Posts about open access paper

Healthy Living Greatly Reduces Likelihood of Dying from Cancer

Lifestyle choices can greatly reduce the incidence and death rates from cancer. 4 factors can reduce the incidence of cancer by up to 40% and death rate by 50%: don’t smoke, don’t drink alcohol in excess, maintain a BMI between 18.5 and 27.5, and exercising at a moderate intensity for at least 150 minutes or at a vigorous intensity for at least 75 minutes every week.

Preventable Incidence and Mortality of Carcinoma Associated With Lifestyle Factors Among White Adults in the United States

A substantial cancer burden may be prevented through lifestyle modification. Primary prevention should remain a priority for cancer control.

Cancer is the second leading cause of death in the United States, with 1.6 million new cancer cases and 0.6 million cancer deaths projected to occur in 2016.1 The cancer mortality rate, age-standardized to the 2000 US standard population, decreased from 199 to 163 per 100 000 between 1969 and 2013.2 However, this decline (17.9%) has been modest compared with the dramatic decrease in heart disease mortality (67.5%) during the same period, highlighting the need for further efforts in cancer prevention and treatment.

The study reviewed previous studies and the makeup of the previous studies and available statistics. As they state in the paper: “Because our cohorts’ participants were predominantly whites, to avoid any influence of different racial distributions on the comparison with the general population, we only included whites in the analysis.” They also excluded about 10% of cancers that are believed to have strong environmental factors.

Table Showing a Comparison of Lifestyle Factors in the Low- and High-Risk Groups

In the 2 cohort studies of US white individuals, we found that overall, 20% to 40% of carcinoma cases and about half of carcinoma deaths can be potentially prevented through lifestyle modification. Not surprisingly, these figures increased to 40% to 70% when assessed with regard to the broader US population of whites, which has a much worse lifestyle pattern than our cohorts.

Notably, approximately 80% to 90% of lung cancer deaths could be avoided if Americans adopted the lifestyle of the low-risk group, mainly by quitting smoking. For other cancers, from 10% to 70% of deaths could be prevented. These results provide strong support for the importance of environmental factors in cancer risk and reinforce the enormous potential of primary prevention for cancer control.

Related: A Healthy Lifestyle is More About Health Care than the Sickness Management That We Call Health Care IsBetter Health Through: Exercise, Not Smoking, Low Weight, Healthy Diet and Low Alcohol Intake (2013)Exercise Is Really Really Good for YouPhysical Activity for Adults: Inactivity Leads to 5.3 Million Early Deaths a Year (2012)

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

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

Lactic Acid Bacteria in Bees Counteracted Antibiotic-Resistant MRSA in Lab Experiments

13 lactic acid bacteria found in the honey stomach of bees have shown promising results as an antibiotic treatment in a series of studies at Lund University in Sweden (Open access paper: Lactic acid bacterial symbionts in honeybees – an unknown key to honey’s antimicrobial and therapeutic activities). The group of bacteria counteracted antibiotic-resistant MRSA in lab experiments. The bacteria, mixed into honey, has healed horses with persistent wounds. The formula has also previously been shown to protect against bee colony collapse.

photo of a bee on a flower

Photo by Justin Hunter

Raw honey has been used against infections for millennia, before honey – as we now know it – was manufactured and sold in stores. So what is the key to its’ antimicrobial properties? Researchers at Lund University in Sweden have identified a unique group of 13 lactic acid bacteria found in fresh honey, from the honey stomach of bees. The bacteria produce a myriad of active antimicrobial compounds.

These lactic acid bacteria have now been tested on severe human wound pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and vancomycin-resistant Enterococcus (VRE), among others. When the lactic acid bacteria were applied to the pathogens in the laboratory, it counteracted all of them.

While the effect on human bacteria has only been tested in a lab environment thus far, the lactic acid bacteria has been applied directly to horses with persistent wounds. The LAB was mixed with honey and applied to ten horses; where the owners had tried several other methods to no avail. All of the horses’ wounds were healed by the mixture.

The researchers believe the secret to the strong results lie in the broad spectrum of active substances involved.

“Antibiotics are mostly one active substance, effective against only a narrow spectrum of bacteria. When used alive, these 13 lactic acid bacteria produce the right kind of antimicrobial compounds as needed, depending on the threat. It seems to have worked well for millions of years of protecting bees’ health and honey against other harmful microorganisms. However, since store-bought honey doesn’t contain the living lactic acid bacteria, many of its unique properties have been lost in recent times”, explains Tobias Olofsson.

This is a very cool: “When used alive, these 13 lactic acid bacteria produce the right kind of antimicrobial compounds as needed, depending on the threat.” As is the note that store bought honey doesn’t contain the living bacteria. My guess is some honey bought directly from farmers or bee-keepers, at farmer’s markets may well still have those live bacteria – but I am just guessing I may be wrong.

