Posts about Science

Using Diatom Algae to Deliver Chemotherapy Drugs Directly to Cancer Cells

I am thankful for scientists doing the time consuming and important research to find new ways to fight disease. Here is an interesting webcast discussing how chemotherapy is used to fight cancer and how scientists are looking to algae to deliver the chemotherapy drugs to better target cancer cells (while not savaging our health cells).

I am also thankful to the funding sources that pay for this research (and for cool explanations of science, like SciShow).

Read more about the genetically engineered algae kills 90% of cancer cells without harming healthy ones. The algae are a diatom and many diatoms look very cool.

Sadly the actual research paper (by government funded university professors) is published by a closed science publisher (when are we finally going to stop this practice that was outdated over a decade ago?). Thankfully those responsible for SciShow are much more interested in promoting science than maintaining outdated business models (in direct contrast to so many science journal publishers).

Related post on cool delivery methods for life saving drugs: Using Bacteria to Carry Nanoparticles Into CellsSelf-Assembling Cubes Could Deliver Medicine (2006)Nanoparticles With Scorpion Venom Slow Cancer SpreadNASA Biocapsules Deliver Medical Interventions Based Upon What They Detect in the Body

Parasite Evolved from Cnidarians (Jellyfish etc.)

This is another instance of science research providing us interesting details about the very odd ways life has evolved on earth.

Genome sequencing confirms that myxozoans, a diverse group of microscopic parasites that infect invertebrate and vertebrate hosts, are actually highly reduced cnidarians — the phylum that includes jellyfish, corals and sea anemones.

“This is a remarkable case of extreme degeneration of an animal body plan,” said Paulyn Cartwright, associate professor of ecology and evolutionary biology at the University of Kansas (KU) and principal investigator on the research project. “First, we confirmed they’re cnidarians. Now we need to investigate how they got to be that way.”

images of myxozoans parasite spores and a jellyfish

Not only has the parasitic micro jellyfish evolved a stripped-down body plan of just a few cells, but via data generated at the KU Medical Center’s Genome Sequencing Facility researchers also found the myxozoan genome was drastically simplified.

“These were 20 to 40 times smaller than average jellyfish genomes,” Cartwright said. “It’s one of the smallest animal genomes ever reported. It only has about 20 million base pairs, whereas the average Cnidarian has over 300 million. These are tiny little genomes by comparison.”

Despite its radical phasedown of the modern jellyfish’s body structure and genome over millions of years, Myxozoa has retained the essential characteristic of the jellyfish — its stinger, or “nematocyst” — along with the genes needed to make it.

“Because they’re so weird, it’s difficult to imagine they were jellyfish,” she said. “They don’t have a mouth or a gut. They have just a few cells. But then they have this complex structure that looks just like stinging cell of cnidarian. Jellyfish tentacles are loaded with them — little firing weapons.”

The findings are the stuff of scientific fascination but also could have a commercial effect. Myxozoa commonly plague commercial fish stock such as trout and salmon.

“They’re a very diverse group of parasites, and some have been well-studied because they infect fish and can wreak havoc in aquaculture of economic importance,” Cartwright said.

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Funding Sources for Independent Postdoctoral Research Projects in Biology

Here is a nice list of funding sources for independent postdoctoral research projects in biology.

Some examples:

Directory of select science and engineering scholarships and fellowships for undergraduates, graduates and faculty on our blog.

Related: Science, Engineering and Math Fellowships (2008)Proposal to Triple NSF GFRP Awards and the Size of the Awards by 33% (2007)HHMI Expands Support of Postdoctoral ScientistsNSF Graduate Research Fellow Profiles (Sergy Brin, Google co-founder)

Chimpanzees Use Spears to Hunt Bush Babies

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

Scientific Inquiry Leads to Using Fluoride for Healthy Teeth

This webcast, from the wonderful SciShow, explores how we discovered fluoride helps prevent tooth decay and how we then used that knowledge and finally discovered why it worked.

I love stories of how we learn for observing what is happening. We don’t always need to innovate by thinking up creative new ideas. If we are observant we can pick up anomalies and then examine the situation to find possible explanations and then experiment to see if those explanations prove true.

When working this way we often are seeing correlation and then trying to figure out which part of the correlation is an actual cause. So in this dental example, a dentist noticed his patients had bad brown stains on their teeth than others populations did.

