Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Bio 322 > Unit 9 > Flashcards

Unit 9 Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

What are the 2 kinds of analyses of microbial communities?

A
  • culture-dependent
  • culture-independent
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the kinds of culture-dependent analyses?

A
  • enrichment
  • isolation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How does enrichment work?

A
  • collect sample to serve as inoculum culture
  • place inoculum into selective media
  • DNA is extracted
  • sequence 16S r RNA to determine community diversity
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is selective media?

A

Media specific for organism of interest

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the step needed to enrich methane-oxidizing organisms?

A

Incubate soil chunk in minimal media with methane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What happens when consumption of methane is detected?

A

Detected via GC then sample is transferred to fresh media and process is repeated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How does isolation work?

A
  • extracted our culture from enriched sample
  • culture played on agar plate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What happens after growth detected in complete isolation?

A
  • streak few times under specific carbon source
  • mix molten agar with liquid culture and creamy dilutions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is a modern method for isolation?

A

Laser tweezers that includes
- laser beam creates force
- force pushes down microbial cell and holds it in place
- laser beam is moved cell moves with it

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the process in laser tweezers?

A
  • laser beam drags cells down via specific forces
  • cells trapped
  • trapped cells flushed from capillary into tube
  • tube contains sterile media
  • place tube at optimal temp to detect growth
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is flow cytometry?

A
  • Counting and examining microscopic particles by suspending them in stream of fluid and passing them through electronic detector
  • cytometers assess size, shape and fluorescent properties of single cells
  • cells are examination when passing through detector
  • machine sorts cells based on measured criteria
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

are the 2 types of microscopic analysis?

A
  • general staining methods
  • FISH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are the kinds of general staining methods?

A
  • fluorescent staining with dyes that bind nucleic acids
  • viability staining
  • fluorescent proteins as cell tags and reporter genes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

fluorescent staining with dyes that bind nucleic acids

A
  • DAPI dye - binds DNA (eukaryotic)
  • SYBR Green I - bright fluorescence for all micro
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

viability staining

A
  • differentiates living from dead cells
  • cells live = membrane intact = no dye
  • cell dead = membrane not intact = dye
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

fluorescent proteins as cell tags and reporter genes

A
  • gene for GFP inserted into genome of bacterium
  • if GFP expressed, cell fluorescence green when observed with UV microscopy
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

FISH

A
  • not GENETIC
  • nucleic acid probe is a DNA or RNA oligonucleotide complementary to sequence in target gene or RNA
  • probe and target together = hybridize
  • nucleic acid probes made fluorescent by attaching dyes to them
  • fluorescent probes used to identify organisms that contain sequence complementary to probe
  • phylogenetic FISH stains are fluorescing oligonucleotides complementary to sequence of 16 or 18S r RNA
  • phylogenetic stains penetrate cells and hybridizes with r RNA directly in ribosome
18
Q

what are the kinds of genetic analysis?

A

pcr
microarrays
omics

19
Q

PCR

A

amplify DNA that is later used in phylogenetic analysis

20
Q

what is useful to distinguish bacteria at species level?

A
  • recA and gyrB
21
Q

what is the genes that encode proteins accumulate?

A

mutations faster than genes for r RNA

22
Q

why is 16S r RNA not helpful to identify species?

A

conserved gene

23
Q

MLST

A
  • multi loci sequence type
  • relies on different housekeeping genes from related organisms that are examined
  • housekeeping genes encode essential functions in cells and located on chromosome not the plasmid
  • alleles of each genes are assigned a number
  • strain assigned an allelic profile
24
Q

what is MLST have good use in?

A

microbiology and used to differentiate strains of various pathogens

25
Q

genome fingerprinting

A
  • rapid approach for evaluating polymorphisms between strains
  • fingerprints are DNA fragments from genomes
  • gene is PCR amplified and characterized
  • characterize 16S r RNA - ribotyping
  • diff genes used to generate fingerprint
  • based on localization of 16S r RNA genes on genome fingerprinting
  • genomic DNA is extracted and digested by restriction enzymes
  • fragments are separated via electrophoresis
  • fragments are transferred to membrane
  • membrane is incubated and labeled 16S r RNA gene probe
  • size and number of bands detected generates a specific pattern
26
Q

what does the ribotype allow?

A

rapid identification of different species and different strains of species

27
Q

what is another genome fingerprinting method?

A
  • repetitive extragenic palindromic PCR
  • multigene and whole genome analyses
28
Q

rep-PCR

A
  • based on highly conserved repetitive DNA elements randomly incorporated in bacterial chromosome
  • number and positions of these repetitions caries between strains in species
  • primers designed to be complementary to elements
  • PCR amplification of genomic fragments between elements
  • PCR products can be visualized via agarose gel electrophoresis
  • pattern profile of fragments that is characteristic for strain in species
29
Q

multigene and whole genome analyses

A
  • gives insights into large role of HGT in microbial evolution
  • reveals dynamic nature of microbial genomes
  • enables comparative analysis of presence or absence of gene, order of genes in genome
  • whole genome used for metabolic reconstruction and characterization of genetic pathways
30
Q

microarray

A
  • lab tool serves to detect expression of many genes at the same time
  • DNA microarray are microscope slides that contain thousands of tiny spots in defined position
  • each spot has known DNA sequence or gene
  • DNA microarray slides called gene chips or DNA chips
  • DNA molecules attached to each slide act as probes to detect gene expression
31
Q

phylochips

A
  • microarrays designed for biodiversity studies
  • developed for screening of microbial communities
  • microarrays designed to detect genes for ammonia oxidation, sulfate respiration, nitrogen fixation
32
Q

how to create phylochips?

A
  • fix rRNA gene to chip surface
  • phylochip designed for specific group of organisms
  • assess the diversity of sulfate-reducing organisms in sulfidic enviro
  • obtain 16S r RNA from all known SRB and attach to phylochip
  • isolate total community DNA from sediment
  • PCR amplification and fluorescence labeling of 16S r RNA genes
  • hybridize environmental DNA with probes on phylochip
33
Q

application of OMICS

A
  • genomic
  • transcriptomic
  • metabolomic
  • proteomic
34
Q

genetics

A
  • study heredity
  • refers to function and composition of single gene
35
Q

genomics

A
  • study genes and functions
  • function and composition of genes and their internal relationships
  • goal is to identify combined influence of genes on growth and development of organism
36
Q

J. Craig Venter

A
  • modern genomics
  • computational approach helped in sequencing human genome

cut all genome with restriction enzymes
separate PAA electrophoresis
analyze sequence fragment by fragment
time-consuming

37
Q

modern types of sequencing

A

illumina sequencing
- sample preparation
- cluster generation
- sequencing
- data analysis

38
Q

compare soil organisms and parasites

A

soil: larger genomes, complex enviro, diff strategies to survive
parasite: small genomes, partially rely on host where they live

39
Q

what was the goal and what was the organism?

A
  • mycoplasma genitalium to mycoplasma laboratorium
  • identify minimal set of genes required to sustain life
  • rebuild genes synthetically to create a new organisms
40
Q

measuring microbial activity in nature

A
  • chemical assays -> measure lactate oxidation to assess activity of SRB
  • radioactive 14CO2 -> measure intensity of phototrophy in some area
  • microsensors -> microneedle embedded in area
  • stable isotopic labeling -> 13C and 34S

Bio 322 (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions