Kyle OliveiraThis week the first portion of class on Monday involved a brief overview of the emerging technologies in the field of eDNA. I am interested in learning more about the microfluidic chips, because in concept they seem so simple and easy to work with. So I would like to find...
dyiuThe emerging methods we discussed this week are pretty interesting. Some of them seem like they have a potential to become really powerful technology in the future. The ones seem the most revolutionary to me are microfluidic chips, mRNA, and nanopore sequencing. I am excited to hear more from Dr....
steven allersThis week we talked about LAMP (loo=mediated isothermal amplification). Prior to this week I had not heard of LAMP before and was surpised to find out that it was 15 years old. The biggest difference between LAMP and regular pcr is mainly concerning the primers. The LAMP method utilizes primers...
Sarah HoslerLearning about LAMP was interesting. Discussing the advantages and disadvantages were similar to all other methods. In a few years, once this method is more developed and tweaked more, I think it will be very useful especially for field work. The microfluidic devices were the most interesting to me because...
Emily PierceReflection week 9 blog post The technology we talked about this week was new to me, and I wish we had more time to talk about it because it seems really interesting! Luckily in my breakout room, Shane was able to talk about benefits of ddPCR over LAMP, and as...
JenThis week’s class covered emerging e-DNA technologies with a student-led presentation by my group about LAMP (loop-mediated isothermal amplification) with highlights from Williams et al.’s 2019 paper “Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.”. I am intrigued by LAMP technology, especially...
Sydney GreenleeThanks for introducing microfluidics chips this week. I had never heard of them before. It’s fascinating that someone capitalized on the very small-scale behavior of fluids to extract DNA from a sample. Additionally, the magnet step that attracts only target DNA is amazing. And the ability to combine an extraction...
Lara WilburI had never heard of LAMP technology until this week, and it seems like a really promising technique for eDNA work. Just the fact that it can be performed in the field and in remote areas is a huge benefit. It eliminates the need for costly thermocyclers, and allows for...
Rene FrancoliniThis week, my project group chose to have the class read the 2017 Williams et al. paper “Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.”. We chose this paper because while the technology of Loop-mediated Isothermal Amplification (LAMP) is not a new...
Zachary A. May (Zmay61)The topic of the week is eDNA methods and using LAMP. The point of using LAMP has some interesting applications and it can be used without a thermocycler like normal PCR. Using this method, we are continuing the strand of DNA instead of copying sections of it. A very different...
Julia SunnarborgThis week’s discussion presented two papers - Lee (2017) and Williams et al (2017) – to introduce the LAMP method of DNA amplification. The latter in particular connected this method to eDNA. One of the highlights of the discussion for me was the comparison between LAMP and traditional PCR methods....
Alex AscherI have to confess I feel like I still do not 100% understand how LAMP works, but I can still see the potential benefits it provides. One thing that stood out to me is the linear nature of its amplification. Errors due to PCR can represent a big issue for...
Sarah RisleyThis week we discussed isothermal loop-mediated amplification, also known as LAMP. Our group chose this emerging technology because it offers an alternative to PCR or qPCR that does not require the use of a thermocycler and produces rapid, specific results. LAMP is extensively used to detect pathogens and viruses, for...
Sam SilverbrandThis week’s discussion on LAMP technology and its applications to eDNA was super foreign to me! I’d heard of this technology once before, I think in a COVID testing sense, but I had never really thought of it in terms of use in eDNA research/ my own research interests. Specifically,...
Samuel TanWhile I’ve heard of LAMP for a while now (and have admittedly always struggled to visualise how it actually works), after today’s discussion, I’m certain that at the moment, it is best used as a complementary approach to regular PCR, especially when convenient, rapid detection is needed (e.g. in the...
Rachel PresleyThis week’s class, we discussed emerging technologies in the field of eDNA. We discussed two different papers by Lee (2017) and Williams et al. (2017). The paper by Lee (2017) describes LAMP, or loop-mediated isothermal amplification, and how it differs from PCR. This paper also delves into its applications and...
Phoebe JekielekThis week we discussed the tool isothermal loop mediated amplification (LAMP). My group picked this emerging technology to discuss for this week. However, I now know that this is not really an emerging technology but more of an evolving technology. It was developed in the early 2000’s and has been...
Shane FarrellThis week’s group discussion was an eye-opener. It was a good reminder that having a laissez-faire attitude to cybersecurity and data management will fail. I think the password thing is the hardest. These days companies like Apple or Google try and streamline logins by remembering password information. This efficiency also...
Kyle OliveiraThis week we discussed bioinformatics and how one can use them for evaluating sequences containing lots of information and millions of DNA reads. The matching process of sequences to the reference database depends on methods that the user chooses (distance based, or model based approaches), and thus the results will...
Shane FarrellThis week’s group discussion was an eye-opener. It was a good reminder that having a laissez-faire attitude to cybersecurity and data management will fail. I think the password thing is the hardest. These days companies like Apple or Google try and streamline logins by remembering password information. This efficiency also...
dyiuLearning about the process of sequencing analysis this week helped reinforce my understanding of how the Illumina MiSeq works, which I did not totally get before. This module discussed the topics that Sue’s amplicon sequencing analysis is all about, including talk on bioinformatic analysis, the merits of ASVs over OTUs,...
steven allersThis week we talked a lot about ASVs and dada2. Dada2 is a tool I use with qiime2 to help assign taxonomy to DNA samples. I would like to learn more about how dada2 works. As it is, my understanding is that dada2 uses similarity scoring, error thresholds, predominance of...
Sarah RisleyI really enjoyed this week because we covered an interesting eDNA debate (OTU’s vs ASV’s), but also learned from our classmates about the very practical (and slightly terrifying) topic of data management. In a sense, the paired discussion and lecture were archetypal of this course experience as a whole: a...
Emily PierceReflection week 8 blog post I wasn’t overly excited about this week’s topics coming in to it; I have some experience with bioinformatics based in the command line using QIIME and hadn’t put much thought into backups or data safety. Most of my assignments and work are done on Google...
