Biology Bytes

Induced pluripotent stem cells (iPSCs) have enormous potential for being used in tissue transplants and therapies. Why is this? It’s because iPSCs can be made using virtually any cells from a person’s body — such as skin or fat samples that wouldn’t be missed. (And since they’re the patient’s own cells, the immune system should not reject them in a transplant.) iPSCs are also pluripotent, which means they can be turned into nearly any cell type. This means that if a patient needs a certain type of retinal cell to treat an eye disease, a skin sample could be taken, turned into the desired retinal cells, and then transplanted into the patient’s eye. And this is exactly what happened for the first time last week.

Even though human iPSCs were first created in late 2007, it wasn’t until last week that they were used in a tissue transplant in a human for the first time. The person was a Japanese woman in her 70s, and the iPSC-derived cells were used to treat her age-related macular degeneration (AMD), a leading cause of blindness in the elderly. Safety studies in mice and monkeys had been previously done to ensure the iPSCs would not cause tumors or be rejected by the immune system.
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Do you like to bird watch using your backyard bird feeder? Or maybe you have fun going bug hunting at a local nature preserve. However you enjoy taking in the natural world around you, there may be a way you can help scientists with important research at the same time! It’s thanks to citizen science, which is basically the practicing of having people — needing no official scientific training — help scientists collect and analyze data.

Previously, Biology Bytes explored citizen biology projects that people can do from the comfort of their own home computer. Here we’ll take a look at citizen biology that gets your hands dirty out in the field! Read on to find out about some of the projects you can get involved with around your home.
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Can you imagine using a plant instead of a light bulb to light up a room? Or a tree to light up a street instead of a lamp post? These inspiring, sustainability-focused ideas were what the Glowing Plant Project used to raise public support in creating plants that glow. And not just simply glow — the plants would ideally produce as much light as light bulbs. The idea was to make plants work as substitutes for electricity-requiring light sources.

Last summer, the small Glowing Plant company raised nearly $500,000 (much more than their goal of $65,000) through Kickstarter to make the glowing plants, and it has been working on creating these plants since then. The main species of plant being used is Arabidopsis thaliana, which is a small flowering plant that belongs to the mustard family. (It’s commonly used in scientific laboratories, making it well-studied.) A glowing rose is also in the works. How are these plants made to glow? They’re essentially forced to incorporate a glowing gene (taken from glowing bacteria) into their own genes.
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With the ALS ice bucket challenge going viral, amyotrophic lateral sclerosis (ALS) has been getting a lot of attention. But what exactly is ALS? It is essentially a poorly understood neurodegenerative disease that kills relatively quickly — with people usually dying within 3–5 years after onset of the first symptoms — and is responsible for the death of about 2 out of every 100,000 people in the U.S. And most people with ALS (90% of them) have no family history with the disease — why they get ALS is unclear.

So what makes the ice bucket challenge ironic? Several lawmakers have chosen to participate in the challenge even though they previously significantly cut funding for research into the disease.
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Just last Thursday, three papers were published in The New England Journal of Medicine that came to very different conclusions about how much table salt (sodium chloride) we should have in our diets if we want to avoid cardiovascular disease and a related death. While two of the studies suggested that most people could safely eat more salt, the third study reported that high numbers of cardiovascular disease-related deaths — specifically 1.65 million in 2010 — are due to eating lower levels of salt than this. It’s clearly a controversial topic that draws a lot of interest because it potentially affects so many people.

First we’ll explore the papers that might make you less afraid of shaking a few dashes of salt onto your next meal. These two papers are a part of the large-scale PURE (Prospective Urban and Rural Epideimological) Study — they basically show that high levels of sodium may not necessarily be harmful unless you are in a certain high-risk group, and that the relationship between eating salt and increasing blood pressure levels is not linear.
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We have a long history with the silkworm (Bombyx mori), which was native throughout Asia and thought to have been domesticated more than 5,000 years ago in China to make silk. Silkworms today are biological silk-producing machines, the products of thousands of years of careful breeding. Silk production is now a multi-billion dollar industry, with around 150,000 tons of silk created every year. But silkworms today make more than just ordinary silk.

