MODULE 1 - Microbial Evolution and Ecology

Question 1

what were the first organisms on earth and how did they create the environment which allowed for new forms of life?

Answer 1

anaerobic bacteria because there was no oxygen on earth. When these anaerobes developed the ability to use light to produce oxygen earth began to change from an anaerobic to an aerobic environment. Because of this aerobic organisms began to evolve and proliferate

Question 2

What is LUCA and what can we assume because of it?

Answer 2

LUCA is the last universal common ancestor, and we can assume that if all life is descended from this, then there will be common biochemistry, architecture and mechanisms between all life e.g. storage of info in DNA, most cells work the same way, most life is made up of proteins etc.

Question 3

what are the major components of all cells and what are these components made of?

Answer 3

the major components of all cells are membranes, nucleic acids (DNA/RNA), proteins and all these are composed of the same basic materials (CHONSP)

Question 4

what is CHONSP and why are they the most common elements?

Answer 4

Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur, Phosphorous

Because they form covalent bonds which are strong enough to hold long-term structure but can be broken down so that we can recycle our building blocks and they can also attach to multiple accessories

Question 5

what is the universal solvent which is required for a chemical reaction to take place?

Answer 5

water hence its importance to all organisms

Question 6

what are the two essential components for life to occur?

Answer 6

CHONSP and water

Question 7

what was the Miller-Urey experiment?

Answer 7

simulated life with all the key elements and the right conditions inside a chemostat to make more complex structures proving that its possible for life to form from simple compounds. The experiment succeeded in creating many organic molecules, most essential amino acids and most nucleic acid bases. They concluded that the organic building blocks of life were generated in the probable atmosphere of early earth

Question 8

why were membranes essential for the development of life?

Answer 8

they enclose and compartmentalise things in environments allowing certain experiments to occur shit loads of times so that a one in a million thing will likely occur in one of a million closed environments where the conditions are perfect

they also allow for gradients to let certain things in and out across the membrane

Question 9

how were the first membranes formed?

Answer 9

they were likely self-assembled and would have been things like coacervates, micelles and liposomes. These would have been semi-permeable membranes and would persist indefinitely without oxygen or decomposers. These became what is called a protocell (closed environment formed by a membrane)

Question 10

why might RNA have been the first biological molecule?

Answer 10

central dogma of molecular biology in the modern world suggests info flows from DNA to RNA to protein, however this might not have been the case for the first life forms. DNA is missing an oxygen atom making it more stable and less reactive in an aerobic world. But when the world was anaerobic (when life started) stability wasn’t an issue as there was no oxygen so perhaps RNA was the first molecule as we wouldn’t have had to worry about protecting it from oxygen

Question 11

what are self-catalytic RNA enzymes?

Answer 11

ribozymes work by folding naturally onto themselves and recognising sequences then catalysing a reaction to cleave themselves

Question 12

why are self-catalytic RNA enzymes/ribozymes the first step in producing life?

Answer 12

because it is the first time we are able to catalyse a reaction ourselves without letting chance rule it i.e we have reproducibility where the same things can happen over and over and we can expect the same outcome

Question 13

what is the RNA world hypothesis for the origin of life

Answer 13

heating and cooling of the prebiotic soup leads to formation of more complex structure and eventually generates RNA and liposomes

liposomes and RNA combine with some other shit in the soup to form probionts (predecessor to early life)

so far these are all random reactions but once we have a ribozyme these reactions are reproducible allowing for production of RNA and proteins which allows for the first cells

so the RNA world hypothesis is generally centred around the idea that RNA was the first nucleic acid and was the building block which allowed life to occur

Question 14

outline how ribozymes are formed

Answer 14

random precursors turn into more complex things like nucleotides which can randomly turn into RNAs which can even more rarely turn into ribozymes

Question 15

once the world transitioned from a chemical world to a biological one, why did the biological one take over?

Answer 15

once you have life you have reproducibility meaning life can take over as it has a blueprint to allow enzymes to produce nucleotides in the same way

Question 16

what is the selfish gene hypothesis?