JenThis week our class covered bioinformatics and data management. In our lecture, Andy made an interesting point about the benefits of open source software in that it is available to researchers worldwide and it is free. Proprietary or paid-for software is also available. But an important consideration should be made...
Samuel TanWhile having some degree of familiarity with standard bioinformatics workflows, the various steps involved, and the basics of what they do (if not the fine details), I have been increasingly sold over my time in Maine-eDNA about the merits of assigning ASVs over OTUs, in order to minimise loss of...
Sydney GreenleeThank you to this week’s group for starting an interesting discussion on data management. Data management was not discussed much during my undergraduate outside of accessing files more easily in R or in ArcGIS, so I found it especially valuable. I thought it was a great wake-up call for me...
Greg LeClairThis week we talked about emerging technologies in eDNA, and man, I always thought I was up-to-date on what was going on - apparently not! It's exciting to see what is up-and-coming, but I'm curious what will actually stick. For example, the chips seem really cool, but also seem more...
Greg LeClairThis week we talked about bioinformatics and data management. I have to say, if I knew about bioinformatics/metabarcoding before starting my master’s, I probably would have gone this route instead of qPCR/something single-species! This is a field that I’m still very much getting my feet wet in but I am...
Lara WilburI was initially surprised by the low degree of overlap between fish species found by eDNA metabarcoding and species found by traditional fish sampling in the Collins et al. (2019) study. This really emphasizes that even primers specifically designed for one taxon will not necessarily work as envisioned. It also...
Phoebe JekielekI’m not gonna lie, the bioinformatics stuff is hard for me to grasp. I thought the group did a great job of walking us through the differences and different applications of OTU’s and ASV’s and did a great job, overall, of engaging folks. I liked the discussion around data storage...
Phoebe JekielekI really appreciated the very engaged discussion we had this week. It was really helpful to have a walk through with this paper as I quickly got lost with the different strains, the primer optimization, and then the different methods used. There were a lot of parts to the paper...
Phoebe JekielekThis week we went into the field for our group project, and it was amazing. Jen, Rene, Sarah and I took the Vinalhaven ferry from Rockland at 7am to then join Captain Jason Day on his boat for a morning of sampling. Jen and Sarah had never collected eDNA data...
Sarah HoslerThis week was one of the most helpful so far, but I also feel like I say that every week in my reflection posts. Maybe I should say it was the most interesting to me. We talked a lot about data management during the Responsible research class I took earlier...
Rene Francolini“Exact Sequence Variants Should Replace Operational Taxonomic Units in Marker-Gene Data Analysis” (Callahan et al., 2017) is a paper that I was familiar with prior to this course, as I have presented it in a lab meeting in 2018. I had chosen it as a presentation paper because I had...
Emmaeve JourdainI enjoyed this week’s discussion on bioinformatics and data management, as these are two areas that I haven’t had much experience with. I enjoyed learning about my classmate’s methods for data management, and I agree that this should be taught at some point in undergraduate because this is definitely a...
Sam SilverbrandThe discussion yesterday on data management and introduction to some bioinformatics analysis for sequencing data/ discussing the difference between OTUs and ASVs was awesome. Data management is something that’s not taught to us very well in undergrad (in my opinion) and its been quite the learning curve to understand organizational...
Rachel PresleyIn this week’s discussion class, we discussed data management and bioinformatic pipelines. As a class, we discussed the importance of data management, storage, and security. Additionally, we read the Data Management Plan document, which outlines the requirements, content, and all other aspects of a data management plan. Data management plans...
Alex AscherI have read this Callahan paper about the merits of ASVs over OTUs before, but it was a revelation that it was written by the same person who developed DADA2. That in mind my reading of this paper for class was a little different from when I’d previously read it....
Zachary A. May (Zmay61)This week was discussion data management and dada pipeline. Being safe and secure in how one protects and copies their data is important. There should be multiple files and copies that include a few onsite and offsite wheres of the data. Verification logons were also discussed as well as multiple...
Julia SunnarborgOur discussion today on best methods for data storage and management was extremely helpful and relevant. I have been trying to find a system to organize my backups in a more intentional way, and today provided some really good starting points and ideas. I love that we have unlimited storage...
Kyle OliveiraThis week in class we discussed next generation sequencing and its applicability to our work in eDNA. Because I focus on a single species approach in my research, sequencing is not the best option for me; however, it was interesting to hear how applicable this technology can be to other...
Emmaeve JourdainThis week we discussed the paper by Collins et al 2019 that compared several universal primer sets for fish biodiversity. I have never had much of an interest in fish so I learned a lot about what primer sets are out there for detecting fish and how effective they are....
Shane FarrellI thought this paper was very enlightening. I think this paper highlights why it’s challenging to make a universal primer set. I wonder why the COI primer set the authors created performed poorly compared with the MiFish 12s. It seems like 12s is becoming the industry standard when metabarcoding fish....
dyiuThe discussion on Collins et al. 2019 this week was surprisingly relevant to a lot of topics I have been thinking about lately. The authors went through some similar steps that we did when looking for the best gene to use as a fish metabarcode for our eDNA work. We...
steven allersThis week we discussed on a paper which examined the efficiency of primers in regards to metabarcoding the results for environmental DNA. Most discussed in the group was the dynamic of the paper which compared primers which targeted CO1 (mitochondrial cyotochrome c oxidase subunit 1), to those which targeted 12s....
Emily PierceReflection week 7 blog post This week was really interesting because I never learned about what actually happens inside of a sequencer. I’ve used a MiSeq before and added on the adaptors, but now I understand the purpose of them as well as the lawn of oligos to make bridges...
JenThis week’s class covered next generation sequencing and general primers and a student-led discussion covering Collins et al.’s 2019 paper “Non‐specific amplification compromises environmental DNA metabarcoding with COI”. I missed the student discussion due to conducting field work with my classmates for our group project. I found the ending conclusion...
