As we continue through our open application window for the Microbiome Awards we are checking back in with some of our previous winners to learn a little more about them and what they have been up to. This week we talk with AndreaTarnecki who is a Postdoctoral Research Fellow at Mote Marine Laboratory in Sarasota, FL and took 3rd place in the 2016 Microbiome Awards.

As we ramp up this year's Microbiome Awards we decided to check back in with some of our previous winners to learn a little more about them and what they have been up to. This week we talk to Dr. Christopher J Stewart who is a post-doctoral associate at Baylor College of Medicine in Houston, Texas and took 2nd place in the 2015 Microbiome awards.

QIAGEN presents the 2017 Microbiome Awards, offering up to $65,000 in prizes!

Our journey towards Ficus phyllospheres started at the front gate of the University of Ibadan’s Botanical garden on the 5^th of November 2015.  The garden is rich, diverse and a distance from the working laboratory but I was not tired of going there because the garden was a worthy reward. The garden is fascinating and serene with abundant ‘first class’ fresh air and smooth floor which tempted me to sit for a while. Thank God for the ever-helpful garden attendants especially Mr. Sam for his patience and readiness to provide answers to my questions. I wish I could be allowed a little time out in the garden on weekly basis.

July 18-20, 2017, Stockholm, Sweden

In a recent study, Willmann and colleagues investigated the impact of ciprofloxacin treatment on the intestinal microbiome. Antimicrobial treatments are known to upset the structure of the intestinal microbiome. Taxonomic profiling can reveal the severity and long term effects of antibiotic treatments on the gut community.

If you’ve figured out how to extract high-quality DNA from an elephant, chances are that without too much trouble, you’d be able to do the same from a moose, a mouse or even a meerkat. However, if you’ve figured out how to extract DNA from an Arabidopsis plant, well that might be about all you’ve figured out. That’s because plants have developed something akin to chemical warfare in order to survive a variety of climactic extremes, pathogens, and predators, without the luxury of being mobile. As a result, plants harbor an enormous variety of organic compounds, some with antifungal and antimicrobial properties and some which make them taste bad to herbivores. Other structures are complex networks of polymers that store water and nutrients for both feast and famine.

It’s all good and well for the plants, but many of these substances muck up DNA extractions....

QIAGEN is a proud sponsor of the Gordon Research Conference - Applied & Environmental Microbiology.

The DNase step is one of the most common causes of degradation or loss of the RNA during your extraction. DNase digestion is frequently performed on the spin column and although this can be a great way to save time on the post extraction processing, it is not an efficient method for samples with large amounts of DNA (for example, spleen, thymus, and even some soils). In these cases, DNase digestion in solution is necessary.

The typical protocols for DNase involve inactivation of the enzyme using EDTA and heat. Both of these things can cause problems in RT-PCR. EDTA can inhibit the RT-PCR enzymes and heating the RNA can cause a reduction in integrity. 

As many of you know, a good percentage of our customers are doing microbiome research. Microbiomes, those localized communities of microorganisms that exist symbiotically with their immediate environment, can be found virtually anywhere; inside human colons, around plant roots, inside coral reefs and even within ant colonies. These little microbial microcosms are a hot topic right now. Recent studies have implicated their role for the wellbeing of people, animals, plants and entire oceans. Variations in microbial numbers and diversity within animals have shown critical involvement in auto-immune disease, obesity, acne, tooth decay, pregnancy and even brain chemistry. Plant studies have shown that symbiotic organisms impart resistance to drought, increase nutrient absorption and prevent attack by pathogens.

QIAGEN is knee-deep in questions about DNA and RNA isolation from stool! One of the most frequently asked questions is how to store fecal samples for shipping and then storage for further processing. We consulted a 2010 paper written by Dr. Rob Knight’s lab¹. Dr. Knight is an expert in the microbiome field working with human gut/stool samples.

QIAGEN is cleaning up...DNA and RNA that is. With the addition of the DNeasy and RNeasy PowerClean Pro Cleanup Kits to our portfolio, we thought it would be a great time to discuss how cleanup kits work and when you'd want to use one. Clean-up kits take dirty nucleic acids and remove contaminants that could interfere with your downstream business. Enzyme-dependent applications like restriction digests, ligations, PCR amplification and sequencing all require squeaky clean DNA and RNA in order to get the best (or sometimes any!) results. 

As part of our research on the best practices for soil microbial DNA extraction, we collect a wide variety of samples for product development. So when we were developing the protocols for the PowerLyzer 24 Homogenizer 24 Homogenizer, we wanted a protocol that worked for most of the samples tested.  Our work on homogenization and bead tubes previously showed that depending on the soil, sometimes a different bead type could give you an increased yield of DNA.  We decided to do a similar study using the PowerLyzer 24 Homogenizer to ask the question: what is the difference in DNA yields and integrity using high powered bead beating between two different soils using the same protocols?  It is not uncommon for people to simply adopt a protocol from a paper for their soil type without doing any optimization.  But, does one protocol really work best for every soil?

One of the most efficient ways to extract nucleic acids from a sample is by smashing it against a hard surface repeatedly under high speed until cell walls and membranes crush from the pressure and release their internal contents. In other words: bead beating.

Bead beating is a great way to do what enzymes take hours to accomplish and sometimes never fully succeed in, which is cell lysis to release DNA or RNA for isolation. While enzymes can be successful for DNA isolation from a limited number of sample types, results are achieved a lot faster if you break down the matrix first. And RNA cannot be isolated in a timely fashion without the use of some kind of mechanical maceration.

The questions inevitably arise though, how hard do I need to beat to lyse my sample and how do I know what bead type to use?

“Just to be clear, and in front of multiple witnesses… you want me to spend my time, at work, designing a microbiome board game?”

“Yes”

Like most projects, it started innocently enough.  Our lab had created a series of educational “trading cards” of bacteria that we were sending the International Space Station. Then someone (jokingly I think) asked if we could gamify them… maybe make something like Pokémon. I thought about it, and decided it wouldn’t work. Then Jonathan Eisen, my supervising professor at UC Davis, said “you know, we really should make a microbiome game” and the rest is history.

This past July, I attended the Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) Workshop at the Michigan State University, Kellogg Biological Station in July 2016 led by Drs. Ashley Shade, Adina Howe, and Tracy Teal. EDAMAME started from the ground up and was a great way to get hands-on experience using cutting-edge metagenomics techniques. Although, I would expect, any one of the organizers to say that a great deal of effort and critical thinking is required to stay abreast on current technologies.

At the interface of land and sea, the coastline is the last barrier before our man-made pollutants hit the ocean. Coastlines in top-notch shape, however, can filter out a lot of these pollutants, cleaning up a pretty big mess in a relatively small amount of space. Impressive, right? Yet, most of our coastlines are so impacted by excessive chemical input, choked rivers, extra sediment, and invasive species (to name a few issues), sometimes we need to help out these coastal zones through restoration.

My dissertation research is focused on the gut microbiomes of lemurs, you know, those bug-eyed primates from Madagascar that happen to be the most threatened group of mammals on earth. I specifically work with indriids, a group of critically endangered lemurs that include the indris, woolly lemurs, and sifakas. Go google them, seriously. They are some of the most exotic and stunning animals on the planet. Ultimately, I hope that my research will not only illuminate the symbiotic relationship between lemurs and their gut bacteria but will also inform conservation strategies for both captive and wild lemurs. 

It was really surprising when I sat down on the forest floor, pressing my knees into the soft organic horizon of the soil, to become quickly enveloped in a foreign mustardy aroma that tickled my nose. Beside each of my legs were emerald green rosettes of Alliara petiolata, a few of which were already beginning to show their delicate white petals adjacent to their heart shaped leaves. As I neared the edge of the forest, A. petiolata had a strong foothold, it was dense, tall, and incredibly aromatic (Image 1). I reached my left hand out and popped off a few leaves, put them in my mouth, and chomped away, enjoying the bitter punch of the invasive plant’s phytochemistry on my taste buds. A. petiolata is closely related to some of my favorite veggies, including broccoli, kale, and radish, but unlike these domesticated cultivars, A. petiolata was introduced into North America from Europe, where it has begun to take over the understory of many deciduous forests in the northeastern USA. If we are to control invasion by A. petiolata, we need to understand how it has become so successful. This is where I stepped in with a sledge hammer soil corer, my PowerSoil® DNA Isolation Kits, a couple pipettes, and an incredible amount of patience! 

My name is Dr Michael Sweet. I’m a lecture at the University of Derby in the UK and researcher who studies aspects of Molecular Ecology. Usually you can find me in the tropics, researching coral reefs and more specifically diseases associated with reef organisms, but this year something different happened. I headed to the poles. 

I recently met Ermanno Federici in Milan, Italy while attending Bacterial Genetics and Ecology (BAGECO 2015).  He described to me a "Wall of MO BIO" in his lab, and sure enough, true story!!  Here is a little bit about what happens in his lab... thanks for sharing!!

"Our main interests is microbial ecology and, in particular, the use of culture-independent molecular methods (qPCR, PCR-DGGE, and Illumina NGS, …) to investigate environmental microbial communities and their role in ecological, biotechnological and pathological processes."