Answer 16

all of life exists because our genes want to survive and so make copies of themselves and everything just came about as a side-effect of this

Question 17

outline the RNA world hypothesis step by step

Answer 17

RNA forms from inorganic substances (proven by miller-urey)

RNA self-replicates via ribozymes

RNA catalyses protein synthesis

Membrane formation changes internal chemistry allowing new functionality

RNA codes both DNA and protein (DNA becomes master template and proteins catalyse cellular activity)

Question 18

what was the first organism and where did it live?

Answer 18

it must have been prokaryotic, anaerobic and chemolithotrophic

it possibly consumed iron sulfide and hydrogen sulfide and could have used the resulting hydrogen to drive ATPase by splitting it

Question 19

why is there so much diversity among microorganisms?

Answer 19

gradients, niches and speciation create lots of different habitats

Question 20

how do microbes create gradients as they grow and what do these gradients allow for?

Answer 20

anaerobes consuming oxygen create areas with less oxygen where anaerobic or fermenting microorganisms may live (oxygen gradient)

microbes create nutrient gradients by consuming certain nutrients resulting in areas with more or less nutrients

microbes create pH gradients through creating waste products or chemical production through quorum sensing

all these gradients allow for diversity

Question 21

what experimental evidence is there for evolution?

Answer 21

a single E. coli was inoculated and grown on a glucose limited media so as to create an environment which forces competition so that organisms change for an advantage. Through this they managed to produce three different strains from wildtype, each with differences in maximum specific growth rates and in glucose uptake kinetics

wild type could convert glucose to acetate to glycerol

in the new system the three strains of the same organism specialised in consuming either glucose, acetate or glycerol in order to reduce competition

Question 22

how do we measure diversity in microbial communities in order to classify organisms?

Answer 22

taxonomy

function

metabolism

Question 23

what classification systems do we have for microbial diversity?

Answer 23

biological

phenetic

cladistic (phylogenetic)

Question 24

explain the biological classification system

Answer 24

organisms grouped based on ability to breed so this system doesn’t work for microbes since they don’t need a partner

Question 25

explain the phenetic classification system

Answer 25

organisms grouped based on overall physical similarity (analogous) with no account of evolutionary history (i.e. only measures the end product) this system is liable to errors due to convergent evolution it also is ineffective at classifying microbes as they all very similar physically

Question 26

what is convergent evolution?

Answer 26

leads to the same phenotypes with no shared recent ancestry e.g. bats, birds and insects all have wings

Question 27

explain the cladistic (phylogenetic) classification system

Answer 27

most commonly used system grouping organisms based on evolution from a shared ancestor (clade) as determined from a shared trait. Involves making trees from genetic sequences where more similarity between genomes means two organisms are more closely related. The more mutations accumulated indicates two organisms are more distantly related the issue with this method is that its liable to ignore useful descriptive traits by being too focused on one evolutionary trait or gene

Question 28

what is a molecular clock and what is the most commonly used molecular clock?

Answer 28

a gene whose DNA sequence can be used as a comparative temporal measure of evolutionary divergence. We are essentially trying to look at mutations in that gene to see how long the species have been separated from each other. This works because there is usually a linear relationship between time and the number of mutations accumulated most commonly this is the 16s rRNA gene which encodes the RNA sequences within the small subunit of the ribosome because it is universally conserved in every living organism

Question 29

what are the four key properties of a molecular clock?

Answer 29

found in all living organisms, maintains its function amongst all living organisms (because you want it to be under the same selection pressure), highly conserved with multiple hyper variable regions (conserved regions used as anchors for alignment and hyper variable regions mutate faster which indicate divergence of a species), sufficient length

Question 30

why is the 16s rRNA gene called the 18s rRNA gene in eukaryotes?

Answer 30

because it is slightly larger and sediments slightly slower

Question 31

what did Carl Woese figure out about the domains of life and how?