Greg LeClairThis week we discussed nextgen sequencing and general primers. This is a field that I would be very interested in learning more about - until now my eDNA ideas and research have been mostly focused on single-species assays and qPCR. However, now that I’m more aware of what nextgen and...
Sarah HoslerThis weeks lesson was very helpful for me because it can be applied to my research as well. Eventually I would like to use metabarcoding to identify and sequence the cow gut microbiome in my samples. The paper we discussed in class along with the discussion was really interesting because...
Rene Francolini“Non-specific Amplification Compromises Environmental DNA Metabarcoding with COI” (Collins et al., 2019) provides a nice comparison of universal primers when looking at the biodiversity of fish in the water. I appreciate that they not only analyzed the efficiency of each primer set, but also took into account the reference databases...
Zachary A. May (Zmay61)A recurring theme to some of these paper that keeps me going is how they are specific to the question. It’s obvious that we want to answer our own questions , but the way that these experiments continue to be set up has that mindset. It is very important in...
Sarah RisleyCollins et al. (2019) conducted a comparison of universal primers through the lens of a case study to detect fish species from estuarine and coastal eDNA samples. Their research showed that there are primers that better detect these species than the commonly used COI primers, but that switching to these...
Sam SilverbrandThis weeks paper by Collins et al. (2019) was aptly chosen, I’d already read it! It was extremely relavant and informative in terms of methodologies other authors use to compare and contrast metabarcoding sets. Additionally, I think it was a great paper for people in the class to discuss the...
Samuel TanAs an aside, while I am roughly familiar with the mechanisms behind how Illumina works, it never fails to awe me as to the level of technological wizardry needed to come up with things like bridge amplification, especially when you watch videos of the process (it isn’t the easiest thing...
Rachel PresleyThis week we discussed the study by Collins et al. (2019). The authors compared multiple different primer sets for targeting freshwater and marine fish. The authors constructed a reference library of both freshwater and marine fish in the British Isles and designed two new COI primers in-silico. Then, they tested...
Lara WilburI was initially surprised by the low degree of overlap between fish species found by eDNA metabarcoding and species found by traditional fish sampling in the Collins et al. (2019) study. This really emphasizes that even primers specifically designed for one taxon will not necessarily work as envisioned. It also...
This week’s paper, Collins et al (2019), gave an interesting overview and comparison between various CO1, cytochrome b, 12S, and 16S primers. I may be slightly biased, knowing a bit more about 12S primers than CO1 primers, but I was relieved to see the performance of the MiFish primers. The...
Alex AscherMetabarcoding is probably the first thing that comes to mind for me when I think of eDNA. Partially because my own work centers around metabarcoding of gut contents of lobster larvae, but also because I have a focus on ecology where metabarcoding techniques have shown promise in helping us measure...
Rene Francolini“Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCT and real-time PCR” (Park et al., 2020) provided a good review of the steps to follow when designing and testing primers for qPCR. While the methods themselves were not novel, it was nice to...
Zachary A. May (Zmay61)On this week’s edition of eDNA, we walked through the importance of creating and working with different primers and probes along with the specifications that come with analyses. Although multiple programs and websites aid in the construction and creation of primers, it is important to play around and even shop...
Kyle OliveiraThe paper for this week, written by Park et al. (2020), brought up many principles discussed in lecture on Monday. Specifically, the paper looked to eliminate primer dimer as well as having the least amount of similarity between other coronaviruses. Although not working on eDNA, there were similarities between methodologies...
The paper by Park et al (2020) on primer optimization for SARS-Cov-2 was very eye opening for me and I enjoyed learning more about the details behind the PCR tests that have become a part of my weekly life. I was shocked to see that some of the primer sets...
Emmaeve JourdainThe paper by Park et al (2020) on primer optimization for SARS-Cov-2 was very eye opening for me and I enjoyed learning more about the details behind the PCR tests that have become a part of my weekly life. I was shocked to see that some of the primer sets...
Shane FarrellPrimer design and PCR optimization are critical for the success of many eDNA studies. I’ve been having many problems with a few primer sets I’ve designed. They are currently amplifying off taxa targets. When I look back at the reference database sequences, there are multiple basepair mismatches in both the...
dyiuThis week we talked about primer design and PCR assay. As we searched for a paper to discuss, we were trying to find one that included discussion on the actual primer design process in addition to using the primers for some sort of “interesting” application. It just so happened that...
steven allersThis article covered the topic of optimization of primer sets for detection of SARS COVID 2 of coronavirus disease 2019 (COVID-19) using PCR. I guess there comes a time in everyone’s life where you have to make a decision, and, sometimes, those decisions aren’t easy. Maybe one day you decide...
JenThis week’s class covered PCR Assays and Primer Design and a student-led discussion covering Park et al’s “Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR”. The students also conducted a real-time experiment with the Biomeme qPCR machine, a definite...
Sam SilverbrandThis was such an interesting class discussion! I was really glad we could discuss as a class some of the important aspects to include when you’re validating a primer set. I think there’s definitely more that could be said about this process since it can be a bit complex, but...
Sarah HoslerBefore this week’s lecture I was familiar with the basics of PCR and the various types such as qPCR and reverse transcription PCR, but the anything related to primers was still confusing to me. After Monday’s lecture and Wednesday’s discussion though, everything makes much more sense. The fact that anyone...
Greg LeClairI know last week I said extractions were my weak point, however, primer/assay design… if it’s not my actual weakest subject in eDNA, it’s my second weakest! I’ve had very little experience until this point designing primers. My master’s thesis is currently using primers designed by a group out of...
Lara WilburI was really excited to learn how to use Primer BLAST this week. I had been using it a little to check to see whether a metabarcoding primer would amplify targeted species. I had a vague idea of what parameters to look for, but learning the specific terms has helped...
