In 2013, the USDA Natural Resources Conservation Service entered into a cooperative agreement with the South Dakota No-Till Association and IGRO, SDSU Extension, for delivering the latest soil health and productivity technology to South Dakota farmers and ranchers. A series of four local events were held in South Dakota in Sioux Falls, Watertown, Belfouche, and Mitchell. I feel like Buck Rogers or something with all this equipment hanging on these belts and tactical wear. I'm guessing by now most of you have heard or are aware that there are a lot of soil microorganisms. A lot, a billion, and about a gram of soil, which is about the end of my thumb, a billion, a billion organisms in that big little chunk of soil. Okay, that's neat. There's actually thousands of different types of organisms in that same little thing. So I'm not going to go over all that with you. I'm thinking that most of you that are here probably are aware at some level that there's a lot of them down there and they're very diverse and they're very important to the soil. It's now been internationally recognized the role of soil microbes in food production. This is the 2013 report by the prestigious American Academy of Microbiology. Pretty, pretty startling title how microbes can help feed the world. So this isn't some guy from Broglie, South Dakota come to tell you about how microbes are going to save the world. There's actually a whole lot of other people that are thinking the same way and that we can take a much greater advantage of the soil microbes that live in the soil. Okay, what are these things doing there? Why do I care? I don't really want to know all about each individual microbe or how diverse they are. I want to know how they affect my farming system. This is just a range of benefits that soil microbes can provide in your farming system. And they provide these benefits simply by living their lives. They're just living just like you and I, they're taken in carbon or some other. They're also getting energy from carbon or some other energy source. They're breeding, they're multiplying, they're doing the same things. But along the way, they're actually doing all this stuff and it really amounts to something substantial because there are so many of them. And I want to just go around the ring here a little bit and talk about things you might not think of. Microbes have been found to suppress weeds, either by directly degrading the weed seeds or by some chemical interference with the weed group. Soil structure and aggregation, what do you think microbes are made of? They're made of carbon, okay? So they're part of the carbon that feeds the soil structure. They exude all kinds of mucus and things that are called polysaccharides and all kinds of stuff all over their bodies that help stick things together. I mentioned that they're soil carbon. They have a huge impact on nutrient retention and nutrient availability and most of what I'm going to present. We'll be talking about these things down here. Of course, many of you were nitrogen fixation, having inoculated your soybean seeds. There's a whole other thing, there's all kinds of chemical warfare and positive things that are happening out there with plant growth promoters. So benefits from soil microbes, you can't put them all in one bin. They're actually, you could probably think of a few more that aren't on this chart. So, okay, you convinced me in two slides, soil microbes are important. They provide a array of benefits. How can I get some in my farming system? And this C3-A is sort of the basis. These are the fundamental pillars. If you want to increase soil biology and get this array of benefits, think about how you can integrate some of these things into your current system. Acknowledging that there's constraints, largely economic in a lot of cases. But there are things you can do. But there's things you can do to reduce the amount of tillage, to increase the crop diversity, to have cover a larger percentage of the year. For instance, by using cover crops, you will in fact increase soil microbiology. Both diversity and numbers, you will start to see the benefits that I showed you in the previous slide. Now, we take a look at a couple fields here. One has cover crops and one doesn't. And these should be pretty fundamental things that most people are aware of. Which one handles the elements better? Okay, and the real, the key issue with cover crops or some other form of keeping cover on your fields all year round is this one right here. If you have something growing on your field, you are pumping free energy, carbon and nitrogen into your soil. Who doesn't want carbon, nitrogen and energy in their soil? Everybody wants it. If you don't have something growing there, you're not taking advantage of building your soil using the sunlight. If you have something growing there, I think it's intuitive to most people that you have better water infiltration, better water storage and less erosion by water for wind. Okay, how about the critters, all right? It's real easy to see if you're a farmer, if you're an outdoorsman, the difference between a field of black dirt and a field that has something growing in it. And the things that you can see, like deer and pheasants and insects, it's really easy to tell that they're going to be more numerous in this field. But I bet what you didn't know is how the microbes react to this.  It gets hotter at the surface and that actually kills some of the microorganism. It gets drier at the surface. That either kills or reduces their activity. The surface is exposed to more UV radiation from the sun. That also kills bacteria on the surface. The more tillage, the more physical disruption of filamentous bacteria, the more susceptible your land will be to water and wind erosion, which will also remove microbes from your field. So in general, these guys are reacting, you can't see them, but there's all kinds of literature out there in different areas that will support. If you have bare soil, you will have less microbes, at least in the top, the top little bit. I don't know how much data there is, deeper, obvious, but let's get to the next slide. What happens deeper, at least in a lot of the soil depth that most farmers are interested in, is affected by having something growing there. Did you know that 10 to 40% of the carbon that your plant's fixed don't go to produce biomass of the plant? They don't go produce grain. They actually leak out of the roots into the soil. Well, why would they do that? Well, I don't know why they do that, but there's a consequence of that. And the consequence of that is all that carbon that the plants are fixing are supporting microbes in the surrounding soil. So it's really important to recognize that if you take the plant out of the system, now you've taken the source of a large part of the energy for soil microbes out of the system. And this is huge. When you think about looking at a field and you see stuff growing, you see animals using it, you see insects and beneficial insects. It's very intuitive, but think about what's going on underground. It's simply not the presence of the roots. It's the carbon. It's the energy. It's all the other things that they're leaking out into the soil. Cells are sloughing off of their roots. That's food. That's food for the microbes. We have been working the last five or six years on using cover crops. Again, simply as a means to keep something growing longer during the season. And we've been looking at how growing cover crops can promote soil biology. That's been a focus of our lab's research. We also have researchers that are looking at how they affect insects, researchers that are how they're looking at weed populations. What I've been looking at is the soil biology of these systems. People talk about soil microbial communities and how they might change with my management and am I doing good or am I doing bad? Do I have good soil or do I have bad soil? Those are the kind of questions I hear. They're really difficult questions to answer. I've got to tell you that. The questions that many of you are asking me are right at the edge of our scientific knowledge. There are some things we can do now. They may not be the best things, but there's something we can do now. We have good reason to believe. More often than not, they're important. And one of these things is the ratio of fungi to bacteria. They're in the soil. And this diagram or this picture here is simply some fungal filaments and these little things here are bacteria sitting on them. The idea is you take a soil sample and measure the ratio of fungi to bacteria in that soil. It is not the be all end all. It's a way to get at this change in soil microbial community due to your management. However, in the literature, there's enough scientific findings that support that soils with a higher fungal to bacterial ratio tend to have higher carbon and nutrient retention. Those are, I don't know, what else do you want? Carbon and nitrogen and other nutrient retention. That's pretty good stuff. Again, it's not a one-to-one correspondence, but it's a pretty good trend. We have some plots at our research farm that were established in 2000. And they feature three levels of residue removal. There's a low, which is where we just take the grain, just like a lot of cashcroppers do. We have a medium residue where we bail the stover, take those bails off as if they're going to be used for cellulosic ethanol production. And we have a high residue removal, which is a silage cut. So three levels of corn residue removal. These are no-till corn soybean systems. They've been in over 10 years. We added splits to them where we had cover crops. They were initiated after both the soybean and the corn phase. I know the question's out there. How do you do that? Well, I have an agronomist, Shannon Osborn, who works on that very issue, and they've tried all kinds of different things. And let me tell you, it doesn't always work. Each year, the cover crops don't always get established. But over 10 years, you can see the differences. These two graphs, the top one is 2009. The lower one is 2010, where we took soil samples. We looked at fungal-bacterial ratios. The black bars are the residue removal without cover crop. And if you look at the black bars, in 2009, 2010, with increasing residue removal levels, you have lower fungal-bacterial ratios. Again, that's an indicator of what the soil is doing. And it's especially important if you look over time how it's progressing. And it tends to be linked to positive things like carbon and nitrogen retention in your system. But the other interesting thing, and it's mostly in 2010 that this shows up, is in the subplots with cover crops, we don't see the reduced fungal-bacterial ratios. So again, what we see is evidence of cover crops overcoming some of the negative changes that might be associated with harvesting cornstone. And what I want to add is we have data on soil carbon. We have data on aggregation. We have data on highly erodible fraction. And largely that data parallels the data on these two slides. If you remove the residue, you end up with less aggregates, less carbon, more highly erodible fraction, and a change in microbial communities to a more bacterial-dominated system. If you add cover crops, you can reduce those changes. So this is a role for cover crops. We also have done a fair amount of work with nitrogen, which is obviously the prime nutrient. Microbes don't just think of nitrogen as a nutrient. I mean, it's important to them. They're going to be roughly 10% dry weight nitrogen in their body, so they need a lot. But nitrogen's more than a nutrient to microbes. They have the ability to take atmospheric nitrogen and fix it into a form that can be used for plants. Why is that important? Well, they actually trade that nitrogen to the plants for some food from the plants. They also take ammonia and oxidize it to nitrate. And in doing so, they actually get energy. That's how they run their cells. That's how they run their metabolism. There's also organisms that you might be aware of that reduce nitrate to ammonia. And those organisms are using nitrate in the same way we use oxygen when we breathe. They also will take combined organic nitrogen and mineralize it to ammonium. And in this study, what we did was look at three cover crops, clover, rye, and vetch, and compare them to a fallow situation. This is no-till corn, no, corn, soybean, wheat. So after the wheat, we planted the cover crops, and then it was coming into corn again. And what I did was look at nitrogen mineralization once the cover crop was killed over the corn growing season. And these three different colors here are different periods of the corn growing system. And what we're measuring here is how much nitrogen was mineralized. So you can see with the two legumes, clover, and vetch, we had a lot of nitrogen mineralized over the corn growing season. And even rye was slightly above fallow, but don't necessarily discount rye out. Because what you've got to remember is what I measured here was nitrogen mineralized over the course of the corn growing season. That didn't mean that rye didn't have something else to give the next year or the year after. So rye took up some nitrogen. It didn't take up as much as the legume because it doesn't have any fixers. And it releases it more slowly because it doesn't decompose as fast. But still, that doesn't mean rye is no good. It just means rye's. The timing of the nitrogen release is different than the legumes. But this is an important role for soil microbes. The more you have, the more diversity you have, the more of these types of benefits that you're going to have. Lately, what we've been looking at is one group of microorganisms called our muscular mycorrhizal fungi. And many might have heard of them. They're a type of fungus that only lives with a plant. It has to have a plant to live. So that's why we're interested in them. They're partners with nearly all your crop species except for brassicas. The fungus, actually, this is a blow-up here of the root. Can't see it very well. But the root surface here, and what the fungus does is the plant sends out a chemical signal, a cum hither signal. And the fungus sits in the soil in a spore and it germinates a filament and attaches to the root and actually invades the root, goes inside the root, and inside the cortical cellular root forms a structure called an arbuscle. And that's a diagram of the arbuscle. And this is a blow-up of the arbuscle. And they call it an arbuscle because it kind of looks like a tree. But I like to think of it, I don't know. They'll get the idea, I think. But it kind of looks like a tree. To me, it looks like a lung or a kidney. And that's exactly what it is. It's got lots of little fingers. And what it does is maximize the surface area between the fungus and the plant. And why do we care about surface areas? Because