Answer 31

by looking at different sequences as molecular clocks, he kept finding that all life would be grouped into three groups rather than the previously believed five groups these groups were eukaryotes, eubacteria (new bacteria) and archaebacteria (old bacteria or the base of the tree which everything evolved from)

Question 32

how have the 16s observations been validated and what has changed?

Answer 32

observations based on 16s have been validated by other genes, by amino acid sequence and by enzyme structure RNA polymerase structure however has now shown that archaeological are more closely linked with eukarya rather than bacteria suggesting they are not the old base of the tree but are instead completely different organisms

Question 33

what is the eocyte hypothesis (two domain hypothesis)?

Answer 33

suggests that eukaryotes branch within the archaea meaning that they are just a sub-group of archaea and there are only two domains of life. it implies that the closest relative to eukaryotes is one or all of the TACK archaea

Question 34

what evidence do we have for the two domain hypothesis?

Answer 34

TACK archaea and eukaryotes share genes no found in other archaea so our ancestors must be TACK archaea

Question 35

what is a limitation to phylogenetics?

Answer 35

horizontal gene transfer

Question 36

what are saprophytic fungi?

Answer 36

decomposers which get nutrition through absorptive nutrition (releasing enzymes which break down something and then they suck up all the nutrients). they convert organic material to fungal biomass, carbon dioxide and small molecules such as organic acids

Question 37

what are mycorrhizal fungi?

Answer 37

mutualistic fungi which colonise plant roots and help solubilise phosphorus and bring soil nutrients to the plant in exchange for carbon from the plant

Question 38

what are the two types of mycorrhizal fungi?

Answer 38

ectomycorrhizae - grow on the surface of roots and are commonly associated with trees endomycorrhizae e.g. arbuscular mycorrhizal fungi - grow within the root cells and commonly associated with grasses, crops, vegetables and shrubs

Question 39

what is the third group of fungi?

Answer 39

pathogens or parasites which cause reduced production or death when they colonise other organisms

Question 40

what is the problem with species classification?

Answer 40

there is a long-standing failure of biologists to agree on how we should identify species and how we should define the word 'species' differing definitions include; taxonomic rank, a group of organisms capable of interbreeding and producing fertile offspring, and a separately evolving lineage that forms a single gene pool

Question 41

what do we focus on currently to define a species?

Answer 41

a phenotypic assignment (organisms phenotype) and genome similarities (so kind of a hybrid of what it looks like/what it can do and the evolutionary history when comparing genomes)

Question 42

what is the definition of a prokaryotic species?

Answer 42

a category that circumscribed a genetically coherent group of individual isolates/strains sharing a high degree of similarity in independent features, comparatively tests under highly standardised conditions

Question 43

what is a bacterial species defined as?

Answer 43

a genomically coherent group of organisms

Question 44

what is required for a strain to belong to a new species?

Answer 44

OrthoANI (average nucleotide identity) should be about 95% (meaning if they are divergent by 5% or more they are classified as a new species) if the above classifies it as a new species and you want to describe it as such, you must carry out additional taxonomic research such as phenotypic characterisations and biochemical tests to show new phenotypes. This is because just cause the gene is there doesn't mean its being used it must also have a type strain that is live which anyone can obtain for taxonomic study. It must be a pure culture so it can be used as a benchmark when comparing new species

Question 45

what is the issue with classification of new bacteria?

Answer 45

it is difficult to quantify differences and define a boundary for a species. This is cause its usually not clusters but a gradient of species making it difficult to decide where to draw the line as a new species

Question 46

what is the practical definition of a prokaryotic species?

Answer 46

a group of strains that are characterised by a certain degree of phenotypic consistency, showing 70% of DNA-DNA binding and over 97% of 16S ribosomal RNA gene-sequence identity

Question 47

what three things do all classification systems share?

Answer 47

they are arbitrary (no reason why we draw the line at that certain point, just cause it works with what we've done previously) they are anthropocentric (based off classic microbiology which focused on classifying pathogens but doesn't fit all microbial diversity) they are rooted in practical necessity (we just make the best choices we can when it comes to classification cause we don't know any better systems)

Question 48

what have bacterial species historically been defined by?