After investigation the natural fluoridation of the water in Colorado Springs, Colorado, USA seemed like it might be an explanation (though they didn’t understand the chemistry that would cause that result). They also explored the sense that the discolored teeth were resistant to decay.

Even without knowing why it is possible to test if the conditions are the cause. Scientists discovered by reducing the level of fluoridation in the water the ugly brown stains could be eliminated (these stains took a long time to develop and didn’t develop in adults). Eventually scientists ran an experiment in Grand Rapids, Michigan and found fluoridation of the water achieved amazing results for dental health. The practice of fluoridation was then adopted widely and resulted in greatly improved dental health.

In 1901, Frederick McKay, a recent dental school graduate, opened a dental practice in Colorado Springs, Colorado. He was interested in what he saw and sought out other dentists to explore the situation with him but had little success. In 1909, he found some success when renowned dental researcher Dr. G.V. Black collaborate with him.
Dr. H. Trendley Dean, head of the Dental Hygiene Unit at the National Institute of Health built on their work when he began investigating the epidemiology of fluorosis in 1931. It wasn’t until 1945 that the Grand Rapids test started. Science can take a long time to move forward.

Only later did scientists unravel why this worked. The fluoride reacts to create a stronger enamel than if the fluoride is not present. Which results in the enamal being less easily dissolved by bacteria.
Health tip: use a dental stimudent (dental picks) or floss your teeth to maintain healthy gums and prevent tooth decay. It makes a big difference.

Related: Why does orange juice taste so bad after brushing your teeth?Microbiologist Develops Mouthwash That Targets Only Harmful Cavity Causing BacteriaUsing Nanocomposites to Improve Dental Filling PerformanceFinding a Dentist in Chiang Mai, ThailandFalse Teeth For CatsWhy Does Hair Turn Grey as We Age?

We Have Thousands of Viruses In Us All the Time

Biology and the amazing interactions within a human body are amazing. Our bodies are teeming with other life (and almost life – viruses). All these microbes have a drastic impact on our health and those impacts are not always bad.

A Virus In Your Mouth Helps Fight The Flu

Hidden inside all of us are likely thousands of viruses — maybe more. They just hang out, harmlessly. We don’t even know they’re there.

But every once in a while, one of these viral inhabitants might help us out.

Young people infected with a type of herpes virus have a better immune response to the flu vaccine than those not infected, scientists at Stanford University report Wednesday. In mice, the virus directly stops influenza itself.

We’re talking about a ubiquitous critter, called cytomegalovirus. About half of all Americans carry it. And so do nearly 100 percent of people in developing countries.

In younger people, CMV had the opposite effect that Davis had predicted: “The virus ramped up the immune system to give better protection from pathogens,” Mark Davis says. “We tested only for the flu, but I speculate it protects against everything.”

So should we all go out and get infected with CMV? No way! Davis exclaims.

You see, CMV has a dark side. It can become dangerous if the immune system is suppressed, which happens after an organ transplant or during treatments for autoimmune disorders. CMV is also a concern for pregnant woman. It’s the top viral cause of birth defects worldwide.

The human microbiome is incredible and teams with thousands of species (bacteria, viruses, members of domain Archaea, yeasts, single-celled eukaryotes, helminth parasites and bacteriophages). The complexity of interactions between all the elements of what is in our bodies and cells is one of the things that makes health care so challenging. It is also fascinating how these interactions provide benefits and costs as they work within our bodies.

The fact that we have evolved in concert with all these interactions is one of the big problems with anti-biotics. Antibiotics are miraculous when they work, but they can also decimate our natural micro-biomes which does create risks.

I would have thought Stanford wasn’t still supporting closed science :-( Sadly this research is not published in an open science manner.

Related: Foreign Cells Outnumber Human Cells in Our BodiesMicrobes Flourish In Healthy PeopleTracking the Ecosystem Within UsPeople Have More Bacterial Cells than Human CellsCats Control Rats With ParasitesSkin Bacteria

2014 Ranking of the World’s Best Research Universities

Shanghai’s Jiao Tong University produces an annual ranking of research universities. The methodology values publications and faculty awards (Nobel and Fields) which belies the focus on ranking research not for example the quality of education provided.