that is where the exchange takes place. Just like in our lungs, we take air in, goes into our lungs, interacts with the blood that's in there, strips the oxygen out, and puts CO2 back in so we can exhale it. If you have a structure like that that's got all kinds of little fingers in surface areas and branches, it's built for exchange. And that's what this does. The mycorrhizae brings water, brings nutrients, particularly phosphorus and other mobile nutrients, into the plant. The plant says thank you by giving the fungus some sugars all through this exchange structure called an arbuscle. Well, we think these fungi are very key in terms of soil microbiology and benefits that you might get to your farming system. And this is one way of looking at it. On the left is a plant without any mycorrhizal fungi. On the right is a plant with mycorrhizal fungi. All those little threads are filaments of mycorrhizal fungi, they're different colors because they represent different types or species. And they attach to the root. Basically what they do is they expand the root system. They don't just expand it into more volume but because these filaments are smaller than the roots, they actually able them to access small pore spaces. And because they're small, they have a high surface area to volume ratio. And again, surface area is what you're after. Surface area is the key to exchanging things. And so this is like, I don't know, this is not what you would like. This is the enhance model. The enhance model, why do we care about this enhance model? Well, it's taking up nutrients. It's taking up water. And you know what else? Because this fungus can only grow with a plant, it needs its plant host. Therefore, it's resistant to pests and pathogens. It does not want its host to die because then it dies. So once you're colonized by mycorrhizal, you tend to be more pathogen and pest resistant. One question that comes up to me is, well, how do they get these nutrients? Well, they have special capabilities. And these mycorrhizae actually produce enzymes that go out into the soil that help mineralize and mobilize nutrients so they can be taken up by the mycorrhizae and transferred to the plant or just the plant themselves. They also produce things called chelators, which is a compound like EDTA that might go out there and complex, say, a copper molecule that's tightly bound to the soil. Break it off there, bring it into the mycorrhizae and transfer it to the plant. They also can change the pH locally. We're talking at the micron scale there, but the micron scale is what matters to whether a nutrient is gonna be available to the plant or not available to the plant. These guys, can you believe it, they reduce erosion and how they do this is two ways. This is a picture of a fungal hyphae on an aggregate and so simply because of the thread-like structure, they help hold aggregates together. But this is a microscopic picture of a fungal filament and these are spores right here. There's a bunch of mucus that hangs off here and it's basically this protonaceous glue that they produce and that protonaceous glue called glomalin or glomalin, pronunciation varies, is very effective at gluing together aggregates. So you never think about it, these invisible organisms that you don't see, you see erosion like that and you think, well, I gotta do this thing or I gotta put up a fence or something. I can't remember what they're called, debris barrier, erosion, landscape cloth, but it's actually these microscopic organisms that can make a big impact on erosion. They can also make a similar impact on water storage. If you have improved soil aggregation, you have improved soil structure and then your structured soil behaves like a sponge where water can infiltrate, more water can be held in that sponge, those are all good things. I believe the NRCS has developed some data this year that for cover crop, folks that cover crop three years, at least three years, they had 10% better yields in a 2012 drought year. And a lot of that has to go with soil structure. Well, I don't know if it had to do with AMF, but AMF, mycorrhizal plunge, I certainly play a big role in that. Why else do we care about AMF? Well, this kind of figure's been shown dozens of times. It's called the big plant, little plant. And on the left is some sorghum, we've added mycorrhizae. What's unique about this picture is this mycorrhizae, the mycorrhizae we added to the pots on the left, actually we collected from a producer's field down by ideal. We took his soil, we extracted the mycorrhizae and we added it to the soils in the sorghum on the left. We did not add them to the right. Those are the dry weights of the plants. You can see there's a big difference in the growth and vigor of these plants with and without mycorrhizae. Ag management, okay, I want more of these. You convinced me there's enough data out there to show that low numbers of these can stress the plants. In general, mycorrhizae are negatively affected by tillage, fallow, because they need a plant to grow, flooding, because they need oxygen. Rotation and host plants, that can go either way depending on what plants you're talking about. And lastly, they respond negatively to inorganic phosphorus inputs. You wonder about that. So if you put a lot of inorganic phosphorus inputs on there, the plant has enough phosphorus. It doesn't necessarily need the mycorrhizae to help bring phosphorus and other nutrients in there. So it doesn't send the come hither signal for the mycorrhizae to colonize the plant. The mycorrhizae sits in there, eventually decays because it cannot reproduce and make more.  We used a kind of rudimentary technique for looking at mycorrhizal numbers. We counted spores. Again, this is not necessarily the best measure, but what we found is if we look in a native prairie, there's a lot of them. If we look in almost any agricultural soil in this region, there's not very many. No big surprise. We then embarked on a multi-year study at several sites where we used another technique to look at the numbers of mycorrhizae. And this technique is based on propagules, which includes things like spores and infected roots and little bits of filament. Anything that can give rise to a mycorrhizal infection. It is hugely labor intensive, involves a multi-step thing for every single sample that you want to say, well, there's this much mycorrhizae in there. You have to grow 15 plants and analyze them to see whether they're effective or not by mycorrhizae. It's a heck of a lot of work. But we did this. And we did this at a producers field where he had put out replicated strip trials. Again, no-till. Again, following wheat before corn. And he had no cover crop. He also had a conventional-till check. And then there's five different cover crops, clover, oats, pea, pea Timothy, canola, radish, pea. And we looked at the number of mycorrhizae in those soils. The numbers we found in his field were pretty low, you know, they're pretty low here. But one thing that was clear was the oats, pea mixture had significantly higher mycorrhizae. We would love to do dozens of these studies. And hopefully you got the idea from the previous study, we simply can't with these methods. But we have done replicated trials at our research farm and we've got two years of data there. We use the same technique looking at mycorrhizae. We had no cover crop, again, no-till, wheat cover crop, going into corn, same kind of rotation. Canola, which is non-mycorrhizal, oats, vetch, and then various combinations that you see there. And again, we saw in both years 2009 and 2010 that oats was able to promote the highest numbers of mycorrhizae. So, in terms of cover crops, we think including oats in your cover crops is a good bet for increasing mycorrhizal numbers. We also went down to a farm, an ideal, and that producer has much longer rotation that includes wheat. And after the wheat, he planted a five-way cover crop mix. And he did that in about half his fields before they went to corn, the following year. So we took paired samples, fields with wheat, and the five-way mix, fields with wheat, and no cover crop. And we took samples back to lab, we did that technique, and we saw much higher numbers in this producer's fields.  