The scientific idea that is most ready for retirement is the scientific method itself. More precisely it is the idea that there would be only one scientific method, one exclusive way of obtaining scientific results. The problem is that the traditional scientific method as an exclusive approach is not adequate to the new situations of contemporary science like big data, crowdsourcing, and synthetic biology.
Hypothesis-testing through observation, measurement, and experimentation made sense in the past when obtaining information was scarce and costly, but this is no longer the case. In recent decades, we have already been adapting to a new era of information abundance that has facilitated experimental design and iteration. One result is that there is now a field of computational science alongside nearly every discipline, for example computational biology and digital manuscript archiving. Information abundance and computational advance has promulgated the evolution of a scientific model that is distinct from the traditional scientific method, and three emerging areas are advancing it even more.
Big data, the creation and use of large and complex cloud-based data sets, is one pervasive trend that is reshaping the conduct of science. The scale is immense: organizations routinely process millions of transactions per hour into hundred-petabyte databases. Worldwide annual data creation is currently doubling and estimated to reach 8 zettabytes in 2015.
University of Houston researchers have developed a concept for MRI-powered millimeter-size “millirobots” that could one day perform unprecedented minimally invasive medical treatments.
This technology could be used to treat hydrocephalus, for example. Current treatments require drilling through the skull to implant pressure-relieving shunts, said Aaron T. Becker, assistant professor of electrical and computer engineering at the University of Houston.
But MRI scanners alone don’t produce enough force to pierce tissues (or insert needles). So the researchers drew upon the principle of the “Gauss gun.”
A team from China grabbed the headlines last month when it announced it had edited DNA in the nucleus of human embryos. Whatever the ethics of such research, the breakthrough raises the question of just how far we will take tampering with our genetic make-up?
The Chinese team’s work was done using a gene-editing technique called CRISPR (pronounced “crisper”) and the results were not spectacular – only four of the 86 eggs injected were successfully modified.
Nonetheless, Harvard Professor George Church believes that within five to seven years it will be possible to snip out and replace stretches of DNA to genetically engineer babies.
But should this kind of research be done at all? And as parents look to guarantee a better future for their children, what should we consider acceptable?
Treating gum disease can reduce symptoms of prostate inflammation, called prostatitis, report researchers.
Previous studies have found a link between gum disease and prostatitis, a disease that inflames the gland that produces semen. Inflammation can make urination difficult.
“This study shows that if we treat the gum disease, it can improve the symptoms of prostatitis and the quality of life for those who have the disease,” says Nabil Bissada, chair of Case Western Reserve’s periodontics department and the new study’s corresponding author.
Bissada explains that gum disease affects the mouth, but is also a system-wide condition that can cause inflammation in various parts of the body. The dental school has previously found a link between gum disease and fetal deaths, rheumatoid arthritis, and heart disease.
Researchers studied 27 men, 21 years old and older. Each had a needle biopsy within the past year that confirmed inflammation of the prostate gland, and a blood test that showed elevated prostate specific antigen (PSA) levels—possible signs of inflammation and cancer.
A genetically engineered virus has ‘cured’ patients of cancer for the first time in a breakthrough which raises hopes of an end to chemotherapy.
In a worldwide study which was led by the Institute of Cancer Research in the UK, scientists showed that the new treatment allowed some patients with skin cancer to live for more than three years – the benchmark many oncologists use to define a cure.
The therapy – called T-VEC - works by infecting and killing cancer cells while also sparking the immune system into action against tumours.
Currently most cancers are treated with using invasive chemotherapy, radiotherapy and surgery, all of which carry the risk of further harm.
The new therapy has far fewer side effects and does not damage healthy tissue or cells.
While the breakthrough came in skin cancer patients, scientists said it raises hopes that the same process could be used for other cancers.
Charities said the development was ‘exciting’ and offered new hope to many patients.
“Patients showing responses beyond three years is something that up until now, we could only have imagined,” said Gillian Nuttall, Founder of Melanoma UK.
Despite extraordinary advances in new drugs and biotechnology, cancer is still one of the leading causes of death worldwide.
