
• New bacteriophages are released to infect other cells

Bacteriophage Replication Cycles: Lysogenic

• Phage DNA integrates into the host cell's DNA, forming a prophage
• The prophage replicates alongside the host's DNA and is passed to daughter cells
• Under specific conditions, the prophage can be induced to leave the host genome and proceed with the lytic cycle

Comparing Lytic and Lysogenic Cycles

Tradeoffs Between Lytic and Lysogenic Cycles

• Lytic cycle benefits include rapid phage replication, leading to quick infection spread, costs the host cell death
• Lysogenic cycle allows phage persistence in the host population without immediate harm
• Lysogenic cycle is slower and less efficient, with the potential for prophage excision leading to the lytic cycle under stress

Bacterial Defenses Against Phages

• Genetic resistance involves altered receptor proteins
• Restriction endonucleases cleave viral DNA lacking methylation
• CRISPR integrates phage DNA sequences, functioning as a bacterial immune system through clustered regularly interspaced short palindromic repeats

Viral Impacts on Ecosystems

• Viral shunts occur by lysing cells and returning carbon and minerals to surface waters, making themAvailable to other organisms
• Viral shunts help balance nutrients
• Viruses terminate algal blooms and control overgrown algal blooms
• Persistent viruses can remain in hosts and evolve traits to benefit a virus-host mutualism

Viral Infection and Entry

• Viruses must contact and attach to a host cell
• Cell-surface receptors facilitate contact and attachment with specific viral components
• Bacteriophages typically deliver their genome into the cell through the cell envelope, leaving their capsid outside

Viral Infection: Three Stages

• Absorption and entry
• Viral replication
• Release

Definitions Related to Viruses

• Oncogenic viruses can cause cancer by transforming host cells through insertion of an oncogene or integration of the viral genome
• Host range is the range of host species a given virus can infect
• Temperate phages can infect and lyse cells, with the ability to integrate their genome
• Lysogeny is a symbiotic relationship where a bacteriophage integrates its DNA into the host's genome

Biosynthesis Overview

• Biosynthesis/anabolism directs central carbon metabolism products toward macromolecules
• The major goal is to build macromolecules
• The process must convert elements from organic to inorganic forms
• Microbes regulate enzyme production based on environmental availability

Microbial Interactions

• Competition and predation occurs when cells are killed for molecules
• Genome loss and cooperation is a challenge

Carbon and Nitrogen Acquisition

• To obtain carbon, microbes can use carbon from other organisms or from CO2
• To obtain nitrogen, microbes can use nitrate/nitrite/ammonium ions, or N2 gas

Carbon Fixation Pathways

• Calvin Cycle fixes carbon using CO2 and water with a ribulose intermediate, using enzyme rubisco
• Reverse TCA cycle fixes carbon using anaerobic bacteria and archaea, a very ancient process
• Reductive Acetyl-CoA Pathway is used by anaerobic soil bacteria to condense two CO2 molecules
• 3-Hydroxypropionate cycle fixes carbon through acetyl-CoA and propionyl-CoA reactions

Rubisco and Carboxysomes

• Rubisco fixes initial carbon by converting atmospheric carbon dioxide into organic molecules
• Carboxysomes enhance Rubisco by concentrating CO2

Nitrogen Fixation Challenges and Strategies

• Reduction of dinitrogen into ammonia requires a significant amount of energy
• The enzyme nitrogenase, is sensitive to oxygen
• Heterocysts are cells that fix N2 instead of photosynthesizing
• Rhizobium colonizes root nodules and the plant produces leghemoglobin to sequester oxygen
• Azospirillum flocculates when fixing N in aerobic conditions

Modular Synthesis

• Modular synthesis is a cyclic pathway that uses products as substrates
• Fatty acid synthase (FAS) elongates fatty acid chains using malonyl-CoA
• Modular elongation is used to create storage polymers such as polyesters and polyhydroxybutyrate (PHB).
• PHB is generated under stress and made into biodegradable plastics and surgical sutures

Culture-Based Technique Limitations

• Traditional ecological concepts can be difficult to apply to microbiology as microbes often look similar under a microscope.
• Great Plate Count Anomaly describes the discrepancy between observed cells and those grown on agar plates

Metagenomics and Amplicon Sequencing

• Metagenomics sums up all DNA sequenced from a sample

Metagenomics Procedure

• Sample microbes in their environment
• Break open the cells to isolate DNA
• Amplify DNA and fragment for size
• Specific regions of the 16S rRNA gene are amplified
• DNA fragments are read using a sequencer
• Overlapping reads are assembled into contigs to generate a metagenome assembled genome (MAG)

Advantages of Culture-Independent Methods

• These methods are relatively cheap and low risk
• They detect unculturable species and lots of data exists

Disadvantages of Culture-Independent Methods

• Culture-independent methods only show species distribution and they assume evolution matches molecular clocks, some species will be lost and spatial information is limited.