Emily PierceReflection week 6 blog post I feel like every week I say that every lecture is really relevant to my thesis, but this weeks was the best yet! I am currently designing species specific primers for invasive invertebrates and am struggling with a few species. Regarding databases, I didn’t realize...
Alex AscherI’ve spoken in a few different forums about the difficulties we’ve had developing lobster blockers for my own research. I think that has given me a little perspective into the difficulties there are in designing a primer specific to an organism. That being said it doesn’t really surprise me that...
Julia SunnarborgThis week was my first ~real~ introduction to primer design and optimization! Both the lecture and the discussion were really helpful in understanding how one moves from understanding what a primer is to actually using your own in your research. It was also great to get a refresher on some...
Sarah RisleyThe discussion this week was an informative dive into primer design and optimization. Overall, I felt like this week exposed me to a lot of new content (plus many new acronyms!) and offered a thorough behind the scene look into primer design, in silico testing, amplification, melt curves, and even...
Samuel TanWhile already familiar with PCR theory, and to a lesser extent, primer design, it was nice to be able to pick up some tips on the more practical aspects of the latter. Admittedly, I haven’t got to the stage where I have to design primers for my PhD project, but...
Rachel PresleyThis week we discussed the study by Park et al. (2020) that aimed to find the best primers and accompanying protocols for detecting SARS-CoV-2, which is the virus responsible for the disease COVID-19 in humans. In the study, the target genes were RdRP, N, E, and S. The authors designed...
Phoebe JekielekI really appreciated the very engaged discussion we had this week. It was really helpful to have a walk through with this paper as I quickly got lost with the different strains, the primer optimization, and then the different methods used. There were a lot of parts to the paper...
JenThis week’s class covered ways to collect, store, and extract eDNA (environmental DNA). The group-led discussion furthered the conversations about these methods and covered two papers, one by Foote et al, “Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals”, and the other by Deiner...
Sarah RisleyThe papers from this week, Denier et al. (2014) and Foote et al. (2012), both explored the complicated decisions surrounding eDNA capture and extraction. Foote et al. (2014) specifically examined how widely varying eDNA protocols can significanlty influence the ability of eDNA to detect biodiversity. As someone completely new to...
Emily PierceReflection week 5 blog post This week’s discussion and readings were very relevant to the current progress of our grant as we’re still trying to finalize which extraction kit to use. Furthermore, my group for the research project in this class have differing opinions on which extraction kits are best...
Sam SilverbrandI had a really great time talking about extraction and collection techniques with everyone this week!! Discussion always really get my brain thinking in ways that I hadn’t thought about before, and gives me new perspective and ideas on how to solve problems. Choosing an extraction technique that is good...
Sydney GreenleeExtraction methods are deceivingly complex- at first glance, they all have similar steps. They even have similar results, though some filter tests reveal differences in DNA yield from the kits. Are these differences in yield significant in downstream applications? I have been thinking about one of our discussion questions this...
The topic for this week was DNA extraction methods. Figuring out which extraction method to use is pretty daunting. It seems like every paper I read uses a different method AND finds different results. For example: Deiner et al. (2014) found that MO Bio’s Power Water kit does not detect...
Greg LeClairThis week we talked about different methodologies for filtration and extraction - while there seems to be a limitless number of approaches and combinations for nearly every step of the eDNA process, these particular steps seem especially limitless! I have read a handful of papers that compare filter material, pore...
Lara WilburIt’s exciting to be getting into the details of how eDNA can be collected, stored, and extracted. The more we discussed the Deiner et al. (2015) paper, the more questions I had about collection protocols for my own project. Which filter type should I use? How will I either filter...
Phoebe JekielekThis week’s papers and discussions have been very relevant to some considerations that I’m very currently thinking on in my work. Specifically, the use of different extraction kits to maximize DNA quantification is at the top of my list. We’ve recently been talking about comparing the DNA extraction efficacy of...
Rene FrancoliniWhat I found to be interesting about Deiner et al. (2016) and Foote et al. (2012) is how these papers, while relatively “old” in the environmental DNA field, have similar conclusions to what we are still reporting today. Specifically for the Deiner et al. paper, while it focuses on different...
dyiuThis week we talked about filtering and extractions. My main takeaways were: Backpack filters exist. This is brilliant. What if there was a mechanism that could rotate or switch between filters to allow for discrete sampling without having to switch them manually? I would like this whole fitration system to...
Shane FarrellWhy is extracting DNA from water so simple yet so hard? When I first started this program, I fell into the trap of scrutinizing the difference between extract kits; as Erin pointed out, these “pilot” tests between extraction kits are never a quick and easy thing. The Rasher Lab has...
Sarah HoslerExperimental methods are very similar to statistical methods in that there are many different options to chose from, but they you need to pick the best methods to get the most accurate results for your specific project. Each project works with different organisms, goals, variables, environment, and many other factors...
Emmaeve JourdainThis week we discussed DNA collection and extraction methods and three words that I feel encompass the gist of our class discussions are compatibility, consistency, and standardization. These three words are linked and become important in the context of eDNA research as scientists need to figure out the level of...
Samuel TanCollection & extraction methods were the topic of the week. Our class came to the conclusion that research questions across the Maine-eDNA program are too different for effective standardisation in most cases. The best techniques to use can differ greatly based on a host of factors, such as environmental parameters...
Julia SunnarborgThis week we talked about collection and extraction methods, standardization, and how the choices we make when choosing methodology impact our results. I think the discussions really hammered home some points that have started coming up more and more, such as the importance of consistency, tailoring your methods to your...
Alex AscherStandardization of eDNA techniques is a lofty goal. There is clear sense in setting out standardized protocols for collection, storage, extraction, and amplification. Studies have shown that altering pieces of these steps can have affects on your results, such as Deiner et al where taxa richness and DNA concentration differed...
Kyle OliveiraIf I took one thing away from class this week it is to really be aware of targets and intentions when conducting a study with eDNA. Lecture on Monday focused on having three things in mind when designing a study: DNA state (extracellular or within the cell), the type of...
