New Method to Predict Protein-Environment Interactions Found

It is well-known that proteins are the cornerstone of life and play a key role in all biological processes. Therefore, understanding how they interact with the environment is critical to developing effective treatments and designing the basis for artificial cells.

Recently, the Protein Design and Immune Engineering Laboratory (LPDI) of the Institute of Bioengineering at the Swiss Federal Institute of Technology (EPFL), in collaboration with the Institute of Computational Science at the USI School of Information, Imperial College, and other units in the United Kingdom, has developed a groundbreaking machine learning-driven technique for predicting interactions between proteins and the environment and achieving a description of the biochemical activity of proteins based only on surfaces. In addition to deepening our understanding of protein function, this approach, known as MaSIF, can also support the future development of protein-based components in artificial cells. The study was published in the December 9 issue of Nature Methods.

In this new study, the research team took a large amount of protein surface data and entered these chemical and geometric properties into a machine learning algorithm and trained them to match them to specific behavioral patterns and biochemical activities. Then, they used the remaining data to test the algorithm.

“By scanning the surface of a protein, our method can define a ‘fingerprint’ that can then be compared between proteins,” said the leadauthor, Dr. Pablo Gainza of EPFL Bioengineering Institute and Swiss Institute of Bioinformatics.

Scientists have developed a new method to predict interactions between proteins and other proteins and biomolecules, as well as to predict their biochemical activity by looking only at their surfaces.

The team found that proteins with similar interactions all share a common “fingerprint”.

“The algorithm can analyze billions of protein surfaces per second,” said Bruno Correia, Ph.D., director of LPDI and corresponding author of the study. “Our research has important implications for the design of artificial proteins that allow us to program proteins to behave in a specific way simply by changing their surface chemistry and geometry.”

The method is published as open source and can also be used to analyze the surface structure of other types of molecules.

CSK All The Way

There is something special about the Chennai Super Kings and I know that I have millions of fans to back me up on this theory. Ever since the conception of the Indian Premier League, they have stood out amongst the rest. Yes, some of that credit can go to the conspicuously bright yellow jerseys they have on as their uniforms but most of it is attributed to the individual efforts that blend in well with the team’s ideology and in turn helps them produce a unified yet and distinctively successful results. And the remaining credit should indubitably go to the captain- Mahendra Singh Dhoni, without whom the fate of the Super Kings would have been significantly different.

The C S K Group started off in the I P L journey with some of the best contemporary cricketers available such as Hayden, Stephen Fleming, Muttiah Muralitharan, M.S.Dhoni and Michael Hussey. An amount of one and a half million dollars was shelled out to rope in Dhoni. They finished the year 2008 as the runners up of the tournament and with $600,000 as prize money.

The next year they paid fifty grants more to bring in English all rounder –Andrew Flintoff to the team. Though they didn’t quite make it to the finals, one of their own- Matthew Hayden, who scored 572 runs in 12 innings at an average of 52 and strike-rate of 145, was adjudged the Player of the Tournament and was given the Orange Cap for being the lead scorer.

The much acclaimed Andrew Flintoff decided to sit the next season out and hence they filled in his slot with talented substitutes. Suresh Raina was particularly efficient and produced the match winning innings in the finals. And they rounded up the 2010 premier league season as the I P L Champions.

Michael Hussey was brought back in the 2001 season while retaining the likes of MS Dhoni, Suresh Raina, Murali Vijay and Albie Morkel. This season was the best that the Chennai Super Kings had seen to date as it not only involved them defending their title as Premier League Champions, but also the Super Kings stood above the rest with a win percentage of 64.11.

For the 2012 I P L auction, the team welcomed Sir Ravindra Jadeja for a whopper of two million dollors, this was a huge mark in the Chennai Super Kings news and history.

According to the current IPL updates, C S K lost to the Pune Warriors by twenty four runs.

Healthy Alternatives to Coffee in the Morning

Coffee in moderation can be a part of a perfectly healthy diet. However, many find themselves depending on that morning cup of coffee a little too much thanks to the delicious flavor and, most importantly, that caffeine boost.

