Using Diatom Algae to Deliver Chemotherapy Drugs Directly to Cancer Cells

Posted on November 26, 2015  Comments (0)

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professors) is published by a closed science publisher (when are we finally going to stop this practice that was outdated over a decade ago?). Thankfully those responsible for SciShow are much more interested in promoting science than maintaining outdated business models (in direct contrast to so many science journal publishers).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

Posted on November 22, 2015  Comments (0)

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.

Read more

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

Posted on November 15, 2015  Comments (0)

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?

Backyard Wildlife: Blue Jay

Posted on November 8, 2015  Comments (3)

photo of a blue jay with a berry in its beak

Blue Jay in Arlington, Virginia (in my backyard). See more of my photos.

This is a picture I simply could not have taken before I bought my new camera (a Canon PowerShot SX60 HS Digital Camera with 65 times optical zoom). Birds are still hard to photograph but now at least occasionally I get a decent photo of birds. If you want to get photos of wildlife it is a great camera. And it is a wonderful camera in general.

I like just planting things that will feed and shelter birds (and others) rather than filling bird feeders myself. There is information on how to use your backyard to promote wildlife. I see many birds flying around in my backyard, which is quite nice. Blue jays are some of my favorites.

Blue jays diet is composed mostly of insects and nuts. They especially like acorns.

Young jays may be more likely to migrate than adults, but many adults also migrate. Some individual jays migrate south one year, stay north the next winter, and then migrate south again the next year. No one has worked out why they migrate when they do.

The pigment in blue jay feathers is melanin, which is brown. The blue color is caused by scattering light through modified cells on the surface of the feather barbs.

Related: Backyard Wildlife: Robins Attack Holly TreeBackyard Wildlife: BirdsBackyard Wildlife: CrowsBackyard Wildlife: FoxBackyard Wildlife: Chimpmunk

Fighting Superbugs with Superhero Bugs

Posted on October 31, 2015  Comments (2)

As concerns over deadly antibiotic-resistant strains of ‘superbug’ bacteria grow, scientists at the Salk Institute are offering a possible solution to the problem: ‘superhero’ bacteria that live in the gut and move to other parts of the body to alleviate life-threatening side effects caused by infections.

Salk researchers reported finding a strain of microbiome Escherichia coli bacteria in mice capable of improving the animals’ tolerance to infections of the lungs and intestines by preventing wasting–a common and potentially deadly loss of muscle tissue that occurs in serious infections. If a similarly protective strain is found in humans, it could offer a new avenue for countering muscle wasting, which afflicts patients suffering from sepsis and hospital-acquired infections, many of which are now antibiotic resistant.

images of E. coli bacteria, salmonella typhimurium and burkholderia thailandensis

Salk scientists found a strain of E. coli bacteria (left) that were able to stop muscle wasting in mice infected with either Salmonella Typhimurium (center) and Burkholderia thailandensis (right). Image courtesy the Salk Institute.

“Treatments for infection have long focused on eradicating the offending microbe, but what actually kills people aren’t the bacteria themselves–it’s the collateral damage it does to the body,” says Janelle Ayres, a Salk assistant professor in the Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis and senior researcher on the study.

“Our findings suggest that preventing the damage–in this case muscle wasting–can stave off the most life-threatening aspects of an infection,” she adds. “And by not trying the kill the pathogen, you’re not encouraging the evolution of the deadly antibiotic-resistant strains that are killing people around the world. We might be able to fight superbugs with ‘superhero’ bugs.”

Once the most powerful and revolutionary of drugs, antibiotics appear to have reached their limits, due to the ability of bacteria to rapidly evolve resistance to the medicines. The rise of antibiotic resistance presents a grave threat to people around the world, as diseases once easily controlled repel all attempts at treatment. A recent study found that up to half of the bacteria that cause infections in US hospitals after a surgery are resistant to standard antibiotics.

In the United States alone, two million people annually become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections, according to the U.S. Centers for Disease Control.

Read more

Funding Sources for Independent Postdoctoral Research Projects in Biology

Posted on October 25, 2015  Comments (1)

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)

Youyou Tu: The First Chinese Woman to Win a Nobel Prize

Posted on October 17, 2015  Comments (1)

The Nobel Prize in Physiology or Medicine 2015 was divided, one half jointly to William C. Campbell (born Ireland, now USA) and Satoshi Ōmura (Japan) “for their discoveries concerning a novel therapy against infections caused by roundworm parasites” and the other half to Youyou Tu (China) “for her discoveries concerning a novel therapy against Malaria”.

Youyou Tu is the first Chinese woman to win a Nobel Prize.

Diseases caused by parasites have plagued humankind for millennia and constitute a major global health problem. In particular, parasitic diseases affect the world’s poorest populations and represent a huge barrier to improving human health and wellbeing. This year’s Nobel Laureates have developed therapies that have revolutionized the treatment of some of the most devastating parasitic diseases.

William C. Campbell and Satoshi Ōmura discovered a new drug, Avermectin, the derivatives of which have radically lowered the incidence of River Blindness and Lymphatic Filariasis, as well as showing efficacy against an expanding number of other parasitic diseases. Youyou Tu discovered Artemisinin, a drug that has significantly reduced the mortality rates for patients suffering from Malaria.

These two discoveries have provided humankind with powerful new means to combat these debilitating diseases that affect hundreds of millions of people annually. The consequences in terms of improved human health and reduced suffering are immeasurable.

image of Artemisinin

via Noble Prize website

Malaria was traditionally treated by chloroquine or quinine, but with declining success. By the late 1960s, efforts to eradicate Malaria had failed and the disease was on the rise. At that time, Youyou Tu in China turned to traditional herbal medicine to tackle the challenge of developing novel Malaria therapies. From a large-scale screen of herbal remedies in Malaria-infected animals, an extract from the plant Artemisia annua emerged as an interesting candidate.

However, the results were inconsistent, so Tu revisited the ancient literature and discovered clues that guided her in her quest to successfully extract the active component from Artemisia annua. Tu was the first to show that this component, later called Artemisinin, was highly effective against the Malaria parasite, both in infected animals and in humans. Artemisinin represents a new class of antimalarial agents that rapidly kill the Malaria parasites at an early stage of their development, which explains its unprecedented potency in the treatment of severe Malaria.

Youyou Tu was born in 1930 in China and is a Chinese citizen. She graduated from the Pharmacy Department at Beijing Medical University in 1955. From 1965-1978 she was Assistant Professor at the China Academy of Traditional Chinese Medicine, from 1979-1984 Associate Professor and from 1985 Professor at the same Institute. From 2000, Tu has been Chief Professor at the China Academy of Traditional Chinese Medicine. She doesn’t have a doctorate, very rare for a Nobel Prize winner in the sciences.

Read the full press release

Related: Nobel Prize in Physiology or Medicine 2012 for Reprogramming Cells to be PluripotentNobel Prize in Physiology or Medicine 2008Parasites in the Gut Help Develop a Healthy Immune System2011 Nobel Prize in Physiology or MedicineVideo showing malaria breaking into cell

Cancer Rates Consistent Across Species Instead of Increasing Due to Body Mass

Posted on October 12, 2015  Comments (0)

It would seem sensible to think cancer should be more prevalent in species with a huge number of cells, and thus more cells to become cancerous. But cancer risk doesn’t increase in this way. This interesting, open source paper, sheds some light on what is behind this.

Solutions to Peto’s paradox revealed by mathematical modelling and cross-species cancer gene analysis

Whales have 1000-fold more cells than humans and mice have 1000-fold fewer; however, cancer risk across species does not increase with the number of somatic cells and the lifespan of the organism. This observation is known as Peto’s paradox. How much would evolution have to change the parameters of somatic evolution in order to equalize the cancer risk between species that differ by orders of magnitude in size? Analysis of previously published models of colorectal cancer suggests that a two- to three-fold decrease in the mutation rate or stem cell division rate is enough to reduce a whale’s cancer risk to that of a human. Similarly, the addition of one to two required tumour-suppressor gene mutations would also be sufficient.

We surveyed mammalian genomes and did not find a positive correlation of tumour-suppressor genes with increasing body mass and longevity. However, we found evidence of the amplification of TP53 in elephants, MAL in horses and FBXO31 in microbats, which might explain Peto’s paradox in those species. Exploring parameters that evolution may have fine-tuned in large, long-lived organisms will help guide future experiments to reveal the underlying biology responsible for Peto’s paradox and guide cancer prevention in humans.

Elephants in Kenya

Elephants in Kenya by John Hunter. See more photos from my trip to Kenya.

In another way it would make sense that large animals would have hugely increased risks of cancer. As they evolved, extremely high cancer rates would be a much bigger problem for them. Therefore it wouldn’t be surprising to find they have evolved a way of reducing cancer risks.

Despite these limitations, we found genes that have been dramatically amplified in specific mammalian genomes, the most interesting of which is the discovery of 12 TP53 copies in the genome of the African elephant. We subsequently cloned those genes and identified 19 distinct copies of TP53 in African elephants and 15–20 in Asian elephants [1]. Another potential lead for solving Peto’s paradox is MAL, which is found to have eight copies in the horse genome and two in microbat. This could be an example of convergent evolution where a large animal (horse) and a small, long-lived animal (microbat) both evolved extra copies of the same gene to overcome their increased risk of cancer. Further analysis and experimentation would need to be performed to determine the function of these copies and whether or not they provide enhanced suppression of carcinogenesis.

The researchers have found an interesting potential explanation for how that has been accomplished.

Related: The Only Known Cancerless Animal (the naked mole rat)Webcast of a T-cell Killing a Cancerous CellResearchers Find Switch That Allows Cancer Cells to SpreadCancer Vaccines

Wristband Thermometer Can Save Many Babies’ Lives

Posted on October 4, 2015  Comments (3)

As I have mentioned many times before, I really love the use of appropriate technology to make a significant contribution to our lives. It is hard to do much better than saving our babies from death.

Hypothermia and infection are among the top causes of newborn deaths for the poor around the world. Regular temperature monitoring can enable early intervention.