This will be the last of the #EDAMAME2015 posts for this year, we are sad to see you go!

MO BIO would like to formally thank EDAMAME 2015 (especially green circled Dr. Ashley Shade) for all the interesting science blogs!!  Great group of hardy scientists!!

Last MO BIO guest blog for 2015:

In the last five years, scientists have seen an increased number of papers assessing the diversity of microorganisms.  However, although knowledge of fungal diversity has increased, it is far behind in comparison.  As a mycologist/plant pathologist, I have been amazed by the diversity of fungi and oomycetes in different environments, and their roles in these habitats.  Just here at KBS, we could observe some of this diversity walking around the gardens.

When the BiOstic® Bacteremia DNA Isolation kit was originally designed, it was optimized for the extraction of bacterial DNA from infected blood. However, it has turned out to be useful for so much more. Bacteremia is the presence of bacteria in the blood and under normal circumstances blood should be sterile, but with the insertion of a catheter into the body or through an open wound, bacteria can gain entry and take hold. Even a small numbers of bacteria can be a real problem...

My advisor always says I should ask this question to myself at every step of my research. Your work may be the best in the world. It can be innovative and exciting for you and your lab. However, you must be able to express it in simple terms, so much so that even your parents who may not come from a science background, understand what you did, why you did it, and what is next. Often, we are deeply engrossed in the complexities of our projects that we often fail to take a step back and look at it from a very simple point of view. Asking yourself whether your research makes sense to the random person allows you to critically analyse your own work and address the loose ends that might be present in your research idea, data, analyses, and finally interpretation. I also think that when striving to simplify our own words, we automatically start transitioning into trying to explain our research in a sequential and logical manner.

There is a saying that “You can’t teach an old dog new tricks.” I am a bit of an unusual candidate for EDAMAME2015. I am an older associate professor in the Biology Department at the University of Puget Sound, and can even remember biology prior to PCR! At the same time, I have been following the recent blossoming of research into communities of microbes over the years, ranging from hydrothermal vents, to insect guts, to acidic cave effluent, to the ever present human microbiome.

One of the most efficient ways to extract nucleic acids from a sample is by smashing it against a hard surface repeatedly under high speed until cell walls and membranes crush from the pressure and release their internal contents. In other words: bead beating.

Bead beating is a great way to do what enzymes take hours to accomplish and sometimes never fully succeed in, which is cell lysis to release DNA or RNA for isolation. While enzymes can be successful for DNA isolation from a limited number of sample types, results are achieved a lot faster if you break down the matrix first. And RNA cannot be isolated in a timely fashion without the use of some kind of mechanical maceration.

The questions inevitably arise though, how hard do I need to beat to lyse my sample and how do I know what bead type to use?  The answers depend on a great number of variables, so to avoid beating your head against the wall to sort through them all, I have written this two-part blog series offering advice on the methods that we have used at MO BIO and found to work best for us.

Formalin-Fixed, Paraffin-Embedded (FFPE) tissues, the most common tissue preparation method for archiving bio-specimens, can be a valuable resource for genetic studies. The fixation process makes it possible for samples to be stored for years at room temperature, for analysis even decades later.

Chemical fixatives like formalin (a mixture of formaldehyde and methanol) preserve the structural integrity and morphology of the tissue by cross-linking neighboring amino groups between proteins. This traps other molecules like carbohydrates, lipids and nucleic acids in place.

While the fixation process preserves the structural integrity of the cells, it also denatures proteins and causes the degradation of RNA and DNA. The longer the fixation process and the age of the tissue the more damaged the nucleic acids.  As a result, the size of the nucleic acid fragments is generally small, in the 100-500 bp range. All this makes the extraction, amplification and analysis of nucleic acids a bit tricky. However, using appropriate protocols and kits it’s still possible and highly worth the effort.

We are starting a new series of blogs that will include a short synopsis of a recently published peer-reviewed paper. We want to keep you (and ourselves!) up to date on the latest and greatest science news.

Psst, don’t forget about our Published Reference program, you get a free kit for sending us (reference@mobio.com) your published paper using our kits!  Not a bad gig!

This month we picked:

Metagenomic Analysis of the Airborne Environment in Urban Spaces

Nicholas A. Be & James B. Thissen & Viacheslav Y. Fofanov & Jonathan E. Allen & Mark Rojas & George Golovko & Yuriy Fofanov & Heather Koshinsky & Crystal J. Jaing

Hello MO BIO!  My name is Jesse McNichol and I'm a graduate student in the MIT/Woods Hole Joint Program and along with my supervisor, Dr. Stefan Sievert, I study the microbiology of deep-sea hydrothermal vents. These ecosystems are extremely unusual on Earth, since they are mostly supported by volcanic activity instead of the sun's light. The oxidation of hydrogen sulfide and hydrogen gas are probably the ultimate source of food for all the teeming life around these hot springs, including the large fishes, tube worms and crabs. 

There’s been some social media buzz lately about #WomenInScience. No better time than the present to update the list from our previous blog!

Ruth E. Ley is an Assistant Professor of Microbiology at Cornell University in Ithaca, NY. She was trained in ecology and natural history at the University of California Berkeley (B.A.) and in ecosystem science and soil microbial ecology at the University of Colorado, Boulder, where she worked with Dr. Steve Schmidt (Ph.D.). 

Blood contains a mixture of plasma, red and white cells and platelets.  It is a unique beast among sample types, because while the quantity of nucleic acids in blood is copious, this genetic gold mine bathes inside a complex soup of cellular debris and protein. These contaminants can interfere with downstream PCR and sequencing.  It is the hemoglobin in particular, within the red cells, which causes major issues in DNA/RNA contamination and PCR inhibition.

Warning ---> If you don't use twitter, this article might give you the extra boost to go ahead start tweeting away..

I met Arwyn's tweet one day and rest is history!  He had posted results from his undergraduate class about how there are essential oils such as lavendar that are actually a more effective bacteriocide than other toxic chemicals such as bleach.  Super Rad result!  I got in touch with him and, over time, learned about his incredible and very global climate change relevent research on microbes that live on ice and snow of the Arctic.

I sent him a few basic questions and voilà!  Enjoy.

Dear MO BIO,

I am using the RNA Power Soil Total RNA Isolation kit with some high saline soil.   I was not able to extract any RNA but was able to extract DNA with the kit.  What's going on?

Thao

My name is Cassie Ettinger and I am a 2nd year PhD student in Jonathan Eisen's laboratory at the University of California, Davis. I am working with Hannah Holland-Moritz, a Junior Specialist, and Jenna Morgan-Lang, the Post-doc in charge of the project, to try to characterize the Seagrass Microbiome, the entire microbial community associated with seagrass.

Why study the seagrass microbiome? Seagrass has an interesting evolutionary history.  Starting out as marine algae, an ancestor of seagrass made the transition from marine to terrestrial with its descendants eventually becoming what we know today as plants.  Some of these plants later returned to the marine home world from whence their ancestors had originated (just like whales evolved from a land-based ancestor that returned to the marine environment!). Seagrasses are the only known flowering plants to have made this return to the sea. This is because surviving in a marine environment poses significant physiological and morphological challenges. We are interested in the role microbes might have played in the adaptation of seagrass to the marine environment and if any co-evolution has occurred between seagrass and its microbiome.

My email dings soon after lunch on Monday, I open the window, and there it is in all its glory. The MiSeq data has arrived! I promptly download the file giddy with excitement…and wait. And wait. The file is huge, and incomprehensible, and somehow contains nearly 15 million sequences.

Luckily, I had signed up to attend the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop hosted by Michigan State University. So here I am at Kellogg Biological Station on Gull Lake taking baby step-by-baby step through the shell, QIIME, Mothur, and R. Many of these I have used in the past, believing that I had taught myself how to run them. But here’s the difference: what I had done was copy and paste some commands, hope it worked, and then compared my results to results from other programs. Very efficient! Now: we are really learning the meat of these programs down to the last –i and / and the knowledge of these details allows the understanding of what happens in each step. My goals while here at EDAMAME 2014 are not to merely analyze this dataset, but to be able to take this knowledge and power and translate it to any dataset.

Hello!  My name is Enid Gonzalez-Orta and I am an Associate Professor of Biological Sciences at California State University, Sacramento, where I teach undergraduate students about the wonderful world of microbes.  In addition, I embed an authentic research experience into my microbial diversity class each spring where we study soil samples collected from CSU Sacramento Arboretum or from local vernal pool sites.  We study the bacterial community of these samples using traditional methods, like culturing samples onto laboratory media, sequencing of the 16s rRNA gene through the Sanger method, and building phylogenetic trees.  However, I began to think about how much the field of microbial ecology has changed and is changing.  I thought about how culture-independent methods allow us to peek into environments seldom studied in the laboratory and how these methods reveal members of bacterial communities that were previously not known to inhabit these niches.  I also thought about how next generation sequencing (NGS) methods are becoming becoming the “tradition” in this field.  And, I thought about how important it is for undergraduate students to have hands-on experience with bioinformatics and computing in order to interpret the volume of sequencing data that is produced through NGS.  But, how I could I do this when I myself had little-to-no experience with processing 16s rRNA NGS data?  Then came EDAMAME to the rescue!

Greetings, Culture Dish followers!

My name is Ashley Shade and I am an assistant professor at Michigan State University in the Department of Microbiology and Molecular Genetics. I am excited to share our first days’ adventures in our new workshop, Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME). EDAMAME is a week-long intensive training in bioinformatics tools and ecological analyses of microbial metagenomics data, held at Michigan State’s Kellogg Biological Station.

I know what you are thinking: Silly new professor! Why dedicate preparation time and a week of your life to a non-credited summer course that won’t count towards your teaching requirements?

Want to play in the mud?  Like the ocean?  If your answer to both questions is “yes,” you may have a tinge of jealousy when it comes to this Where in the World project.  François Thomas, PhD, works as a postdoctoral scientist with Stefan Sievert, PhD, at Woods Hole Oceanographic Institution on Cape Cod in Massachusetts.  His collaborative project* funded by the National Sciences Foundation studies microbes in New England salt marshes. By sampling sediments and roots of the salt marsh grass known as Spartina, he uses both cultivation and molecular techniques to understand the microbial communities in each environmental niche. In particular, he is studying sulfur-oxidizing microbes, which can profit from the release of oxygen from the roots and might play a critical role in linking the carbon, nitrogen and sulfur cycles. To get back to your childhood memories, check out this video from the field.

One of the top five technical concerns we get at MO BIO relates to low yields of DNA.   Whether it be sediment, swabs, waste water or sludge, at some point we've probably heard that you didn't get enough DNA out of it.  After all, there is no such a thing as getting too much DNA.   Nope, haven’t heard that grievance even once!

When someone tells us they didn’t get enough DNA, we rule out the obvious offenders. It could be that your lab-mate left your samples out all night at room temperature and didn’t tell you. It might also be that you’ve made an error in the way you’ve interpreted or conducted a protocol or perhaps you’re using an inappropriate kit. The list goes on and on.  However, the answer could be a lot simpler.  Low DNA yields (defined here as those that can't be easily measured with an absorbance spectrophotometer, for example, a Nanodrop) may not indicate that something went wrong at all.   It might just be that there wasn't a lot of DNA to begin with.  This is very common with low biomass samples like swabs, filters or sediment.

Last week marked the deep sea submersible Alvin’s 50th Birthday.  This translates to 50 years of unprecedented ocean exploration and discovery!

MO BIO Laboratories, Inc. would like to thank Alvin and the very dedicated folks that make Alvin’s story so historic in scientific discovery!

Thanks to Chris Linder, Alvin and MO BIO's cultivating curiosity were united on R/V Atlantis during the first scientific expedition with the newly outfitted Alvin, awesome sauce!  I can't help but share my own special moments with Alvin, thanks for checking in!

Considering a move to high throughput DNA/RNA isolation? Many of our customers, who’ve been using MO BIO single prep kits for some time, now want to scale up.  We’ve been getting a lot of questions as to what equipment is required to make the switch.  Scaling up usually means moving sample preps over from 2 ml tubes to standard 96 well microplates. While many customers have experience with multichannel pipetting for these plates, many have never done any bead beating in 96 well format.

Most MO BIO kits take advantage of bead beating to assist in cell lysis because it is an exceptionally good method for isolating gram+/- and spore and oocyst DNA & RNA.  But bead beating, while easily done on a vortex in 2 ml bead tubes, requires much beefier equipment for 96 well plates.

Craig Cary, a friend of the MO BIO Laboratories' family came by to say hello and also updated us on his work. Craig works on soils from Antarctica in a region called the Dry Valleys in Victoria Land.   Talk about extreme!  Imagine glaciers, extremely cold temperatures, very dry air, rocky salty soils, lack of vegetation, “Kadabatic” winds derived from the mountains, 24 hours of sunlight during “summer”, and to top it off mummified seals!  This place has been described as one of the most extreme environments on the planet, and is used as a model ecosystem to better understand the conditions on Mars, a planet akin to this “freeze dried environment”. In 1989, an important treaty called the Montreal Protocol was put into effect banning the use of CFC’s in any commercial products due to its deleterious effects on our ozone layer.  It turns out it this treaty has made a profound effect on positively regenerating the ozone layer which is concentrated in the upper atmosphere of the poles.  This comes with concern about how this will effect the environment in Antarctica, ozone traps heat including the climate changing CO₂ we are pumping in to it.  Will Antarctica continue to warm?  We know that the Antarctic Peninsula, a fingerlike projection sticking up towards South America, is one of the fastest warming regions on the planet.  What will happen with the rest of the continent, will it warm too?  This is what Craig wants to know.

Three years ago we published a tech article in which we went into detail on using swabs with MO BIO DNA Isolation kits.   Recommendations depend both on levels of PCR inhibitors and whether one wants microbial or eukaryotic DNA.  The article included details on how to transfer swab samples to bead tubes and collection tubes for use in each kit.  Swabs continue to be one of the fastest and easiest methods for sample collection and remain a popular subject for tech support questions.

Since the previous swab article, we’ve developed two new kits that we recommend for swabs, one for RNA Isolation and the other, for high through-put rapid mechanical lysis of microbial cells on swabs from low biomass/low inhibitor samples.

Most of the time choosing a DNA Extraction kit is pretty straight-forward.   If you want to isolate DNA from lung tissue, then use a tissue DNA isolation kit.   If you want DNA from microbial culture, then use a microbial DNA isolation kit.    But what if you want microbial DNA from the lung tissue?  Do you choose the tissue kit or the microbial kit?  And what if you want animal tissue DNA from a soil sample?  Should you use a tissue or a soil DNA isolation kit?  It gets a little tricky.  These kinds of mixed up situations make up a good fraction of our technical support questions.   We have worked out protocols for many of these scenarios.   Below we discuss three of the most common mixed-up circumstances and give suggestions as to which kit and protocol will work best for them.

A few years ago the folks here at MO BIO technical support were contacted by a customer from UC Berkeley who was trying to extract microbial DNA from Western Blue Bird fecal sacs. She’d tried several sample kits of PowerSoil. Yet, despite her best efforts, she could not get any measurable DNA from this particular sample type. We knew that the DNA had to be in there. After all, fecal samples are chocked full of microbial DNA. We went down our normal list of troubleshooting suggestions. The sample was collected properly, stored properly and she was following the normal protocol. But still no luck! So what the heck was going on? We  had extracted DNA from many different types of fecal samples in the past without any difficulty. In efforts to figure out the answer, we suggested that she send us a few of the bird fecal samples so we could do some experimentation.

Whether you don't know which DNA isolation kit to buy or you just have a protocol question, MO BIO technical support it here to help. More often than not, we've heard a similar question before and we can answer you pretty quickly. Occasionally, however, it takes some brain wracking. It might be that you've managed to throw something unique our way. But usually, it's because we don't have enough information to go on. In that case, we will write or call you back, ask for more specifics and then (depending on the answers) we might ask some more. While we all enjoy the back and forth banter, we know you'd really like to get back to your research as quickly as possible. So we thought maybe we should come up with some tips for you to make the process more stream-lined. We were able to get it down to five key elements. This list is not comprehensive. But, we think if you can give us this information right off the bat, we'll be able to get you back on track fast.

This will be my final blog post as MO BIO Lab's Director of R&D.  I wanted to leave you with some last words as I make the next transition and continue to be a part of the microbiology world, just from another side- as a customer of MO BIO just like all of you.

I have had the most amazing experience being a part of this wonderful family. I am so grateful for the opportunity given to me 5 years and 9 months ago to be the director of the science coming out of MO BIO Labs, for the chance to stretch my brain and be creative every day,   and to work with the most talented people I've ever known.  Thank you for the opportunity to travel to amazing places to represent MO BIO and for all the close friendships with customers that I've made because of my time here.  Many of you I will continue to tweet with and email for mentorship and dialogue and I am grateful.

Dedicated bead beating instruments are costly. For a device that can hold more than just a couple of bead tubes, prices quickly rise into the thousands of dollars. Fortunately, a less expensive alternative, the humble and multipurpose vortex, can do the trick nicely for most bead beating applications. For optimal results, we recommend that you use a vortex adapter, a detachable horizontal tube holder, for efficient and consistent homogenization of your samples.  MO BIO manufactures such adapters in a variety of tube sizes from 2 ml up to 50 ml.

While the majority of our customers use these adapters, sometimes their MacGyver instincts take over and they will rig up something of their own.  And while they have come up with some pretty clever and unique constructions, the results are not always favorable. Though it may seem like a remarkably simple device, much testing and optimization has gone into the design of our vortex adapters. From the orientation of the tube holders to the number of tube holders on each platform, each one has been designed to work best for a particular type of bead tube. 

I am sure that in the back of many a scientist’s mind is the idea that it would be fun or better yet a good career move to start a biotech company. I told myself that very thing many years ago and decided to give it a try. I had recent experience with a startup that some of you may remember if you are old enough. It was called BIO 101 and was the first company ever to sell DNA kits. In fact, I am on the first ever patent for a DNA isolation kit that used silica resin to purify DNA in the presence of binding salts, followed by washing and then eluting the pure DNA into water. This is pretty much the industry standard today for how DNA and RNA get purified.
Wow, it brings back memories of what it is like to have no competition and have the opportunity to sell a product that has a huge impact on the industry. That was 1986. Fast forward to 1993 when I decided to go out on my own with many product improvement ideas I had that did not fit with the BIO 101 plans.

How DOES science fare in the online space? Communication of complex scientific processes is difficult enough one-on-one. With Twitter and Facebook, communication is now not just between two people but hundreds, maybe thousands. This is the topic to be addressed at the next MO BIO Labs sponsored BiteSize Bio webinar.

You may remember our previous webinar with Dr. Joseph Petrosino from Baylor College of Medicine and his talk on Metagenomics and Type 1 Diabetes (T1D).  Dr. Petrosino described the undertakings of an exciting collaborative effort to find the cause of T1D and eventually a cure.

For our next webinar we wanted to do something quite a bit different.  This time around we want to focus on a very important subject that impacts everyone in the community. That is, as scientists, how do we communicate our science and our knowledge of science online.

The olive tree, derived from the domestication of wild olive, is the main oleaginous crop of the Mediterranean Basin. Spain is the world leading country for olive production, with more than 2.4 million ha, of which 63% are located in Andalusia (southern Spain). Olive cropping systems include agroforestry stands (in marginal soils and hills), traditional groves and new intensive orchards. 

Pavilion Lake, in northern British Columbia, holds a uniquely diverse array of microbialites that may offer information for equally diverse applications, spanning from the ancient past to vitality at the far reaches of our solar system! PhD Student Rick White, along with the Suttle Lab at the University of British Columbia, describes his research endeavors at this exciting site. 'The Pavilion Lake Research Project (PLRP) is an international, multi-disciplinary, science and exploration effort to explain the origin of freshwater microbialites in Pavilion Lake, British Columbia, Canada. Fossil microbialites represent some of the earliest remnants of life on ancient Earth, and were common from ~2.5 billion to 540 million years ago. Today, microbialites are found in environments where conditions are often too harsh for most organisms. However, the microbialites in Pavilion Lake have provided a new environment for the scientific community to study that demonstrates that large, and uniquely shaped structures can also occur in non-extreme environments that support fish, plants and other species.

Led by Dr. Chinh Doa, undergraduates of Drake University are delving into a project to assess microbial ecosystems within the prairies and waterways of central Iowa through molecular fingerprinting. The major goals of this project are to measure the changes in microbial diversity over time in a given water or soil microenvironment, quantify the fluctuations, and determine how sensitive microbial communities are to ‘normal’ changes in their environment.  These students sampled the state parks and two rivers in the Des Moines area, the Des Moines River and the Raccoon River, as well as an area near the city dump. 

The infamous LA river winds through the center of Los Angeles, heavily polluted with waste from the city. It may not quality as a southern California scenic destination, but as far as bioremediation projects go, this locale is ideal! The river provides a fertile source of microorganisms accustomed to living with and degrading pollutants. Nikki Thadani and a team of fellow California Institute of Technology (Caltech) undergraduates have chosen this urban river as their site of choice for the iGEM synthetic biology competition. They hope to produce a bioremediation system for endocrine disruptors. Endocrine disruptors such as DDT and BPA have a significant detrimental impact on the reproductive systems of organisms living

"How many organisms live on a square centimeter of your skin? What do they do, and how do they differ from those of your neighbor? Each person’s microbial jungle is so rich, colorful, and dynamic that in all likelihood your body hosts species that no scientist has ever studied. Your navel may very well be one of the last biological frontiers. It is time to explore!" proposes Jiri Hulcr, PhD, of the Belly Button Biodiversity project. 

Ryan Adams, Greg Barnes, and Taylor Foulger, of Southern Utah University, in collaboration with mentors Terri Hildebrand and Paul Spruell, are wading their way into utilizing DNA analysis to describe irrigation water bacterial communities. They state, "access to clean water is essential to life.  Around the world, water is used for both drinking and agricultural purposes; therefore, pathogen free water is paramount to healthy living.  Methods that test for specific pathogenic bacteria in water samples have been developed.  However, these approaches are limited in scope and do not detect non-pathogenic or atypical bacteria.  Our research seeks to describe the bacterial communities of irrigation water found in Iron County, Utah using DNA sequencing analysis.  During the course of this research bacterial DNA has been isolated, using the UltraClean® Water DNA Isolation Kit, ...

Anchialine habitats are defined as coastal ponds and pools that lack surface connections to the open ocean, but are influenced by both seawater and freshwater sources via subterranean connections to the ocean and underlying freshwater aquifers. Habitats fitting this definition are found worldwide, but are concentrated in the Hawaiian Islands, with 600 of the world’s ~1000 habitats. These Hawaiian anchialine habitats host diverse and often endemic macro- and microbiotic communities. Unfortunately, anchialine habitats in Hawaii are threatened by habitat destruction and alteration due to coastal development and invasive species. 

The US viticulture industry generates >$30 billion revenue each year and employs more than 24,000 people. It is also a growth industry, but one that is highly susceptible to the vagaries of climate and changing weather patterns. There is exceptional merit in exploring the “quality” of soil and the vine microbiome when growing wine as there is a fundamental link between plant health and productivity and the microbial dynamics in the biogeochemical cycling nutrients.

Lee Ripma ( Graduate Student) : The objective of my master’s thesis research project is to elucidate the evolutionary relationships within the genus Oreocarya (Boraginaceae). Oreocarya has long been treated as a subgenus of Cryptantha and defined by perennial (or biennial) duration and production of only chasmogamous flowers. Past treatments by Payson and Higgins treated Oreocarya as a generic section or subgenus. A forethcoming paper by Hasenstab and Simpson recovers Oreocarya as a monophyletic clade and resurects the group to genus level. Their molecular phylogeny of Cryptantha s.l. finds that the genus as currently treated is polyphyletic and warrants a split into 5 genera. The group will be split into Cryptantha s.s., Oreocarya, Eremocarya, Greeneocharis and Johnstonella.

S

table Isotope Lab use MoBio products at the Toolik Field Station located in northern Alaska. They are investigating microbial communities in arctic tundra soils and how different metabolic pathways are utilized. 

Jessica examines shifts in soil microbial community structure, activity, and functionality as a result of increased soil temperature and moisture, increased thaw depth, and altered vegetation caused by excess winter snow accumulation in a permafrost tussock tundra ecosystem.  Mobio's products have been extremely helpful in the field where I am using Mobio's LifeGuard soil preservation solution to instantly stabilize soil microbial RNA and DNA on the spot, giving me plenty of time to finish field work without worrying about instantly freezing my samples. Thanks Mobio!! - Says Jessica.

Guizhou, China, studies gut microbes in Asian leaf eating monkeys.  Specifically, She is comparing gut microbes between wild and captive Guizhou snub-nosed monkeys (Rhinopithecus brelichi) and other closely related colobines - including the Francois' langur (Trachypithecus francoisi), the proboscis monkey (Nasalis larvatus), the Sichuan snub-nosed monkey (Rhinopithecus roxellana), and the Yunnan snub-nosed monkey (Rhinopithecus bieti).  These species are all leaf-eating monkeys - which can be difficult to maintain in captivity.  Gastrointestinal issues or disease often plague captive colobines - not infrequently resulting in their deaths.  This study will evaluate differences in the gut microbiota found in wild and captive monkeys in attempt to determine how we can better support the health of captive colobines like the Guizhou snub nosed monkey and the Francois langur. The study will also assess the gut flora of closely related monkeys to determine if the gut microbiome reflects host phylogeny.  (She uses  MoBio kits to extract DNA from the monkey feces and then have my samples sequenced through the Earth Microbiome Project.)

Working with samples from rare and endangered bird species such as White-tailed Sea Eagles, Golden Eagles and Temminck’s stints, Dr. Laura Kvist and her colleagues at the University of Oulu, Linnanmaa consider each collected sample to be precious and switched to MO BIO products after experiencing PCR amplification problems.

Nestled below the dramatic Dolomites, an expanse of vineyards cloaks the Trentino region of northern Italy. Nestled below these vineyards, lies an even more complex expanse of microbes. Claudia Longa, PhD at the IASMA Research and Innovation Center, Edmund Mach Foundation, along with colleagues of the plant-environment interaction program, has the most romantically-set research backdrop we have seen our kits experience. She and her team are studying the molecular profiling of microbial communities in soil and in the rhizosphere of vineyards from Trentino, ...

In Ph. D. student Andy Canion's own words: "Greetings from the Arctic archipelago of Svalbard!  The lab of Dr. Joel Kostka, at Florida State University, recently participated in an international research expedition to study the microbes that live in the marine muds at the bottom of Arctic fjords.  The expedition was organized by the Max Planck Institute for Marine Microbiology in Bremen, Germany, and took place in the Svalbard archipelago (79°N), north of Norway.  Svalbard is a majestic place, with striking mountains, glaciers calving right into the water, and no shortage of polar bears.  There is also no shortage of researchers in the town of Ny-Ålesund, which has been converted from a coal-mining town to a year-round research station (the northernmost permanent residence in the world!).  

Dr. Laurie Casalot, from the French Research Institute for Development (Marseilles, France), Department of Microbiology and Biotechnology of Hot Climates, extracts really complex samples from a settling tank at a semi-industrial olive oil factory in Morocco. The samples were collected at two different periods: 2 weeks after the oil-production campaign and 7 months after this campaign. In the meantime, the outside temperature reached more than 40ºC and the water evaporated leaving only an extremely viscous solution (see picture below), making the samples quite challenging for extracting DNA

Alexandre de Kochko from the “Centre IRD” in Montpellier (France) is working in collaboration
with two Malagasy Colleagues, Jean-Jacques Rakotomalala and Josiane Razafinarivo, (pictured above) on the evolution of Malagasy Coffea species. Coffea (coffee) is a large genus (containing more than 90 species) of flowering plants in the family Rubiaceae.

At the southernmost-tip of the East African Rift Valley in Kenya, lies a, at times, virtual pool of sodium carbonate, the Lake Magadi. This lake is replenished primarily by surrounding saline hot springs, setting the scene for an extremely challenging environment for life of any form. With soda covering around 80% of the lake surface in the dry season, and areas within the lake containing salt up to 40 meters thick, there is only one surviving species of fish withstanding the conditions.

Thulani Makhalanyane, PhD candidate at the Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, South Africa, along with Professor Donald Cowan, recently took a trip to the Namib Desert, to conduct research focused on understanding the microbiology of hyperarid desert microbial communities, particularly, the hypolithic communities. Hypoliths, which are microbes found underneath translucent rocks, are particularly exciting microbial niche communities. "We are interested in understanding the composition and community dynamics of hypoliths. This involves the analysis of microbial (prokaryote and eukaryote) diversity, and building a relationship between community composition and local physiochemical properties such as pH, relative humidity and temperature. One of the microenvironmental dynamics which is particularly exciting is water relations - we would like to understand the relative contributions of rain, fog (condensation) and ground water."

Princeton University Professor Tullis Onstott and his team used the MO BIO UltraClean^® Mega Soil DNA Isolation Kit to remove bulk DNA from filtered fracture water for downstream metagenomic analyses. The water was collected from South African gold mines that stretch nearly a mile below the earth. A large scale DNA isolation kit was required for this project because of the enormous volume of water required for a complete metagenome – up to 8000 liters! While hot, salty water samples were collected from multiple boreholes, one specimen collected from a 2.8 km borehole yielded remarkable results. Using the16S rRNA gene to examine the biodiversity present in the fracture water, Tullis’ group discovered that 99.9% of the sample was comprised of a single bacteria. 

Kevin Redd, PhD candidate, and colleages at the School of Zoology, Marine Research Laboratories, Tasmanian Aquaculture and Fisheries Institute (TAFI)-University of Tasmania use UltraClean® Fecal DNA Isolation Kit and UltraClean-htp® 96 Well Soil DNA Isolation Kit for their research.

The goals of the project are to examine the range of prey consumed by the southern rock lobster (Jasus edwardsii) and to further the understanding of the role that this predator has in the marine environment. In Australia, rock lobsters are the basis of important commercial and recreational fisheries and are sold live to discerning international markets. We have developed non-lethal techniques to collect fecal material from live rock lobsters so that our sampling efforts can be conducted in marine protected areas and in conjunction commercial fishing operations.

The Hidden Secret of Soil: A team of scientists at ESR, Catriona Macdonald, Jacqui Horswell, Rachel Parkinson, Jill Vintiner, are using MO BIO’s PowerSoil® DNA Isolation Kit for soil to extract DNA from soils for forensic purposes.
In forensic science, soil is frequently encountered as trace evidence (e.g. on the sole of a shoe or the tread of a tire) but detailed soil analysis is seldom carried out in routine forensic examination for numerous reasons (e.g. cost, insufficient sample size, access to expertise).
ESR has been developing a technique to compare the microbial “fingerprint” of soils collected from realistic crime scenarios. The soil profiles are representative of the site of collection and therefore could potentially be used as associative evidence to prove a link between suspects and crime scenes.

Developing a biological reduction cell to remediate heavy metal and acid-containing industrial and mine leachates: Alison Dann is a Ph.D. candidate whose project is to study the environmental impact of an old industrial production plant in Tasmania. It was operated between 1948 and 1996 in Heybridge, located on the north coast of Tasmania on the Blythe River catchment. During the plant’s operation sulfuric acid/iron oxide waste was discharged directly into Bass Strait, resulting in elevated metal concentrations and a highly visible red plume along the coastline locally suppressing the marine benthic biota and altering biodiversity. The leachate is very similar to acid mine drainage

Dr. Leda Christina Mendonca-Hagler and her colleagues at the Rio de Janeiro Federal University characterize mangrove sediments in a highly-polluted region of the Guanabara Bay, Brazil. It is a challenge to identify the most efficient oil degrading bacteria in a polluted environment. They isolate DNA of soil-degrading bacteria from the rhizospheres of mangrove plants using our UltraClean® Soil DNA Isolation Kit.

Dr. Maria A. García-Amado, Researcher from Laboratorio de Fisiología Gastrointestinal (Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas (IVIC), Mrs Sanz posdoctoral student from Centro de Ecologia (IVIC), both from Venezuela and Mrs Rodríguez-Ferraro, doctoral student from the Department of Biology, University of Missouri-St. Louis (USA) work in Venezuela in the detection of the Helicobacter genus in feces of wild birds. 

They isolate DNA of bacteria from the fecal samples using UltraClean® Microbial DNA Isolation Kit. Dr. Garcia-Amado quoted: “This kit is easy to use and we have excellent results!”The wild birds are caught with mist nets, Dr. Garcia-Amado and her colleagues took morphometric measurement and collected the feces, and then the birds are liberated.” (No harm is done to the birds during the process)

Milagro Fernández (see right picture) is currently a Ph.D. student in Biological Sciences at Simon Bolivar University, Venezuela. Her Ph.D. thesis subject is on detection and isolation of Vibrios in a marine coastal environment of Venezuela. She uses our UltraClean® Microbial DNA Isolation Kit for DNA extraction of Vibrio cultures from seawater, plankton, and oyster tissue.
The aim of her research is to detect and isolate pathogenic Vibrio spp. from seawater, plankton, and mollusks in a touristic area of Venezuela exposed to fecal contamination. These samples are analyzed by culture techniques, PCR and 16S rRNA gene sequencing. Milagro Fernandez quoted that "For total genomic DNA extraction from bacterial cultures, the UltraClean® Microbial DNA Isolation Kit has been very useful"
She is now using the UltraClean® Water DNA Isolation Kit for the direct detection of these bacteria in the environmental samples, whose presence is a public health concern.

Water up to 400°C shoots skyward carrying hoards of toxic chemicals from cracks in the earth's crust at the depths of our seas!  Aspects of the newly explored deep-sea hydrothermal vents are nothing short of absolutely captivating. Previous expeditions to these vents have identified strange and exotic sea floor dwellers, but the National Science Foundation's "Extreme 2008: A Deep-Sea Adventure" was the first to investigate the viral and protozoan extremophiles that play a vital role in vent ecosystem balance. Led by University of Delaware marine scientist, Craig Cary, this international research team set sail aboard the R/V Atlantis to the Pacific and Sea of Cortés, to explore this foreign and extreme environment.

Jennifer Kerekes is currently a Ph.D. student in the Department of Plant and Microbial Biology at the University of California, Berkeley. Her recent work at the Barro Colorado Nature Monument in Panama focused on the effect of repeated and long-term exposure of macronutrients and micronutrients on saprotrophic fungal diversity. She used the PowerSoil® DNA Isolation Kit  for total genomic DNA extraction from soil and leaf litter environmental samples. “The PowerSoil DNA Isolation Kit has been very useful for isolating total genomic DNA and has had great results in amplifying microbial DNA,” said Jennifer. She also had positive results with the PowerSoil DNA Isolation Kit in El Salvador at the Walter Thilo Deininger Park where, where in collaboration with the Instituto Salvadoreño de Turismo and the local community, she is studying the diversity and community structure of soil fungi in a dry tropical forest.

Deep, deep below the surface, at 2000m depth in the Gulf of California, lies an intriguing and unique hydrothermal vent system of microbial wonder. This system is unlike any other in that this hydrothermal fluid does not erupt through black smokers, but instead, slowly percolates upward through a layer of organic-rich thick sediment. A collaborative team of researchers from around the globe, including a group from UNC Chapel Hill led by chief scientist Andreas Teske, make up a multidisciplinary team, aboard the Guaymas Expedition- 2009, analyzing the geochemistry and microbiology of Guaymas hydrothermal seeps. These studies notably include analysis of the mats of Beggiatoa organisms that often form on top of active hot areas of fluid escape.