Sequencing Reads

• Overlapping short sequences are aligned
• These alignments are called contigs
• Contigs that are mapped to a reference create a scaffold
• Contigs are the largest pieces of DNA assembled

Genome Assembly

• Genome assembly can be mapped to a reference sequence
• Alternatively, genome assembly can be done de novo
• Mapping to a reference sequence is faster but less informative

Metagenomics vs Functional Analysis vs Transcriptomics

• Metagenomics contain total DNA sequence from a community
• Metagenome functional analysis describes what metabolic pathways are encoded
• Transcriptomics show what tasks the community is capable of

Metatranscriptomics

• Metatranscriptomics study RNA transcripts
• Metatranscriptomics offer insights into dynamic activities

FISH Overview

• Detects specific DNA in cells using probes
• Genomic data create probes to reveal interactions through rRNA
• Fix the DNA, denature it, then label it
• Wash and visualize

Symbiosis Types

• Symbiosis involves relations between interactions between species.
• Mutualism is mutually beneficial
• Synergism is beneficial but optional
• Commensalism benefits one partner
• Amensalism harms one partner
• Parasitism harms one partner

Factors That Show Symbiosis Is In Effect

• No interaction, independent mircocolonies
• Synergism
• Distinct boundaries

Multiomics

• Multiomics integrates other perspectives

Flux

• Flux shows the flux of molecules between ecosystems

Steady State

• Steady state says that input is output

Residence Time

• Residence time says the average time in a reservoir
• amount in reservoir / flows in and out

Carbon Cycle Components

• The carbon cycle involves photosynthesis that is turned to glucose using sunlight
• Respiration is breakdown of matter with CO2 back to the atmosphere
• Fermentation is when glucose is converted to ethanol etc
• Methanogenisis produces CH4, whereas methanotroph consumes it

Oceanic and Terrestrial Cycles

• Oceanic is fixed by photosynthesis, but ocean has deep anoxic reginos
• Terrestrial is aided by fermentation and produces fossil fuels

Water Cycle Role

• Nutrient pollution happens, growing organisms, more nutrients, then depletion

Bloom Formations

• Blooms happen from a heavy amount of nutrient growth and depletion events
• Death leads to bacterial decomposition, which leads to O2 depletion
• Consequences: fish and etc will suffocate

Areas of the Environment

• The deep can often lead to anoxic sediments and there are areas that are deadzones
• The zone is nitrogen

The Nitrogen Cycle

• The nitrogen cycle contains Nitrogen Fixation, Nitrification, Denitrification, and ammonification

Nitrogen Fixation

• Uses inert gas to amonium
• Catylzed to N2, tremendous energy

Nitrification

• Uses energy, is oxidized, used via nitrite/Nitrous
• Can be be taken up by microbes and plants

Denitrification

• Anaerobic condition that uses n2 gas and denitrifying bacteria

Anammox Reaction

• Requires oxygen gas

Iron Needs and Use

• Iron is a cofactor, is needed
• It is hard to acquire because not soluble or oxidezed, and there are HNLC low content areas
• Iron is low on chlorophyll as well

Sideophores

• Siderophores increase iron uptake
• Some secret to scavenge iron and bring it in
• Bacteria also steal eachothers

Definitions

• Biochemical oxygen demand measures how much oxygen is used
• Omz happens when layers mix
• Haber process provides fertilizer

Fermentation and Microbes

• Fermentation is metabolic and bacteria use carbs without O2
• HomoLactic acid- turns to cheese
• Fermenting microbes turns to starter
• Protein is cleaved etc, curd happens
• The curd is then shaped to what can be used

Acid and Fermentation

• Propio acid turns into swiss chhese
• Heterolactic acid turns to vegetables
• Ethanolic makes bread and beer
• Alkaline and bacillus turn to soybeans

Different Product Outcomes

• Nutrients add flavors and nutrients
• This can influence the substrate and microbes used
• Envirornemtal conditions affect it as well
• All cheese is different

Cheese Production

• Curd is then strained

Different Types of Cheese

• Swiss uses lost CO2
• Feta is ripened in brine

Products

• Temph is fermentation based and MSG is a product

More Substrates

• Lueconostoc is used for cabbage

Chocoloate Subtrates

• Product of cacao, a complex fermentation
• Yeasts can be used along with aerobic and anaerobic types

Alcohols

• Ethanolic with sach
• Beer and wine

Bread

• Makes a gluten with carbs

Fermentattion

• Prevents harm

Spoilage and Poisoning

• Spoilage is unfit and unpaltable
• Oxidation happens and alkalinity happens
• Proteins are putfiied

Food Borne Illness

• Bacteria has pathogens and some can remain for years
• Dangerous when toxin has fusion

Typically Eukaryotic

• We eat these because cannot eat bacteria due to high NA content
• Contains purines that lead to acid and lack an enzyme

Bacteria for Us

• Bacteria is needed for some processes
• Can also be used to make vitamin
• Made of different genes and promotes

Challenges from These

• Need to create the right expressions

Mass Problems

• How to keep and mass and prevent contaminattion

Bacteria Extraction

• Need to extract product and purify

Definition Methodds

• Include dehydration, regrigerattion, acids
• And pack in wierd methods and chemicals

Food Borne Illness

Answers

• Rbisco, demand, reductuve, plaque
• Psychotrohpic, etc
• Fixation
• High survival, etc
• Food spoilgae and multinommial methods