What else do silkworms make? Thanks to some inventive genetic engineering, larvae have been made that can produce modified silk — such as silk that’s stronger than steel and fluorescent silk used in designer wedding dresses — as well as proteins for medical purposes. This is accomplished by changing the genetics of the silkworms so that they make modified silk, or medical proteins, instead of their ordinary silk.
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Ebola has been in the headlines a lot lately, mostly because the current outbreak is the largest one we’ve ever seen. There have also been people transported into the United States who were infected, raising concerns about an Ebola outbreak happening in the country. However, while Ebola is a terrifying disease, it is unlikely to spread in the U.S. Here we’ll explore what Ebola is, what makes it so scary, and why there won’t be an outbreak in the U.S.

Ebola (also called hemorrhagic fever) is a disease caused by a virus. (It specifically belongs to the RNA virus family Filoviridae, which are filamentous viruses, in the genus Ebolavirus.) It was first discovered in 1976 in the Democratic Republic of the Congo, near the Ebola River, which it is named after. Researchers have since then identified five subspecies of the Ebola virus, four of which cause the Ebola disease in humans (the fifth causes it in nonhuman primates). An outbreak usually happens when people come in contact with infected wild animals (typically fruit bats [a highly suspected reservoir], rodents, pigs, or primates), and then the virus is transmitted from person-to-person.

When a person becomes infected by the Ebola virus, it can take 2 to 21 days before they show symptoms (although it’s typically 8 to 10 days). Symptoms include fever (above 101.5°F), chills, muscle aches, and a headache initially. By the fifth day, a rash may appear on the skin. Symptoms can progress to nausea, vomiting, diarrhea, and chest and abdominal pain, and then to jaundice (yellow skin), confusion, bleeding (hemorrhaging), severe weight loss, and organ failure. Ebola usually kills 50% to 90% of infected people (although the current epidemic has about a 55% to 60% fatality rate).
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Have you heard of the chikungunya virus? The virus (pronounced chik-en-gun-ye) was discovered in 1952 in Africa, and has been slowly making its way around the world… although the pace has been quickened in recent years. The first U.S. case was reported just earlier this month, on July 17, 2014, and a second case soon followed it, so the virus is definitely in the country now.

Luckily, the infection is not usually fatal, but can be extremely painful and debilitating. The virus, which is spread by certain mosquitos from person to person, primarily causes a fever and joint pains in 4 to 7 days after being bitten, but other symptoms include headaches, joint swelling, muscle aches, and rashes. (The virus’s name, “chikungunya,” actually means “that which bends up” in an African language because of how people bend up due to joint pains.)
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Last week, we took a look at the amazing diversity of microbes (bacteria, fungi, and others) that live on, and inside of, our bodies. This week we’ll dig deeper into our microbiomes and explore what’s known about how they help keep us healthy, and why they sometimes make us sick.

How are our microscopic neighbors connected to our health? And why is it so important that researchers try to answer this question? The idea is that by understanding which microbes are beneficial and help keep us healthy, we could develop ways to promote the growth of such microbes (and figure out how to deter populations of pathogenic, or disease-causing, microbes). This sounds simple enough in theory, but in reality things get a bit complicated — it can be difficult to know which are the “good” microbes and which are the “bad” ones (especially since this sometimes varies from person to person). Read on to find out what’s known about our microscopic neighbors, both the good and the bad.
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Our bodies are made up of many more microbe cells — bacteria, fungi, and other microscopic critters — than human cells. These microscopic organisms are clearly important for making us who we are. And yet, there’s so much we don’t understand about them. How do our microbiomes help keep us healthy, and why do they sometimes make us sick?

Here we’ll do a survey of what’s known about the various microbiomes than live on, and inside of, our bodies, while next time we’ll dig deeper into how these microscopic communities may be connected to our health.
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You may have heard the news that the Earth’s magnetic field (also called the geomagnetic field) is changing. (The field itself is created by the molten iron in the Earth’s outer core and other factors.) Specifically, it’s been significantly weakening over the last 200 years (by about 15%), and the geomagnetic North pole has been moving… and its movement is accelerating. The geomagnetic poles may in fact switch, with the North becoming the South and vice versa.