Rachel PresleyThis week we discussed two different studies. The first by Deiner et al. (2015) explored whether different eDNA sample capture and extraction methods affected the detection rates for various species. They compared two different capture methods and three different DNA extraction protocols using samples from two different freshwater sites. They...
Zachary A. May (Zmay61)These two papers were great representations of how eDNA is evolving. Both the collection and detection have changed throughout the novel (novel) approaches of eDNA. 15ml for species detection in 2012/2015 to nearly 4L in our study. It does show that even small amounts of a water sample can provide...
steven allersThese two articles covered different topics, with the first article focused on different combinations of different protocols, and the second article on dectection of long finned-pilot whales. The first article described how different combinations of different extraction/sampling protocols can result in large differencecs in in DNA yield amounts as well...
dyiuThis week we discussed a paper on eDNA from suspended particulate matter. It made me face how important it is to read about the sampling design of any study before drawing inferences. In this paper, it seeemed like the lack of rigor in the sampling design took away from confidence...
Shane FarrellThis article had both good and bad parts. The concept of deploying SPM traps to catch and collect sinking particulate is fascinating. In reality, I don’t know how someone could control what/where the sediment is coming from. As we discussed in class, there could be a risk of old sediment...
This week we discussed using eDNA extracted from suspended particulate matter (SPM) to monitor fish communities. I chose this paper because it is relevant to my own work on the EPSCoR project. My first task on the grant is to recreate fish communities from current sediments, before they settle on...
steven allersReflection on ‘Aquatic suspended particulate matter as source of eDNA for fish metabarcoding’ This article discusses the idea of obtaining samples from suspended particulate matter as a kind of compromise between soil sampling or water sampling. Whereas water sampling contains more contemporary, possibly relevant information, soil sampling contains higher amounts...
Emily PierceReflection week 4 blog post The readings this week really made me reflect on work in my own laboratory and think about potential for future projects. For example, one of the master’s students in my lab studies green crabs and has found that their eDNA is really only detectable near...
JenDuring class this week we read Díaz et al’s 2020 paper, “Aquatic suspended particulate matter as source of eDNA for fish metabarcoding”. This paper is particularly interesting to me this week because I had the opportunity to accompany Maine-eDNA researchers in the field as they collected eDNA water samples through...
Sam SilverbrandI was really jazzed about this paper by Diaz (2020) after reading it. It brought up a lot of questions for me, as well as brought to light some interesting parallels to my own research. I think that SPM has great potential in the field of eDNA, but it clearly...
Sydney GreenleeI thought this week’s discussion on the Diaz et al. suspended particulate matter (SPM) paper was quite exciting. Sediment sampling, including this SPM sediment trap method, is new to me. I deal primarily with water samples, and my target organisms are phytoplankton and bacteria rather than large metazoans. Utilizing SPM,...
Sarah HoslerI had a lot of similar feelings/opinions about this paper (using eDNA in SPM) and last weeks paper (comparing seasonality) because they were both proof-of-concept papers. What I find interesting is how everyone in the class responds to the paper differently. What I might find could be improved upon or...
Greg LeClairThis week, we discussed a new source of eDNA - fine particulate matter. Since DNA is charged (negatively I think?), it sticks to other items in the environment - including clay, cellular material, plant matter, etc. Because of this, stored soil samples and filters with particulate material could provide eDNA...
Lara WilburThe Diaz et al (2020) paper presented by Group 6 raised many interesting questions about suspended particulate matter (SPM) and eDNA. I was definitely excited by this study and the idea that SPM can be a source for high eDNA yields. As I plan my upcoming surveys for rare bridle...
Phoebe JekielekThis week I thought a lot about this work in relation to the questions I’m asking. Truthfully, sediment traps are something I’ve been considering to compare fertliziation success in wild and cultured populations of scallops. The eggs are neutrally buoyant, fertilized or unfertilized, so sediment traps would be a great...
Rene FrancoliniThe paper “Aquatic suspended particulate matter as a source of eDNA for fish metabarcoding” (Diaz et al., 2020) addressed a pilot study that was conducted to determine whether suspended particulate matter (SPM) could be used for eDNA extractions. This paper brought up a few interesting aspects of the potential of...
Zachary A. May (Zmay61)Our reading this week included methods in eDNA using suspended particulate matter. This study went through applications in attempts to detect fish species in German river systems. These SPM sampling used sediment traps and different eDNA extractions kits. 29 taxa were resolved using metabarcoding after sediment DNA was extracted using...
tktdvmThis week our class discussed the paper by Diaz et al. (2020) regarding eDNA detection of fish from suspended particulate matter (SPM) in German rivers. I was pretty amazed by the fact that frozen, banked river samples (in the German Environmental Specimen Bank) were a thing, as I did not...
Emmaeve JourdainThis week we discussed a paper by Diaz (2020) detailing a pilot study on extracting eDNA from suspended particulate matter (SPM). The paper made me appreciate the complexities surrounding field sampling in a project like this and we felt that there were many field related details that the research didn’t...
Samuel TanThis week, we discussed the proof of concept paper Diaz et al. 2020, but I felt it was a little sloppy in many aspects, which gave a feel of a paper more in line with the earlier days of eDNA. To be a little harsh, it felt more similar to...
Alex AscherIsolating eDNA from SPM is a really interesting idea that raises a lot of questions. I think a lot of my class mates had been wondering whether suspended particulate matter was a viable source of eDNA, and this week’s paper did a good job of demonstrating that it is. One...
Kyle OliveiraJulia, Sharon, and Grayson presented their paper (Diaz et al. 2020) this week which was a proof of concept study revolving around extracting eDNA from suspended particulate matter (SPM). I have a lot of questions regarding this paper in terms of their methods, along with contamination of bacteria and the...
Sarah RisleySomething that continues to surprise me in this course is the many ways in which you can sample and analyze eDNA. Learning about these different methods, despite the fact that it further muddies the already complex sampling design decision-making process, is always exciting to me. The more I learn, the...
