Posts about university research

Stanford Research Scientists Discover 99% of the Microbes Inside Us are Unknown to Science

Readers of this blog know I am fascinated by the human microbiome. It is amazing how much of our biology is determined by entities within us that are not us (at least not our DNA) (bacteria, viruses etc.). This whole area of study is very new and we have quite a bit to learn. There are scientists across the globe studying this area and learning a great deal.

Stanford study indicates that more than 99% of the microbes inside us are unknown to science

Of all the non-human DNA fragments the team gathered, 99 percent of them failed to match anything in existing genetic databases the researchers examined.

The “vast majority” of it belonged to a phylum called proteobacteria, which includes, among many other species, pathogens such as E. coli and Salmonella. Previously unidentified viruses in the torque teno family, generally not associated with disease but often found in immunocompromised patients, made up the largest group of viruses.

“We’ve doubled the number of known viruses in that family through this work,” Quake said. Perhaps more important, they’ve found an entirely new group of torque teno viruses. Among the known torque teno viruses, one group infects humans and another infects animals, but many of the ones the researchers found didn’t fit in either group. “We’ve now found a whole new class of human-infecting ones that are closer to the animal class than to the previously known human ones, so quite divergent on the evolutionary scale,” he said.

Related: We are Not Us Without The Microbes Within UsWebcasts on the Human MicrobiomePeople are Superorganisms With Microbiomes of Thousands of Species (2013)We Have Thousands of Viruses In Us All the Time (2015)Tracking the Ecosystem Within Us (2007)

Large Scale Redox Flow Battery (700 megawatt hours)

Scientists and engineers in Germany have created the largest battery in the world with redox flow technology.

Redox flow batteries are liquid batteries. The Friedrich Schiller University of Jena has developed a new and forward-looking salt-free (brine) based metal-free redox flow battery. This new development will use salt caverns as energy storage.

schematic for salt-free (brine) based metal-free redox flow battery

Schematic for salt-free (brine) based metal-free redox flow battery by Ewe Gasspeicher. Two caverns each have a volume of 100,000 cubic meters.

A redox flow battery consists of two storage tanks and an electrochemical cell in which the reactions take place. Storage for solar and wind sources of power is an important challenge being explored in many ways today. Efforts such as this one provide a path to continue the rapid adoption of more solar and wind power.

In the electrochemical cell the two storage liquids – catholyte and anolyte – are separated from one another by a membrane. This prevents the large storage liquids from mixing with one another. The ions, however, can pass unimpeded through the membrane from one electrolyte solution into the other.

When charging the battery, the charging current ensures that electrons are deposited on the polymers of the anolyte. At the same time, the catholyte releases its electrons.

The charged catholyte and anolyte molecules are pumped from the cell into storage containers and replaced by uncharged ones. When the battery is discharged, the reaction is reversed. The anolyte molecules emit their electrons, which are available as electrical current.

Both charged electrolytes can be stored for several months. The maximum storage capacity of this redox-flow battery is limited only by the size of the storage containers for the electrolyte liquids.

The project is being ramped up now, going through a test phase before bringing the full system online; they are aiming to achieve this in 6 years. The electrical capacity of 700 megawatt hours will be enough to supply over 75,000 households with electricity for one day.

Related: Molten Salt Solar Reactor Approved by California (2010)Battery Breakthrough Using Organic Storage (2014)Chart of Global Wind Energy Capacity by Country from 2005 to 2015

Small Farm Robots

The IdaBot was created by researchers at Northwest Nazarene University (Idaho, USA).

Using robots in farming is limited today but the future could see a huge growth in that use. Benefits of introducing more robots to farming include reducing the use of pesticides and chemicals to control weeds.

Reducing labor costs is also a potential benefit but at current market prices (due to high costs of robotics and available cheap labor) that is more something for the future than today. However that can change fairly quickly – as for example the collapse in solar panel costs have made solar energy economically very attractive. In areas with high labor costs (Japan etc.) or areas where there are active efforts to reduce the supply of labor (in the USA where a significant portion of labor does not have proper visa to work in the USA and the current administration is seeking to reduce that labor availability) robots become more attractive economically.