Bempu is a new startup based in India that is developing a wrist-band for newborns that monitors their temperature and gives an audio-alarm if the temperature is unsafe. This isn’t an Apple-watch but it is just as worthy of publicity.

Baby thermometer wristbands

These wristbands can save the lives of newborns.

The Gates Foundation, and others, have contributed money to bring this product to market.

From an article on the new wristband:

UNICEF estimates that preventing and effectively responding to hypothermia could save 18 to 42 percent of newborns who die each year in developing countries in their first month of life. That’s anywhere from between 600,000 and 1.4 million babies. And that doesn’t even account for those who survive a drop in temperature, but have developmental problems because they struggle to gain weight and fight off infection when they become too cold.

We know what the problems are, we know what to do about it and it’s not happening,” says Karsten Lunze, a doctor and expert in newborn hypothermia at Boston University. If Bempu, which is still in prototype and will likely get to market by the end of 2015, succeeds, “it would be a miraculous catalyzer that everyone has been looking for over a decade,” he says. It’s testing well so far: A prototype, used on 25 newborns this year, detected a temperature drop a full 24 hours before hospital workers noticed.

Bempu was born after Narain followed his nose to the global south at 27, where he worked as an engineering fellow at Embrace, a nonprofit that makes a cheap, portable and rechargeable incubator for newborns. He noticed something clear: No one was really watching closely. Nurses lacked thermometers; some couldn’t even read them and mothers didn’t know the difference between Celsius and Fahrenheit.

Related: Manufacturing Biological Sensors Using Silk and Looms in IndiaCheap vinegar test cut cervical cancer deaths in India; could help many poor countriesUsing Drones to Deliver Medical Supplies in Roadless AreasAppropriate Technology and Focus on Improving Lives at MITWater Wheel

Backyard Wildlife: Deer

Posted on September 27, 2015  Comments (1)

deer in woods

Deer in backyard by John Hunter – see more of my nature photos

Deer populations have been exploding across the USA in the last century. Before that deer populations had collapsed largely due to hunting. In the last 10 or 20 years populations of deer have been largely stable (though varying quite a bit by area).

The deer populations had increased (many predators were largely wiped out and with a dramatic decline in hunter) so much that more and more complaints were being made to local governments of problems with deer grazing on property and damaging cars when the cars hit deer crossing the road.

My neighborhood is urban and I have never seen deer in the neighborhood. About 5 blocks away there is a bike path with a tree lined strip of nature where I have very occasionally seen deer. The deer in the photos I imagine got here from that strip of habitat. There is a small area (next to a school which has trees that wouldn’t be so bad for a deer for 1 night). I figured the deer would leave.

But a few days later I saw new evidence of a deer eating some small trees in my backyard – though I wasn’t sure if I missed it before. Then a couple nights later I saw a deer grazing after dark in my backyard.

I have posted about other interesting wildlife in this backyard previously: Backyard Wildlife: Fox and Backyard Wildlife: Sharpshinned Hawk (see more below).

Read more

Highest Paying Fields at Mid Career in USA: Engineering, Science and Math

Posted on September 20, 2015  Comments (0)

Payscale has again provided details on average salaries by major for various fields. Once again engineering, math and science dominate. For this data they define mid-career as those with 10+ years of experience.

The top 15 bachelor degrees by mid-career salary were all from those 3 fields. And the median salary was $168,000 for petroleum engineering degrees (at the top) to $107,000 for Aerospace Engineering and Computer Science and Mathematics (tied for 14th).

The starting salaries for those with these degrees ranged from $58,000 for Actuarial Mathematics (though by mid-career salary they were in 3rd place at $119,000) to $101,000 for petroleum engineering. My guess is petroleum engineering salaries will decline from their current highs (as they have done in previous oil price busts). The second highest paying bachelor degree starting salary was for mining engineering at $71,500 – with most of the other fairly close to that amount.

Nuclear engineering pay started at a median of $68,200 before rising to the 2nd highest mid-career level of $121,000.

Payscale also provided data based on master’s degree field. Again petroleum engineering was in first place by mid-career ($173,000). Nurse anesthesia was in second at $159,000 and held the first spot for starting median salary ($139,000).

Taxation is the only filed that is obviously not STEM (science, technology, engineering and math) related which had the lowest initial median salary of $60,700 but was tied for 5th for mid career salary at $126,000. Technology management and operations research are also not STEM fields though are a bit related to the STEM area.

PhD degree’s with the highest mid-career median earning are again all STEM fields. Economics is one many people probably don’t think of as STEM but it is (as a social science) and really it is largely mathematics at this point.

Many of the PhD starting salaries are at $100,000 (or close). The disciplines with the highest mid-career median salaries are: Electrical and Computer Engineering $142,000; Computer Engineering $139,000; Chemical Engineering $138,000; Biomedical Engineering, $137,000; and Economics $134,000.

Related: No Surprise, Engineering Graduates Pay Continue to Reign Supreme (2012)The Time to Payback the Investment in a College Education in the USA Today is Nearly as Low as Ever, Surprisingly (2014)Engineering Again Dominates The Highest Paying College Degree Programs (2011)Earnings by College Major” Engineers and Scientists at the Top (2013)Looking at the Value of Different College Degrees

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