Article Review 6 Read the following article: Rasmussen S, Allentoft Morten E, Ni
ID: 176917 • Letter: A
Question
Article Review 6
Read the following article:
Rasmussen S, Allentoft Morten E, Nielsen K, et al. Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell.163(3):571-582.
For this paper, you will need to submit a Grammarly report along with your paper (must be uploaded with your paper). The Grammarly score must be above 80%. MAKE SURE YOU HAVE THE PLAGIARISM CHECK ON!
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Important reminders:
Do not use superlatives or hyperbole. (don't waste text with unnecessary dialog or comments).
Do not repeat the text of a question.
Make sure your paper is logical, that you have answered every point you raised, and that it is divided into appropriate paragraphs.
Remember to write a reflection at the end.
Your file MUST be in one of the following formats: .rtf, .doc, .docx, or .pdf. No other format is acceptable.
What must be in your paper:
State the goal/purpose of the article.
State the working hypothesis.
Discuss the importance of Yersina pestis, including the importance of the YMT gene.
Explain the concept of a molecular clock (how do researchers determine the age of a divergence?).
Explain the importance of divergence?
Discuss the concept of phylogeny, and how it is determined.
Explain figure 2 and 4
Discuss the authors' conclusions.
Reflection: three things you learned from this paper.
Explanation / Answer
The main goal of this article is to know the origin of the Yersinia pestis which is an etiological agent of plague and responsible for human pandemics and in addition to this they tried to find out how it has acquired more virulence and was able to cause bubonic plague. The working hypothesis is Y.pestis strain which is a virulent and flea borne has evolved from a less pathogenic Y.pestis lineage infecting human populations.
Yersinia pestis is responsible for the cause of plaque and will be transmitted through human to human contact and is responsible for three major historic human pandemics. The pandemic which has occurred in Europe has killed nearly 30 to 50% of European population resulting in economic and political collapses.
In Y.perstis genomes, 55 genes were found to be associated with the virulence and Yersinia murine toxin (ymt) gene alone was found on the pMT1 plasmid. This ymt genes is known to encode a phospholipase D and this enzyme will provide protection to Y.pestis inside the gut of flea and thus this arthropod will act as a vector for the transmission of Y.pestis. One more finding is ymt gene is not present in Y.pestis before 1686 cal BC, but Y.pestis acquired this gene only after 951 cal BC and is by horizontal gene transfer.
As we all know, the molecular clock is a technique which with the help of mutation rate of biomolecules (DNA or protein sequences) will try to tell us the when actually the lifer form has diverged. In this article through molecular clock, it was estimated that Y.pestis was diversified between 2600 and 28000 years ago from this more prevalent and environmental stress tolerant, less pathogenic Y.pseudotuberculosis bacterium. Later research showed that the divergence actually happened before 5783 years ago and it is done by taking temporally stamped ancient DNA data and by doing time series for the molecular acquisition of the pathogenicity elements and immune avoidance systems.
Divergence has played an important role in the emergence of this virulence strain of Y.pestis and with the help of SNPs the branch length of the Y.pestis clade to Y.pseudotuberculosis was estimated. A Bayesian Markov Chain Monte Carlo approach implemented in BEAST2 on a subset of the supermatrix method was used to known the recent common ancestor of Y.pestis and Y.pseudotuberculosis. Like this it was found that the Y.pestis was branched 5783 years ago.
Through phylogeny, the authors got the diagrammatic hypothesis which can explain actual history of the evolutionary relationship of Y.pestis with other group of organisms. Here they chose RISE505 and RISE509 and mapped the reads from Yersinia similis (n = 5), Y. pseudotuberculosis (n =25), and Y. pestis (n = 139), to the Y. pseudotuberculosis reference genome (IP32953).RAxML was used to construct a Maximum Likelihood phylogeny from a supermatrix concatenated from 3,141 genes and a total of 3.14 Mbp.
In figure 2, three plasmids pCD1, pMT1, and pPCP1 (0.12 to 50.3X in average depth) were mapped and the latter two of which played a crucial role for distinguishing Y. pestis from its highly similar ancestor Y. pseudotuberculosis. The analysis helped us to locate the ymt gene at 74.4-76.2 kb on the pMT1 plasmid and this ymt of 19kb region was found only in the youngest sample (RISE397, 951 cal BC)
Through this work, the authors concluded that Y.pestis was originated 5783 years ago and Y.pestis has acquired pathogenicity elements and immune avoidance system through a time series and this has helped it to evolve as a most deadly bacteria from a less virulent bacteria with zoonotic potential. Ancient Y.pestis strain was able to cause only pneumonic and septicemic plague, but the evolved strain caused bubonic plaque. Only after 1st millennium BC, the Y.pestis has become fully adapted lea borne mammalian pathogen.
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