The next step is further studies to investigate wider clinical use against topical human infections as well as on animals.

The findings have implications for developing countries, where fresh honey is easily available, but also for Western countries where antibiotic resistance is seriously increasing.

Related: People are Superorganisms With Microbiomes of Thousands of SpeciesThe Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria CellsOur Dangerous Antibiotic Practices Carry Great RisksPotential Antibiotic Alternative to Treat Infection Without Resistance
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Crows can Perform as Well as 7 to 10-year-olds on cause-and-effect Water Displacement Tasks

In Aesop’s fable about the crow and the pitcher, a thirsty bird happens upon a vessel of water, but when he tries to drink from it, he finds the water level out of his reach. Not strong enough to knock over the pitcher, the bird drops pebbles into it — one at a time — until the water level rises enough for him to drink his fill.

Highlighting the value of ingenuity, the fable demonstrates that cognitive ability can often be more effective than brute force. It also characterizes crows as pretty resourceful problem solvers. New research conducted by UC Santa Barbara’s Corina Logan, with her collaborators at the University of Auckland in New Zealand, proves the birds’ intellectual prowess may be more fact than fiction. Her findings, supported by the National Geographic Society/Waitt Grants Program, appear today in the scientific journal PLOS ONE: Modifications to the Aesop’s Fable Paradigm Change New Caledonian Crow Performances.

photo of Corina Logan

Researcher Corina Logan with a great-tailed grackle and a night heron at the Santa Barbara Zoo. The zoo is one of the sites where Logan is gathering data to compare and contrast the cognitive abilities of grackles and New Caledonian crows.
Photo Credit: Sonia Fernandez

Logan is lead author of the paper, which examines causal cognition using a water displacement paradigm. “We showed that crows can discriminate between different volumes of water and that they can pass a modified test that so far only 7- to 10-year-old children have been able to complete successfully. We provide the strongest evidence so far that the birds attend to cause-and-effect relationships by choosing options that displace more water.”

Logan, a junior research fellow at UCSB’s SAGE Center for the Study of the Mind, worked with New Caledonian crows in a set of small aviaries in New Caledonia run by the University of Auckland. “We caught the crows in the wild and brought them into the aviaries, where they habituated in about five days,” she said. Keeping families together, they housed the birds in separate areas of the aviaries for three to five months before releasing them back to the wild.

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Goats Excel at Learning and Remembering a Complex Tasks

I like research showing animals using intelligence that seems advanced, for example: Crow Using a Sequence of Three ToolsInsightful Problem Solving in an Asian ElephantBird-brains smarter than your average apeTropical Lizards Can Solve Novel Problems and Remember the SolutionsPigeon Solves Box and Banana Problem.

I also like open access science, and this has both: Goats excel at learning and remembering a highly novel cognitive task

The majority of trained goats (9/12) successfully learned the task quickly; on average, within 12 trials. After intervals of up to 10 months, they solved the task within two minutes, indicating excellent long-term memory. The goats did not learn the task faster after observing a demonstrator than if they did not have that opportunity. This indicates that they learned through individual rather than social learning.”

The individual learning abilities and long-term memory of goats highlighted in our study suggest that domestication has not affected goat physical cognition. However, these cognitive abilities contrast with the apparent lack of social learning, suggesting that relatively intelligent species do not always preferentially learn socially. We propose that goat cognition, and maybe more generally ungulate cognition, is mainly driven by the need to forage efficiently in harsh environments and feed on plants that are difficult to access and to process, more than by the computational demands of sociality. Our results could also explain why goats are so successful at colonizing new environments.

The experiment was done with domesticated goats. I also learned this from the article, which I didn’t know before:

Domestication is known to strongly affect brain size. Consistent reductions in brain size relative to body size, as well as in brain size parts, have occurred in many domestic species.

Related: Orangutan Attempts to Hunt Fish with SpearFriday Fun: Bird Using Bait to FishPhoto of Fish Using a Rock to Open a Clam

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Better Health Through: Exercise, Not Smoking, Low Weight, Healthy Diet and Low Alcohol Intake

These 5 activities/state reduce the risk of chronic diseases: regular exercise, not smoking, healthy bodyweight, healthy diet and low alcohol intake. How these were defined

  • not smoking
  • body mass index (BMI): 18 to under 25
  • diet: target was to be 5 portions of fruit and/or vegetables a day, but since almost no one meet that target they reduced the acceptable rate to 3 as accepted as ‘healthy.” Also a diet with less than 30% of calories from fat was required.
  • physical activity: walking two or more miles to work each day, or cycling ten or more miles to work each day, or ‘vigorous’ exercise described as a regular habit
  • alcohol: three or fewer units per day, with abstinence not treated as a healthy behaviour.