He puts a little bit of manure every four or five years. We found really pretty good overall numbers there, and we saw about a doubling in mycorrhizae with the cover crops. So those are numbers, but the other thing you can measure, and that's important, is diversity, mycorrhizal diversity. Again, using this kind of basic spore technique, we've looked at crop fields in our area, and prairie. And again, what you see is not so much diversity in the agricultural fields quite a bit of prairie, probably not a surprise. But why should we care about diversity? And this is data from another researcher. It's been 15 years ago, it was published. But if you look at the number of our muscular mycorrhizal species, that's the X-axis for all these graphs. It is positively correlated with chute biomass, root biomass, plant tissue pee, and negatively correlated with soil, Olsen pee. So you see a lot of benefits, and it sort of looks like you don't have to use as much input to get all these benefits if you increase the diversity of mycorrhizal. So that's what we care about diversity. That's what we're working on now, is trying to develop and adapt techniques to examine the diversity of mycorrhizal species as it's reflected by ag management. We think that's a very important potential indicator. The problem is the techniques are very difficult, complex. We're using some DNA-based techniques that we took us over a year to kind of get them where they could tell us about the diversity of mycorrhizae in these crops.  And we looked at the diversity of mycorrhizal fungi in a prairie, again, right here. And you don't have to know all those names, but the point is there's a lot of different colors in that pie. And they represent a different mycorrhizal species. So as you would expect, the prairie's very diverse. Then what we did was we took this soil and inoculated four different candidate cover crops to see which one actually retained the most amount of diversity. And we, old clover and veg, this is a type of diagram that shows how many species were in each one. And the bottom line here is, again, old retained the most diversity in the system. Wheat retained the least diversity. And clover and veg were about intermediate. So that's where we are. We probably got another, I'm hoping, year till we get an approach where we can actually go out in the field and run these same tests on a more routine basis. But that's where we're going with this. In terms of building soil boating on your farm, there's only a couple of things you really need to think about. What do they need? They need food, more diverse crops, more diverse plants, equals more diverse types of foods. Each plant exudes different kind of compounds into the soil. If you have more continuous cover, you have a more continuous source of food.  To live in, some of them don't like to be disturbed too much. If they've got filamentous growth structures, like migraecal fungi, so they need habitat. They need stable aggregates. And they also would like to have diversity of plants, equals more niches, equals more diversity. And the vision, and I've kind of put this thing together to think of a vision. If you think of a farm system and you think about it as a sandbox where you've got to put everything in every year and then take it out, and I call it a pass-through system because a lot of that stuff just passes through, or is actually, you add some nutrients and they get fixed to surfaces and never to be seen again. It's a pass-through system or a self-sustaining system where you can put nutrients and pest protection in at smaller amounts and get some of those services here. And the real key thing here is how much you lose. You don't want to lose these inputs that you've purchased. You put it into your system. You can add less and lose less and maintain your yields. Those are all, I think, the goal. And obviously as a producer, this is the most important thing is balancing your bottom line in these systems. And this is a way I've been thinking about this whole issue about nutrients. And I want to use phosphorus as an example. You put phosphorus on, lots of inorganic phosphorus, or you put a little bit and hope the soil biology takes care of the rest. And this analogy is, let's say you needed one liter of water a day. You're out there in the field somewhere and need one liter of water a day, right? There's two approaches. One approach is you can take a big cattle trough. It may have a few holes in it. Who knows? Fill it up with 1,000 liters of water, right? You only need 100. You need one liter a day for 100 days. So it turns out you're going to get your 100 out of that 1,000, but you're going to lose 900. 900 of those liters is going to work out of the holes, go into the soil, whatever, evaporate. The other way to do it is to lock your phosphorus up in microbes, in plants, in some kind of organic matter in the soil and have just a little bit come out at a time. So you've got a little dish here that only holds one liter, but it's always full. You can always get your one liter of water you need that day because you've got a one liter dish. But because it's a small dish, you don't have very much evaporation. You don't have very much loss as long as you keep everything tied up in here. And that's one way of looking at a system that could provide the same amount to a plant and yet be conservative in terms of imports and exports in the system. And this is my last slide. And I think it became more apparent when I gave a talk a couple of months ago, and people are still struggling with this. And the bottom line is it can be done. I mean, you have people here in this state, producers here, that have demonstrated these concepts that I just showed you. And then the last year or two, there was a big publication out of the Iowa State Lab. And I just want to read this one quote. So as results of our study indicate that more diverse cropping systems can use small amounts of synthetic agrochemical inputs as powerful tools with which to tune rather than drive agroecosystem performance while meeting or exceeding the performance of less diverse systems. So it can be done. And I think that's important to show people because you're going to have some struggles trying to do these things. But folks need to know that there's work out there that shows it can be done. And with that, I'd like to thank you for your attention, acknowledge some collaborators and sponsors. And if there's time, I'll entertain questions. Yeah, we have some time for some questions. We have a question for Mike. Is the reader happy? All right. Have you needed research? We do not generally engage in any sort of commercial product evaluation that historically