However, such a reversal may not really have a huge impact on life on Earth. This is because this kind of switch is thought to actually happen a lot (speaking in geological times) — it last happened about 800,000 years ago, and we haven’t found any mass extinctions related to the event. But that doesn’t mean that such a change wouldn’t disrupt lives. Read on to find out about some of the many critters that use Earth’s magnetic field to figure out their location and how to navigate to a different location. We have lots to learn about how such animals use this ability, called magnetoception.
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A new study may not only make you want to head to bed on time tonight, but also try to make sure you don’t get any interruptions during the night. Why is that? It turns out that not getting enough sleep can be just as detrimental as repeatedly getting woken up at night. (This may be an obvious finding for many parents, but it’s still reassuring to see scientific data justifying the crankiness of a newborn’s parents.)

Specifically, this study found that having one interrupted night of sleep (8 hours in a bed but with four interruptions, where each interruption needed a 15-minute, purposeful response) is just as bad as having a night with only 4 hours of sleep. This was measured by testing cognitive abilities and attention spans the next day through an activity online, as well as self-reporting moods. Overall, awoken and sleep-restricted volunteers similarly omitted more answers and made more mistakes when doing the activity, and reported more depression and fatigue, compared to when getting a night with a solid 8 hours of uninterrupted sleep.
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Last week, the Supreme Court ruled that, due to religious objections, Hobby Lobby (and other for-profit companies) does not have to provide health insurance coverage for contraceptives that are part of the Affordable Care Act. Specifically, Hobby Lobby objected to four contraceptive methods – Plan B, Ella, and two intrauterine devices (IUDs) – because Hobby Lobby’s owners “believe” that these contraceptives cause abortions, calling them abortifacients. But, this just isn’t true.

Despite Hobby Lobby’s owners’ beliefs, scientific evidence shows that these contraceptives don’t actually cause abortions. Instead, they primarily work by preventing fertilization, which happens before a woman is even technically pregnant. Furthermore, these contraceptives cannot terminate a pregnancy once it is established. Consequently, these contraceptives do not cause abortions. To understand this, a brief refresher on reproductive biology helps.
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Have you ever had a lucid dream? Lucid dreams can be quite fun and freeing — they are when the dreamer realizes that they are in a dream, and can control the dream to be what they want it to be. And recently, researchers found out how they could cause somebody to have a lucid dream. It turns out that it just needs the right kind of electrical stimulation, and the dreamer is off to be the commander of their dream world.

Typically, when a person has dreams, they are in the “rapid eye movement” (REM) phase of their sleep (so-called because their eyes really do rapidly, and randomly, move around). And while dreams occur during the REM phase, different parts of the brain can be active depending on the type of dream. Specifically, in lucid dreams, areas of the brain that are associated with higher cognitive function are active, but these areas are inactive during non-lucid dreams. The recent study found that, during REM, when some of these inactive areas are stimulated with the right electrical signal (having a certain frequency), they become active and induce lucid dreams.
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Are we alone, or is there life beyond Earth? It’s a question we’ve been trying to actively answer for decades now, with increased interest in more recent times. While there almost certainly is life outside of our world, we have yet to find it. Based on our understanding of the spectrum of organisms that live on Earth and the conditions that life needs to thrive, we can hypothesize what other life-bearing planets may look like. Using this basic approach, a newly developed computation method estimates that there may be more than 100 million planets in our Milky Way galaxy that could be home to complex life.

This computation method takes into account several factors that affect whether life can survive on a planet. For example, a planet’s size and temperature are two main ones to consider — a planet should be 0.1 to 10 times the mass of Earth (to support the right type of atmosphere), and not too much hotter or colder than Earth (to allow water to be in a liquid form). The distance of the planet from its central star is also essential and affects the planet’s temperature. (Its similarity in size and likely temperature are reasons why the recently-discovered Earth-sized planet of Kepler-186f attracted much attention as a possible life-bearing planet.)
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In the past six months, several interesting and promising studies have been published on Alzheimer’s disease. They’ve ranged from how what we eat might affect our odds of developing it, to discovering the underlying mechanisms. Taken together, researchers are definitely making progress in developing treatments — and preventative measures — for Alzheimer’s. For those of us who have watched older family members mentally decline due to the devastating effects of this genetic disease, these studies may help give some hope that the same fate does not await us.