Rachel PresleyThis week we discussed the study by Díaz et al. (2020), which discussed using suspended particulate matter (SPM) as a source of eDNA for detecting fish. In this study, they used sediment traps to collect their SPM. They used different methods for extraction and purification of DNA and found that...
Julia SunnarborgThanks everyone for a great discussion today! It was awesome to hear your ideas and critiques regarding the paper, and on the impact of SPM and sediment in general. As many of you did, I had questions and reservations about the methods used in this study, and am interested to...
Greg LeClairStudy design is something that can get very complicated very quickly, however I always find it to be the most engaging and exciting part of a project for me (at least for eDNA; I am a big fan of planning a project and seeing the results, the in between stuff…...
Kyle OliveiraThis week we discussed study design, focusing on different methods of forming hypotheses, sampling approaches, and understanding needs for metadata. In developing our study designs, there are multiple limits to consider (funding, time, resources, etc.); these constraints may prevent us from accomplishing all we set out to do, but they...
tktdvmThis week our class discussed the paper by DeSouza et al. (2016) and the authors’ approach to identifying the seasonality of eDNA detections of two imperiled species in a river basin in Alabama. The authors concluded that there is a difference in seasonality in detecting these species from eDNA samples....
Sarah HoslerTo me, survey design is one of the most important and difficult parts of the scientific process as it encompasses every part of it. To have a good survey design you need to be thinking about what you already know, what you want to know, and what kind of analysis...
Sydney GreenleeFrom our exercise in budgeting this week for the term project, study design appears to be an art of balancing tradeoffs. Molecular reagents and consumables, like tips and PCR plates, add up unbelievably quickly! Add in the number of samples from your “dream” experiment, and the thought of processing 600+...
dyiuMy most exciting part of this week’s module on study design was learning about occupancy modeling. I vaguely heard of it in fisheries applications, but not for eDNA until this week’s lecture. Given the vast uncertainty surrounding eDNA, I like the idea that you can use this analysis to account...
steven allersReflection on ‘Environmental DNA (eDNA) Detection Prbobability is Influenced by Seasonal Activity of Organisms’ This article discusses the important of understanding the context of the species in question being investigated by eDNA. In this case, the Black Warrior Water Dog and Flatwater Musk Turtle. The Black Warrior Dog has a...
Sarah RisleyOne of the most important take-aways for me from our group discussion this week is this: know your study organism in and out. I feel that it is often easy to get bogged down in the technical aspects of research, from sampling protocols to site selection, and lose sight of...
JenDuring class this week we read Díaz et al’s 2020 paper, “Aquatic suspended particulate matter as source of eDNA for fish metabarcoding”. This paper is particularly interesting to me this week because I had the opportunity to accompany Maine-eDNA researchers in the field as they collected eDNA water samples through...
JenDuring class this week we read de Souza et al’s paper, “Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms,”. During our group discussion of the paper, some interesting points rose to the surface that have stuck with me, especially as some members of our class embark...
Sam SilverbrandI really liked this week’s discussion from deSouza et al. (2016) around study design, specifically the aspects of multiple competeing hypotheses and the use of occupancy modeling when planning your research. I’ve read a lot about the use of occupancy modeling in eDNA through my lab’s work, as many of...
This was my first time taking a deeper dive into occupancy modeling. However, I was familiar that an organism’s biology and the surrounding environment will influence detection rates.I have multiple questions surround this… What aspectsof an organism’s biology are most important to understand detection rates? In marine systems, what are...
Rachel PresleyThis week we discussed module 3 - study design and introduction to data management. In the class, we reviewed multiple competing hypotheses (MCH), definitions of “sample” and “replicate,” and occupancy models. The study by De Souza et al. (2016) examines the effect of seasonality on detection in eDNA samples for...
Lara WilburI think that study design and data management are likely the most difficult aspects of research. One especially difficult aspect of study design may be somewhat unique to wildlife work (or wildlife work within government agencies). Researchers may suddenly find themselves with funding and equipment to study a particular species...
Julia SunnarborgI’m glad that we had a dedicated lecture for study design. It’s not only helpful for our projects, but for current and future research endeavors. It’s also nice to see that conversation happen ‘formally’ in a course, instead of just being taught through the grapevine or by trial and error....
Phoebe JekielekSomething that is challenging to me is translating eDNA methods and experimental designs from aquatic or terrestrial systems to marine systems. I’m experiencing this challenge in my other course as well (Eco-evolutionary dynamics) and lose some of the understanding if I can’t relate the systems. However, the discussion that we...
Alex AscherI really enjoyed the authors focus on natural science in this paper. It feels like sometimes these basic facts, such as range, behavior, activity level, and breeding season are frequently overlooked. That can go doubly so for eDNA analyses as you can make it through an entire research project without...
The theme for this week’s lecture and paper was Survey Design. I was surprised to learn how many replicates are needed in field and laboratory samples. I am used to working with DNA in large quantities- such as plant clippings or colonies of bacteria. It makes sense that field and...
Samuel TanIt was interesting to read about the earlier days of eDNA in the deSouza et al. paper. Even today, seasonality is not given as much consideration as it should deserve in many eDNA studies, and seasonality itself can be highly organism- and location-specific. Nevertheless, the paper had several flaws that...
Zachary A. May (Zmay61)This week (Feb 7) we discuss a 2016 eDNA paper looking at two different species and their detection at multiple sites over seasonal differences. This paper was very specific when discussing the overall findings and methods. Their criteria was very strict as to what they concluded to be a positive...
Grayson HustonThe paper we read for discussion this week was frustrating because it was so annoyingly obvious. Environmental DNA concentrations are higher when an organism is actually present or is more abundant? It seems like common sense. Yet as I sit here analyzing my frustration, I realize that this is a...