that's been a role of the land grant universities. And I do know one quick route, specifically that Ron Gelderman at SDSU has done some work. Oh, the part where they put on Starter Foss, if you say putting on too much Foss, they make the plant not called to be a thing. How much is too much? Well, that's a really good question. It's really hard to nail down the exact amount, mainly because of differences in soil type and soil test. And so whatever if you use Bray, Olson, May Lake, whatever, you're getting a different fraction of that phosphorus. And then what that relates to in terms of the plant and its ability or propensity to give off the signal is also unclear. I mean, there's curves. Like the one I showed you with a reducing curve. And I think for any given set of circumstances, a soil and a test, a particular test, you could develop these curves. If you took a soil type, a plant type, and a particular phosphorus test, you could develop and get that information. But there's not a real comprehensive database of that information. Is there a difference in different types of plants? Well, generally the organic sources don't seem to show that repression. Mostly what the repression is is related to inorganic. In terms of different inorganic sources, I'm not clear on that. But there is a difference between organic and inorganic. I've been reading a lot about spring foster. Fungal size, which you see, what you think. What I just heard today is you're actually going to try to kill these fungus by putting the fungus size on. Is that true or false? I've heard that question before. And actually, I have a small project going with South Dakota State University looking at that very thing. I did a little literature review of that last, I don't know, six months. And what it shows is the fungus size that are systemic, right, are particularly inhibitory. The fungus size that are applied as a soil drench seem to have the most inhibition. Those are the only rules in terms of gathering all the data in that I see. If the fungus size is not systemic, there's generally less of a chance that it will negatively affect micro-IC. In terms of more specific data, we are working on that right now. Pete Sexton and I are doing that.


Anxious people will often say that sometimes they feel like the world isn't real anymore or they feel like they're not real anymore That's an actual anxiety symptom. It's incredibly common and we call it Depersonalization or derealization. Sometimes you might hear it called DPDR for short When you experience Depersonalization or derealization suddenly either you don't feel quite real anymore or you feel weird or you feel detached from your own self you might look in the mirror and Really kind of feel strange about what you see looking back at you or you might look down at your hands and have a hard time Sort of recognizing them where you might feel like you're detached from your body And when you look around you the world just seems off like there's a pane of glass between you and it and it's not real anymore And you can't connect to it sounds are strange colors are strange smells are strange. This is really really common It's very scary and it's very disturbing But it's also not dangerous many anxious people experience this and mistakenly become afraid of that Sensation because they interpret it as a sign that they are slipping away disintegrating losing themselves dying or maybe having a psychotic break or losing their sanity But that's not what that is. It's just another symptom of anxiety and down the road We'll talk about it more But if you are frantically trying to make that go away when it happens You may actually be making it worse and then you're learning to be really afraid of the next time it happens Even though it never really hurts you so that's DPDR in a nutshell It feels really bad really scary and really disturbing, but I promise it's not dangerous. You'll be okay


Once the template search is finished, we land on this page. This view shows a list of templates that have been found for your target protein. The list is already sorted according to a template score, meaning that good templates are most likely to be found further up in the list. But let's see what we are presented with. First is a box to select and deselect templates. If we select them, they are shown in the 3D viewer. In addition, selected templates will be used for modeling when we click the build model button. The second row is the name of the template in the Swiss model template library. I come back to this one in a bit. The third is the coverage, meaning how much of our sequence is covered by the template. We are very lucky in this case, since our sequence is completely covered. But often we can learn a lot about a protein, even if we can only build part of it, if the important domains are included. Identity shows how many amino acids are exactly aligned. Identity is only one criterion for choosing a template. But obviously, higher identity tends to give better models. Resolute and resolution should be self-explanatory. If the resolution is too low, we might want to use a different template. The oligomeric state is of course very important. Sometimes you get a warning, like here for 1e90.1.b. Whenever the oligomeric state of the template cannot be used for the model, it is estimated to be different, a warning and explanation are shown. The last column shows the ligands in the template. Depending on what we want to do with the model, this might be very important. Out of experience, getting a ligand in the right place with the right confirmation can be very challenging. However, a word of warning. This model is very conservative, meaning it will remove ligands relatively quickly if it causes steric clashes with the model, or if the binding site is not conserved. This arrow here opens the Detail tab. Let's use it on the top two and the fourth template. As I mentioned, those are the most likely to be suited for modeling. Here we see an image of the template structure and some more information. GMQE stands for Global Model Quality Estimate, which is a number between 0 and 1. The closer to 1, the better. As the name suggests, this number estimates the expected quality of the model, given this alignment we have. Sequence similarity shows the similarity between the two sequences. Next, we have the Quartinary Structure Quality Estimate. This score, again between 0 and 1, reflects how well the inter-chain interactions are, given the alignment. Simply said, a score above 0.7 is a very strong indication that the Quartinary Structure of the template is a good representation of the Quartinary Structure of our model we want to build. Lastly, the Oligomeric State of the Bio Unit. Here you can override the Oligomeric State that was automatically assigned for the model. All in all, we have four scores that indicate how suitable a template might be. The GMQE and the QSQE scores, as well as sequence identity and similarity. From these templates, I would probably not pick the top one, since it has no copper. You might have noticed that the second and the fourth templates have the same name, but have slightly different scores. One template was found with Blast, and the other with HH Splits. As we see later, the sequence alignments are not exactly the same. And this has an effect on the scores, and more importantly, on the final model. In order to find the correct Quartinary State, we should go to the Quartinary Structure tab.


