lecture questions Flashcards
Microbial life first appeared:
a) ~50 million years after Earth’s formation
b) ~65 million years ago
c) ~3.8 billion years ago
d) ~3 million years ago
e) ~3000 years ago
c) 3.8 billion years ago
When aligning sequences; a basic alignment software (like MUSCLE) works
by:
a) Changing sequences to match a consensus
b) Inserting missing basepairs to make sequences align
c) Deleting extra basepairs marked by —- to make sequences align
d) Aligning sequences and inserting gaps
e) Predicting function and clustering on function
d) Aligning sequences and inserting gaps
What are molecular clocks? Describe features of an effective molecular
clock?
-temporal information stored in genomic sequences, follows gene changing over time
-gene function stays the same
-average mutation rate
-constant generation time
The LTEE experiment demonstrated that there is a fitness advantage for ‘evolved’ strains of E. coli vs the parental strain in the glucose and citrate containing media tested. You ask for these strains for your lab, and want to test fitness in 100 media types with different carbon sources under both aerobic and anaerobic conditions.
Do you expect the ‘evolved’ strains of E. coli to outcompete the parental strain in most conditions? Why or why not?
no, fitness it dependent on the environment you’re analyzing so the aerobic and anaerobic environments will create different fitness levels
How could you setup an experiment to test relative fitness?
-differences in growth kinetics
-compete two strains at equal density, track growth over time
“VRE often expands in the gut of hospital patients receiving antibiotics. Since VRE is already adapted to hospital settings/patients, there is no evidence for the accumulation of new mutations in the gut of colonized
individuals”.
Is this statement True or False, explain.
False, VRE is always acquiring new mutations and adapting as every patient is different, changes in diet, selective pressures, and microbiota differences cause mutations and adaptation
In studies of bacterial diversity, the core genome refers to:
a) The genome of ancient microbes
b) The component of the genome performing functions of the central dogma
c) The collection of all genes identified in a group of isolates
d) The genes shared between a group of related bacteria
e) The genes that are not shared between a group of related bacteria
d) the genes shared between a group of related bacteria
What are some key steps in genome annotation? What types of features are annotated?
- identify and annotate the core genes, tRNA’s and rRNA’s
- predict functions of open reading frames
- BLAST all hypothetical proteins to attempt to determine function
What is a Draft genome? Explain how long-read sequencing can help overcome some challenges in assembling a bacterial genome encountered with short-read sequencing.
draft genome is all of the short read sequences (contigs) that are broken apart by repeat sequences. long read sequences stitches contigs together and reads through repeat sequences
Nitrogenase, an enzyme required to ________________, requires anaerobic conditions to function. How is this accomplished in oxygenic cyanobacteria?
fix atmospheria nitrogen -> ammonia, accomplished with heterocysts and temporal segregation in oxygenic cyanobacteria
What are dimension reduction techniques? Why do we use them?
dimension reduction - represent data set using lowest number of features while still capturing important features
-used to show inter species diversity
Why would using genes that are syntenic reducing binning errors in MAG assembly? Explain
syntenic: located in the same location on different species genomes
-lots of mutations in one area, contigs are binned together ensuring similar species are binned together still
Using the ___ operon, Salmonella can use ___________ as a
_________________ in ____________ respiration
ttr, tetrathionate, terminal electron acceptor, anaerobic