Lake Tai (or as it is known to the local, Taihu) is the third largest lake in China - over 30 million people rely on it as a source of potable water and for various aquaculture, industrial and transportation purposes. Over the last few years though it has been inundated with massive algal bloom dominated by the potentially toxic cyanobacterium Microcystis. Dr. Jennifer DeBruyn and Ms Sarah Farnsley accompanied Professor Steven Wilhelm, all from the University of Tennessee,  to Taihu in May 2009 to collect samples from the lake in order to begin to develop an understanding of the factors that control the proliferation of these toxic algae. 

China's booming population, along with that of the rest of the world, demands an equally booming food and resources supply. In this light, Ning Ling, a Ph. D. student from the College of Resources and Environmental Sciences, Nanjing Agricultural University, China, is investigating a key aspect to our species survival. He is currently working on soil microbial ecology, researching the food crop nemesis, soil-borne watermelon pathogen, Fusarium oxysporum. In his studies, Ning Ling isolates DNA from diseased soil infested with Fusarium oxysporum (shown in the above photo, left side), and soil restored with various bio-organic fertilizers (above right). Using molecular biological methods, Ning Ling studies the differences in soil microflora between these soils to optimize crop stability.

Subramanya Rao, PhD student at the University of Hong Kong, part of the Extremophiles Research Group run by Dr Steve Pointing, has taken an expedition to the Thar Desert to obtain samples from arid and semi arid regions within Rajasthan, India. The aim of this research is to examine the soil microbial community from arid and semi-arid regions of the desert and to understand ecosystem functioning in desert soil.

"Soil samples were collected in sterile tubes, one groups containing stabilization solution (used to extract RNA) and the other without (used to extract DNA). The soil samples were then transported to the laboratory for further analysis. Immediately cultivable microbes...

Every summer since 2008, a cadre of scientists from the University of Pennsylvania, the Academy of Natural Sciences and the National University of Mongolia head out to the Lake Hövsgöl Long-Term Ecological Research (LTER) site. Camp staff, project coordinators, undergrads, grad students, post-docs and faculty members are the backbone of this team united through the PIRE Mongolia Project (Partnerships in International Research and Education). Through this project, plant ecologists, biogeochemists, soil scientists, climate modelers, and others are empirically documenting the effects of climate and land-use change on this arid ecosystem, which has been grazed for a millennia by the livestock of local nomadic herders. How the microbial ecology of this ecosystem shifts with climate change and how this correlates with shifts in the plant community are some of the central questions under investigation.  

Anthropogenic influences on the global nitrogen cycle have resulted in a series of environmental problems including global acidification, increased emission of the greenhouse gas N2O, and eutrophication in estuaries and coastal seas. Yangtze River is the third-largest river in the world. In recent years, the Yangtze River has a high load of anthropogenic nutrients from increased agricultural activities, fish farming, and wastewater runoff due to the increase in population and economic development, which has resulted in severely eutrophic status in the estuarine and coastal area. Since the 1980’s, harmful algal blooms have occurred frequently in this area, due to excessive inputs of inorganic nitrogen. Hence, the nitrogen transformations are of major concern in the Yangtze Estuary.

Approximately 99% of bacteria present in soil are uncultivable making it impossible to study by culture dependent methods. Estuaries and mangroves are important ecosystems in Asia consisting of 42% world mangroves playing crucial role in coastal and ocean nutrient cycling. It is vital to study these habitats in detail through culture independent approaches in order to understand the ecosystem functioning and biotechnological potentials.

infection become prey for a number of scavengers in the region. Vultures are among the most abundant scavengers here and they may play a role in the distribution of Bacillus anthracis endospores. However, this role has not been quantified, and a misguided belief that vultures transmit disease over long distances has led to an extreme decline in numbers. Dr. Ganz informed us that both of their study species, lappet-faced vultures (Torgos tracheliotos) and white-backed vultures (Gyps africanus), are currently listed as threatened species. Their research, then, not only seeks to better understand population disease transmission, but also seeks to strengthen coonservation efforts. 

A group of 33 people including Emelia DeForce (shown at right), a graduate student from University of Massachusetts Boston, sailed the tall ship SSV Corwith Cramer to collect and study plastics in the North Atlantic subtropical gyre.  The research and teaching vessel of Sea Education Association in Woods Hole, MA left out of Bermuda and covered over 3800 nautical miles going east passing over the mid Atlantic Ridge on a 34 day journey.  This was a follow-up cruise to sample an area that had not been surveyed for plastics.  To collect the tiny pieces of plastic, mostly millimeters in size, they towed a neuston net several times a day overboard then sieved and counted over 48,000 tiny plastic pieces by hand! Emelia and other microbial ecologists on board also preserved pieces of plastic for further investigation back in the labs at Woods Hole Oceanographic Institution and Marine Biological Laboratories.

Forest fragmentation has been a prominent threat to the conservation of biodiversity, especially in tropical habitats. Costa Rica, nestled in the Central American isthmus, houses an extensive amount of biodiversity, and so is an area where crucial examination and careful monitoring of land fragmentation and its effects are pertinent. The Organization for Tropical Studies (OTS), in Costa Rica, takes a large part in this very important role. OTS is a nonprofit organization that brings together 63 research institutions in the United States, Latin America and Australia to "provide leadership in education, research and the responsible use of natural resources in the tropics." 

We speak with many scientists who work with filtered water for isolating microbial DNA and RNA. Water samples can be difficult because of their typically low biomass (depending on the water source) and because these samples are often from precious and unique sources.

Why is molecular research on microbes in water difficult?

For some people, getting back to the original source of water may not be possible for months or even years. For example, we talk to scientists collecting samples at hydrothermal vents in the middle of the ocean, in the Antarctic, and in the Baltic Sea.  For some researchers, water samples may have been collected after a certain event, such as a flood or heavy rain and so the conditions of the water will not be the same in a week or even after a day. They need to get answers from every sample collected and they need it to accurately reflect the current microbial content.

I would like to meet whoever is responsible for perpetuating the myth that scientists area stuffy and dry bunch and introduce him or her to the amazingly creative and artistic scientists we have the pleasure of interacting with at MO BIO.  This month we invited our usersto submit a poem about their MO BIO experience. The results were quite impressive. The topics ranged from our kit's unparalleled ability to remove inhibitors to our great customer service. In return for their very kind words, we offered up a t-shirt and discount code.

Be sure to check out the video links of MO BIO employee's reading the submitted poems.

We start off our MO BIO Poetry Corner with a poem from our CFO/owner, Liz Brolaski. Mark Brolaski, CEO/owner, reads Liz's poem that gives a shout out to the awesome employees at MO BIO.

Thank you to everyone that submitted a creative piece this month. Have your own poem to share? We would love to hear it, leave it in the comments or e-mail us at customercare@mobio.com for your own shirt and promo code!

Who hasn't pondered the age old question: Which came first, the chicken or the egg?

Debates on this subject have kept philosophers busy for centuries, lending to rich discussions on everything from evolution of chickens to the beginning of life and the universe. One could ponder this question from a literal point of view and discuss the evolution of egg laying species and whether or not this pre-dates the appearance of chickens. Or one could set forth on a metaphysical journey and focus on the possibilities of how one life form can exist without its developmental precursor or how a precursor exist without its original maker?

Here at MO BIO, this discussion led us down a different path. The question we propose to you is: Which came first, the DNA or the protein? You need DNA to know what proteins to make and how to make them, but, you need proteins to synthesize more DNA, to transcribe the DNA into RNA, and to hold it all together.

This week we want to discuss a technique that is very common but still causes many people to suffer from separation anxiety.  What could that possibly be? It is cleaning up dirty genomic DNA.

Here's the scene: You have a precious soil sample collected from the roots of an ancient never-before seen orchid located on a remote island in the middle of the South Pacific. You isolated the DNA from microbes in this soil using a method other than the PowerSoil Kit. It's still dirty and won't amplify in PCR so it needs to be cleaned of humic acids and other humic substances. You need every last molecule for whole genome shotgun sequencing.... what do you do?

Jan 24, 2013
69°56.9S X 76°17.2W (Most Southern Point)
West of the Antarctic Peninsula
Sunrise  2:50am
Sunset  12:19pm

We’ve all got our groove on. Sampling and processing seems like a breeze despite it’s challenges.  The flow of efficiency has finally set in and it feels good!

Last week we dropped off the birding duo at Avian Island, a “Antarctic Specially Protected Area” where you need special permits to land.   With the help of a few shipmates, they set up a camp and spent five days researching the massive Adelie penguin colonies breeding there.  During the set-up (which took about a half day), others were able to take the small boat to a deserted Chilean Base for some exploration.  It is a relief to be on solid ground and take an afternoon off, boosts morale especially when you have the opportunity to listen to the sounds of the elephant seals that we encountered.