Robot farmers are coming to a field near you

In Japan, using robots to harvest strawberries is roughly cost-equivalent to human labor if the ‘bots are shared between multiple farms, Lux Research said.

“With strawberry-picking being slow and labor-intensive, and labor scarce and expensive ”” the average agricultural worker in Japan is over 70 years old ”“ the robot is quickly likely to become the cheaper option,” it said.

Lux Research also forecast European lettuce-growing ”” a major industry on the continent ”” would become automated by 2028.

“Automated lettuce weeding is already competitive with human labor in Europe, thanks to regulatory limitations on agrochemicals. Lettuce thinning is still accomplished manually at lower cost, but robots are likely to reach breakeven with human labor in 2028,”

The global market for agricultural robots will explode to $73.9 billion by 2024, up from $3.0 billion 2015

Related: For Many Crops Ants Can Provide Pest Protection Superior or Equal to Chemicals at a Much Lower CostSustainable Ocean FarmingCool Robot Locomotion: Transforms from Wheeled to Walking For Stairs and Rough Terrain (2012)Lean Science: Using Cheap Robots to Aid ResearchMoth Controlled Robot (2009)

Eating Nuts May Reduce the Risk of Heart Disease, Cancer and Other Diseases

A large analysis of current research shows that people who eat at least 20g of nuts a day have a lower risk of heart disease, cancer and other diseases. The analysis of all current studies on nut consumption and disease risk has revealed that 20g a day – equivalent to a handful – can cut people’s risk of coronary heart disease by nearly 30%, their risk of cancer by 15%, and their risk of premature death by 22%.

While this is reassuring news to those of us (like me) that frequently eat nuts I am not sold on their evidence. Heath research is prone to overstating the benefits. Still there is little reason to avoid making nuts part of a healthy diet. That is a big part of the reason I have. They offer benefits and maybe even great ones (as indicated in this research) without much risk.

An average of at least 20g of nut consumption was also associated with a reduced risk of dying from respiratory disease by about a half, and diabetes by nearly 40 percent, although the researchers note that there is less data about these diseases in relation to nut consumption.

The study, led by researchers from Imperial College London and the Norwegian University of Science and Technology, is published in the journal BMC Medicine, Nut consumption and risk of cardiovascular disease, total cancer, all-cause and cause-specific mortality: a systematic review and dose-response meta-analysis of prospective studies (open access paper).

The research team analysed 29 published studies from around the world that involved up to 819,000 participants, including more than 12,000 cases of coronary heart disease, 9,000 cases of stroke, 18,000 cases of cardiovascular disease and cancer, and more than 85,000 deaths.

While there was some variation between the populations that were studied, such as between men and women, people living in different regions, or people with different risk factors, the researchers found that nut consumption was associated with a reduction in disease risk across most of them.

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The Challenge of Protecting Us from Evolving Bacterial Threats

I have long been concerned about the practices we continue to use increasing the risks of “superbugs.” I have written about this many times, including: The Overuse of Antibiotics Carries Large Long Term Risks (2005)Are you ready for a world without antibiotics? (2010), Antibiotics Breed Superbugs Faster Than Expected (2010), Entirely New Antibiotic (platensimycin) Developed (2006), Our Poor Antibiotic Practices Have Sped the Evolution of Resistance to Our Last-Resort Antibiotic (2015).

I do also believe the wonderful breakthroughs we make when we invest in science and engineering have made our lives much better and have the potential to continue to do so in many ways, including in dealing with the risks of superbugs. But this is something that requires great effort by many smart people and a great deal of money. It will only happen if we put in the effort.