Answer 48

growth characteristics (morphology, gram stain, growth medium) (classic species were generally fast growing pathogens) disease caused

Question 49

what is DNA-DNA hybridisation?

Answer 49

involves comparing the genome of two organisms to see how well they hybridise to each other. It is considered phenotypic as well as genotypic because if you compare the genome you should be able to predict what the phenotypes are actually going to be essentially measures the degree of genetic similarity between complete genomes by measuring the amount of heat required to melt the hydrogen bonds between the base pairs that form the links between the two strands of the double helix of duplex DNA

Question 50

outline the DNA-DNA hybridisation process?

Answer 50

put genomic DNA in tube and add dye, apply heat and eventually DNA melts and releases dye (so we are looking for when the dye disappears) you apply a second genome to the same mix and melt it again so that it anneals to the other genome strand. You then get a hybrid genome with one strand from one organism and one from the other any difference in temperature to melt this hybrid suggests there is a difference in similarity of those genomes the DNA melting temperatures from both organisms can be graphed to show two peaks (one for one organism and one for the other)

Question 51

what does DNA-DNA hybridisation provide a standardised means for?

Answer 51

identifying and classifying prokaryotes that lack well defined morphological or phenotypic characteristics

Question 52

what are the pros of DNA-DNA hybridisation?

Answer 52

greater than 70% similarity means its the same species good correspondences with phenotypically coherent clusters of strains in Enterobacteriaceae

Question 53

what are the cons/issues of DNA-DNA hybridisation?

Answer 53

unclear how it relates to whole-genome relatedness (i.e. you are looking at melting not actually comparing DNA sequences) time consuming carried out properly by few laboratories ill-suited for rapid identification only suited for pair-wise comparison previous classification must be present unavailable for non-culturable organisms (and only 1-2% of prokaryotic cells are cultivable)

Question 54

how do you sequence the 16S rRNA gene?

Answer 54

isolate DNA heat to seperate strands and add specific primers primer extension with DNA polymerase repeat above steps to obtain many copies of 16S rRNA gene run agarose gel and check for correct sized product purify and sequence PCR product

Question 55

what were the major impacts of DNA-DNA hybridisation?

Answer 55

established a base line for species delineation allows us to affirm whether or not a species is the same after high-level classification with 16S (>70% binding value and >97% 16S rRNA gene sequence similarity = same species)

Question 56

what is the issue with 16S rRNA sequencing?

Answer 56

<97% 16S rRNA sequence similarity always = different species BUT >97% sequence similarity doesn't always mean the same species and as a result may not be >70% binding value (think gorilla and humans sharing >97%) so basically 16S good to confirm when things are different but not when they are the same

Question 57

what are some limitations of using the 16S rRNA gene for gene comparison?

Answer 57

lacks resolution compared to DDH (16S gene small compared to whole genome) can't discriminate between highly related species (>97%) doesn't relate to metabolic capabilities or provide fine details as only relies on a single gene (16s gene highly conserved so doesn't change except for over long periods of time but rest of genome under lots of different selection pressures thus can gain/lose functions without changing 16s gene so might not capture more recent evolutionary events)

Question 58

what is ANI (average nucleotide identity) and how does it work?

Answer 58

used to figure out how different two organisms are works by running a BLAST or alignment which compares base pair to base pair over the entire genome for two genomes. But its done through informatics on a computer so can compare the whole genome very quickly it has replaced DNA-DNA hybridisation with a new threshold of 95% (as opposed to 70% with DDH) so there is a much tighter boundary for what a species is supposed to be ANI won't give you a new organisms taxonomy at phylum, family or genus level so for this you still have to rely on 16S sequencing

Question 59

even though it has replaced DNA-DNA hybridisation, what are some limitations of ANI?

Answer 59

we are simply updating the way we measure/compare differences no biological definition/explanation for why we use 95% ANI or 70% DDH DDH was a biased system and ANI is just the same biased classification system only faster

Question 60

what is AAI (average amino acid identity)?