We know many of our customers like to be selective about their RNA. That's because, most of our RNA technical questions involve a desire to retain or exclude certain varieties of RNA. It’s not always possible to get what you want;  but sometimes by making slight adjustments to the extraction protocol, it is possible to get what you need. In fact, in a previous MO BIO blog article [microRNA from Fresh Tissue and FFPE Samples using MO BIO Kits with Modified Protocols] we discussed how to bring in very small sized RNA when using our tissue extraction kits. 

Since many of our customers are now turning their efforts towards extracting RNA from more difficult samples (AKA dirtier), we figured it would be a good time to talk about some of our newer RNA kits: PowerMicrobiome RNA, PowerPlant RNA, PowerWater RNA and PowerBiofilm RNA. All four of these RNA Isolation kits use the same combination of two solutions to bind the RNA in your cell lysate to a silica spin column. It's the ratio of these two binding solutions that determines the size of the RNA that will bind and subsequently the size of the RNA you extract. Everything smaller than the cutoff point will wash off the column.  Everything above the cutoff will stay on the column and will come out in your elution. You can alter the binding solutions to change the cutoff point but you’ll always lose everything smaller than the cutoff.

It's Valentine's Day and love is in the air at MO BIO! To celebrate this special (not so special for some) day, we thought we'd tell you about the cutest and nerdiest proposal of all time. Watch out guys, if your girlfriend sees this and is expecting a ring sometime soon, the pressure's on!

You may have heard some buzz floating around recently about the guy who cleverly proposed to his girlfriend via agarose gel. Yes, we know, it's incredible.  We wanted to ask him a few more questions about this amazing, geeky proposal,  so we tracked down the proposer, Eric (currently a Post-Doc at UCSD) , to get the whole story.

How did you two meet?

We were both graduate students at Stanford. We met at a grad student event and played volleyball together. We ran into each other again later at a department happy hour.

Where did you get the idea from?

Regional Climate Warming: West of the Antarctic Peninsula

Jan 17, 2013
68°00.2S X 69°30.8W
Sunrise  11:37pm
Sunset  9:49pm

MO BIO Labs is going to collaborate with our friends at the popular science blog site, Bitesize Bio to sponsor a couple of webinars for their readers.  Since MO BIO Labs has a primary focus in microbiology and ecology, we want to sponsor seminars that are going to highlight the research and scientists working in this exciting field.

As I was pondering potential speakers, I thought about the women in science I've heard speak, who are an inspiration to me. But my experience is also limited being in the private sector. I don't get to interact with as many women thought leaders as I would like. The question then became: who are the leading women in the field right now?  What women scientists do we have to draw insight and inspiration from?

I attend the Gordon Research Conference in Applied Microbiology every other year where I get to meet so many outstanding scientists from across the globe and of course ISME (also every other year) is a chance to network with many in Europe who don't make it to ASM each year. ASM is a great meeting as well, however, we know many environmental science labs save their money for smaller more intimate meetings and avoid the crowds of ASM.

Boondoggle!
by Emelia DeForce
Jan 10, 2013
66°15.0S X 67°21.9W
West of the Antarctic Peninsula
Sunrise  2:50am
Sunset  12:19pm

I have to pause for a minute to pay homage to and tell you about the humbling power of Palmer Station.  There are only about 30 people that live there in the summer months (Sept-April) but all of them are responsible for running not only a station, but a home.  There are cooks, seamstresses, metal workers, electricians, doctors, scientists, etc. many of them acting in multiple roles on a daily basis.  Each individual plays an integral part to make the station a success even if it means scrubbing someone else’s bathroom floor after lunch.

The Drake Passage

By Emelia DeForce

Jan 4, 2013
64°46.50S X 64°03.00W
sunrise: 2:58am
sunset: 11:42pm
United States Antarctic Program Palmer Station, Antarctica

Honestly, I slept through leaving the dock at Punta Arenas as we forged South towards Antarctica.  The travel, preparations, and constant sunlight have left my body exhausted.  I vividly remember waking up on the ship after leaving and immediately saying to myself, “there is no way we are underway, the ship is hardly rolling!”  It turns out this was a foreshadow of our crossing of the Drake Passage.

The infamous LA river winds through the center of Los Angeles, heavily polluted with waste from the city. It may not quality as a southern California scenic destination, but as far as bioremediation projects go, this locale is ideal! The river provides a fertile source of microorganisms accustomed to living with and degrading pollutants. Nikki Thadani and a team of fellow California Institute of Technology (Caltech) undergraduates have chosen this urban river as their site of choice for the iGEM synthetic biology competition. They hope to produce a bioremediation system for endocrine disruptors. Endocrine disruptors such as DDT and BPA have a significant detrimental impact on the reproductive systems of organisms living

 Dr. Emelia DeForce visited us at MO BIO Labs in December after the Plastics at SEA voyage was complete and provided us an amazing presentation of her travels at sea and the important work they are undertaking to determine the effects of plastic in the ocean ecosystem.  It was great to see the effort and passion Emelia and the whole crew has for our precious oceans.

Emelia's next trip takes her to Antarctica where she has the unique opportunity to be a part of the 2013 field season of the Antarctic “Long Term Ecological Research” program. Rather than me tell you all about it, I thought it would be better left in the words of the expert extreme traveler and scientist adventurer herself.  So here is the first post of Emelia's web diary of her trip to "The Ice". She'll be sending us more stories of her chronicles as she has time to write and reflect.  For those of you curious about the life and times of an extreme microbial ecologist,  we hope you enjoy what you read.  If you have any questions for Emelia, let us know!

Enjoy!!

Touch the Toe Before You Go!

Microbes outnumber the human cells in our bodies by about 10 to 1. So wouldn't you like to know which ones are hitching a ride? Well now, thanks to a new open-access project known as “American Gut” nearly anyone can find out about their own personal community of microbes.  In association with the Human Food Project, researchers at the University of Colorado Boulder along with nearly thirty researchers at other institutions around the world, are on a mission to understand the interaction between diet, lifestyle and our microbes. The project builds upon previous efforts, including the five-year, $173-million NIH-funded Human Microbiome Project, to characterize the microorganisms living in and on our bodies. However, unlike other projects that worked with just a few hundred hand-selected test subjects, the American Gut project allows anyone in the public to get involved.  In fact the hope is that tens of thousands of people will do so.

The project is not just an exercise in curiosity.

Today I wanted to talk about a method that you’ve been doing forever in your science career. Something so basic, so easy, that I bet you don’t even have to think about it. I bet you can do this type of prep in your sleep. What am I talking about? Plasmid preps, of course!

Plasmid DNA isolation is so routine today in labs that you pretty much expect to get DNA back, even when you make a mistake.  But are you getting back only DNA?  It turns out that plasmid preps are the perfect application to demonstrate a basic difference in two methods for DNA quantification: spectrophotometry (Nanodrop) vs. fluorescent dye (Picogreen).

If you want to isolate microbial DNA from environmental water samples, you need to first separate the microbes from the water.   And since size exclusion filtering is one of the easiest methods to isolate microbes from large volumes of water, this is usually the preferred method.  With this in mind the MO BIO PowerWater DNA and RNA Isolation kits were designed for the isolation of nucleic acids from microbes captured on water filters.   These kits contain 5 ml bead tubes that are large enough so that a standard 47 mm water filter can be rolled up and easily slid into the tube.  Virtually any 0.2 or 0.4 micron size exclusion membrane filter will work, with one caveat.   Bacteria, fungi and protists will be captured on the membrane.    However, virus won’t.  Extracting virus from environmental water samples is a bit trickier.

We recently received the following technical question regarding virus in water.  It’s a common question we get here at MO BIO technical support.

Our team came back from the 4th Annual Argonne Soil Metagenomics Conference held in the Chicago area October 3-5 last week and a hot topic of discussion was filamentous fungi.  Seems that ears were burning all over the cosmos as our technical support lines were also lighting up with questions about recommendations for isolation of DNA and RNA from filamentous fungi. So it looks like this tough critter deserves a blog post all its own.

Fungi are a funny breed of microbe.  What other species can range in size from a single cell to the largest known organism on earth encompassing almost 4 square miles of soil (in the Blue Mountains of Oregon)?  That's right: Fungus. Fungus are everywhere, many beneficial, some tasty, and others deadly.  No matter what you think of them, there is no denying that these are the toughest of microbes.

What makes them so tough?

A great excursion is about to take place! Thanks to Emelia DeForce, Chief Scientist in the expedition for letting us know about an important research project taking place this month in the North Pacific Ocean. The health and maintenance of our oceans is a subject near and dear to our hearts here at MO BIO, and those of many of our customers. That's why we are excited to tell you about a research voyage embarking this week that seeks to understand the fate of plastic in the oceans and the microbes that make plastic their new home.

A team of 38 scientists, sailors, and students led by PIs, Kara Lavender Law, Erik Zettler, and Giora Proskurowski sets sail out of San Diego, California October 2nd, en route to Honolulu, HI to study the effects of plastic marine debris on the ocean ecosystem. The expedition is called Plastics at SEA: North Pacific Expedition 2012 and is being conducted by the Sea Education Association (SEA). The goals of this research are to better understand the impact of plastic on the ocean ecosystem, while also providing updated estimates of floating plastic concentrations in the region dubbed the “Great Pacific Garbage Patch”.

