Genome sequencing meets chocolate

ORIGINAL: IBM Research

How analyzing cacao plant genes could save chocolate

Plants have DNA, too. So just as genome sequencing has been conducted on fruit flies and humans, scientists have also discovered the genomes of rice, mustard, and a few trees - including as of 2010, the cacao.

IBM, the United States Department of Agriculture’s Agricultural Research Service (USDA-ARS), and candy-maker Mars Inc. teamed up in 2008 to sequence the cocoa genome in an effort to help farmers grow tastier, more disease-resistant and more productive cocoa trees. The initial phase of work yielded a surprising result: identifying the genes that dictate the color of the plant may be the best indicator for better-tasting, healthier plants.

Why sustain cocoa?

• 70 percent of today’s global cocoa is produced in equatorial Africa
• 2,000,000 small-scale cocoa farms in West Africa depend on this crop
• 1/3 of all cocoa produced in Africa is lost to drought, pests and fungal disease
• $800 million (U.S.) lost due to failed cocoa crops

IBM and Mars use Deep Analytics to Map the Cocoa Genome

IBM and Mars use Deep Analytics to Map the Cocoa Genome(2:52)

Genome sequencing: how computers deciphers genetic code

In order to sequence the cacao’s genetic material, scientists had to first crush the leaves, pods and other parts of the plant at the USDA’s Agricultural Research Service lab. A DNA sequencer then extracted the nucleotides that make up the plants unique set of genes. And while the team at IBM, Mars and the USDA finished the sequence three years ahead of schedule, the real work is in deciphering the more than 30,000 estimated cacao genes.

The 30,000 is arrived at by using algorithms to identify patterns of genes embedded in the genome. The algorithms “spot” the genes by comparing similarities with known genes from other species.

While this fully automated process can estimate the total number of genes, specific genes are handled by in silico-in vitro screenings – a combination of experimental biology and computer analysis. The analysis is a delicate problem that, in IBM's efforts to identify cacao pod color, demanded algorithmic precision at a different scale (a sort of “genome whisperer”) that analyzed hundreds of pods collected from different geographies.

“Typically, the hardest task is in finding gene(s) responsible for a phenotype in the "mass" of genes in the genomes. The breakthrough here is being able to pinpoint the genes responsible for pod color. ”

Dr. Laxmi Parida, computational genomics manager at IBM Research

Traits of flavor and sustainability through pod color

Classification of cacao cultivars using
the IRiS algorithm, developed by
the IBM scientists

The color coding identified within these cacao candidates, as suggested by these specialized algorithms, were put through an additional vetting process of targeted sequencing, as well as RNA analysis of the relevant tissues in these target plants. The combination of these processes identified which genes expressed pod color, and where they reside within the genome.

The red pod color trait is positively correlated with an undesirable flavor characteristic in the cacao. On the other hand, the green pods taste better but have a lower yield. The ability to screen young cacao seedlings with red or green molecular markers – and then select only those carrying the alleles genes that result in green pods – would greatly reduce the population sizes required for the laborious and expensive evaluations of unlinked flavor and yield traits.

In other words, using marker assisted selection, versus naturally breeding the plants (which takes years), will greatly speed up the effort of identifying and selecting the most flavorful and sustainable cacao plants.

Analyzing any genome

IBM's work to identify the cacao’s pod color is genetic selection, not modification.

IBM conceived, designed and developed these specialized algorithms to identify candidate genes, to provide guidance for specific experiments that support Mars’ work to improve cocoa taste and sustainability. Mars hopes to use these results to rapidly accelerate breeding programs to improve the quality of chocolate produced from cacao beans. All of IBM’s algorithms are available for any research community to apply to their own plant or animal studies.
Explore other food technologies from IBM

Cacao vs. Cocoa

“Cacao” refers to the tree Theobroma cacao and its seeds (and the beans inside of the seeds). The word “cocoa” refers to the processed product of the tree, seed and bean.

This article refers to the gene sequencing of the “cacao” plant.
Meet the researcher

Laxmi Parida
Manager, Computational Genomics Group,
Thomas J. Watson Research Center


Learn more about genome sequencing
Download the algorithms used in the project
Computational genomics at IBM Research
Using genome sequencing to map humanity's family tree
Learn more about IBM Analytics

The 10 healthiest foods on the Planet

ORIGINAL: My Amazing Earth
by Amazing Earth
May 25, 2013

These 10 super-foods are proven disease fighters and energy boosters according to our pals at fitnessmagazine.com.

Lemons: Just one lemon has more than 100 per cent of your daily intake of vitamin C, which may help increase ‘good’ HDL cholesterol levels and strengthen bones. And the citrus flavonoids found in lemons may help inhibit the growth of cancer cells and act as an anti-inflammatory.

Broccoli: One medium stalk of broccoli contains more than 100 per cent of your daily vitamin K requirement and almost 200 per cent of your recommended daily dose of vitamin C — two essential bone-building nutrients. The same serving also helps stave off numerous cancers.

Dark chocolate: Just one-fourth of an ounce daily can reduce blood pressure in otherwise healthy individuals. Cocoa powder is also rich in flavonoids, antioxidants shown to reduce ‘bad’ LDL cholesterol and increase ‘good’ HDL levels.