Healthy Lifestyles Reduce the Incidence of Chronic Diseases and Dementia: Evidence from the Caerphilly Cohort Study (PLoS open science publication).

The numbers of men judged to be following a healthy lifestyle were as follows: 179 (8%) followed none of the five behaviours, 702 (31%) followed one behaviour, 814 (36%) followed two, 429 (19%) followed three, 111 (5%) followed four or five behaviours and only two (0.1%) followed all five behaviors.

Within a representative sample of middle-aged men, the following of increasing numbers of healthy behaviours was associated with increasing reductions in several important chronic diseases and mortality: an estimated 50% reduction in diabetes, 50% in vascular disease and 60% for all-cause mortality. These results therefore confirm previous studies and provide further data on the association of lifestyle with cognitive impairment and dementia, with a reduction of about 60% in cognitive impairment and about the same in dementia. These reductions, and especially those in cognitive function, are of enormous importance in an ageing population.

Healthy habits reduce dementia risk (Cardiff University press release):

The people who consistently followed four or five of these behaviors exp
experienced a 60 per cent decline in dementia and cognitive decline – with exercise being the strongest mitigating factor – as well as 70 per cent fewer instances of diabetes, heart disease and stroke, compared with people who followed none.

Principle Investigator Professor Peter Elwood from Cardiff University’s School of Medicine. “What the research shows is that following a healthy lifestyle confers surprisingly large benefits to health – healthy behaviours have a far more beneficial effect than any medical treatment or preventative procedure.

Christopher Allen, Senior Cardiac Nurse at the British Heart Foundation, which part-funded the study, said:

“The results of this study overwhelmingly support the notion that adopting a healthy lifestyle reduces your risk of cardiovascular disease and dementia.

Related: Examining the Scientific Basis Around Exercise and Diet ClaimsHealthy Diet, Healthy Living, Healthy WeightStudy Finds Obesity as Teen as Deadly as SmokingPhysical Activity for Adults: Inactivity Leads to 5.3 Million Early Deaths a YearToday, Most Deaths Caused by Lifetime of Action or Inaction

Another Bee Study Finds CCD is Likely Due to Combination of Factors Including Pesticides

Abstract of open access science paper funded by the United States Department of Agriculture (USDA) Crop Pollination Exposes Honey Bees to Pesticides Which Alters Their Susceptibility to the Gut Pathogen Nosema ceranae:

Recent declines in honey bee populations and increasing demand for insect-pollinated crops raise concerns about pollinator shortages. Pesticide exposure and pathogens may interact to have strong negative effects on managed honey bee colonies. Such findings are of great concern given the large numbers and high levels of pesticides found in honey bee colonies. Thus it is crucial to determine how field-relevant combinations and loads of pesticides affect bee health.

We collected pollen from bee hives in seven major crops to determine 1) what types of pesticides bees are exposed to when rented for pollination of various crops and 2) how field-relevant pesticide blends affect bees’ susceptibility to the gut parasite Nosema ceranae. Our samples represent pollen collected by foragers for use by the colony, and do not necessarily indicate foragers’ roles as pollinators. In blueberry, cranberry, cucumber, pumpkin and watermelon bees collected pollen almost exclusively from weeds and wildflowers during our sampling.

Thus more attention must be paid to how honey bees are exposed to pesticides outside of the field in which they are placed. We detected 35 different pesticides in the sampled pollen, and found high fungicide loads. The insecticides esfenvalerate and phosmet were at a concentration higher than their median lethal dose in at least one pollen sample. While fungicides are typically seen as fairly safe for honey bees, we found an increased probability of Nosema infection in bees that consumed pollen with a higher fungicide load.

Our results highlight a need for research on sub-lethal effects of fungicides and other chemicals that bees placed in an agricultural setting are exposed to.

The attempts to discover the main causes of bee colony deaths and find solutions continues to prove difficult years after the problems became major. The complex interaction of many variables makes it difficult. And special interest groups pushing pesticides and the like, which have seemed to be major contributors to the problem for years, make it even more difficult (by preventing restrictions on potentially damaging pesticide use).

The challenges in determining what is killing bees are similar to the challenges of discovering what practices are damaging human health. The success of studying complex biological interactions (to discover threats to human health) is extremely limited. I am concerned we are far too caviler about using large numbers of interventions (drugs, pesticides, massive antibiotics use in factory farms, pollution…).

Related: Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep DyingGermany Bans Chemicals Linked to Bee Deaths (2008)Virus Found to be One Likely Factor in Bee Colony Colapse Disorder (2007)Study of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear

Huge Human Population Boom 40,000 to 50,000 Years Ago

Interesting open access paper on looking at the Y-chromosome to explore our ancestry: A calibrated human Y-chromosomal phylogeny based on resequencing. I can’t understand all the details but the basic idea isn’t that complicated. It is interesting to see these details as are the conclusions that can be drawn: that we had a big explosion of human population o 41,000–52,000 years ago.

