I became interested in this article because I am currently recovering from a bout of sinusitus. I originally saw it written up at http://www.sciencedaily.com/releases/2013/02/130218173302.htm (a reprint from a press release by Newcastle University
Full article: Efficacy of a Marine Bacterial Nuclease against Biofilm Forming Microorganisms Isolated from Chronic Rhinosinusitis.
Robert C. Shields, Norehan Mokhtar, Michael Ford, Michael J. Hall, J.
Grant Burgess, Mohamed Reda ElBadawey, Nicholas S. Jakubovics. PLOS ONE published on: 18th February 2013
As with any scientific article, go to the end of the introduction to (very briefly) see what they actually did:
"The exogenous addition of NucB to biofilms formed by Escherichia coli, Bacillus subtilis or Micrococcus luteus resulted in almost complete removal of bacterial cells from surfaces."
Their explanation is that NucB breaks down extracellular DNA (eDNA) and wipes away biofilms. Simple enough.
A little background: A few years back, they isolated a strain of Bacillus licheniformis from red dulce (sea lettuce) which created antimicrobial compounds and red pigments in a bioreactor (from an article by the same author in Applied and Environmental Microbiology, 2003). The antimicrobial compound was determined to be bacitracin, a widely known antimicrobial derived from the same species, and the pigment was unidentified. Later, they published on the NucB enzyme, derived from the same strain and growth conditions, saying that it causes biofilms to break up (reference 33).
Here, they get mucus from 20 sick folks and fix some of it from two of the patients up for electron microscopy. Figure 1 shows you their EM micrographs and it looks much like you would expect mucus to look. Not sure what the purpose of this is, other than to do some EM on snot, which is kind of cool, I guess...
Thankfully they wised up and stained the bacteria with a FISH probe, which binds to bacterial DNA and is fluorescent green (Figure 2). The probe is supposed to target DNA from living cells, but can get caught up in extracellular DNA giving larger fuzzy areas as seen in 2B. I wonder why the epithelial (blue) cells are in focus in panel A and not in panel B. I also wonder why the probe only showed up in parts of the field, but the authors ascribe this to the handling of the specimens during prep.
This is all warmup. Now we get to the 'meat of the paper'. They isolated 75 strains of bacteria from the patient's mucous and screened them for nuclease producers (11 out of 20 patients had them). They selected 20 representative strains (24 individual isolates) of nuclease producing and non-nuclease producing bugs to test for biofilm formation and there was hardly a difference between the two groups. Then they treated these 24 biofilms and found that 9/9 of the nuclease producing strains and 5/15 of the non-nuclease types were dispersed by their NucB enzyme when compared to a buffer treatment. In reality only 50-75 of the biofilm was dispersed, but that was significant when compared to their negative control.
I wish that they had used another nuclease for comparison. Of course the DNA degrading enzyme is going to disperse biofilms better than buffer solution. Why is this exotic isolate worth more than one found in your backyard (or nose for that matter)?
And now we get to Figure 5. Part A shows the difference in eDNA and iDNA size (obvious that eDNA is smaller than inside the cell) but FH29 seems to be lacking the so-called 30kbps band (it also doesn't produce nuclease). I say so-called because the first lane which is the ladder, does not go that high. It also looks like the DNA could have gotten trapped at the top of the gel. Part B shows that there is clearly more iDNA than eDNA, and their quantification showed just as much DNA for FH29 as the other two strains. Then part C shows the eDNA for some of the other strains in the study and some of them appear to be lacking on the gel, but does not follow the nuclease/non-nuclease pattern. The thing that really bothers me about part C is that the ladder looks like it has been photoshopped onto the image, and the two halves of the gel have been spliced together as well. Also, the samples with nothing showing up in the gel have some of the highest values through their other quantification method. Sounds like either cross contamination or (more likely) nanodrop is not an accurate measure of DNA quantity.
Overall, not a bad study, but when you look at the science that's actually being reported, they are a LONG way away from putting this onto the drugstore shelves. I would like to see a study comparing NucB enzymes from different species and, of course, clinical trials on animals and perhaps humans if all else goes well. Until then, I will just have to tough it out, neti some seawater, or gargle some hydrogen peroxide. I think I will tough it out.
Tuesday, February 19, 2013
Wednesday, October 24, 2012
How to read a scientific article
Although each scientific journal has it's own formatting rules on things such as order of presentation, length limitations, and citation style, there are commonalities which can make them easier to comprehend. Experts in the field should be able to understand the essence of a paper after reading most of the abstract, the last section of the introduction, and the figures and tables, but everyday people can also take advantage of these tips to get a quick understanding when trying to tackle a scientific paper.
Abstract: The first sentence or two usually deal with critical background information that form the basis that the study is design upon. The next sentences present a brief description of the experimental or theoretical design, followed by a sentence or two of results. The final sentences of the abstract are reserved for conclusions or a statement to the work's significance. (250 -300 words)
Introduction: The introduction is obviously going to be focused on background information and will be the most citation laden section of the paper. The presentation goes from broad to specific, starting out with an intro to the subject matter, followed by some corollary studies. If the work is about a group of organisms, there is usually some descriptive information which will give the reader insight into the meaning of the results. Often it is in this section that an author will point out gaps in current knowledge as well as studies which were stepping stones for the research being presented. If one is an expert in the field, you can skip the beginning of the introduction completely, except to maybe check that you are up to date with the more recent citations and that your own work is being referenced! However, no inquiring mind should skip the end of the introduction, which is the place that I read first (after the abstract). The second last paragraph will present the hypotheses and the final paragraph explains how they were put to the test. The final sentence of the introduction is supposed to be the 'hook' that keeps a reader intent on delving into the details of the paper.