Potatoes: One red potato contains 66 micrograms of cell-building folate — about the same amount found in one cup of spinach or broccoli. One sweet potato has almost eight times the amount of cancer-fighting and immune-boosting vitamin A you need daily.

Salmon: A great source of omega-3 fatty acids, which have been linked to a reduced risk of depression, heart disease and cancer. A three-ounce serving contains almost 50 per cent of your daily dose of niacin, which may protect against Alzheimer’s disease and memory loss.

Walnuts: Contain the most omega-3 fatty acids, which may help reduce cholesterol, of all nuts. Omega-3s have been shown to improve mood and fight cancer; they may protect against sun damage, too (but don’t skip the SPF!).

Avocados: Rich in healthy, satisfying fats proven in one study to lower cholesterol by about 22 percent. One has more than half the fiber and 40 percent of the folate you need daily, which may reduce your risk of heart disease.

Garlic: Garlic is a powerful disease fighter that can inhibit the growth of bacteria, including E. coli. Allicin, a compound found in garlic, works as a potent anti-inflammatory and has been shown to help lower cholesterol and blood-pressure levels.

Spinach: Spinach contains lutein and zeaxanthin, two immune-boosting antioxidants important for eye health. Recent research found that among cancer-fighting fruits and veggies, spinach is one of the most effective.

Beans: Eating a serving of legumes (beans, peas, and lentils) four times a week can lower your risk of heart disease by 22 percent. That same habit may also reduce your risk of breast cancer.

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How the Food You Eat Makes You More (or Less) Productive

ORIGINAL: Life Hacker

Leo Widrich

There are tons of cliché wisdoms about nutrition: Eat at least five servings of fruit every day. Drink plenty of water. Eat three separate meals. Do this, do that, that's "healthy." What's true? Buffer co-founder Leo Widrich explores the science behind what we eat and how it affects the brain's performance.

Every seven years, the body will change completely. This means that each and every one of your cells will have been renewed and exchanged for another one that your body has produced. I am always amazed by this. Science suggests that this gives us a unique chance to change and erase any mistakes we've made in the past. How? Through a focus on the food we eat. Fortunately we don't have to wait seven years. Day-to-day changes in our diet can have a massive impact on our productivity. Something like this:

"Adequate nutrition can raise your productivity levels by 20 percent on average." -WHO

How food interacts with your brain

One of the most fascinating things about eating is how various ingredients enter the brain through your blood stream. The elements that make it through to power your brain will help you to either focus or lose focus.

Most of what we eat will be broken down to one thing: Glucose. Glucose is our fuel, keeping our brains awake and alert. So at all times, we have a certain glucose level in our blood (kind of like gasoline in a car).

The most important part here is that we are in full control of how we release glucose to our blood and our brains. Certain foods release glucose quickly, while others do so more slowly, yet sustainably. Researcher Leigh Gibson found this to be optimal:

"The brain works best with about 25 grams of glucose circulating in the blood stream—about the amount found in a banana."

The way you can get those 25 grams of glucose into your blood stream is pretty easy. You can eat a donut. You can eat a small bowl of oats. There is virtually no difference in the very short term for your brain activity.

Over the stretch of a normal 8-hour day however, the differences are spectacular. After eating the donut, we will release glucose into our blood very quickly. We will have about 20 minutes of alertness. Then our glucose level will drop rapidly, leaving us unfocused and easy to distract. It's like putting the foot down on the gas pedal until you've used all your fuel.

The oats, on the other hand, release their sugar as glucose much slower. This means we will have a steady glucose level, better focus, and higher attention levels. Another important factor are your Leptin levels. Leptin will signal to your brain how full you are. If you are now guessing that a donut won't signal your brain to be full for a long time, while oats will, well, you are right.

What we are also measuring here as the difference between a donut and a bowl of oats is called your "glycemic index," coined by the Franklin Institute:

"Foods with a low glycemic index number gradually release glucose into your bloodstream. This gradual release helps minimize blood sugar swings and optimizes brainpower and mental focus."

In fact, the lowest glycemic index of all comes from soy, at only 18, and the highest comes with white rice, at 88. [Check out more from Lifehacker on how eating affects your brain.]

What really matters with eating: when, where, and who you're with

That's funny. We're going through all this stuff about blood streams and brain fueling only to find out it doesn't actually matter?

Rest assured, it still matters, yet the context of when, where, and with whom we eat has an equally powerful impact on our eating activities, and hence, our creativity.

Let's start with the "when." The most important part here is that you make sure you are never hungry. To put this better: Hungry judges give harsher sentences.

For our case, being hungry or skipping breakfast can ruin several hours of your productivity until you get your first bite. Let's take a look at this study:

All the children in a class were told to skip breakfast one morning, and then, by random assignment, half of the children were given a good breakfast at school. The others got nothing. During the first part of the morning, the children who got breakfast learned more and misbehaved less (as judged by monitors who didn't know which children had eaten). Then, after all the students were given a healthy snack in the middle of the morning, the differences disappeared as if by magic.