This population explosion occurred, between the first expansion of modern humans out of Africa 60,000 to 70,000 years ago and the Neolithic expansions of people in several parts of the world starting 10,000 years ago.

“We think this second, previously unknown population boom, may have occurred as humans adapted to their new environment after the first out-of-Africa expansion,” says Dr Qasim Ayub, lead author from the Wellcome Trust Sanger institute. “We think that when humans moved from the horn of Africa to Asia, Australia and eventually Europe, they remained in small groups by the coasts. It took them tens of thousands of years to adapt to the mountainous, forested surroundings on the inner continents. However, once their genetic makeup was suited to these new environments, the population increased extremely rapidly as the groups travelled inland and took advantage of the abundance of space and food.”

The work highlights how it is now possible to obtain new biological insights from existing DNA sequencing data sets, and the value of sharing data. The majority of the DNA information used for this study was obtained from freely-available online data-sets.

This is the first time researchers have used the information from large-scale DNA sequencing to create an accurate family tree of the Y chromosome, from which the inferences about human population history could be made.

Full press release

Related: Laser Tool Creates “blueprints” of Archeology SitesHHMI on Science 2.0: Information RevolutionScientists crack 40-year-old DNA puzzle

Should Giant Viruses Be Included on the Tree of Life?

A new study of giant viruses supports the idea that viruses are ancient living organisms and not inanimate molecular remnants. The study may reshape the universal family tree, adding a fourth major branch to the three that most scientists agree represent the fundamental domains of life. But I am not sure that makes sense. The reason given for viruses not being “life” is that they cannot reproduce themselves – they hijack living cells to reproduce. The research in the past history of viruses as they evolved into current viruses is interesting but I don’t see the reason to classify current viruses as life.

The researchers used a relatively new method to peer into the distant past. Rather than comparing genetic sequences, which are unstable and change rapidly over time, they looked for evidence of past events in the three-dimensional, structural domains of proteins. These structural motifs, called folds, are relatively stable molecular fossils that – like the fossils of human or animal bones – offer clues to ancient evolutionary events, said University of Illinois crop sciences and Institute for Genomic Biology professor Gustavo Caetano-Anollés, who led the analysis.

“Just like paleontologists, we look at the parts of the system and how they change over time,” Caetano-Anollés said. Some protein folds appear only in one group or in a subset of organisms, he said, while others are common to all organisms studied so far.

“We make a very basic assumption that structures that appear more often and in more groups are the most ancient structures,” he said.

Most efforts to document the relatedness of all living things have left viruses out of the equation, Caetano-Anollés said.

“We’ve always been looking at the Last Universal Common Ancestor by comparing cells,” he said. “We never added viruses. So we put viruses in the mix to see where these viruses came from.”

The researchers conducted a census of all the protein folds occurring in more than 1,000 organisms representing bacteria, viruses, the microbes known as archaea, and all other living things. The researchers included giant viruses because these viruses are large and complex, with genomes that rival – and in some cases exceed – the genetic endowments of the simplest bacteria, Caetano-Anollés said.

Related: Plants, Unikonts, Excavates and SARsBacteriophages: The Most Common Life-Like Form on Earth8 Percent of the Human Genome is Old Virus GenesMicrobes Retroviruses

Open access paper: Giant Viruses Coexisted With the Cellular Ancestors and Represent a Distinct Supergroup Along With Superkingdoms Archaea, Bacteria and Eukarya

The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

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A single spot in the Sahara that provides huge amounts of nutrients to the Amazon

The Bodélé depression: a single spot in the Sahara that provides most of the mineral dust to the Amazon forest

About 40 million tons of dust are transported annually from the Sahara to the Amazon basin. Saharan dust has been proposed to be the main mineral source that fertilizes the Amazon basin, generating a dependence of the health and productivity of the rain forest on dust supply from the Sahara. Here we show that about half of the annual dust supply to the Amazon basin is emitted from a single source: the Bodélé depression located northeast of Lake Chad, approximately 0.5% of the size of the Amazon or 0.2% of the Sahara. Placed in a narrow path between two mountain chains that direct and accelerate the surface winds over the depression, the Bodélé emits dust on 40% of the winter days, averaging more than 0.7 million tons of dust per day.

Even understanding how connected the global ecosystem is, research like this provides amazing reminders of those connections.

Related: The Amazon Rainforest Would Not Be Without Saharan Dust (podcast interview)Ancient Whale Uncovered in Egyptian DesertNigersaurusThe Sahara Wasn’t Always a DesertElusive Saharan cheetah and Sandcat

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