In many cases, the problem lies not with the drugs but rather the difficulty in successfully delivering them to the site of a tumour. In healthy tissue there is a regular structure of blood vessels supplying oxygen and nutrients to cells, which divide and grow at a steady rate. In cancerous tumours, however, cells divide and grow in an unregulated way, producing a chaotic vessel structure and regions of tissue with little or no blood supply.
This means when drugs are ingested or injected into the blood stream, they don’t reach all parts of the tumour and there is a high risk of cancer recurring after treatment. On top of this, the pressure inside many tumours prevents a drug from being absorbed from the blood, meaning only a very small fraction of it is actually delivered. The rest of the drug circulates around the body and is eventually absorbed by healthy tissue, often leading to intolerable side effects.
One of the major goals of the research being carried out in the Oxford Institute of Biomedical Engineering (IBME) is to develop new methods for delivering anti-cancer drugs that overcome these barriers. While engineers are perhaps more commonly thought of in the context of large construction projects, we are using precisely the same combination of applied science and problem solving.
Last year Tony Perry made mice that would have been brown-furred grow up white instead. That Perry, a molecular embryologist at the University of Bath, tweaked their coat colour isn’t new – scientists have been making so-called knock-out mice, in which certain genes are disabled, since the technique was invented in 1989. It is a long and cumbersome procedure that involves combining pieces of DNA in embryonic stem cells and mouse breeding.
But Perry, who published his study in December, didn’t use this method. Instead he used a new genome-editing technology that has been taking the scientific world by storm since it was first developed from the bacterial immune system in 2012, and shown to work in human cells in 2013.
The powerful tool, known as Crispr, allows the precise and easy manipulation of the DNA in the nucleus of any cell. Make the manipulations in sperm, egg or a one-cell embryo, which is just about to start replicating its DNA, and they can become permanently sealed in the so-called germ line, to be inherited by future generations. Using the procedure on the germ line, Perry inactivated a key gene for mouse coat colour.
But Perry’s work added a unique flourish. He did the editing not in a one-cell mouse embryo – which is how most animal germ-line editing by Crispr has been done to date – but earlier, during the process of fertilisation, by injecting the Crispr components and the mouse sperm into the mouse egg at the same time. It is the same technique – intracytoplasmic sperm injection (ICSI) – widely used in IVF. And it worked. “This or analogous approaches may one day enable human genome targeting or editing during very early development,” notes the paper published in the journal Scientific Reports. If human germ-line editing were ever to be used clinically, incorporating Crispr into the ICSI phase of IVF is how it might be.
Mood disorders such as depression are devastating to sufferers, and hugely costly to treat. The most severe form of depression, often called clinical depression or major depressive disorder (MDD), increases the person’s likelihood of suicide and contributes significantly to a person’s disability-adjusted life years (DALYs), a measure of quality of life taking into account periods of incapacity. The healthcare burden of MDD is large in most countries, especially when the person requires a stay in hospital. Putting these factors together, it’s clear we need to develop effective treatments to combat depression.
The mechanisms of depressive disorders are not well understood, and it seems likely that there is no single cause. Most modern therapies use drugs that target neurotransmitters – the chemicals that carry signals between neurons. For example, the class of drugs known as SSRIs, or selective serotonin reuptake inhibitors, prevent the neurotransmitter serotonin from being reabsorbed by a neuron; this means that more serotonin is available to wash around between the nerve cells, and is more likely to activate cells in the brain networks that area affected in MDD.
With over 584,000 deaths due to malaria each year, fighting the mosquito-transmitted disease is a major world health priority. Now, reports Popular Science’s Alexandra Ossola, there’s a new ally in the fight against malaria — Viagra.
A new study shows that Viagra can increase the spleen’s ability to filter malaria from the blood. Ossola explains that once Plasmodium falciparum, the parasite that causes malaria, hits the human body, it “spends one very important [developmental] stage in human red blood cells found in bone marrow.” These blood cells are soft and malleable, which allows them to elude the blood-filtering spleen, which looks for firm or dead blood cells instead.
By bypassing the spleen’s filtering abilities, malaria is able to spread through the blood. But researchers were able to put a stop to that process with Viagra when they learned that the enzyme inhibitor that gives the pill its popular effects stiffens infected blood cells, too. In the lab, they used an artificial spleen to filter infected, Viagra-stiffened blood cells — and learned that they were “less likely to circulate through the spleen.”