Emmaeve JourdainThis week in class we discussed the many considerations associated with study design. One of my major takeaways was the emphasis on determining an analytical approach for the data set before data collection actually occurs. This decreases the need to sort through large amounts of data trying to find some...
Emily PierceReflection week 3 blog post This week’s lecture and discussion focused around experimental design. It was interested to learn about experimental design in a classroom setting because I’ve had it touched on in statistics before, but in my experience it’s not commonly taught as specifically as it has been this...
Zachary A. May (Zmay61)The discussion this week on open access and open data sources was very informative in multiple ways. This information relayed through the paper and discussion was eye opening in how others think about relaying research and findings to curious people. While publishing is newer to most of us, it’s imperative...
Rene FrancoliniThe paper “Environmental DNA (eDNA) Detection Probability is Influenced by Seasonal Activity of Organisms” (L. de Souza et al., 2016) provided a great reminder to truly consider your organisms or ecosystem of study as you design an eDNA study - how a “big-picture” mindset is vital when studying the natural...
Kyle OliveiraThis week we discussed study design, focusing on different methods of forming hypotheses, sampling approaches, and understanding needs for metadata. In developing our study designs, there are multiple limits to consider (funding, time, resources, etc.); these constraints may prevent us from accomplishing all we set out to do, but they...
tktdvmHaving not been directly involved in research for several years, I was relieved to read that the perceived stigma formerly associated with open access (OA) journals is diminishing. McKiernan et al. 2016 provides considerable encouragement to researchers pursuing OA publications. In addition to the flexibility OA forums can provide to...
Sam SilverbrandThis week’s reading on the paper by McKiernan et al. (2016) generated really interesting conversation in our group and left me with a lot to think about when trying to publish scientific work. Overall I think that one of the biggest things I took away from this reading were the...
Sarah HoslerIn a perfect world, I think that everything should be open access. I do not see any advantage to subscription journals except for it being cheaper to publish, and maybe the work being seen by people more interested in it. Other than the cost, open access is pretty great. As...
dyiuUntil joining the eDNA program last year, the human dimension of DNA was always separate in my mind from eDNA as we apply in ecological contexts. Because these connections are relatively new to me, the TallBear paper was an interesting one to read. I enjoyed learning more about the conflict...
Shane FarrellI think it is widely agreed that journals should be open access. There are many reasons for both benefits to the author(s) and reader(s). Quick aside… I am always shocked by the cost to publish in open access journals. Just the other day, I read a tweet by @mightdropout saying,...
steven allersReflection on ‘How open science helps researchers succeed’ This article discusses the benefits of using ‘open’ publishing for science journals. ‘Open’ here mainly referring to the availability of the articles in question. Some articles or papers can be read only after paying a subscription or one-time fee to a publisher,...
Kyle OliveiraThis week’s readings centered around a report written by McKiernan et al. (2016); the purpose of this paper was to address concerns about open access (OA) that hindered scientists from publishing in OA journals. Throughout discussions held in the breakout room I was a part of, I brought up the...
Sarah RisleyAs scientists we all know that data is a powerful tool. But who has access to data and in what form data is shared or communicated makes a world of difference in the ultimate outcomes of our research. Since the beginning of my graduate degree I’ve wrestled with how to...
Sydney GreenleeBefore and after our discussion, I am a strong proponent of open data. Isn’t research conducted to discover and share new information? McKiernan et al. (2016) did an excellent job outlining the pros and cons of open data, as well as how scientists can contribute to the mission of open-access...
Emily PierceBlog post 2 This week’s lectures focused on communicating science through online platforms such as GitHub, the benefits/downfalls of using open source journals, and places to store data which are open source. Much of this material was new to me; I’ve used R before and have an account with OSF,...
JenDuring class this week we read McKiernan et al’s paper, [“How Open Science Helps Researchers Succeed,”] (https://elifesciences.org/articles/16800) and then discussed it in our small group discussions. The paper makes the argument that there is a strong movement towards open science: “Each year, more studies are published showing the open citation...
Lara WilburI was excited by the perspective embodied in the McKiernan et al.(2016) paper that science and research should aim to become more open-access. As a first-year MS student, I’ve never published any research, but I have frequently been frustrated by the lack of accessibility to research articles. I think that...
Rene FrancoliniThe paper “How open science helps researhcers succeed” (McKiernan et al., 2016) provided thoguhtful insights on open science as it relates to publishing, funding, resource management and sharing, as well as career advancement. The studies they presented on publishing in Open Access (OA) articles that showed a higher percentage of...
Emmaeve JourdainI appreciated our discussion this week on the McKiernan et al. (2016) paper as I previously did not have much knowledge about the extent of open access publishing and data. It was good to see that the stereotype centered around open access journals seems to be switching as researchers are...
Samuel TanPersonally, I have only published one paper thus far, on taxonomy of bivalves in South-East Asia, with several more on the topic in the works. Given the hardly ground-breaking nature of this work, and the fact that my subjects are far from charismatic taxa and have limited socioeconomic or cultural...
Julia SunnarborgI was really glad to see that open access was a topic we were addressing so early in the semester! To me it is one of those things that is best introduced early on to students and young scientists, and talked about throughout one’s career. I was introduced to it...
PhoebeFirst of all, thank you for the papers that were selected for this first week together. The Cristescu and Hebert paper will be a really great reference and foundational resource that I feel like I’ll be able to come back to again and again. Although you mentioned that it’s already...
PhoebeFirst of all, thank you for the papers that were selected for this first week together. The Cristescu and Hebert paper will be a really great reference and foundational resource that I feel like I’ll be able to come back to again and again. Although you mentioned that it’s already...
Alex AscherI think most of us can agree that the future for science is open access. One of the greatest tools a scientist in any field can have is the ability to communicate their research in a compelling and accessible manner. But good communication doesn’t count for much if your work...
Zachary A. May (Zmay61)This is ZMay’s Test_1 Reflection: The readings this first week were a great way to start the semester. A simple yet complex overview of how DNA research has advanced throughout the decades and the processes that were discovered was very interesting. The amount of work that has come before our...