The studies that will be explored here are specifically on: how eating fruits, vegetables, and other components of a healthy diet may decrease the risk of developing Alzheimer’s; the effects of other risk factors; and how some chemicals affect the formation of amyloid plaques or dementia (but not both). Read on for the details.
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Heart attacks and strokes have been thought to be prompted by stress. But why is this — why does stress trigger these dangerous medical events? Based on a study published earlier this month, a key player may actually be some specific species of bacteria.

Researchers examined plaques in the arteries of 15 patients with advanced atherosclerosis and found that at least 10 species of bacteria lived closely with the plaques. (Plaques are created by the buildup of a variety of biological substances on arterial walls, including fat, cholesterol, calcium, other debris, and clearly bacteria too.) What are the bacteria doing there? It turns out that some are making biofilms, which are clumps of bacteria that harmoniously grow together to cover a surface. And when the harmony is disrupted, researchers found that bits of the plaque may break off, which could cause blood clots that result in heart attacks and/or strokes.
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As we become more aware of the resources that we’re quickly using up, we increasingly look for ways to recycle and reuse what we’ve got. For example, some people have been figuring out how to “reuse” food waste by turning it into plastic. And not just any type of plastic — it’s actually biodegradable plastic, which makes the exchange even more exciting and desirable.

The biodegradable plastic, which is specifically polybutylene succinate (PBS), is made using a chemical called succinic acid. Succinic acid can be produced using various types of chemical reactions, from different source materials. Succinic acid has typically been petroleum-based, but recently people have been working on making bio-based succinic acid. Such as by using food waste.
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How our diet affects our health is a very complicated topic. For example, while drinking tea is thought to possibly help reduce the risk of a number of diseases and health conditions, many studies have had inconsistent results, and the chemical mechanisms that go on in our bodies are not well understood. However, a recently published study has helped us better understand how drinking green tea — both as a one-time event and as a habit — may lower DNA damage in a person. (Preventing DNA from getting damaged, and fixing damaged DNA, is important for keeping a person’s cells, and their entire body by extension, in a healthy condition.)

The researchers found that after a person drinks green tea, DNA damage in their cells decreased, which has obvious implications for people wanting to eat certain foods to stay healthy. At the same time, an enzyme that’s involved in the DNA-repairing process became much more active. It definitely looks like a promising correlation to explore.
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In January, two papers were published in the prestigious journal Nature showing how to make stem cells using a shockingly simple and completely novel approach — by putting cells in an acid bath. The resultant mouse stem cells were called STAP cells (for stimulus-triggered acquisition of pluripotency). However, since then, other researchers have had great difficulty making their own STAP cells following the procedures in the papers, and there have been accusations of misconduct, specifically falsification and fabrication of data. After a great deal of controversy, the lead author, Haruko Obokata, announced last week, on June 4, that she agreed to retract both articles. Official retraction of the promising, and then disappointing, papers is imminent. (Nature generally wants all authors to agree to a retraction, and she was the last obstacle — all other authors appear to have also consented to retraction.)

Obokata, a researcher at the RIKEN Center for Developmental Biology in Japan, long defended the validity of the papers’ results and the creation of STAP cells, even after a RIKEN committee found that data had been “inappropriately handled” in March and then
evidence of misconduct (which they define as a malicious act, such as knowingly falsifying data) in early April. This was due to various duplicated and manipulated images in the papers.
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Because they help us fight bacterial infections, antibiotics are an amazing invention that has let us greatly improve our quality of life and life expectancy. However, their overuse has led to some extremely dangerous pathogens — antibiotic-resistant bacteria. Specifically, last fall it was found that more than 2 million people in the U.S. get infected with antibiotic-resistant bacteria, and at least 23,000 people die from the infection. But there are two new antibiotic drugs on the horizon — they should be available in mere months — that have been shown to be effective against some common antibiotic-resistant bacteria.

