Principles of Biology
2nd Edition
ISBN: 9781259875120
Author: Robert Brooker, Eric P. Widmaier Dr., Linda Graham Dr. Ph.D., Peter Stiling Dr. Ph.D.
Publisher: McGraw-Hill Education
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Chapter 24.1, Problem 1TYK
Summary Introduction
Introduction:
The microbiome consists of all the genetic material of the entire collection of microbes in a specific environment. Species of archaea, bacteria, protists and
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Ihsan is a biologist working with the genetics of a psychrophilic bacterium. He cloned an
antifreeze gene from the bacteria for further analysis. After cloning, he isolated the plasmid
carrying his gene of interest for sequencing. Ihsan finally received the nucleotide sequence of
his gene. Explain in detail how he could verify whether the nucleotide sequence matches his
gene of interest using the bioinformatics databases available.
Jackson Wang is a biologist working with the genetics of a thermophilic bacterium. He cloned
a heat shock gene from the bacteria for further analysis. After cloning, he isolated the plasmid
carrying his gene of interest for sequencing. Jackson finally received the nucleotide sequence
of his gene. Explain in detail how he could verify whether the nucleotide sequence matches his
gene of interest using the bioinformatics databases available.
You are cloning a gene called ice, which will help strawberry plants
survive in cold weather, into a test group of strawberry plants. Select
the events you would use to genetically engineer these plants.
Insert the ice gene into the T-DNA region of a Ti plasmid;
transform Agrobacterium tumefaciens with this plasmid; Inoculate a
culture of strawberry plant cells with Agrobacterium tumefaciens; Select
plant cells that have taken up the ice gene.
Insert the ice gene into the T-DNA region of the Agrobacterium
tumefaciens chromosome; Inoculate a culture of strawberry plant cells
with Agrobacterium tumefaciens; Select plant cells that have taken up
the ice gene.
O Insert the ice gene into a Ti transposon; Introduce the transposon
into Agrobacterium tumefaciens Ti plasmid: Inoculate a culture of
strawberry plant cells with Agrobacterium tumefaciens: Select plant cells
that have taken up the ice gene.
Insert the ice gene into a Ti bacteriophage; transduce Agrobacterium
tumefaciens with this…
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- You are performing an experiment using CRISPR-cas9 to genetically modify the LacZ gene of a culture of E. coli. After you run the experiment, you decide to use gel electrophoresis to genotype the different bacterial cultures to determine if the gene editing was successful. How could your electrophoresis results confirm that the PCR was successful? And how could your electrophoresis results confirm that you successfully extracted genomic DNA from your bacterial samples?arrow_forwardThe idea behind PCR-based diagnostics is that a very small number of microbial genomes in a patient sample can be multiplied by PCR and more easily detected by the clinical team managing the patient’s care. Also, genetic-based diagnostics are very useful for viral infections because we don’t have biochemical tests, etc. to distinguish one virus from another (remember, viruses are metabolically inactive). However, a lot of work goes into the development of these tests. For instance, PCR requires primers that are complementary to the viral genome that is being copied. If primers are complementary to the target genome, what must scientists know to design primers that bind to the viral genome to be copied? (I mean this to be a general question; don’t look up the details of designing primers)arrow_forwardWhen we discussed microbiome analysis, we used a popular example in which you perform PCR using primers specific to a region of the 16S rRNA. This means that bacteria and archaea sequences will be represented in the PCR product and can be taxonomically assigned after deep sequencing, while eukaryotes will be excluded from the analysis. True Falsearrow_forward
- Q7) What are things that are common in cloning vectors? Why are they useful?Q8) Using the pCR 2.1 vector, what antibiotics would a cell with the vector be resistant to?Q9) What does B-galactosidase do?arrow_forwardCloning vectors are not just limited to bacterial plasmids. Bacteriophages and M13 phage vectors are also commonly utilized in the cloning process. State any five (5) key criteria to be an effective cloning vector.arrow_forward1)Find a plasmid map for pET11a and create a basic procedure for cloning a gene into this vector. Which selection method and substance would you use for this plasmid after transformation? 2) Which organism would be your first choice for transformation: a bacterium, earthworm, fish or mouse? Describe your reasoning. 3) What is the main difference between plates before and after centrifugation? What may be the purpose of concentrating the media and perform a second plating?arrow_forward
