Chat with AIExam 9: Microbial Systems Biology
The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.
(39) 
VerifiedFALSE
Recommend what type of data should be collected and analyzed in a systems biology approach to investigate how a non-pathogenic bacterial strain becomes pathogenic. Describe what scientific fields and methods would be involved in your recommendation.
(43) VerifiedA systems biology approach integrates multiple methods and fields to model or analyze a problem. One approach would be to compare the genome and the proteome of non-pathogenic and pathogenic strains of a particular species to find the genes and proteins that are different and may be related to pathogenicity. This research would involve 3rd or 4th generation sequencing, 2D polyacrylamide gel electrophoresis of proteins, and bioinformatics to process and analyze all the data. Further experimentation could involve genetic manipulations to investigate the effect of removing or mutating the implicated genes and biochemical characterization of the implicated proteins. (Answers could vary significantly, but any reasonable discussion of how various ʺ-omicʺ techniques and methods could be applied to this problem could be acceptable as long as the discussion is consistent and logical, linking the appropriate data types and methods to detect differences between pathogenic and nonpathogenic organisms. The answer should include the definition of systems biology.)
The Human Microbiome Project is a large research program that aims to understand all of the microorganisms on and in the human body. Which ʺ-omicʺ methods could be applied directly to a sample from the human body to study the microorganisms in the sample? Propose a general experimental approach for analyzing a sample containing a complex mixture of microorganisms.
(38) VerifiedA sample from the human body, such as stool or tooth swab, would be collected and the DNA or RNA extracted. RNA would be converted to cDNA. The cDNA would then be sequenced. This approach is metagenomics (and metatransciptomics for RNA). After sequencing, the short sequences must be assembled into longer stretches (genes or whole genomes). An alternative answer could outline the procedure of single-cell genomics from cells obtained from samples from the human body or the use of a gene chip for identification of organisms. Any answer that shows understanding of general steps and uses terms appropriately and consistently throughout the answer would be acceptable.
Explain horizontal gene transfer and demonstrate how this phenomenon has complicated evolutionary studies using a diagram that illustrates phylogenetic relationships between organisms and genes.
(37) Within Archaea and Bacteria, one megabase pair (Mbp) of DNA encodes about ________ open reading frames.
(34) Transcriptome analysis is useful in relation to genome analysis because
(37) Genes for DNA replication and transcription make up only a small fraction of the typical prokaryotic genome.
(31) In addition to chromosomes, some mitochondria also contain other genetic material known as
(35) A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are
(41) Genes encoding compounds such as pyruvate, acetyl-CoA, fructose-6-phosphate, oxaloacetate, and other small organic compounds could be part of a(n)
(43) The relative percentage of genes devoted to protein synthesis in small-genome organisms is high compared with that of large-genome organisms.
(45) Explain the terms ʺcore genomeʺ and ʺpan genomeʺ and describe how each contributes to the genome of a bacterial species. Give an example of genes that are part of a core genome versus those that are more often in the pan genome.
(27) After transcription, mRNA may undergo significant editing. Compare and contrast RNA editing in prokaryotes and eukaryotes and connect how these differences affect genome size and gene content.
(32) You want to know whether the virulence genes present in Bordetella pertussis are evolutionarily related to genes in the less pathogenic species B. bronchiseptica or if the virulence genes were acquired via horizontal gene transfer. What characteristic(s) would you compare to answer this question?
(38) The core genome of a prokaryotic species is the genomic content that is
(36) Why are the words ʺaboutʺ and ʺapproximatelyʺ used in discussing the results of genomic analysis? Predict what advances in knowledge or methods could change our understanding of a genome sequence.
(28) In general, prokaryotic genome size is linked to its metabolism and interaction with the environment. Which type of prokaryote typically has the smallest genome?
(39) Microorganisms that grow in extreme environments typically contain larger genomes when compared to microbes that grow in non-extreme environments.
(45) 
Filters
- Essay(0)
- Multiple Choice(0)
- Short Answer(0)
- True False(0)
- Matching(0)