This isn’t the first time Viagra has been found to have effects that have nothing to do with the bedroom. For example, doctors now use the drug to treat pulmonary arterial hypertension (high blood pressure between the heart and the lungs) and altitude sickness.
Will malaria eventually make its way to that list? Researchers hope so. “This discovery could help find new ways to stop the spread of malaria in a population,” the team said in a release.
People with tinnitus “hear” ringing, buzzing, or hissing in their ears much like an amputee might “feel” pain in a missing limb. While exposure to loud noise may contribute, some cases have no apparent trigger.
Though it’s not known yet exactly where and how tinnitus occurs in the brain, says Richard Salvi, director of the Center for Hearing and Deafness at the University at Buffalo, functional MRI studies with rats show the abnormal activity underlying tinnitus and a related condition called hyperacusis isn’t confined to a specific brain location, but actually involves a neural network.
Salvi and colleagues induced tinnitus in rats by administering the active ingredient in aspirin, which has long been known to produce tinnitus and hyperacusis symptoms in humans.
“Certain brain regions become very active once tinnitus is induced, much more so than it is for an animal with normal hearing,” says Salvi, one of the authors of the study published in the journal eLife. “Even though high-dose aspirin induces a hearing loss and less information is being sent from the ear to the brain as a result, the brain responds with greater activity. “It’s paradoxical, like a car getting better gas mileage with a less efficient engine.”
The chances of having a heart attack, stroke or dying young may be hidden in the palm of the hand, a study suggests.
A trial on nearly 140,000 people in 14 countries, published in the Lancet, suggests grip strength is better than blood pressure at predicting risk.
The international research team said it would be a "simple, inexpensive" tool for doctors.
Experts argued the link between grip and the heart was unclear and needed more study.
The maximum crushing force you can exert in your grip naturally declines with age.
But those whose grip strength declines fastest may be at greater risk of health problems, the study suggests.
Women in their mid-20s have a grip strength about 75lb (34kg), which falls to 53lb in a 70-year-old. The equivalent figures for men are 119lb (54kg) falling to 84lb.
The huge trial, in 14 countries, showed each 11lb (5kg) reduction in grip strength increased the odds of an early death by 16%.
The odds of a fatal heart problem increased by 17% and a stroke by 9%.
Doctors currently calculate the chances of a heart attack or stroke by filling out a questionnaire with the patient by assessing age, whether they smoke, obesity, cholesterol levels, blood pressure where they live and family history.
The researchers argue grip strength makes more accurate predictions than blood pressure alone and could be a new tool for assessing risk.
Cuba has for several years had a promising therapeutic vaccine against lung cancer. The 55-year trade embargo led by the US made sure that Cuba was mostly where it stayed. Until—maybe—now.
The Obama administration has, of course, been trying to normalize relations with the island nation. And last month, during New York Gov. Andrew Cuomo’s visit to Havana, Roswell Park Cancer Institute finalized an agreement with Cuba’s Center for Molecular Immunology to develop a lung cancer vaccine and begin clinical trials in the US. Essentially, US researchers will bring the Cimavax vaccine stateside and get on track for approval by the Food and Drug Administration.
Research into the underlying causes of a genetic disorder that causes premature aging and death has revealed a key driver of aging in all people. Better yet, this mechanism is reversible – and with it, perhaps, scientists may be able to slow or reverse the aging process.
People with Werner syndrome age faster than normal because of a genetic mutation that disrupts normal DNA cell processes. It affects around one in every 200,000 people in the United States, with sufferers plagued by early-onset age-related diseases, such as cancer, cataracts, type 2 diabetes, osteoporosis, skin ulcers, and more.
It was previously known Werner syndrome is caused by a mutation to the Werner syndrome RecQ helicase-like gene (WRN for short), and that the normal form of the protein is responsible for maintaining the structure and integrity of a person's DNA. However, it was unclear how this happened.