- Much of what we know about the human microbiome – the microbial communities associated with various parts of our bodies – comes from genome sequencing. Here, DNA is extracted from all cells in samples collected from various body sites and randomly sequenced, typically generating huge volumes of short-read sequencing data. These reads thus represent a random, mixed snapshot of genes encoded within any cell in the original sample. As human cells are commonly collected along with the bacteria, researchers first remove human DNA sequences from the dataset. To do this, they computationally remove any reads that are highly similar to the human reference genome; the remaining gene sequences are then assumed to belong to the microbial community. Researchers studying the human microbiome have frequently been interested to find that these bacterial communities seem to contain a number of highly unusual genes that are unique to human-associated microbes. a) Briefly describe one feature of…arrow_forwardThe following DNA sequence is from a bacteriophage that infects a pathogenic bacterium and scientists want to know if this bacteriophage could prove to be a potential treatment against it. But first scientists need to discover if different strains of this pathogen have restriction endonucleases that it may use for its own protection. They try 3 different RE’s:a) EcoR1 b) HaeIII c) BamH1 Look up the recognition sequences for the 3 Res. Enzymes above and check whether the phage genome (a snippet of which is shown below) will or will not be ‘cut’. Tell me how their experiment worked out and what their conclusion was.G A A A A G G C C A C A A G G C C G T C G A C T T T T A A A A G G C C A C A T G C G G C T T T T C C G G T G T T C C G G C AG C T GA A A AT T T T C C G G T G T A C G CCarrow_forwardIf you made a cDNA library from human brain cells and one from human liver cells would the clones in your two libraries be the same? a)Yes, the libraries would be identical. b)You cannot make cDNA libraries from these cell types. c) No, the libraries would have few overlapping clones. d) The libraries would have a number of similar clones for common cellular proteins but would have a number of unique clones associated specifically with each cell type.arrow_forward
- In order to construct a genome library, which statement most accurately describes the correct order of steps in the process? Fragment chromosomal DNA, digest plasmid vector, ligate genomic DNA and digested plasmid vector, transform ligation into bacteria, select for plasmid marker Fragment chromosomal DNA and plasmid vector, ligate genomic DNA and plasmid vector, transform ligation into bacteria, select for gene marker Fragment chromosomal DNA and plasmid vector, ligate genomic DNA and plasmid vector, transform ligation into bacteria, select for plasmid marker Fragment chromosomal DNA, ligate genomic DNA and plasmid vector, transform ligation into bacteria, select for plasmid markerarrow_forwardImagine that there is an E. coli outbreak in your area, and you would like to test the kangkong from your local grocery store. How could you modify this protocol to extract DNA from the kangkong (to identify the species) and check for presence or absence of E. coli.? Keep in mind that (i) E. coli is free-living and not an endosymbiont, and (ii) plant cells are encased in both a cell membrane and cell wall.arrow_forwardA graduate student isolates two new retroviruses: Virus A and Virus B. To determine whether these viruses could cause cancer, the student infected human cells with each of the viruses and then transfered the infected cells to nude mice to see if the viruses would cause formation of tumors. The student was able to determine by PCR that both viruses are integrated into the genome of the host cells before transplanting cell in mice. The data for this assay are shown in the figure below. Explain how the mechanism of transduction may be different for these two viruses to yield the observed data (limit 4-5 sentences). Retrovirus Transformation Assay % Cells Cause Tumors 120 100 80 60 40 20 0 0 10 -Virus A -Virus B 30 20 Days Post Infection 40arrow_forward
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8C - How to do genetic analysis; Author: Useful Genetics;https://www.youtube.com/watch?v=HIa7nPyGn4s;License: CC-BY