Questions 1-6 Flashcards
Give the definition of Phylogeny and Taxonomy and Domain
Phylogeny
Branch of biology, about evolutionary history of organisms
(phylogenesis: evolutionary development of species and organisms
Taxonomy
Science of identification, classification and nomenclature
Domain
Taxonomic sense, the highest level of biological classification
Definition of Archea, Bacteria Eukarya
Archea
A group of phylogenetically realted prokaryotes distinct from bacteria
Bacteria
A group of phylogenetically related prokaryotes distinct from archea
Eukarya
All eukaryotic cells (Algea, protozoa, fungi, slime molds, plant and animal cells)
Give the definition of phylum, family, genus and species
Phylum
A major lineage of cells in one of the three domains of life
Family
In biological classification, an intermediate level of the taxonomic hierarchy. Contains one or more genera, each of which consists of one or more species.
Genus
A collection of different species, each sharing one or more (usually several) major properties
Species
In microbiology, a collection of strains that all share the same major properties but differ in one or more significant properties from other collections of strains
What is the binomial system?
The system established by Carl Linnaeus for naming living organisms, by which an organisms is given a genus name and a species epithet
How can we use ribosomal sequences for understanding of phylogeny?
Ribosomal RNA gene sequencing is used to get a phylogenetic tree of microorganisms:
- Cells are broke up and DNA is isolated
- The gene encoding ribosomal RNA is isolated and multiplied by PCR
- The PCR product is sequenced
- Based on similarities and differences in sequence a phylogenetic tree is calculated (neighborhood analysis): Sequence alignment & analysis, Calculation of evolutionary distance, phylogenetic tree
Define evolutionary distance and evolutionary chronometer
Evolutionary chronometer
A molecule, such as ribosomal RNA, whose molecular sequence can be used as a comparative measure of evolutionary divergence.
Evolutionary distance
In phylogenetic trees, the sum of the physical distance on a tree separating organisms; this distance is inversely proportional to evolutionary relatedness.
What is a universal tree
A phylogenetic tree that shows the position of representatives of all domains of living organisms.
What is a 16S ribosome and why is it important?
- A large polynucleotide (~1500 bases)
- Functions as part of the small subunit of the ribosome of prokaryotes
- Sequence evolutionary information can be obtained from this 16S ribosome
- Eukaryotic counterpart, 18S rRNA
What are some taxonomical tools?
Comparative analysis of phenotype
* Morphology (Shape, size, gram reaction)
* Motility (by flagella, gliding, gas vessels, nonmotile)
* Nutrition and physiology (mechanism of energy conservation (photo-, chemoorgano/lithotroph)
* Relationship to oxygen, temperature, pH, and salt requirements/ tolerances, ability to use various carbon, nitrogen, and sulfur sources)
* Other factors (pigments, cell inclusions or surface layers, pathogenicity, antibiotic sensitivity)
* Biochemical tests: Fatty acid methyl ester analysis (FAME); in fungi e.g. yeasts or filamentous,…
Comparative analysis of the genotype
- GC ratio: determination of the content in guanine and cytosine in the genome
- DNA hybridization: DNA pieces of both species are mixed, hybridisation, how much attaches?
- Ribotyping: DNA digestion via restricition enzymes, fragments in gel electrophoresis + hybridisation with rRNA probes, pattern detection + analysis
- Gene amplification analysis: Microarray, MLSt Multi-Locus-Sequencing-typing of several conserved gene regions
What is comparative analysis of phenotype?
- Morphology (Shape, size, gram reaction)
- Motility (by flagella, gliding, gas vessels, nonmotile)
- Nutrition and physiology (mechanism of energy conservation (photo-, chemoorgano/lithotroph)
- Relationship to oxygen, temperature, pH, and salt requirements/ tolerances, ability to use various carbon, nitrogen, and sulfur sources)
- Other factors (pigments, cell inclusions or surface layers, pathogenicity, antibiotic sensitivity)
- Biochemical tests: Fatty acid methyl ester analysis (FAME); in fungi e.g. yeasts or filamentous,…
What is comparative analysis of genotype?
- GC ratio: determination of the content in guanine and cytosine in the genome
- DNA hybridization: DNA pieces of both species are mixed, hybridisation, how much attaches?
- Ribotyping: DNA digestion via restricition enzymes, fragments in gel electrophoresis + hybridisation with rRNA probes, pattern detection + analysis
- Gene amplification analysis: Microarray, MLSt Multi-Locus-Sequencing-typing of several conserved gene regions
What are important sources for drinking water?
What types of water resources do exist and how can they be used for drinking water supply?
Groundwater: good water quality (filtration through soil)
- Springs: natural sources of groundwater, protect against contamination!
- Artesian wells: pressure applied, comes from confined aquifer
- Groundwater story (aquifer), water-bearing stratum
Surface water: more or less contaminated → in most cases treatment necessary (flocculation, filtration, disinfection), or use water from specifically constructed and protected reservoirs, hygienic quality of river decreases from spring to estuary mouth
Rainwater: is collected in cisterns but preservation is main problem, no good quality (especially industrialized countries), cannot be used without any treatment as drinking water for humans (limited for animals)
Seawater: Utilization requires desalting treatment like evaporation and condensation, reverse osmosis, ultra-filtration, electrodialysis → after that hygienic quality is good
What are some parameters for the evaluation of the quality and hygiene of drinking and recreational water?
BOD = biological oxygen demand → amount of oxygen used by MO to decompose organic waste, high value = bad
**Mostly only the presence of indicator organisms is analyzed ** + allows more samples, better microbial evaluation
- E.coli, fecal Streptococci and enterococci = fecal contamination + specific
- Faecal coliforms: indicate fecal contamination from warm-blooded animals + for disinfection susceptibility
- Sulfite-reducing Clostridiae = spore formation, indicate remote fecal pollution
- Clostridium perfringens
Pseudomonas: associated with recreational waters, highly resistant to disinfectants - Coliphages (FRNA Phage) = presence of human enteric viruses + easy isolation from env.
- Enteroviruses
General requirements for water for human consumption:
- Parametric value (Number cfu/100ml): E. coli, Enterococci, Coliform bacteria: **has to be 0
- Water offered for sale in bottles or containers: E. coli, Enterococci, Pseudomonas aeruginosa, Coliform bacteria: **Value different from 0 possible.
→ enough to consider a few species, tests with standardized volumes
Bacterial load total (bioburden): heterotophic plate count, enumeration of all aerobic bacteria capable of growing on commonly used media - space and time consuming
What are the basic steps of the Gram staining? How does it function?
Gram staining: dependent on the composition of the cell wall
→Gram-positive blue
→ Gram-negative red
- Gram +: lipid membrane, thick peptidoglycan layer
- Gram -: lipid membrane, thin peptidoglycan layer, outer lipid membrane, lipopolysaccharides (anchor is toxin!!)
→ Peptidoglycan layer of G+ has pores where color particles get stuck when Lugol alcohol dehydrates the layer
Steps
1. Air drying fixes bacteria on slides
2. Dye violet, remove after 2 min
3. Add lugol solution, remove after 2 min
4. Discoloration with ethanol, works only on G-
5. Counterstain with red color
