Brock Biology of Microorganisms (15th Edition)
15th Edition
ISBN: 9780134261928
Author: Michael T. Madigan, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley, David A. Stahl
Publisher: PEARSON
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Textbook Question
Chapter 1.13, Problem 3MQ
- List three reasons why rRNA genes are suitable for phylogenetic analyses.
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Carl Woese has recognized that genes encoding rRNAs are excellent candidates for phylogenetic analysis. Identify at least 4 characteristics/properties of these rRNA genes which make them good molecular chronometers.
Carl Woese discovered that genes encoded for rRNAs are good candidates for phylogenetic analysis. Determine at least four characteristics/properties of these rRNA genes that make them effective molecular chronometers.
The phylogenetic tree of the OCTN homologs below was generated with the following accession numbers as basis:
NP_957143.1 - OCTN of unknown function
CDM63451.1 - OCTN specific for ergothioneine transport
XP_021324939.1 - OCTN specific for carnitine transport
Design the phylogenetic tree to make it look more interesting by highlighting the distinct clades or putting a visual emphasis on the gene you are trying to analyze. Provide a caption for this figure.
Chapter 1 Solutions
Brock Biology of Microorganisms (15th Edition)
Ch. 1.1 - In what ways are microorganisms important to...Ch. 1.1 - Why are microbial cells useful for understanding...Ch. 1.1 - What is a microbial colony and how is one formed?Ch. 1.1 - What are bacterial colonies and how are they...Ch. 1.2 - What structures are universal to all types of...Ch. 1.2 - Prob. 2MQCh. 1.2 - What structures can be used to distinguish between...Ch. 1.2 - Prob. 1CRCh. 1.3 - How old is Earth and when did cells first appear...Ch. 1.3 - Prob. 2MQ
Ch. 1.3 - Why were cyanobacteria so important in the...Ch. 1.3 - Prob. 1CRCh. 1.4 - Prob. 1MQCh. 1.4 - Prob. 2MQCh. 1.4 - Prob. 3MQCh. 1.4 - Prob. 1CRCh. 1.5 - Define the terms magnification and resolution.Ch. 1.5 - Prob. 2MQCh. 1.5 - Prob. 1CRCh. 1.6 - Prob. 1MQCh. 1.6 - Prob. 2MQCh. 1.6 - How can cells be made to fluoresce?Ch. 1.6 - Prob. 1CRCh. 1.7 - Prob. 1MQCh. 1.7 - Prob. 2MQCh. 1.7 - Prob. 1CRCh. 1.8 - Prob. 1MQCh. 1.8 - Prob. 2MQCh. 1.8 - Prob. 1CRCh. 1.9 - Prob. 1MQCh. 1.9 - Prob. 2MQCh. 1.9 - Besides ending the controversy over spontaneous...Ch. 1.9 - Explain the principle behind the Pasteur flask in...Ch. 1.10 - How do Kochs postulates ensure that cause and...Ch. 1.10 - What advantages do solid media offer for the...Ch. 1.10 - Prob. 3MQCh. 1.10 - Prob. 1CRCh. 1.11 - What is meant by the term enrichment culture?Ch. 1.11 - Prob. 2MQCh. 1.11 - What were the major microbiological interests of...Ch. 1.12 - Describe the experiments that proved DNA was the...Ch. 1.12 - Why are microbial cells useful tools for basic...Ch. 1.12 - Describe the experiments that proved DNA to be the...Ch. 1.13 - What kinds of evidence support the three-domain...Ch. 1.13 - What is a phylogenetic tree?Ch. 1.13 - List three reasons why rRNA genes are suitable for...Ch. 1.13 - What insights led to the reconstruction of the...Ch. 1.14 - How are viruses different from Bacteria, Archaea,...Ch. 1.14 - What four bacterial phyla contain the most...Ch. 1.14 - Prob. 3MQCh. 1.14 - What features (or lack of features) can be used to...Ch. 1 - Pasteurs experiments on spontaneous generation...Ch. 1 - Describe the lines of proof Robert Koch used to...Ch. 1 - Imagine that all microorganisms suddenly...