Both of the new drugs — Dalvance (dalbavancin) and Oritavancin — can fight methicillin-resistant Staphylococcus aureus (MRSA) infections and other skin infections. Last fall, the U.S. Centers for Disease Control and Prevention (CDC) identified MRSA as being among 12 microorganisms that have a “serious” threat level. Impressively, a single dose of Oritavancin can effectively fight a MRSA infection (while most antibiotics, if they can be used against MRSA at all, require multiple days of treatment). A single-dose treatment like this should clearly cut down on the time that a patient with an antibiotic-resistant infection spends in a hospital, which is where antibiotic-resistant microorganisms can easily spread to vulnerable patients and cause serious (and ongoing) problems.
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While human embryonic stem cells (hESCs) were originally created in 1998, it wasn’t until 2009 — over a decade later — that they were approved by the FDA for use in a clinical trial in people. It was a long wait, but the trial was quite the promising one. The clinical trial, undertaken by the Geron Corporation, was for using hESCs to treat patients with spinal cord injuries and paralysis.

Very unfortunately, the trial became stalled in late 2011, mostly due to financial concerns (but it did undoubtedly help pave the way for other hESC-based clinical trials to get FDA approval starting in 2010). At that point, Geron stated that they’d withdraw from the stem cell field entirely — in early 2013, Geron’s hESC-related assets, including the FDA-approved clinical trial, were bought by another company, BioTime Inc. But now, at long last, it looks as though the trial may resume through BioTime Inc.
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Since it was first discovered in a person in mid-2012, MERS (short for Middle East respiratory syndrome) has been a looming viral threat. MERS is a disease caused a type of virus called a coronavirus (CoV), which typically infects the respiratory and gastrointestinal systems. (Many common colds and even cases of pneumonia are caused by coronaviruses.) But unlike common colds, MERS-CoV has a high fatality rate, around 30%. Since its discovery, there’ve been nearly 600 people in the world infected with MERS. While this is a relatively low number of infected individuals, MERS-CoV continues to spread — it’s now been found in 12 different countries, recently including the United States.

The first people infected with MERS-CoV were in Saudi Arabia, and still all known cases of MERS-CoV infections can be traced back to Saudi Arabia and the surrounding countries on the Arabian Peninsula. It’s now thought that the virus came from camels in Saudi Arabia, as camels have been found carrying similar viruses and can be infected with MERS-CoV, but details on any specific cases of transmission between people and camels are unknown. While in people the virus appears to only be spread through close contact, it still continues to spread, crossing country boundaries, and leading to the first two known cases in the U.S.
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Note: The Biology Bytes blog will only be updated on Tuesday this week (the author is traveling in Japan). Regular Tuesday/Thursday updates will resume on June 3.

Whenever I travel internationally, I make a point of visiting science museums. It’s fascinating not only to learn scientific concepts from them, but also to see what specific topics and interactive activities have been chosen to be turned into exhibits; the exhibits are the end result of a careful selection process (due to limited space and resources). Last week, I had the pleasure of visiting Miraikan, the National Museum of Emerging Science and Innovation in Tokyo, Japan. (I’ve visited it once before, five years ago.) It’s one of the best (if not the best) science museums I’ve been to because nearly all of its exhibits are great examples of this process.

Miraikan has many exhibits that clearly were created because they highlight a cutting-edge, key scientific idea, and do so in a way that really engages visitors. Here I’ll explore some of the current biology-related exhibits that were surely made with these criteria in mind. If you’re a biology fan (or just enjoy learning more science in general) and will be visiting the Tokyo area any time soon, you’ll want to be sure to drop by Miraikan to check them out (along with the other incredible exhibits)!
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Note: The Biology Bytes blog will only be updated on Tuesdays during this week and next week. Next week will feature a special tidbit on biology-related exhibits at the Miraikan National Museum of Emerging Science and Innovation in Tokyo, Japan, which the author will be visiting. Regular Tuesday/Thursday updates will resume on June 2.