Scientists at the Salk Institute for Biological Studies, who worked in collaboration with researchers at the Chinese Academy of Science, now have a possible answer. They found a link between the WRN gene and heterochromatin, which is a small, tightly-packed bundle of DNA found in irregular patches inside a cell's nucleus. This bundling serves as a kind of cell switchboard, regulating the complex molecular machinery.
A group of drugs being tested for cancer could also be used to treat spinal cord injuries, a study in mice suggests.
Mice treated with cancer drugs called nutlins recovered much more movement than those left untreated.
The Imperial College London researchers said the drugs should now be tested in rats and could be tested in human patients within 10 years.
There are currently no proven effective treatments for spinal cord injuries.
Such injuries can affect patients' ability to feel or move parts of their body below the injury.
The damage is often permanent because it is very difficult to make spinal cord nerves regrow. The study, published in the journal Brain, used drugs which have been found to be safe in early cancer trials.
MIT researchers have found they were able to reactivate memories in mice that could not otherwise be retrieved, using optogenetics — in which proteins are added to neurons to allow them to be activated with light.
The breakthrough finding, in a paper published Thursday (May 28) in the journal Science, appears to answer a longstanding question in neuroscience regarding amnesia.
Damaged or blocked memory?
Neuroscience researchers have for many years debated whether retrograde amnesia — which follows traumatic injury, stress, or diseases such as Alzheimer’s — is caused by damage to specific brain cells, meaning a memory cannot be stored, or if access to that memory is somehow blocked, preventing its recall.
The answer, according to Susumu Tonegawa, the Picower Professor in MIT’s Department of Biology and director of the RIKEN-MIT Center at the Picower Institute for Learning and Memory: “Amnesia is a problem of retrieval impairment.”
Memory researchers have previously speculated that somewhere in the brain network is a population of neurons that are activated during the process of acquiring a memory, causing enduring physical or chemical changes.
If these groups of neurons are subsequently reactivated by a trigger such as a particular sight or smell, for example, the entire memory is recalled. These neurons are known as “memory engram cells.”
Alzheimer’s disease may have evolved alongside human intelligence, researchers report in a paper posted this month on BioRxiv.
The study finds evidence that 50,000 to 200,000 years ago, natural selection drove changes in six genes involved in brain development. This may have helped to increase the connectivity of neurons, making modern humans smarter as they evolved from their hominin ancestors. But that new intellectual capacity was not without cost: the same genes are implicated in Alzheimer's disease.
Kun Tang, a population geneticist at the Shanghai Institutes for Biological Sciences in China who led the research, speculates that the memory disorder developed as ageing brains struggled with new metabolic demands imposed by increasing intelligence. Humans are the only species known to develop Alzheimer's; the disease is absent even in closely related primate species such as chimpanzees.
Tang and his colleagues searched modern human DNA for evidence of this ancient evolution. They examined the genomes of 90 people with African, Asian or European ancestry, looking for patterns of variation driven by changes in population size and natural selection.
Stem-cell scientists at McMaster University have developed a way to directly convert adult human blood cells to sensory neurons, providing the first objective measure of how patients may feel things like pain, temperature, and pressure, the researchers reveal in an open-access paper in the journal Cell Reports.
Currently, scientists and physicians have a limited understanding of the complex issue of pain and how to treat it. “The problem is that unlike blood, a skin sample or even a tissue biopsy, you can’t take a piece of a patient’s neural system,” said Mick Bhatia, director of the McMaster Stem Cell and Cancer Research Institute and research team leader. “It runs like complex wiring throughout the body and portions cannot be sampled for study.
“Now we can take easy to obtain blood samples, and make the main cell types of neurological systems in a dish that is specialized for each patient,” said Bhatia. “We can actually take a patient’s blood sample, as routinely performed in a doctor’s office, and with it we can produce one million sensory neurons, [which] make up the peripheral nerves. We can also make central nervous system cells.”
More than a quarter of a middle-aged person's skin may have already made the first steps towards cancer, a study suggests.
Analysis of samples from 55- to 73-year-olds found more than 100 DNA mutations linked to cancer in every 1 sq cm (0.1 sq in) of skin.
The team, at the Sanger Institute, near Cambridge, said the results were "surprising".
Experts said prevention was the best defence against damage from the Sun.
Skin cancer is one of the most common cancers.