Answer 60

AAI is the same principle as ANI but instead of comparing the whole sequence you are comparing the amino acid sequence across all proteins in that genome

Question 61

what is the correlation between DDH, ANI and 16S rRNA?

Answer 61

there is good correlation between all three more than 70% DDH is equivalent to more than 95% ANI is equivalent to more than 98.5% 16S rRNA (but all these are still based off old classification systems so even though there's good correlation there is no theory to support them)

Question 62

what is MLST (multilocus sequence typing)?

Answer 62

a method for the genotypic characterisation of prokaryotes at the infraspecific level, using the allelic mismatches of a small number (usually 7) of housekeeping genes. Housekeeping genes are essential for the organism and found in all the strains. Designed as a tool in molecular epidemiology (so usually used during epidemics) and used for recognising distinct strains within named species precursor to MLSA

Question 63

what is MLSA (multilocus sequence analysis)?

Answer 63

a method for the genotypic characterisation of a more diverse group of prokaryotes (including entire genera) using the sequences of multiple protein-coding genes so basically the same as MLST but instead of using 7 housekeeping genes can use any genes which are in all the genomes that you are comparing

Question 64

what does MLSA allow us to do?

Answer 64

different species can be clearly separated ecotypes can be identified (ecotypes are populations that are genetically cohesive and ecologically distinct)

Question 65

what are the pros and cons of MLSA?

Answer 65

pros: higher resolution, uses multiple genes, provides a species or lower classification as opposed to 16S rRNA gene analysis which provides a genus classification cons: genes must all be a single copy, must all be present in all the organisms being analysed, still the problem of what really constitutes a species

Question 66

what is metabolism?

Answer 66

the sum total of all chemical reactions that occur in a cell composed of two opposing reactions: - catabolic reactions (energy releasing metabolic reactions) - anabolic reactions (energy requiring metabolic reactions)

Question 67

what is the issue with current knowledge of microbial metabolism?

Answer 67

most of it is based on study of laboratory cultures

Question 68

what nutrients do cells need and why?

Answer 68

cells need nutrients for a supply of monomers (or precursors of) which are required for growth. This includes macronutrients (CHONSP) which are nutrients required in large amounts and micronutrients which are required in trace amounts and many of which are cofactors or part of catalytic site of enzymes despite needing larger volumes of macronutrients than micronutrients both are equally important for a cell

Question 69

why are many micronutrients transition metals?

Answer 69

they have multiple states which allows them to mediate redox reactions

Question 70

what is Gibbs free energy?

Answer 70

energy released that is available to do work in a biological context this would be the energy released when you break a bond which is actually available for use by the cell

Question 71

what is the electron donor in a redox reaction?

Answer 71

the substance being oxidised

Question 72

what is the electron acceptor in a redox reaction?

Answer 72

the substance being reduced

Question 73

if something gets reduced, does it have more or less electronegativity and does it have more electrons?

Answer 73

more electronegativity more electrons

Question 74

redox reactions occur in pairs by pairing opposite reactions, what is the energy from these oxidation-reduction reactions used for?

Answer 74

synthesis of energy-rich compounds e.g. ATP (i.e. anabolism)

Question 75

what are the two ways in which we can use the energy from redox reactions?

Answer 75

stored in chemical compounds/bonds as 'batteries' for use at a later time e.g. ATP used immediately as an energy source e.g. NADH goes straight into membrane, is converted to NAD and the electrons lost are used to physically drive a flagella or motor

Question 76

where on the redox tower would you find electron rich (donors) compounds?

Answer 76

top

Question 77

where on the redox tower would you find electron poor (acceptors) compounds?

Answer 77

bottom

Question 78

what does a bigger drop between donor and acceptor on the redox tower mean?

Answer 78

more energy harvested

Question 79

redox reaction usually involve reactions between intermediates. What are these intermediates called and what are the two classes they can be divided into?

Answer 79

electron carriers divided into prosthetic groups (attached to enzymes) and coenzymes (diffusible) e.g. NAD+ and NADH (so these coenzymes facilitate redox reactions)

Question 80

electron carriers don't get broken down, what happens to them instead?