Eric Barker, one of the best productivity bloggers out there, put it like this: "Across the board, yeah, food puts you in a better mood. To be more exact, research has shown that two cheeseburgers = one orgasm."

Using context to control your eating is one of the most important aspects. If you are like me, you always end up eating portions that are too big, which makes me overly full at lunch and very tired a few hours afterwards.

One of the best proven techniques here is to eat from a smaller plate. Why? Because Delboeuf told us so a long time ago with his illusion experiment of thinking the right circle looks bigger:

The portion on the smaller plate will always fill you up more. This can make the difference of an hour of productivity gained each day, simply by reducing the size of your plate and being less full. Joining the small plate movement is definitely something worth trying.

Another aspect comes in regarding the people you are with as Barker points out: "Eating with overweight friends? You'll eat more. Is your waitress overweight? You'll eat more. Are you a woman eating with a man? You'll eat less. Wide variety of food? You'll eat more."

Three most important aspects to get the most out of eating food

It's time to get our hands dirty. I think we've got a basic understanding of how food determines our daily output. But what are the best ways to act on this information?

Reorganize the positioning of food stored in your cupboard: One of the most interesting aspects about eating is that we are extremely likely to eat what is in close sight. In fact, famous researcher Brian Wansink mentions that, "You are three times more likely to eat the first thing you see in your cupboard than the fifth thing you see." Make sure you organize your food in way that brain powering foods get more exposure. It's an incredible trick to start eating better food that will give you more daily alertness.

Learn to graze: From the first section in this post, we've learned that the brain needs very specific portions of food. Too much will give you a spike that rapidly declines. Too little won't bring your brain up to speed. A great way to go about it, I've found, is to make your three daily meals a bit smaller (potentially by making the plates smaller), and then add two very specific, healthy snacks in between meals to keep your brain plugging away at full speed. This way you don't have to change your core habits too much, yet can still fuel up your brain efficiently.

These foods will give your brain the most power: Here is a great list of brain powering foods that you can eat, especially for snacking. The WHO particularly emphasizes the following: dark chocolate, nuts, seeds, and fish.

Some further brain powering foods are the following: blueberries, raw carrots, whole grains, and avocado.

Quick last fact: What you eat will also decide your grandchildren's productivity

As a last quick tip, here is something that blew my mind. Yes, what you eat will affect your productivity today. But even more so, it will determine the productivity of your children and grandchildren's productivity. "Evidence indicates that what you eat can affect your grandchildren's brain molecules and synapses," Gómez-Pinilla said. What you eat can, according to Gomez-Pinilla, rewire your genes, and the more you strengthen the synaptic connections, the better your kids and their kids will perform.

Note: We wrote yesterday about the food organization tricks Leo mentions above. Check out that post here.

The science behind how your productivity is chosen by what you eat | Buffer

Leo Widrich is the co-founder of Buffer, a smarter way to share on Twitter and Facebook. Leo writes more posts on efficiency and customer happiness over on the Buffer blog. Hit him up on Twitter @LeoWid anytime; he is a super nice guy.

Image by Yuganov Konstantin (Shutterstock).

Desarrollan un chocolate que retrasa la vejez

ORIGINAL: Mas Verde Digital

Expertos británicos de la Universidad de Cambridge llegaron a una conclusión unánime: el chocolate sí puede ser un medio perfecto para retrasar el proceso del envejecimiento humano.

Los científicos de la empresa ‘Lycotec’ elaboraron una tecnología que ayuda al cuerpo a absorber de una manera mucho más rápida los compuestos orgánicos, llamados flavonoides que contiene el cacao. Estas moléculas mejoran la saturación de oxígeno en la piel, necesario para reducir la velocidad del proceso responsable del envejecimiento.

Así, los expertos cambiaron la composición del chocolate con un solo ingrediente, conocido como ‘Coco-Lycosome’ que aumenta el poder de los flavonoides hasta 20 veces.

Ya se conocía que el chocolate goza de este efecto milagroso, aunque la noticia podía consolar tan solo a los verdaderos amantes del producto, capaces de devorar al menos dos barras enteras diarias, necesarias, según los especialistas, para alcanzar el resultado prometedor.

Ahora los expertos aseguran que un pequeño trozo del nuevo producto es equivalente a la norma, ‘prescrita’ anteriormente. “Dos barras diarias pueden ser una buena noticia para los aficionados, pero no a todo el mundo le encanta el chocolate en estas cantidades”, sostiene el fundador de la compañía, Iván Petyaev.

De acuerdo con el experto, la pequeña transformación en la composición del chocolate no afecta de ningún modo al sabor o la textura del producto, mientras que la seguridad del ingrediente añadido está demostrada por los médicos. Por lo tanto, el nuevo producto está listo para entrar en el mercado mundial.

Sin embargo, la nutricionista Dra. Carrie Rakston expresó sus dudas sobre que se trate de un producto totalmente sano. “Los flavonoides se absorben mal por el organismo. Pese a que la idea es interesante, se necesita obtener la confirmación específica de la eficacia del desarrollo”, destacó la dietista.

Fuente: RT, Agencias