Sam SilverbrandOverall, this weeks review paper were similar to other reviews I’ve read in the eDNA field and were very familiar to me. I still think that even for someone with more exposure to eDNA, the Cristescu paper still provided good insight into the field and raised some interesting questions. The...
Lara WilburReading both the TallBear (2013) and Cristescu and Hebert (2018) papers reminded me of the importance of caution in science. It is always tempting to immediately use new technologies and methods in biology, especially if the new technology is cost-effective and yields more results per unit effort than previous methods....
Cristescu & Hebert, 2018 seemed to focus on the more qualitative aspect of eDNA and metabarcoding as a biodiversity monitoring tool rather than using eDNA for absolute quantification. eDNA seems like the wild west. To answer ecologically interesting questions, we need to accept many assumptions about eDNA (degradation, retention, etc.)....
steven allersSteven Allers - Reflection One Tallbear’s paper is a declaration of the indignation of indigeneity. In it, they explain how attempting to categorize tribes by haplotypes, in essence, genetically stereotypes the tribes by their genetic novelty. For instance, a person of a tribe not containing the prerequisite distinctness of said...
Sarah RisleyI felt that both the TallBear TallBear (2013) and the Cristescu and Herbert Cristescu and Hebert 2018) papers provided different, but valuable perspectives on the complex landscape of genetics. Cristescu and Herbert discussed the technical challenges of eDNA research: the potential sources of contamination and the limitations of the available...
Kyle OliveiraAs a student new to eDNA and genetics in general, this week was informative in providing a little background of the uses and interpretations of eDNA and genetic material. It was surprising to hear a consensus among students that there was concern about the lack of involvement of eDNA science...
Andy RomingerI really like the idea that eDNA has its own ecology (depicted in Figure 2 from Cristescu and Hebert 2018) that we have to consider when analyzing it. It’s not like there’s an impartial record of biodiversity hiding out there in eDNA—the record is imperfect and biased and our analyses...
Andy RomingerI really like the idea that eDNA has its own ecology (depicted in Figure 2 from Cristescu and Hebert 2018) that we have to consider when analyzing it. It’s not like there’s an impartial record of biodiversity hiding out there in eDNA—the record is imperfect and biased and our analyses...
Emmaeve JourdainI found the discussion papers from this week really interesting and each gave me a different insight on eDNA research. The paper by Tallbear (2013) made me take the time to consider the moral obligations and complications associated with genetics work and eDNA research. I think it is understandable that...
Sydney GreenleeWe covered a large range of topics this week and I have focused on Tall Bear 2013 for my submission to keep it (relatively) brief. I appreciated the assignment of this paper as I was not familiar with the discourse on the use of genetic information as a basis for...
JenThis week’s readings were helpful in learning about eDNA as a scientific method and provocative for thinking about the ethics of DNA. Critescu and Hebert’s paper illuminated the strengths and weaknesses of eDNA methods and pointed to gaps in knowledge (as of 2018). It is written in clear, understandable language...
Emily PierceReflection week 1 blog post (Attempt 2) The readings and course material this week made me excited for the semester ahead. I recently completed my master’s thesis on eDNA and the background literature is not foreign to me, but it will be good to have this platform to discuss other...
Samuel TanRegarding the Cristecu & Herbert (2018) review, while I was already familiar with a significant number of the points discussed, I was surprised that even though much progress has been made in the realm of eDNA research in the last decade, such methods have failed to have been properly adopted...
Rachel PresleyThis week we went discussed how you can use GitHub and R simultaneously to improve research communication and collaboration efforts. On Monday, we discussed the differences between “markup” and “markdown.” We went over markdown syntax. Then, we walked through a tutorial on setting up GitHub and R Studio in order...
Rachel PresleyDuring this module, we made our introductions and talked a little about perceptions of eDNA, what it is, where it comes from, its development and history of use, and its applications. It was interesting to hear from others in the course about their personal experiences of the various perceptions of...
Julia SunnarborgWhat really stuck with me from this week’s reading was the section on the Kennewick Man in the TallBear paper. I had never heard of this issue or the debate that surrounds it. Reading the paper, it seemed so logical and clear why indigenous groups were upset. However, when I...
Rene FrancoliniThe first paper of the week, “Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation” (Cristescu et al., 2018) provided a satisfactory overview of the current state of eDNA work, however, there were not any new revelations regarding the methods, limitations, or applications of eDNA in conservation work....
Alex AscherA lot of the concepts in the Cristescu paper felt familiar to me, owing mostly to my participation in the eDNA Friday seminar meetings last semester. Although, like everyone else in class I was really surprised to learn about how long-lived eDNA can be in sediments. I work mostly with...
Andy RomingerThese are some written instructions for connecting RStudio and GitHub. These instructions assume you’ve already successfully done the following: made a free account with github.com downloaded and installed git (or checked that it’s alread availible on your computer) downloaded and installed R and RStudio (or checked that they’re already availible...
linden schneiderAndy is really doing a great job. He added a hyperlink, see markdown refs for how to add this. He also added a really cool figure and he used the img markdown and added to a folder, so that image is avaiable too all of you. You can do this...
Sarah HoslerAs someone who is completely new to the eDNA world, I found both of the papers very interesting. The Tallbear paper really emphasized the issues that many tribes face relating to their genetics and spirituality. I thought the tribal politics regarding genetic testing were interesting and it would definitely be...
dyiuThis unit caused me to think about the benefits of open access publications and the transition we are attempting to undergo as a community towards open access. We talked about how the subscription journal system works, how this model made sense when paper subscriptions were the main way of disseminating...
Andy RomingerI really like the idea that eDNA has its own ecology (depicted in Figure 2 from Cristescu and Hebert 2018) that we have to consider when analyzing it. It’s not like there’s an impartial record of biodiversity hiding out there in eDNA—the record is imperfect and biased and our analyses...