Answer 80

they get recycled/reused but they must be recharged in order to be used again

Question 81

despite the different ways in which a cell can store energy, what do they all hinge on?

Answer 81

bonds

Question 82

what are the three fueling reactions which are crucial to an organism?

Answer 82

energy source, carbon source, electron source

Question 83

what does energy source in an organism look at?

Answer 83

how does it drive metabolism

Question 84

what is carbon source looking at in an organism?

Answer 84

what things can it actually degrade

Question 85

what is electron source looking at in organisms?

Answer 85

the physical carrier that is carrying that energy from the energy source

Question 86

what does the breakdown of carbon/glucose lead to?

Answer 86

energy harvesting (used to generate energy) carbon harvesting (intermediate compounds) (used to build things)

Question 87

what is the energy source for chemotrophs?

Answer 87

chemicals

Question 88

what is the energy source for chemoorganotrophs?

Answer 88

energy from C molecules

Question 89

what is the energy source for chemolithotrophs?

Answer 89

energy from inorganic molecules

Question 90

what is the energy source for phototrophs?

Answer 90

sunlight

Question 91

what is the energy source for photoheterotrophs?

Answer 91

energy from sun and C from organic molecules

Question 92

what is the energy source for photoautotrophs?

Answer 92

energy from sun used to fix C

Question 93

why does aerobic respiration lead to the highest amount of energy?

Answer 93

because the transfer of electrons in very easy

Question 94

what do good electron acceptors have either of?

Answer 94

an abundance of oxygen or a lack of hydrogen (oxidised)

Question 95

what do good electron donors have?

Answer 95

an absence of oxygen and an abundance of hydrogen (reduced state)

Question 96

what do organisms that can't use organic compounds use as electron donors/acceptors?

Answer 96

inorganic compounds

Question 97

do you need oxygen present to perform respiration?

Answer 97

no its just that aerobic respiration is the preferred method for organisms cause more energy produced

Question 98

what is anaerobic respiration dependent on?

Answer 98

electron transport, generation of a proton motive force and ATPase activity

Question 99

what is used as electron acceptors in anaerobic respiration?

Answer 99

anything other than oxygen egg, nitrate, ferric iron, sulfate, carbonate and certain organic compounds

Question 100

why is more energy produced under aerobic conditions than anaerobic (other than oxygen being at bottom of electron/redox tower)?

Answer 100

because when an organism realises there is no oxygen it will turn on certain genes that code a bunch of other proteins and fill the membrane in the electron transport chain with them the process is the same but the organism is now using three or more electron acceptors to get it to the terminal electron acceptor so it would get a much more efficient electron transport chain under aerobic conditions combine this with oxygen being a better electron acceptor and you see why anaerobic conditions are preferred

Question 101

what have been the main technological advancements in microbiology?

Answer 101

direct cell counts (great plate count anomaly) culturing (the rare biosphere) 16S surveys (biological "dark matter") metagenomics

Question 102

what is the great plate count anomaly?

Answer 102

the finding that microscopic and culture enumerations differ by orders of magnitude for three possible reasons - different nutritional requirements - cells may be in non-dividing state - organisms may rely on other organisms (can't grow alone) basically a lot of micro-organisms are unculturable

Question 103

what is enrichment bias?

Answer 103

each culture media selects for only a few organisms microorganisms cultured in the lab are frequently only minor components of the microbial ecosystem

Question 104

what are the reasons for why we have a tendency towards common fast growing microbes when culturing?

Answer 104

nutrients available in the lab culture are typically much higher than in nature narrow set of conditions in lab culture selects for organisms that can grow alone (even though many organisms are auxotrophic)

Question 105

why is a dilution of inoculum performed?

Answer 105

to eliminate rapidly growing but quantitatively insignificant weed species

Question 106

what are two culture-independent analyses of microbial communities?

Answer 106

PCR methods of microbial community analysis Environmental genomics and related methods

Question 107

what is the rare biosphere?