Winning war against ”˜superbugs”™

hey won this particular battle, or at least gained some critical intelligence, not by designing a new antibiotic, but by interfering with the metabolism of the bacterial “bugs” ”” E. coli in this case ”” and rendering them weaker in the face of existing antibiotics

ROS, or “reactive oxygen species,” include molecules like superoxide and hydrogen peroxide that are natural byproducts of normal metabolic activity. Bacteria usually cope just fine with them, but too many can cause serious damage or even kill the cell. In fact, Collins”™ team revealed a few years ago the true antibiotic modus operandi: they kill bacteria in part by ramping up ROS production.

We need to continue to pursue many paths to protecting us from rapidly evolving bacterial risks. Many promising research results will fail to produce usable solutions. We need to try many promising ideas to find useful tools and strategies to protect human health.

An Eukaryote that Completely Lacks Mitochondria

If you don’t have any idea what the title means that is ok. I probably wouldn’t have until the last 15 years when I found how interesting biology is thanks to the internet and wonderful resources online making biology interesting. I hope you find learning about biology as interesting as I do.

Look, Ma! No Mitochondria

Mitochondria have their own DNA, and scientists believe they were once free-living bacteria that got engulfed by primitive, ancient cells that were evolving to become the complex life forms we know and love today.

What they learned is that instead of relying on mitochondria to assemble iron-sulfur clusters, these cells use a different kind of machinery. And it looks like they acquired it from bacteria.

The researchers say this is the first example of any eukaryote that completely lacks mitochondria.

However, the results do not negate the idea that the acquisition of a mitochondrion was an important and perhaps defining event in the evolution of eukaryotic cells, he adds.

That’s because it seems clear that this organism’s ancestors had mitochondria that were then lost after the cells acquired their non-mitochondrial system for making iron-sulfur clusters.

Biology is amazing and mitochondria are one of the many amazing details. I wish so much that my education could have given biology a tiny fraction of the interest I have found it in after school.

Related: Human Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticOne Species”™ Genome Discovered Inside Another”™sParasite Evolved from Cnidarians (Jellyfish etc.)Plants, Unikonts, Excavates and SARs

International Science Research Scholar Grants

The Howard Hughes Medical Institute (HHMI), Bill & Melinda Gates Foundation, Wellcome Trust, and Calouste Gulbenkian Foundation have announced the International Research Scholars Program which aims to support up to 50 outstanding early career scientists worldwide. The program”™s aim is to help develop scientific talent worldwide.

The new international competition is seeking top early career researchers from a wide variety of biomedical research fields. Applicants must have started their first independent research position on or after April 1, 2009. Awardees will be invited to participate in research meetings with scientists supported by the funders. These meetings facilitate the exchange of ideas, stimulate new research, and provide an opportunity for collaborative endeavors within the international scientific community.

  • Awardees will receive a total of $650,000 over five years.
  • Applications are due June 30, 2016.
  • Awardees will be notified in April 2017.

HHMI and its partners have committed a total of $37.4 million for the International Research Scholars Program and will award each scientist who is selected a total of $650,000 over five years. The competition is open to scientists who have trained in the U.S. or United Kingdom for at least one year. Additionally, eligible scientists must have run their own labs for less than seven years, and work in one of the eligible countries.

Nieng Yan

Although Nieng Yan had several grants when she started her lab at Tsinghua University in 2007, she barely had enough money to pay her eight lab members. “In China, there is a limit on the percentage of a grant that you can use to pay people ”” your graduate students, your postdocs, your technicians, your assistants ”” to a decent level,” she explains. After struggling to balance her budget for several years, Yan”™s scientific achievements and potential landed her an international grant from HHMI in 2012. “The amount of money provided by Hughes is relatively small compared to other programs, but it has the advantage that you can freely decide what to do with it,” says Yan. In fact, HHMI”™s science officers encouraged Yan to use her five-year International Early Career Award (IECS) to cover the cost of paying her lab team, explaining that the money could be used in any way that assisted her research. Today, Yan has 15 people working in her lab helping to elucidate the structures of proteins that move molecules in and out of cells. The protein channels and transporters they study are mutated in a number of diseases ”” including diabetes and cancer ”” and understanding how they work could help in the development of drugs that block their ill effects. For example, the team recently solved the structure of GLUT1 ”“ a glucose transporter that is often overexpressed in malignant tumor cells. Their data may provide clues for how to inhibit the transporter and perhaps even reveal a way to use it to deliver chemotherapeutic drugs. Photo Credit: Kevin Wolf (AP)