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- Why is sequence alignment critical to phylogenetic analysis?arrow_forwardExplain how the different “-omics” involved with the three major parts of the central dogma can be used to study this new species. What are molecular techniques/tools (sequencers) that can be used to study each of these? How would you sequence the genome efficiently (i.e., lowest amount of time and money)?arrow_forwardselect the correct options: A) For organisms that diverged >74 mya, ignore 3rd base positions within codons because they will offer little phylogenetic information for organisms. B) use different parts ofthe genome to estimate different parts of a phylogeny C) Use only 1st base positions within codons because they increase rapidly at first, then level off as result of single subsitituions at the same sites D) Use slowly evolvong sites in the squecne, such as 2nd base positions within codonsfor analyzing the oldest relationships among organisms.arrow_forward
- What are three reasons that functional traits might notcorrespond with distinct phylogenetic groups as defined by16S ribosomal RNA gene sequences?arrow_forwardHere is some information about the sequences: There are two images given; one with sequences and the other with a figure. All these sequences, “SEQUENCE_21” to “SEQUENCE_27” are in the same subfamily or “clade” of a large phylogenetic alignment of all Rab proteins in these three species (see “Image with a figure” for a full view of gene family in humans, plants and yeast, see the “D” branch towards the bottom of the tree in Figure). “SEQUENCE_28” is a different Rab protein (actually it is the Rab39 protein at the bottom of the tree). “SEQUENCE_21” is from yeast. “SEQUENCE_22” to “SEQUENCE_25” are from the plant, Arabidopsis. “SEQUENCE_26” and “SEQUENCE_27” are from humans. Question: Based on the information above, what can you speculate about the possible evolution of the genes that “SEQUENCE_21” to “SEQUENCE_27” represent?arrow_forwardWhat are the two advantages of using sequence analysis of ribosomal components in determining the relatedness of organisms? please explain why each is an advantage.arrow_forward
- Here is some information about the sequences: All these sequences, “SEQUENCE_21” to “SEQUENCE_27” are in the same subfamily or “clade” of a large phylogenetic alignment of all Rab proteins in these three species (see “Figure 1.pdf” for a full view of gene family in humans, plants and yeast, see the “D” branch towards the bottom of the tree in Figure 1). “SEQUENCE_28” is a different Rab protein (actually it is the Rab39 protein at the bottom of the tree). “SEQUENCE_21” is from yeast. “SEQUENCE_22” to “SEQUENCE_25” are from the plant, Arabidopsis. “SEQUENCE_26” and “SEQUENCE_27” are from humans. Question: Based on the information above, what can you speculate about the possible evolution of the genes that “SEQUENCE_21” to “SEQUENCE_27” represent? (write 5 points at least).arrow_forwardLet's say that you're a scientist trying to analyze newly sequenced bacterial DNA genomes from an environmental sample of rainforest soil, and your first task is to organize all of the genomes you find into a phylogenetic tree. If you couldn't use the 16S rRNA gene sequence to create the tree, which of these alternative genes would work best for your task of creating a tree that works for all the bacteria in your sample? The gene for Bacteriochlorophyll A A gene for an RNA polymerase component protein The first gene in the histidine biosynthesis pathway The first gene in the LPS synthesis pathwayarrow_forwardThere 27 sequences from 27 individuals belonging to an unidentified group of organisms. Eleven (11) sequences were mined from NCBI while the rest are unpublished sequences from Mindanao. Sequences labeled with "SSL" are from Agusan Marsh while sequences labeled with "CKL/CITLR" and "CWL" are from Camiguin Island and Dinagat Islands respectively. Finally, sequences labeled with "MSLA" are from Mt. Magdiwata. (a) What species is considered as the outgroup? (b) What genetic marker is utilized to generate the sequences? (c) Which specimen group is more closely related to "SSL"? CKL or MSLA? Justify your answer. (d) Based on the BLAST results, what possible species name can be assigned to the MSLA group?arrow_forward
- A) What module can we use to run BLAST over the internet in Biopython: Bio.Blast.NCBIWWW Bio.Blast.NCBIXML WWW NCBIXML B) Which one of the following modules is not part of the Bio.Blast package in Biopython: NCBIStandalone FastaIO ParseBlastTable NCBIXML 3. Question 3 Using Biopython find out what species the following unknown DNA sequencearrow_forwardYou isolate bacteria from several different pools at the recreation center. Curious about which bacteria likely have a common ancestor with your reference pool (the Buffalo-pool), you BLAST the 16S ribosomal gene from the Buffalo pool bacteria against the 16S ribosomal genes from the other pools. The results are shown below. Which of the bacteria likely have a common ancestor with the Buffalo-pool bacteria? Use e as a cutoff for homology. Organism Dive-well bacteria Competition-pool bacterial Practice-pool bacteria Puddle bacteria Puddle bacteria Practice-pool bacteria Competition-pool bacteria Dive-well bacteria E-value 9e-175 -300 8e 4e-2 4arrow_forwardMetagenomics has revolutionized our understanding of the microbial world by allowing the study of organisms that had been impossible to culture. Understanding the Lokiarchaeota required metagenomics analysis, which has also led to the identification of the eukaryotic signature genes in other environments. The terms below relate to genes and genetic analysis. Drag each term to the correct description. Drag and drop the terms on the left to match the description on the right. ▸ View Available Hint(s) Submit Homologous Monophyletic Metagenomics Orthologs Paralogs and that has a different function (this occurs through gene duplication) : the study of genetic material from an environmental sample Reset : a group of organisms in a phylogeny that have a common ancestor : a gene that is related in different species by being inherited from a common ancestor Help and that has the same function : a gene that is related in different species by being inherited from a common ancestor : a gene that…arrow_forward
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