Answer 107

a concept describing the observation that a very large proportion of the taxa in microbial communities are extremely uncommon i.e. there is massive diversity found in low abundances, so a few organisms make up the vast majority of sequences you get from a sample cause a few species make up the majority of organisms in any ecosystem

Question 108

what led to the discovery of the rare biosphere?

Answer 108

new technologies such as 16S sequencing this enabled the detection of these rare populations as prior techniques lacked the resolution to detect the rare biosphere

Question 109

what is a genome?

Answer 109

entire complement of genetic information including genes, regulatory sequences and noncoding DNA genomes are also somewhat moulded by an organisms lifestyle

Question 110

what is genomics?

Answer 110

discipline of mapping, sequencing, analysing and comparing genomes

Question 111

what is bioinformatics?

Answer 111

multidisciplinary field that combines biology, computer science, information engineering, mathematics and statistics to analyse and interpret biological data explores gene functions, who carries what genes and where these genes are found

Question 112

what is comparative genomics?

Answer 112

involves making alignments to compare genes and genomes across many different organisms so that we can identify trends such as highly conserved genes many genes can be identified by sequence similarity to genes found in other organisms (comparative analysis) comparative analyses allow for predictions of metabolic pathways and transport systems

Question 113

what is the number of genes with a role that can be clearly identified in a given genome?

Answer 113

70% or less of total open reading frames (ORFs) detected

Question 114

what are hypothetical proteins?

Answer 114

uncharacterised open reading frames (ORFs) so basically proteins that likely exist but whose function is not known hypothetical proteins likely encode nonessential genes (e.g. in E. coli there are lots and they are thought to encode regulatory or redundant proteins) considered to be biological 'dark matter' which is parts of the genome that are consistently being detected but we have no idea what their purpose is

Question 115

what is metagenomics (environmental genomics)?

Answer 115

DNA from whole microbial community (in a sample) is extracted and directly sequenced no primers needed so metagenomics is unbiased

Question 116

why can the primers and polymerases used in PCR methods of microbial analysis create a bias?

Answer 116

they may preferentially amplify one target over another to make primers you also need to know the sequence of the part of DNA you want to flag creating further bias against unknown organisms

Question 117

what is the metagenome?

Answer 117

the total genetic content of all organisms present in an environment

Question 118

what are the pros of metagenomics?

Answer 118

detect as many genes as possible yields picture of gene pool in environment can detect genes that are not amplified by current PCR primers powerful tool for assessing the phylogenetic and metabolic diversity of an environment

Question 119

how does total DNA extraction occur in metagenomics?

Answer 119

environmental single-gene surveys shotgun studies of all environmental genes

Question 120

what does the DNA sequencing in metagenomic allow us to identify?

Answer 120

identify common genes within a community identify genome contents favoured by current environmental conditions

Question 121

what is the difference between 16S and metagenomics?

Answer 121

16s targets a single gene while metagenomics sequences all the information in a sample

Question 122

what is transcriptomics?

Answer 122

targets RNA (transcripts from genome) the transcriptome is the entire complement of RNA produced under a given set of conditions and this is what transcriptomics is looking at

Question 123

what is proteomics?

Answer 123

genome-wide study of the structure, function and regulation of an organisms proteins equivalent of sequencing all the proteins in a sample to see what is actually made

Question 124

what is metabolomics?

Answer 124

the complete set of metabolic intermediates and other small molecules produced in an organism can be broken down into glycomics (sugars), lipodomics (lipids), and fluxomics (changes in concentration of things)

Question 125

why might one use all of the omics together?

Answer 125

just because a gene is their doesn't mean it is being used if a gene is found by genomics is found to be turned on by transcriptomics, then we don't know if the actual phenotype shows as there may be post-translational modifications. So we then use proteomics

Question 126

what can be learned from RNA experiments?

Answer 126

expression of specific groups of genes under different conditions expression of genes with unknown function; can yield clues to possible roles comparison of gene content in closely related organisms identification of specific organisms