When it comes to isolating DNA and RNA from all kinds of samples, the fastest and most thorough approach is bead beating.  Whether you have microbes, mouse tissues, plant seeds and leaves, or difficult soils, homogenization using beads will break open both cell walls and membranes and release the desired DNA and RNA so it can be isolated and purified.

Today there are many choices for beads and it can get confusing trying to figure out which is best for what you want to do. To make it easier, here we will summarize the characteristics of all of the bead matrices we use at MO BIO Labs and what types of samples we recommend for them.

In a previous article, we discussed in great detail the homogenization conditions  recommended for RNA extraction. Today's discussion will give you an overview of the entire selection of bead choices for both DNA and RNA.

MO BIO Laboratories, Inc. becomes exclusive sponsor of Nature’s Human Microbiota Special

Carlsbad, CA; August 21, 2012 – MO BIO Laboratories, Inc., the leader in microbial nucleic acid purification, is pleased to announce their sponsorship of Nature’s Special: Human Microbiota, enabling free access to four of Nature’s recent human microbiome publications.

“MO BIO is committed to furthering human microbiome research through the development of nucleic acid isolation kits optimized for difficult samples, including stool and gut material”, Mark Brolaski, President and CEO of MO BIO Laboratories, said. “We are proud to have the opportunity to make these important human microbiome publications freely available to the scientific community.”

Tips and tricks for isolation of RNA from cells and tissues remains a very popular subject.  I can't tell you how many discoveries in science depend on identifying that elusive low-copy mRNA with the 5 second half-life!

Joking aside, we've covered quite a few of the basics so far.  For example, I've explained how a strong and complete homogenizationin denaturing lysis buffers performed very quickly is the key to denaturing nucleases and releasing the maximal amount of RNA. And we've talked about the options for homogenization of samples, beginning with liquid nitrogen and ending with all the types of beads available for bead beating using high powered instruments.  All the methods work, so the choice comes down to what is available to you and how many samples you have to do in a day. Bead Beating can easily process many samples at one time with equal and efficient lysis, so consistency between preps is maintained.  Methods that are performed one sample at a time, such as mortar and pestle or rotor-stator homogenizers are better if only a few samples are involved but increase the risk of cross-contamination if cleaning the equipment between the samples is required.

The article this week is about a subject we don't receive many questions about, because, quite simply, the method is so straightforward and consistent that it always works. What am I talking about?  I'm talking about isolation of DNA from formalin-fixed paraffin embedded (FFPE) tissues.

What are FFPE tissues?

FFPE samples are derived from tissues (usually suspected tumor samples) that are fixed with formalin to preserve the cytoskeletal and protein structure and then embedded in a type of paraffin wax so the tissue can be sliced on a microtome, an instrument used to prepare very fine slices, 5-10 microns thick.  Formalin irreversibly cross-links proteins via the amino groups thus preserving the structural integrity of the cells so they can be stained with dyes used to analyze for abnormalities in the tissue that indicate cancer. However, the effect of these cross-linking fixatives on the nucleic acids is detrimental. Isolation of nucleic acids is impaired by both the paraffin wax and the cross-links that block DNA polymerases and inhibit PCR if they are not removed

Since Next Generation Sequencing (NGS) was introduced onto the market less than a decade ago, the technology has undergone rapid growth and improvement. Run speeds have increased, costs have gone down, and the sheer number of bases sequenced per run has improved so significantly that NGS is now within reach for most researchers. Consequently, scores of scientists are trying NGS for the first time. And they have a lot of questions, some of which have been thrown our way here at technical support. The most common question we get is whether or not DNA isolated using a particular MO BIO DNA Isolation kit is suitable for Next Generation Sequencing.

I wanted to spend some time writing on our blog to tell you about our exciting new products for high throughput microbial DNA isolation. It's been a LONG time coming.   And it was worth the wait!

How it Began...

We started onthe development of magnetic bead based nucleic acid purification for environmental samples over two years ago. At that time, all of the current technologies available for magnetic bead surface coatings used for DNA isolation were not suitable for dirty, inhibitor containing samples.   Any residual fulvic or humic acids in the lysate stuck to the beads and co-eluted with the DNA.  We knew there had to be a way to make this work and that with increasing sample numbers for the Human Microbiome Project and the advent of the Earth Microbiome Project, a hands-free method for DNA purification from soil and stool was going to be a necessity.

This weeks technical tip is a great question because, as we are all aware, no two environmental samples are ever quite alike. And when working with microbes, they exist anywhere and everywhere, so the substrate often complicates the matter. That's why choosing a method for DNA isolation can be confusing. Luckily, here at MO BIO, we've seen and heard it all and we know what to do.

Take this question, for example.....

Hi MO BIO Technical Support,

I'm considering using one of your PowerSoil kits for an experiment I'm doing. I'm not actually extracting from soil, however. I'm extracting fungal DNA from wood and paper that I've allowed to be colonized by fungi in the environment.

It sounds like combining the Powersoil kit with the Powerlyzer bead-beating would take care of fungal cell disruption and humics from the wood & paper.

However, I'm concerned about polysaccharides and polyphenolics, which may potentially be present in high concentrations in these samples. Would "inhibitor removal technology" be able to remove these inhibitors? Could you fill me in as to whether this kit would be good to use on substrates that might contain high amounts of polysaccharides and polyphenolics? If so, are any changes to the protocol provided for soil necessary?

Thanks for your help.

A. Vortex

B. PowerLyzer

C. FastPrep

D. Precellys

E. All of the Above......

The answer is E! MO BIO Kits work with everything!

The tech tip for today is a great question!  Many people ask us about the adaptability of our kits with all the various bead beaters. Everything we make is compatible with any bead beater on the market. Read more.....

Hello,

I am interested to use the PowerSoil® DNA Isolation Kit. I want to use it with a FastPrep. Is that a problem? Are your tubes adapted for this machine as well?

Best regards,

PhD student

Scientists often come to us with their dirty little DNA problems.   Samples like soil, feces, and blood (oh my!) can make extracting DNA challenging because they are high in compounds like humic acids, polysaccharides, heme, or dyes.  These bind to the DNA and inhibit enzymes used in downstream applications like PCR and sequencing.   MO BIO uses patented Inhibitor Removal Technology® (IRT), a method to remove these substances in many of our kits.   It is very effective at removing the inhibitory compounds without significantly decreasing DNA yield.   But how well does it really work?   Good scientists want to see the data. Recently we received the following request...

MO BIO is very excited to sponsor a special seminar by distinguished scientist Jim Prosser from the Department of Biological and Environmental Sciences at the University of Aberdeen. Dr. Prosser is on sabbatical for several months in the lab of Mary Firestone from the University of California, Berkeley, so we've convinced him he needs to come down to San Diego and share his knowledge with our local community of scientists.

Don't miss this chance to meet one of the world's leading microbiologists!

The presentation begins at 10 am on Tuesday May 22nd at the Venter Institute. Click the flier to expand your view.

If you are interested in attending, please RSVP to customercare@mobio.com

Seating at the Venter Institute is limited.

Welcome back readers! After a short break from blogging, we're back with some new and different ideas to share with you. We'll start off with a new weekly feature called Tech Tip Thursday (#MBTTT on twitter) where we share some of our customer's questions and our answers with you. What better way of saving you time for life then to post a few of the frequently asked questions we get from all the scientists out there using our products and our answers to those questions? We figured you'd agree.

This week I'd like to share a question about the storage of environmental samples in ethanol as a preservative and why this is NOT a good idea. 

Welcome back readers! After a short break from blogging, we're back with some new and different ideas to share with you. We'll start off with a new weekly feature called Tech Tip Thursday (#MBTTT on twitter) where we share some of our customer's questions and our answers with you. What better way of saving you time for life then to post a few of the frequently asked questions we get from all the scientists out there using our products and our answers to those questions? We figured you'd agree.

This week I'd like to share a question about the storage of environmental samples in ethanol as a preservative and why this is NOT a good idea. Read on....

A person of great significance to MO BIO Laboratories has passed away.  Michael Moroney, father of our CFO, Liz Brolaski, and one of MO BIO's first employees passed away on October 25th, 2012. He was 81 years old.

Mike was an accomplished geological engineer.  He received his degree from the University of Missouri in engineering and joined the US Army in 1951.  Following his time in the military, he went to work in Calgary, Alberta where he met his wife and spent many years working in the oil industry. He moved the family to San Diego in 1975 where he would eventually retire.

In 1985 when his daughter and son-in-law, Liz and Mark Brolaski helped start one of the first life science biotech companies, called BIO 101,they put Mike to work again.  After 8 years of running BIO 101, Mark and Liz set off to start their own biotech company, MO BIO Laboratories in 1993.  (Bio 101 would eventually be sold to Q-Biogene.) Mike worked alongside them, doing the various tasks that brand new start-up companies need to do.  The UltraClean Soil Kit was under development and Mike observed the R&D scientists trying to work with bead tubes taped down to their vortex and the occasional bead tube flying across the room.