Ultraviolet-radiation from sunlight bombards our skin and transforms it from healthy to cancerous tissue. Seeds of cancer
Many of the mutations that culminate in skin cancer are already known, but the team wanted to know when they first started to appear.
The researchers analysed excess skin that had been removed from the eyelids of four patients.
They then drilled down deeply into the skin's DNA to discover the very first steps being taken on the journey to cancer.
Dr Peter Campbell, the head of cancer genetics at Sanger, told the BBC News website: "The most surprising thing is just the scale, that a quarter to a third of cells had these cancerous mutations is way higher than we'd expect, but these cells are functioning normally."
Does the world really need men? It has been suggested that, in the age of cloning – and with enough sperm banks around to populate several future generations – the question is legitimate. However, new research suggests that the reason that we need two sexes is because it improves the overall genetic quality of a species and reduces the risk of population extinction.
The question of why sex is so widespread across nature has intrigued and puzzled scientists for a very long time. From a biological perspective, the purpose of life is to pass on your genes to the next generation. Asexual organisms, such as bacteria, do this simply by duplicating themselves. The offspring is an identical copy of the parent, which passes on all its genes.
Sexual organisms, however, need a partner to reproduce. Sexual species have two sexes, but only one of these can bear young. This means that sexual populations can only grow half as fast as asexual populations. Sex is also inefficient for the reason that you need to find a mate, which takes time and energy. Overall, life would be a lot simpler if we could just split in two to reproduce.
So why did sex evolve? The explanation may lie in mutations. Mutations are typos that occur as DNA is copied. The result is that we all have new variants of DNA that our parents don’t have. Most mutations have no effect, but some can be useful, and help an organism to survive. Other mutations, however, result in a loss of function in the gene they affect.
When Elizabeth Wright smacks her right leg on a table, she says “ow.” That’s only interesting if you know one more thing: that her right leg is made out of carbon fiber and metal. It’s also part of her. “It is my right leg, just as my left leg is my left leg, and just as your right leg is your right leg.”
Wright was born with something called congenital limb deficiency—neither her right arm or right leg grew to their full length in the womb. At 2 years old, she was fitted with a prosthetic leg, something she describes as “a revelation.” Around the time she was 6 years old the doctors decided it was time for her to try a prosthetic arm. That didn’t go as well. “This was in the 80s,” Wright says, “before the fancy hands you can use to pick up eggs and not break them. The arm that I got it was purely for aesthetic reasons, it just hung there like some kind of weird dead arm, and I couldn’t do anything with it. I could actually do less. So I think it lasted two or three days and then it got relegated to the cupboard. I refused to wear it.” And it stayed there. Today, Wright still uses a prosthetic leg, one that is wholly hers, entirely a part of her identity, and she still rejects the use of a prosthetic arm. She says she’s learned how to do things without it.
The most detailed study to date of skin wound healing, conducted by University of Manchester scientists with 40 volunteers, has provided new evidence that electrical stimulation accelerates wound healing.
In the new research, half-centimeter harmless wounds were created on each upper arm of the volunteers. One wound was left to heal normally, while the other was treated with electrical pulses over a period of two weeks. The pulses stimulated angiogenesis — the process by which new blood vessels form — increasing blood flow to the damaged area and resulting in wounds healing significantly faster.
A multi-year study led by researchers from the Simons Center for Data Analysis (SCDA) and major universities and medical schools has broken substantial new ground, establishing how genes work together within 144 different human tissues and cell types in carrying out those tissues’ functions.
The paper, published today online by Nature Genetics on April 27, also demonstrates how computer science and statistical methods may combine to aggregate and analyze very large — and stunningly diverse — genomic ‘big-data’ collections.
Led by Olga Troyanskaya, deputy director for genomics at SCDA, the team collected and integrated data from about 38,000 genome-wide experiments (from an estimated 14,000 publications). These datasets necessarily contain not only information about cells’ RNA/protein functions, but also information from individuals diagnosed with a variety of illnesses.
Using integrative computational analysis, the researchers first isolated the functional genetic interconnections contained in these rich datasets for various tissue types. Then, combining that tissue-specific functional signal with the relevant disease’s DNA-based genome-wide association studies (GWAS), the researchers were able to identify statistical associations between genes and diseases that would otherwise be undetectable.