Countries that are not eligible for this competition include the G7 countries (Canada, France, Germany, Italy, Japan, United Kingdom and United States), as well as countries identified by the U.S. Department of Treasury, Office of Foreign Assets Control (OFAC) as being subject to comprehensive country or territory-wide sanctions or where current OFAC regulations prohibit U.S. persons or entities from engaging in the funding arrangements contemplated by this grant program. For this program, such sanctioned countries or territories currently include Iran, North Korea, Sudan, Syria, and the Crimea region of Ukraine.

Related: Directory of Science and Engineering Scholarships and FellowshipsFunding Sources for Independent Postdoctoral Research Projects in BiologyScientific Research Spending Cuts in the USA and Increases Overseas are Tempting Scientists to Leave the USA (2013)HHMI Expands Support of Postdoctoral Scientists (2009)Science, Engineering and Math Fellowships

Webcasts on the Human Microbiome

The human microbiome is a very interesting aspect of our health and biology.

The 99% figure they quote is mainly silly. It might be technically accurate, but it is much more misleading than accurate (if it is accurate). We have more non-human cells than human but those cells are much smaller and we are overwhelmingly made up of human cells by weight (95+%).

The complexity of healthy bodies is far from understood. It is interesting to watch our understanding of the balancing act going on inside of us. Many foreign “invaders” are critical to our health.

Related: People are Superorganisms With Microbiomes of Thousands of SpeciesPeople Have More Bacterial Cells than Human CellsFighting Superbugs with Superhero BugsWe Have Thousands of Viruses In Us All the Time

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200,000 People Die Every Year in Europe from Adverse Drug Effects – How Can We Improve?

A new integrated computational method helps predicting adverse drug reaction more reliably than with traditional computing methods. This improved ability to foresee the possible adverse effects of drugs may entail saving many lives in the future.

Most computer tools employed today to detect possible adverse effects of compounds that are candidates for new medicines are based on detecting labile fragments in the drug’s structure. These fragments can potentially transform to form reactive metabolites, which can have toxic properties. This is what is known as idiosyncratic toxicity and is a big headache for the pharmaceutical industry, as it tends to be detected in late development stages of the drug and even when it is already on the market, often causing the drug to be withdrawn.

Jordi Mestres, coordinator of the IMIM and UPF research group on Systems Pharmacology at the Biomedical Informatics Program (GRIB) states ”˜With this study we have contributed to complementing the detection of these quite unstable fragments, with information on the mechanism of action of the drug, based on three aspects: similarity to other medicines, prediction of their pharmacological profile, and interference with specific biological pathways. The optimal integration of these four aspects results in a clear improvement of our ability to anticipate adverse effects with higher confidence, which entails an extremely positive impact on society”™.

In Europe, nearly 200,000 people die every year from adverse drug reactions, seven times more than in traffic accidents. An estimated 5% of hospitalisations are due to adverse effects and they are the fifth most common cause of hospital death. In addition, elderly people tend to take more than one drug at the same time, which multiplies the chances of suffering from adverse effects due to potential drug-drug interactions. In an increasingly aging society, this problem is becoming much more serious.

I think interactions is a hugely important area that needs a great deal more research. Doing so is very complex, which means it isn’t surprising so much more work is needed. The work of my father (and George Box and others) on multi-factorial experimentation is a powerful tool to aid this work (and that connection is likely one of the reasons I find the area of interactions so interesting – along with the realization there is so much benefit possible if we focus in that area more). Previous post on this Curious Cat Science and Engineering blog: Introduction to Fractional Factorial Designed Experiments.