Have you ever wondered why it’s so hard to remember things from when you were a little kid, before the age of 3 or so? Within the first few years of a person’s life, parts of the brain that are involved in creating memories — like an area of the brain called the dentate gyrus — are still developing, which is thought to cause well-known childhood amnesia.

How is the dentate gyrus region of the brain “developing” exactly? It’s largely done by creating new neurons (which are specialized cells that send signals and are made through a process called neurogenesis). While it’s been thought that neurogenesis is the basis for memory, a study published earlier this month shows that instead of creating memories, neurogenesis may actually cause people to forget them. Not only does this helps explain the phenomenon of childhood amnesia, but it has other fascinating implications as well.
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Have you ever felt like your reaction time isn’t as good as it should be? Or, if you’re male, have you ever had people comment that you look particularly masculine? These traits might seem unrelated, but they actually can be due to the same thing — infection by a very common parasite called Toxoplasma gondii (which infects people through exposure to cats and eating undercooked meat). A little while ago we talked about the Toxoplasma parasite, how it’s thought that about one in three people in the U.S. (and other developed countries) are infected with it, and that it makes mice less afraid of cat urine. Infection in people has been typically considered asymptomatic, but it turns out that this isn’t really the case — surprisingly, and concerningly, studies are showing that infection can affect human development, immune response, personality, and much more.

A paper published in 2013 took a look at studies done over the past two decades on the effects of Toxoplasma infection in humans — primarily college students, pregnant women, and military personnel — and made some interesting conclusions. It was found that infection with the parasite not only affects our behavior (which is not too surprising considering the effect of infection on mice), but also our immune response, which has far-reaching consequences, such as potentially changing which embryos are selected by a woman’s body for pregnancy.
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The bacteria Clostridium difficile is pretty terrifying — if it infects a person’s gut, it can cause severe diarrhea, bloating, and potentially death. In the U.S. alone, it hospitalizes nearly 250,000 people and kills at least 14,000 people each year. Why not just fight it with antibiotics, like we use to fight other bacterial infections? Well, antibiotics is actually part of how C. difficile infections get started.

A lot of people normally have a small amount of C. difficile in their gut, and when a person takes broad-spectrum antibiotics, this can kill most of the gut’s bacteria except for antibiotic-resistant C. difficile bacteria, which can then grow and take over. (Just one more reason to not take antibiotics when they’re not really needed!) It is a particularly big problem in hospitals, where antibiotic-resistant C. difficile can spread between patients who are on antibiotics. So how are we to fight antibitioc-resistant C. difficile if our antibiotics don’t help? The answer appears to be fecal transplants… and fecal banks.
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With Mother’s Day coming up, it can be fun to talk about some of our family’s genetic traits, like eye color, hair color, or having mid-digit hair (yup, that’s genetic too!). We all know that we get our genetics — the basic blueprints that make us who we are — from Mom and Dad, but it turns out that how they lived their lives before we were conceived affects who we are as well. Specifically, it’s been recently shown that a parent’s epigenetics — in addition to their genetics — get passed on to their offspring. What does this mean exactly, and what are the implications?

While our genetics are a collection of our genes (together making up our genome), epigenetics are certain factors that control which genes we’re using. And according to two recent studies, because of epigenetics, what your mother ate before you were even conceived, and whether your father had a stressful childhood or not, may affect who you are today.
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Are you not a scientist by training but you’d like to help scientists do real research? Or maybe you are a scientist and would like to aid others in doing more investigations in your spare time. Whatever your background, there are actually many ways that you can now do real scientific research in your spare time, most of them from your own home computer. It’s thanks to citizen science, which is basically the practice of having people — needing no official scientific training — go through scientists’ mountains of data, or help collect data for scientists. Analyzing the data can range from categorizing pictures of distant galaxies to playing a game where you get points for solving the structure of a protein, and so much more in between.

Doing citizen science really helps researchers who have collected more data than they can feasibly analyze on their own. And there are many biology-based projects that people can participate in. Read on to find out about some that you could get involved with to start doing real science at home on your computer!
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