The resulting technique, which they called a ‘network-guided association study,’ or NetWAS, thus integrates quantitative genetics with functional genomics to increase the power of GWAS and identify genes underlying complex human diseases. And because the technique is completely data-driven, NetWAS avoids bias toward better-studied genes and pathways, permitting discovery of novel associations.
Supplementing the plant-based Mediterranean diet with antioxidant-rich extra virgin olive oil or mixed nuts has been associated with improved cognitive function in a study of older adults in Spain, according to an open-access article published online by JAMA Internal Medicine.
Previous research suggests following a Mediterranean diet may be associated with better cognitive function and a lower risk of dementia. However, the observational studies that have examined these associations have limitations.
The researchers compared a Mediterranean diet supplemented with olive oil or nuts with a low-fat control diet.
The randomized clinical trial included 447 cognitively healthy volunteers (223 were women; average age was nearly 67 years) who were at high cardiovascular risk and were enrolled in the Prevencion con Dieta Mediterranea nutrition intervention.
Of the participants, 155 individuals were assigned to supplement a Mediterranean diet with one liter of extra virgin olive oil per week; 147 were assigned to supplement a Mediterranean diet with 30 grams per day of a mix of walnuts, hazelnuts and almonds; and 145 individuals were assigned to follow a low-fat control diet.
The authors measured cognitive change over time with a battery of neuropsychological tests and they constructed three cognitive composites for memory, frontal cognition (attention and executive function), and global cognition.
Mediterranean-diet subjects showed improved memory or cognition
The study found that individuals assigned to the low-fat control diet had a significant decrease from baseline in all composites of cognitive function. Compared with the control group, the memory composite improved significantly in the Mediterranean diet plus nuts group, while frontal and global cognition improved in the Mediterranean diet plus olive oil group.
At the end of the follow-up, there were 37 cases of mild cognitive impairment: 17 (13.4 percent) in the Mediterranean diet plus olive oil group; eight (7.1 percent) in the Mediterranean diet plus nuts group; and 12 (12.6 percent) in the low-fat control group. No dementia cases were documented in patients who completed study follow-up.
“Our results suggest that in an older population, a Mediterranean diet supplemented with olive oil or nuts may counteract age-related cognitive decline,” the researchers suggest.
“The lack of effective treatments for cognitive decline and dementia points to the need of preventive strategies to delay the onset and/or minimize the effects of these devastating conditions. The present results with the Mediterranean diet are encouraging but further investigation is warranted.”
Scientists at the Salk Institute have discovered a novel type of pluripotent stem cell that develops into a tissue type that is based on the stem cell’s region, or location, in a developing embryo.
Pluripotent stem cells are cells that are capable of differentiating (developing) in the embryo into any of the three germ layers: endoderm (interior stomach lining, gastrointestinal tract, the lungs), mesoderm (muscle, bone, blood, urogenital), or ectoderm (epidermal tissues and nervous system), normally based on what stage of development they are in.
Generating new therapies in the lab with “region-selective pluripotent stem cells” (rsPSCs)
In the paper, published May 6, 2015 in Nature, the scientists report using these new stem cells to develop the first reliable method for integrating human stem cells into nonviable mouse embryos in a laboratory dish in such a way that the human cells began to differentiate into early-stage tissues.*
“The region-specific cells we found could provide tremendous advantages in the laboratory to study development, evolution, and disease, and may offer avenues for generating novel therapies,” says Salk Professor Juan Carlos Izpisua Belmonte, senior author of the paper and holder of Salk’s Roger Guillemin Chair.
The researchers dubbed this new class of cells “region-selective pluripotent stem cells” (rsPSCs). The rsPSCs were easier to grow in the laboratory than conventional human pluripotent stem cells and offered advantages for large-scale production and gene editing (altering a cell’s DNA), which are both desirable features for cell replacement therapies.
The researchers found rsPSCs showed distinct molecular and metabolic characteristics as well as novel epigenetic signatures — that is, patterns of chemical modifications to DNA that control which genes are turned on or off without changing the DNA sequence.
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