The human and financial costs of adverse effects are very high. That is why the discovery of new medicines is increasingly focused more on predicting possible adverse effects at the initial stages of developing a new drug. This work hopes to contribute to setting the path toward a new generation of more reliable computational tools with regard to predicting the adverse effects of therapeutically-relevant small molecules. Advancing large-scale predictive safety at the pre-clinical phase is now becoming closer than ever, with expectations to lead to safer drugs for the entire population.

The research is published in closed science journal so I don’t link to it. I happily link to open science publications. Read the full press release which includes a link to the closed science journal.

Related: Lifestyle Drugs and RiskRoot Cause, Interactions, Robustness and Design of ExperimentsOne factor at a time (OFAT) Versus Factorial DesignsThe Purpose of Mulit-Factorial Designed Experiments11 Year Old Using Design of ExperimentsOver-reliance on Prescription Drugs to Aid Children”™s Sleep?

In Many Crops Ants Can Provide Pest Protection Superior or Equal to Chemicals at a Much Lower Cost

Ants are as Effective as pesticides

The review [of over 70 studies] was conducted by Aarhus University”™s Dr Joachim Offenberg, an ecologist who has studied ants for almost 20 years. It includes studies of more than 50 pest species on nine crops across eight countries in Africa, South-East Asia and Australia.

Most of the studies in Offenberg”™s review are on weaver ants (Oecophylla), a tropical species which lives in trees and weaves ball-shaped nests from leaves. Because weaver ants live in their host trees”™ canopy, near the flowers and fruit that need protection from pests, they are good pest controllers in tropical orchards.

All farmers need to do is collect ant nests from the wild, hang them in plastic bags among their tree crops and feed them a sugar solution while they build their new nests. Once a colony is established, farmers then connect the trees that are part of the colony with aerial ”˜ant walkways”™ made from string or lianas.

After that, the ants need little, except for some water in the dry season (which can be provided by hanging old plastic bottles among the trees), pruning trees that belong to different colonies so that the ants do not fight, and avoiding insecticide sprays.

The review shows that crops such as cashew and mango can be exceptionally well protected from pests by weaver ants.

One three-year study in Australia recorded cashew yields 49% higher in plots patrolled by ants compared with those protected by chemicals. Nut quality was higher too, so net income was 71% higher with ants than with chemicals.

Similar studies in Australian mango crops found that ants could produce the same yield as chemical control, but because the ants were cheaper, and fruit quality better, net income from mangoes produced with ant protection was 73% higher.

Those crops are special cases in which the ants are vastly superior. But in many other cases ants are as effective and much cheaper than chemical options. Different species of ants are suited to protecting different types of drops. Weaver ants require a canopy, other ants can protect crops without a canopy.

I hope more farmers adopt ants to help protect their crop yields.

Related: Pigs Instead of PesticidesWhy Don”™t All Ant Species Replace Queens in the Colony, Since Some DoHow To Make Your Own Pesticide with Ingredients from Your KitchenAnother Bee Study Finds CCD is Likely Due to Combination of Factors Including Pesticides (2013)

Chimpanzees Use Spears to Hunt Bush Babies

Video replaced with new one because original was removed 🙁

Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools by Jill D. Pruetz and Paco Bertolani

Although tool use is known to occur in species ranging from naked mole rats to owls, chimpanzees are the most accomplished tool users. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these.

Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.

The full paper, from 2007, was available as a pdf when I visited (I don’t really trust these publishers and what articles by professors they will block access to later when they don’t clearly say it is open access – in fact the journal broke the link on the post I made about this in 2007 now that I checked – sigh).

The full paper isn’t filled with overly complex scientific jargon (as scientific papers can be). In that sense it is an easy read; it is a bit graphic for those that are squeamish.

Dr. Jill Pruetz maintains an interesting blog the Chimpanzees she studies: Fongoli Savanna Chimpanzee Project

Related: Chimps Used Stones as HammersOrangutan Attempts to Hunt Fish with SpearBird Using Bread as Bait to Catch FishCrows can Perform as Well as 7 to 10-year-olds on cause-and-effect Water Displacement Tasks

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