Title of my talk is Breathe Into the Node, which is interesting because this predates me, so I'm not sure if we can really breathe into the Node.js, but we're going to talk a little bit about what we do and why it's cool and why you should be interested. So I think most of you raised your hands and already are doing things with Node. So we'll talk a little bit about the foundation, the project, where we're heading and what people are doing with Node and give you an idea of the state of the union and then we'll let the smart people talk for the rest of the two days. So, as I said, I'm Mark Hinkel. I have slowly moved up the stack. I started out in Internet support in the 90s and I think I've hit every layer and now I'm all the way at the top in the app space, which is sort of cool for me. I am an open source guy, too, so I've spent the last 20 years or so working in open source. I'm an Apache Committer on an Apache Cloud stack. I've spent a lot of time building open source communities and it's pretty important to me. So Node seemed like a good fit. So real quickly, my Node story. The reason I decided to get involved with Node is before this I was the VP of Marketing to the Linux Foundation. Linux Foundation provides governance for all sorts of projects, including Linux, Cloud Foundry, a lot of networking projects like Open Dayblade, Open NFV and I didn't know a lot about Node so I went to Node Interactive, which is the annual Node conference last fall and just wanted to see what was going on there so I could help better market it and what I saw was pretty exciting. It was probably the most impassioned community of developers I'd seen in quite some time. There was really cool things going on and the usage was amazing and it was sort of puzzling to me because back in the 90s I was a tech support rep and we did JavaScript support which just animated menus and didn't do very interesting things and now people are writing full stack applications in JavaScript with the help of Node and it's progressed quite a bit. So I was really excited about the conference so I walked out in the street at Austin and called my boss who's the head of the Linux Foundation and I said this marketing gig is cool and all but I really want to work on Node.js and he's like really? And I'm like yeah, really there's something here so that started a process of me getting to where I am today which is running the Node.js foundation. I'm very lucky to be here. So the five W's of Node, the who, what, why, when, where the Node.js is now governed in a foundation, the Node.js foundation which is supported by the Linux Foundation. It's very similar to the way Cloud Foundry is governed. I think we all know what Node.js is and from what you said you're all pretty much engaged. It's very cool because now that we can do end to end JavaScript development for full stack applications, it does expand the usefulness of JavaScript via the Chrome V8 engine. And since 2009 we've grown quite a bit so it was developed initially at a company called Joant by a guy named Brian Dahl and now we have over eight million installations worldwide and we know that because people are calling home for downloading their MPM packages through for Node and we're at Node.js.org. So that's the high overview of Node. Let's talk a little bit about Cloud Foundry. So when I was looking to come to the summit I wanted to see what they said about Cloud Foundry so it makes developers' lives easier, sort of their mantra that gives you speed and control and it's backed by the industry heavyweights like IBM and others, Pivotal, etc. So then I said well what do we say about Node and Node's about developers' ease, speed and control and backed by industry heavyweights so I said ah we probably get along pretty good so I think your chocolate fell in our peanut butter and actually somebody told me that they had no idea what that meant and then I realized that I was old but that's the old Reese's Peanut Butter Cup commercial from the 80s so if you remember it you're not old, you're just nostalgic is what I told them and if you don't remember it it's a delicious combo that we should all work gobble up every time. So one of the other things that I hear when I hear Cloud Foundry is they're a polygot so they have build packs for all these different languages it provides that control and that deployment and that automation for applications but what I'm going to talk about mostly today is just one of those and that's JavaScript and so if you look at the Stack Overflow did their annual survey with over 64,000 developers this year the number one language that they talked about was JavaScript which back to my original story it's amazing that 20 some years later in my career I'm still talking about JavaScript and it's still growing but it is for various reasons one of them is I'd like to think is the advances of things like Node. How many people here consider themselves a Java developer? How many people also consider themselves a JavaScript developer? How many people are using more JavaScript and less Java these days? I'm just curious and actually I don't have a preference I'm just it's just fascinating to me that that's with all the frameworks that are out there and the ecosystem expanding things like Angular and React and other development frameworks and things like Node that this is becoming a accepted platform for enterprise application development. Just a little bit more on that last week Redmonk the analyst firm released their analysis the most talked about programming languages and they took data from Stack Overflow cross referenced it with GitHub and once again JavaScript was at the top of the list. So there is a movement and an expansion of JavaScript development on top of the other things I mean Java and Python and C sharp and all these other languages are fine it's just there is a growing ecosystem and there are a lot of opportunities to develop applications with this frameworks and tools that weren't there 10 years ago. This year and this is the first time this data is being seen in the wild but we did a survey of the Node.js community and a lot of these graphs where you see a source is a Q4 and Q32 and such that's from the Node.js community so it's a really good representative sample of what we do and what our users are doing so you know where we're going but in the last 12 months as you would expect JavaScript is the top of our list there's some versioning for the language version from the last six months of 2016 as well but JavaScript as you would expect is at the top of the list. Here's the thing that I think is really interesting is that the growth that we see is JavaScript we also see Go as an emerging language, Swift, Scala, Python, you also in the grey you can see where our users are telling us they're decreasing usage so you see that a lot of people are just moving into JavaScript and Node and not decreasing their usage at all some of the things that are declining are PHP and the sample size for this I believe was like 1300 so it's not a