You could argue one measure does partially address teaching as the Nobel and Fields prizes to alumni are created to the institution (that is separate from a measure of faculty that receive those honors). I would agree it partially measure the education though it also measures the ability of that school to attract the absolute best candidates (whether they would have been just as successful going elsewhere is a fair question).

Results from the 2014 rankings of top 500 universities with the number of schools by country:

location Top 100 % of World
% of World GDP % of top 500
USA 52     4.5%   22.2%  29.2%
United Kingdom   8  0.9  3.5 7.6
Germany   4  1.1  5.0 7.8
Canada   4  0.5  2.4 4.2
France   4  0.9  3.8 4.2
Japan   3  1.8  7.8 3.8
Australia   4  0.3  1.5 3.8
China   0  19.2  11.7 8.8
Netherlands   4  0.2  1.3 2.6
Sweden   4  0.1  0.8 2.2
Switzerland   5  0.1  0.8 1.4
South Korea   0  .7  1.7 2.0
India   0  17.0  1.9 0.2

The top countries for top 100 and top 500 schools are listed above, but I skip over many after the top 7 or 8 to include a few countries I like to watch, see the ranking site for the full list. Country population and GDP data were taken from the World Development Indicators 2013, by the World Bank.

There is little change in top 100 since 2008, which I think is a good sign, it wouldn’t make much sense to have radical shifts quickly in this type of ranking. The USA lost 2 schools in the top 100, UK lost 3, Germany lost 2, Switzerland gained 2, Netherlands gain 2…

There is more change in the top 500 where changes are more sensible (there is probably not much separating schools ranked in the 300’s from those in the 500’s so variation and strong pushes (from countries like China) can have an impact. China gained 14 more schools in the top 500. China’s GDP also increased from 6.6% of global GDP to 11.7%.

University of Wisconsin – Madison is 24th, it was 17th in 2008 My father taught there while I grew up.
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Ranking Countries by Scientific Publication Citations: USA, UK, Germany…

The SCImago Journal and Country Rank provides journal and country scientific indicators developed from the information contained in the Scopus database. I posted about this previously (in 2014, 2011 and 2008).

The data in the post is based on their data from 1996 through 2013. The web site also lets you look at these ranking by very specific categories. For example biotechnology #1 USA, #2 Germany, #3 UK, #4 Japan, #12 China or human computer interaction #1 USA, #2 Germany, #3 UK #4 Japan, #13 China).

I like looking at data and country comparisons but in doing so it is wise to remember this is the results of a calculation that is interesting but hardly definative. We don’t have the ability to measure the true scientific research output by country.

The table shows the top 6 countries by h-index and then some others I chose to list.

Country h-index 2010
% of World
% of World GDP total cites
USA 1,518 1,139 793     4.5%   22.2% 152,984,430
United Kingdom 918 689 465  0.9  3.5 37,450,384
Germany 815 607 408  1.1  5.0  30,644,118
France 742 554 376  0.9  3.8  21,193,343
Canada 725 536 370  0.5  2.4 18,826,873
Japan 635 527 372  1.8  7.8 23,633,462
Additional countries of interest (with 2013 country rank)
16) China 436 279 161  19.2  11.7  14,752,062
19) South Korea 375 258 161    .7  1.7  5,770,844
22) Brazil 342 239 148  2.8  3.0 4,164,813
23) India 341 227 146  17.5  2.6 5,666,045

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Manufacture Biological Sensors Using Silk and Looms

The fabric chip platform from Achira Labs in India uses looms to manufacture biological sensors.

Image of process for creating silk test strips

image by Achira Labs

Yarn coated with appropriate biological reagents like antibodies or enzymes is woven into a piece of fabric at the desired location. Strips of fabric are then cut out, packaged and can form the substrate for di erent biological assays. Even a simple handloom could produce thousands of these sensors at very low cost.

The resulting fabrics can be used to test for pregnancy, diabetes, chronic diseases, etc.. Achira Labs, an Indian start-up, received $100,000 in Canadian funding in 2013 to develop a silk strip that can diagnose rotavirus, a common cause of diarrhea and can be used in diapers.

The company is planing to start selling silk diabetes test strips using there process this year and expects costs to be about 1/3 of the existing test strips using conventional manufacturing processes.