Methods and Materials: This section is the one most often moved around from journal to journal. If there are very strict page limits, there will be an abbreviated M&M section with supplemental information available on the web. Basically this section should provide all of the details on how the study was conducted to such a degree that the work is repeatable. If you read something in the results that don't make sense and the discussion does not resolve it for you, usually the answer will be found in this section.
Results: The results section is typically the worst section to try to read through and comprehend in one sitting. It is often easier to look at the figures and tables and read the captions and then looking through the text for where that information is described. The results are often presented in the order in which they will be discussed in the following section.
Discussion: The discussion is the most fluid section of all, but it serves a very good purpose. It is in this section that the author draws conclusions from their results and observations and has the opportunity to compare their results to those that have previously been published. It is important to read the discussion to see if the conclusions that you drew from the rest of the paper match those of the author. The discussion should present all possible interpretations of the data and settle on what the authors agree upon as the conclusion. Some journal formats allow for a full section for the conclusion, which will often tie in a global perspective to a study, but if there is no clearly designed section, the conclusion can be found in the final paragraphs of the discussion.
Abstract: The first sentence or two usually deal with critical background information that form the basis that the study is design upon. The next sentences present a brief description of the experimental or theoretical design, followed by a sentence or two of results. The final sentences of the abstract are reserved for conclusions or a statement to the work's significance. (250 -300 words)
Introduction: The introduction is obviously going to be focused on background information and will be the most citation laden section of the paper. The presentation goes from broad to specific, starting out with an intro to the subject matter, followed by some corollary studies. If the work is about a group of organisms, there is usually some descriptive information which will give the reader insight into the meaning of the results. Often it is in this section that an author will point out gaps in current knowledge as well as studies which were stepping stones for the research being presented. If one is an expert in the field, you can skip the beginning of the introduction completely, except to maybe check that you are up to date with the more recent citations and that your own work is being referenced! However, no inquiring mind should skip the end of the introduction, which is the place that I read first (after the abstract). The second last paragraph will present the hypotheses and the final paragraph explains how they were put to the test. The final sentence of the introduction is supposed to be the 'hook' that keeps a reader intent on delving into the details of the paper.
Methods and Materials: This section is the one most often moved around from journal to journal. If there are very strict page limits, there will be an abbreviated M&M section with supplemental information available on the web. Basically this section should provide all of the details on how the study was conducted to such a degree that the work is repeatable. If you read something in the results that don't make sense and the discussion does not resolve it for you, usually the answer will be found in this section.
Results: The results section is typically the worst section to try to read through and comprehend in one sitting. It is often easier to look at the figures and tables and read the captions and then looking through the text for where that information is described. The results are often presented in the order in which they will be discussed in the following section.
Discussion: The discussion is the most fluid section of all, but it serves a very good purpose. It is in this section that the author draws conclusions from their results and observations and has the opportunity to compare their results to those that have previously been published. It is important to read the discussion to see if the conclusions that you drew from the rest of the paper match those of the author. The discussion should present all possible interpretations of the data and settle on what the authors agree upon as the conclusion. Some journal formats allow for a full section for the conclusion, which will often tie in a global perspective to a study, but if there is no clearly designed section, the conclusion can be found in the final paragraphs of the discussion.
Tuesday, October 23, 2012
Mission Statement
The intent of this blog is to publish reviews of primary scientific literature, focused on open access articles, on a variety of topics of personal interest to myself. I studied anammox (anaerobic ammonium oxidizing) bacteria in grad school so many of the articles that I want to write about will be in the field of molecular microbial ecology, marine science, general ecology, molecular biology, astrobiology, interactions between humanity and the environment, and perhaps forays into things like particle physics or anything else really.
The number one aim, however, is for this to be a place for me to write reviews of scientific literature as a means of personal development in hopes that I will delve further into the scientific literature to broaden my own knowledge. The secondary outcomes may be that I will improve upon my writing skills and ability to interpret the literature, find new sources of articles which are free to the public, be a place for me to publish examples of my writing, and last but not least, to hopefully inform everyday people and scientists alike about exciting new research. I also hope to review some of the classic literature and even create an educational section to explain key concepts, as well as build a glossary of terms. I have hopes that one day I will obtain an informed audience who will provide feedback and maybe even submit some original reviews in subjects of their own interest.
I will try to limit my article choices to ones that are not only interesting to me, but will appeal to a wide audience. This will probably be an impossible task, but it's worth a shot. This blog has been an idea of mine for quite some time, and I never really had time in grad school to read the literature as much as I would have liked. I am hoping that this will aid in my personal and professional development, especially in my current situation of looking for a job.
Feedback is much appreciated!
The number one aim, however, is for this to be a place for me to write reviews of scientific literature as a means of personal development in hopes that I will delve further into the scientific literature to broaden my own knowledge. The secondary outcomes may be that I will improve upon my writing skills and ability to interpret the literature, find new sources of articles which are free to the public, be a place for me to publish examples of my writing, and last but not least, to hopefully inform everyday people and scientists alike about exciting new research. I also hope to review some of the classic literature and even create an educational section to explain key concepts, as well as build a glossary of terms. I have hopes that one day I will obtain an informed audience who will provide feedback and maybe even submit some original reviews in subjects of their own interest.
I will try to limit my article choices to ones that are not only interesting to me, but will appeal to a wide audience. This will probably be an impossible task, but it's worth a shot. This blog has been an idea of mine for quite some time, and I never really had time in grad school to read the literature as much as I would have liked. I am hoping that this will aid in my personal and professional development, especially in my current situation of looking for a job.
Feedback is much appreciated!
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