small sample and here's some of the things that we're seeing the development of Node in its web apps and enterprise, big data and embedded systems especially IoT. I think it's telling that the Node is a moving into the enterprise because before you know 10 years ago what would you have said you're developing your enterprise apps in Java what else would you do it I'm not risking it maybe .NET but JavaScript is becoming an enterprise app development platform. Here's some of the things that we see affinity with some things I will say that they may be as far as relevance maybe more interesting than others I think that obviously you would expect Node.js frameworks to be something that we work with but containers almost 50% of our users are deploying Node and containers, databases obviously, MongoDB there's something that we call the mean stack, Mongo, Node Express, Angular and Node as a full stack development stack. We see a lot of people that are front-ending with load balancing like Nginx etc and then messaging systems obviously CI I think that CI thing is funny to me because I've been in the development space that perhaps maybe everybody should be using continuous integration and only not just 49% but I think maybe that might have been the way the question was phrased. There's also the framework the front-end frameworks is another thing I'm going to harp on a little bit is with things like React and Angular and Electron you have really good tools to develop applications that you can get up to speed with really quickly I think that's one of the attractions of Node is just time to value is really short. Being a tech guy in the early days everything was about the best like I need the best so I was spending all that money for Solaris servers back in the 90s and then Linux was good enough and we started using Linux and now utility and speed is our ways that we measure IT return whereas in my early days I had metrics around uptime now you have people like Amazon they're like we might be down for 30 seconds but we'll get all these updates up a month sooner than waiting till a maintenance window so the utility, the speed to value and all those things are ways that I see in the sort of new digital age people measure their success so we like to talk about digital transformation it's a great word if you walk into your company or talk to your CIO he's reading about digital transformation and it's really you know taking a lot of these systems into the into the current you know web enabled world I guess web 3.0 we have and we have 8 million node instances running every day and we see every the vast majority of our community using more and more of that every time we also see huge growth in China their second largest population outside of the US using the survey and what they're doing with that is they're bringing legacy systems to the cloud they're building micro services their node is a great great solution on serverless framework mobile application delivery I'll talk a little bit about that a bit API burkering it's just a good solid integration platform and and it's very flexible and that JavaScript is great as a cost for cross-platform delivery this is sort of the breakdown of how people are using that so we see a lot of people using it for back-end services full stack I think full stack is always a great solution I got an email yesterday that said for $30 I can get trained on how to be a full stack developer which I'm sure most of you would laugh because it's $30 and probably five years to really become a very good full stack developer but I mean obviously I did pay my $30 and I'll have my certificate in four to six weeks but I think think the thing that is distinguishing about node.js as it has been brought a whole new population developers in the full stack development because of the ability of running Java on the back end JavaScript on the back end but this is sort of our breakdown we see good traction and IOT I have some other examples of that that I'll share shortly but let's start with serverless so serverless is the hot new thing it's the things like Amazon, Lambda, Google Cloud Functions, Azure Functions, Bluemix is open-wisk all these things are are just the level of abstraction on top of the cloud that is really interesting makes it easier for developers to get into production node.js was the first language and runtime on Azure Functions Cloud Functions, Lambda, Twilio just last week or the week before launched a new cloud function service that is built on node.js and we have lots and lots of examples but node.js and serverless are like peas and carrots I guess they just go together and we see a lot of our community being successful there. We see people like Netflix who's breaking up their big job applications into small microservices running in discreet containers things in Lambda things things in the container services in Amazon in general. Web application services that's another one of our strong spots and the thing that's really interesting is because of the ability to utilize some of these frameworks it's easy for them to develop cross platforms so mobile to desktop and we see some good success there so Lowe's the home improvement aggregated their services layer and now they can completely redesign their high traffic website really quickly and easily there are huge success story for us as is Capital One using the disaggregation tier as well and it makes it makes the platform and delivery less dependent on the technology because JavaScript. Mobile we're great in mobile and I gotta I gotta admit I'm like that guy at the kids baseball game who thinks he's doing all this cool stuff and he just bragging about his kid that's what an executive director does is he brags about all this the work that people like Michael Dawson and other people do so hopefully this gives you an idea of what we're doing but I think the it's worth noting because honestly I think node is probably one of the most humble projects out there like this is this is huge to have eight million instances running every day at the scale that we're running at the in the places we're running without having a lot of formal coordination the cloud foundry people they have a they have a large staff of people that are coordinating this event coordinating the foundation we have huge member base node.js is is very very organic and despite not having that high-level coordination the people that are working on node are doing some pretty crazy complicated things at and there it's everywhere but obviously in the mobile space the difference in in the way asynchronous leaps work versus callbacks there's some advantages there for the mobile traffic. The fact that we support run on TCP and not ACTP there is some low overhead for client server communication and probably one of the best examples of that is Twitter so Twitter announced in February that they had moved a hundred percent of their mobile traffic to a node.js framework that's that's pretty impressive that's that's a use case that that shows just massive massive