However, caffeine is a drug. In fact, research shows that caffeine (usually in the form of coffee) is the United States’ most commonly used drug.

If you find yourself getting headaches without that morning (and sometimes afternoon) cup, there’s a good chance you’re actually addicted to coffee, which can lead to anxiety, withdrawal symptoms, teeth yellowing, nutritional problems, and more.

Not great, is it? That’s why we’ve compiled this list of healthy alternatives to coffee in the morning, and in general. Let’s get started.

Tea

Before you quit caffeine cold turkey, you might want to consider weaning off of it instead. This can reduce the withdrawal symptoms you’ll feel and boost your chances at success.

As you wean yourself off caffeine, try switching to various types of tea. Caffeinated tea usually has a lower amount of caffeine compared to coffee, which will give you a little kick you need without going overboard.

If you want to go all-in with your health, we highly recommend mushroom tea. Mushroom and adaptogenic tea (aka tea packed with amazingly healthy compounds called adaptogens) provide amazing nutrients, antioxidants, and benefits without relying on caffeine. You’ll feel focused, energetic, and healthy without caffeine.

Matcha green tea is another healthy option. Matcha is packed with antioxidants and has been linked to lowered cholesterol, better digestion, relaxation, reduced stress, and more.

Kombucha

The tea section leads perfectly into “kombucha” because, well, kombucha is a type of tea-based drink, too!

Specifically, kombucha is a drink made from fermented tea, yeast, and sugar. This creates a drink loaded with natural probiotics to promote digestion. Because it’s made with either black or green tea, it does contain some caffeine, but nowhere near the amount of caffeine found in coffee.

Kombucha made from green tea is especially healthy thanks to all of the benefits of green tea that we mentioned in the matcha section. Evidence also shows that kombucha can kill harmful bacteria, is filled with powerful immune-boosting antioxidants, and can even reduce your risk of heart disease.

Coconut Water

Ready to make the jump into a caffeine-less existence? Try replacing that morning cup of coffee with coconut water.

Coconut water is the liquid found inside young green coconuts. This drink is packed with nutrients, antioxidants, electrolytes, and minerals that many people don’t get enough of in their everyday diet.

Perhaps the most beneficial properties of coconut water are the electrolytes, which promotes hydration and proper cellular balance. This can help you during workouts, after exercise, and is extremely helpful for those cutting back on sugar. It’s also packed with essential vitamins and minerals like calcium, potassium, magnesium, and sodium.

Celery Juice

Celery juice is definitely one of the trendiest options on this list with it being virtually non-existent until the last couple of years. However, it recently exploded in popularity thanks to the various benefits people experience with it.

One of the most lauded benefits of celery juice is how it can aid in digestion. Celery juice can help balance the acid in your stomach, which makes digestion easier and more efficient. Celery juice also has been linked to:

Lower cholesterol
Lower blood pressure
Improved liver function
Increased antioxidants and immunity
Lower inflammation
Celery juice is also chock full of vitamins and nutrients like vitamin B6, folate, potassium, vitamin C, and vitamin K. These can help you feel healthier and boost your energy as well, which makes it the perfect replacement for coffee in the morning.

Golden Milk

Let’s end with a little bit of an odd-ball, shall we? Golden milk sounds a bit strange, but it’s actually one of the most delicious and nutritious options on this list.

Golden milk is a concoction of turmeric, cinnamon, black pepper, and ginger in warm milk or milk substitutes. Many also add vanilla, honey, or agave to make it a bit sweeter.

Turmeric is the star of the show with this beverage option, providing you with powerful compounds called “circumins” that are powerful antioxidant and antiinflammatories. The black pepper helps your body absorb the circumin from the turmeric, and the honey and vanilla are there to provide a little bit of sweetness to start your day.

This beverage is a lot like a latte, so you’ll still get the feeling of a warm and delicious beverage like you would with a cup of coffee. It’s a lot like chai tea as well, also mimicking another beloved caffeinated beverage without the unhealthy effects.