Related: Appropriate Technology Health Care Solution Could Save 72,000 Lives a YearWater WheelUsing Drones to Deliver Medical Supplies in Roadless AreasAppropriate Technology: Self Adjusting Glasses

Deinocheirus is a Totally Bizarre Dinosaur

A very strange dinosaur has been uncovered, studied and explained by scientists. The dinosaur is from Mongolia about 70 million years ago.

“Deinocheirus is a totally bizarre dinosaur,” explains Phil Currie, professor and Canada Research Chair in Dinosaur Paleobiology at the University of Alberta. At 11 meters long and with an estimated weight of 6.4 tons, Deinocheirus was a behemoth to be sure—but hardly the giant tyrannosaur its massive arms may have suggested. Rather, the apparently disproportionately large forearms were more likely used for digging and gathering plants in freshwater habitats, or for fishing. Among its other unusual attributes are tall dorsal spines, truncated hoof-like claws on the feet to prevent sinking into muddy ground, and bulky hind legs that indicate it was a slow mover.

“Although the arms have been known since 1965 and have always aroused speculation because of their enormous size and sharp, recurving claws, we were completely unprepared for how strange this dinosaur looks,” says Currie. “It almost appears to be a chimera, with its ornithomimid-like arms, its tyrannosaurid-like legs, its Spinosaurus-like vertebral spines, its sauropod-like hips, and its hadrosaur-like duckbill and foot-hooves.”

Currie notes that Deinocheirus is a descendant of ostrich-like dinosaurs that were only slightly larger than humans, so its evolution into a giant, multi-tonne creature is almost certainly responsible for most of its unusual characteristics. “Its great size probably gave it some protection from the tyrannosaurid Tarbosaurus, which appears to have been relatively common in that part of Mongolia some 70 million years ago,” says Currie. To feed its great bulk, Deinocheirus was apparently an omnivore that ingested both plants and fish, as evident from fish remains found in its stomach contents.

“The study of this specimen has shown that even in dinosaurs like Deinocheirus, an animal that has been known for almost half a century, we can still learn surprising things about their anatomy,” says Currie. “Furthermore, it underlines the fact that even today, dinosaurs are still relatively poorly known. The fact that Deinocheirus is from the Nemegt Formation of Mongolia, one of the richest and most diverse dinosaur faunas known, hints that there are probably thousands of dinosaurs that we still do not know about from the majority of dinosaur localities in the world.”

Including poached dinosaur bones (stealing bones has long been a problem to the advancement of science) with the existing bones available to scientists allowed the new understanding of this amazing dinosaur. The now near-complete Deinocheirus specimen has been returned to its home for further study in the Mongolia Centre for Paleontology.

Full press release

Related: Ancient Whale Uncovered in Egyptian DesertNigersaurus, the Mesozoic CowDinosaur Remains Found with Intact Skin and TissueLobopodians from China (“the walking cactus” – an animal)Korea-Mongolia International Dinosaur Project

Epigenetics, Scientific Inquiry and Uncertainty

Science is full of fascinating ideas. Epigenetics is one area I find particularly interesting. This previous post has a few links to learning more: DNA Passed to Descendants Changed by Your Life.

Angela Saini is one 109 people I follow on Twitter. I don’t see the point in “following” people on Twitter that you have no interest in, I only follow the small number of people that post Tweets I want to read.

In, Epigenetics: genes, environment and the generation game, Angela Saini looks at the confused state of current scientific understand now. It is very difficult to tell if, and if so, to what extent, epigenetic inheritance happens in people.

Professor Azim Surani, a leading developmental biologist and geneticist at the University of Cambridge, adds that while there is good evidence that epigenetic inheritance happens in plants and worms, mammals have very different biology. Surani’s lab carried out thorough studies on how epigenetic information was erased in developing mouse embryos and found that “surprisingly little gets through” the reprogramming process.

Professor Timothy Bestor, a geneticist at Columbia University in New York, is far more damning, claiming that the entire field has been grossly overhyped. “It’s an extremely fashionable topic right now. It’s very easy to get studies on transgenerational epigenetic inheritance published,” he says, adding that all this excitement has lowered critical standards.

Related: Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeMedical Study Findings too Often Fail to Provide Us Useful KnowledgeScientific Inquiry Process Finds That Komodo Dragons Don’t have a Toxic Bite After All

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