scale we also have a good footprint in IoT we see that there's a lot of packages for Arduino we see that there's projects like node regs popping up and we see actual use cases like this company Skycatch Skycatch builds drones they build drones not so you can fly them for fun but they build them to gather data and their real product is data aggregation and manipulation and they actually run their infrastructure on Amazon Lambda they gather all this data from drones mapping buildings etc and then pull it together in a really robust way so in the software world this is what's called the NASCAR slide because you try and put as many logos in the smallest space as possible to impress people and but it should be impressive because if you look at all the police places that node is in production and running I mean from the Wall Street Journal to things like wired and all the Kanda Nasta product properties from Uber Uber's apps written to node Airbnb etc etc etc it's it's very very large footprint of users and very very very robust so I think I I moved that slide so I'm not going to hit that one here's the other thing that's interesting is where people are deploying node so at the time of this survey was the middle of last year so Amazon Web Services was there the gray lines are indicating people that are going to increase their usage on those platforms people are doing on premise infrastructure the reason I I think that I would add to the survey it didn't have it specifically would be how many people are deploying the cloud foundry either via IBM's blue mix or on premise I don't think that calls out that well but all the places you'd expect obviously they're developing as well they're developing it in on premise heroku is pretty high up on that list I was a little surprised by that as well as digital ocean but but people are deploying that the the majority of node to cloud infrastructure as they probably are with many other apps reason we like node is because increases productivity earlier on I said developer ease but 68% of our our survey results say that developer productivity was was one of the main reasons that they invested in node along with reduced deployment cost and increased performance and over time we see that those benefits get bigger and bigger so in every category the more they use node the better their experience was so there's this this the other thing it's nice is that we're when you compare node to other open-source projects that are popular we're really really high and if you look at this was the battery open-source software index the boss index and they listed Linux as the number one on their index and I think get in my SQL we're number two and number three node was number four Docker was a little farther down the list and Hadoop and Elastic and some of the other popular open-source projects but of the hundred or so projects they ranked we're the top five and just sort of a node by the numbers overview we had 8 million node users as I've said over and over again I like to brag about that because I used to be in a little open-source project and I'd be like we have 10,000 users sounds good 8 million sounds real good we have over a billion platform a billion package downloads per week we have 36,000 stars on GitHub over 1100 contributed to node core 400 packages published every day and 100% growth year every year we also the thing that's really impressive to me this is from node source node source is a member of our foundation they this node by the numbers this is our contributor growth over the last couple years so it's not just an active user ecosystem it's an active contributor use ecosystem and the downloads are growing accordingly too once again from the source but you can see the blue the purple and the sort of bright blue line at the top is year every year so the bottom is 2014 2015 2016 that's huge growth if we map that out it would be that awesome hockey stick like the last graph and here's another interesting fact is the fact that so W3 text is one of those companies that surveys websites to see what they're running and I just saw this in the last actually I pulled it on June 10th so it's real fresh data but they're showing position and they've actually positioned node alongside Apache and engine X and IS lightspeed and the other ones and what they showed was that node.js is has a huge adoption at high high traffic sites so they're right there in that upper they're the high high upper left so they're the sites that are doing massive amounts of traffic are also using node.js and they're identifying as node.js which is interesting to me our footprints growing not just in the US but all over the world obviously China has been huge other Asia-Pacific countries so everywhere like nodes hot my boss said to me I think nodes are like an established project now I'm like it's still a growth project and and it's growing at exponential rates it's just amazing this is sort of a overview of our users and their usage profile so what versions they have in production obviously Michael told talked about our LTS plans this is a little dated because we just came out with eight but the thing that I wanted to point out to you is in the upper right hand corner is the years using node and those those numbers are somewhat telling because there is a large percentage of 35% with three plus years in nodes so it is it is mature but it's still growing and it's it's it's growing a little bit more about our speakers so while we are very English centric as most of IT is we do see a huge uptick in other countries and we see Germans obviously Chinese Portuguese is the interesting one there so as I noted earlier node is governed by a foundation we're there to provide governance and resources to make sure that the ecosystem is healthy and growing and supported with all the resources that we need so that is my job is to make sure that we are creating ecosystem around a node that that you can depend on over the years and here's just a little slide of who supports nodes so IBM and tell joy it which is now part of my Samsung Microsoft PayPal and Red Hat are our Platinum's then we have GoDaddy and Nodesource and then we have quite a few silver platforms but because of that we do exist to actually help bridge the the financial support to our development community and our community in general there is an individual member opportunity and we are getting together for our annual conference in October you're all invited hope to see you in Vancouver and thanks questions from Mark so I'm not the best person to ask about that but we actually have two companies that joined the foundation that specialized that and that is SNCC and Lyft security and Lyft security is donating all of their secure data so that we get a good footprint on on that so we can make an informed decision on that we also have an ecosystem of of experts from IBM to Nodesource to others who who part of their offering is their expertise in helping to to provide you know secure deployments and they do one more question okay