Red, White and Grape: From Jumping Genes to Wrapping Leaves

Red, White and Grape: From Jumping Genes to Wrapping Leaves

Red or White? Even King Tutankhamun (1332-1322 B.C.) prudently stashed away amphorae of both red and white wines to enjoy in the afterlife. Biochemically, a single class of pigments found in grape skin, the anthocyanins, separates the red from white. White grapes arose from their wild, dark berried ancestors by not one, but two rare and independent genetic events: either one alone would not have given us the white grape. In fact, all ~3000 white cultivars today carry these same gene disruptions, pointing back to a common ancestor that arose millennia ago. The disrupted genes code for transcription factors, aka master regulators of biochemical pathways that can turn other genes on or off.

Science sleuths have peeked back into the gene history of Vitis vinifera to figure this out.

First, the MybA gene duplicated, giving two side-by-side copies, both active in making anthocyanins and red berries. Somewhere along the way, one of them, the MybA2 gene accumulated two mutations (depicted as stars) that rendered the resulting protein non-functional.

Independently, a “jumping gene” or retrotransposon, (green triangle) landed within the adjacent backup gene MybA1, knocking it out as well. The resulting plant, termed heterozygous, still bore red berries, because the unmutated genes on the other chromosome were active. Eventually, two heterozygous plants bred together and some offspring received both chromosomes with two nonfunctional MybA genes.

Voila, white grapes!

If you’ve ever snacked on delicious dolmas, then you know that the goodness of the grape vine goes beyond berries. Legend has it that the gods of Mount Olympus feasted on the tender leaves of the grape wrapped around morsels of rice or meat, alongside ambrosia and nectar! Although stuffed grape leaves are common around the Mediterranean, Greeks claim that dolmades were co-opted by the army of Alexander the Great to parcel out limited rations of meat during the seige of Thebes.  Luckily, you only need to lay seige on your local Middle Eastern grocery store to find jarred leaves, preserved in brine. Unfurl them gently and give them a good wash to get started. It doesn’t hurt to have a glass of your favorite vintage, red or white, on hand before embarking on this project!

For the recipe on stuffed rice dolmas, visit my blog at: https://madamescientist.wordpress.com/2016/02/20/red-white-and-grape-from-jumping-genes-to-wrapping-leaves-for-dolma/

REF:White grapes arose through the mutation of two similar and adjacent regulatory genes. Walker et al., 2007 http://www.ncbi.nlm.nih.gov/pubmed/17316172

Posted in Rajini Rao | 72 Comments

Red, White and Grape: From Jumping Genes to Wrapping Leaves for Dolma

IMG_4066

Red or White?

Even King Tutankhamun (1332-1322 B.C.) prudently stashed away amphorae of both red and white wines to enjoy in the afterlife. Biochemically, a single class of pigments found in grape skin, the anthocyanins, separates the red from white. White grapes arose from their wild, dark berried ancestors by not one, but two rare and independent genetic events: either one alone would not have given us the white grape. In fact, all ~3000 white cultivars today carry these same gene disruptions, pointing back to a common ancestor that arose millennia ago. The disrupted genes code for transcription factors, aka master regulators of biochemical pathways that can turn other genes on or off.

Grape Color

How White Grapes Arose: From Walker et al., 2007 

 Science sleuths have peeked back into the gene history of Vitis vinifera to figure this out.

First, the MybA gene duplicated, giving two side-by-side copies, both active in making anthocyanins and red berries. Somewhere along the way, one of them, the MybA2 gene accumulated two mutations (depicted as stars) that rendered the resulting protein non-functional.

Independently, a “jumping gene” or retrotransposon, (green triangle) landed within the adjacent backup gene MybA1, knocking it out as well. The resulting plant, termed heterozygous, still bore red berries, because the unmutated genes on the other chromosome were active. Eventually, two heterozygous plants bred together and some offspring received both chromosomes with two nonfunctional MybA genes.

Voila, white grapes!

If you’ve ever snacked on delicious dolmas, then you know that the goodness of the grape vine goes beyond berries. Legend has it that the gods of Mount Olympus feasted on the tender leaves of the grape wrapped around morsels of rice or meat, alongside ambrosia and nectar! Although stuffed grape leaves are common around the Mediterranean, Greeks claim that dolmades were co-opted by the army of Alexander the Great to parcel out limited rations of meat during the seige of Thebes.  Luckily, you only need to lay seige on your local Middle Eastern grocery store to find jarred leaves, preserved in brine. Unfurl them gently and give them a good wash to get started. It doesn’t hurt to have a glass of your favorite vintage, red or white, on hand before embarking on this project!

IMG_4071

We start with the stuffing: by now you know that I am an obligate vegetarian (although sorely tempted toward venison when the deer enroach on my lilies), so I opted for a rice filling. In a tablespoon of olive oil, saute a cup of chopped onions until translucent. Add a clove or two of minced garlic, a cup of diced tomatoes and a cup of rinsed rice (any kind will do). That’s it, turn off the heat. Now season the mix: salt and pepper, of course. A cup of chopped parsley. A teaspoon of ground cumin. Some cayenne or smoked paprika, if you like it (love!). A handful of pine nuts or chopped walnuts for texture. A handful of raisins or currants for an unexpected burst of sweetness. A tablespoon of pomegranate molasses (or substitute a good squeeze of lemon). Recipes and variations abound!

IMG_4061

Rice stuffing for dolmas: savory with a touch of sweetness, a bite of nuts and the tang of pomegranate molasses.

Let cool while you chill with the wine. This last step is important because you will need to be patiently mellow for the next step.

Working on a clean counter with a big platter (and glass of wine) close at hand, begin by laying a grape leaf vein side up. Add a teaspoon of rice stuffing to the leaf center, just off the base. Yes, only one teaspoon. I find it easy to first press it into an oblong in the palm of my hand. Follow the directions on any YouTube video to fold in the leaf, first the bottom lobes, then the sides, and finally into a neat little cigar. Mine are not so neat, but I blame the wine. Repeat n-times, until (i) the stuffing or (ii) your patience is used up. Pile the parcels on the platter, seam side down as you go along.

IMG_4062

Do not worry if some of the stuffing busts out before or after cooking. These are the ones that get eaten first!

Bring 3 cups of water to boil. Lubricate a heavy bottomed pot with a swirl of olive oil, and arrange a layer of sliced potatoes on it. These protect the dolmas from sticking to the bottom. You can also line with grape leaves, but the sliced potatoes make for a tasty garnish when done. Next, arrange the stuffed grape leaves in layers. Top with slices of lemon. Finally, add the juice of one lemon and a tablespoon of olive oil to the hot water. Pour it into the pot until it is level with the top layer of dolmas. The amount of water is not critical, as it will eventually get absorbed into the dolmas. Hold the dolmas in place with a heat proof plate and weigh it down with something heavy. Let simmer away for a good hour or so. Cool completely, as dolmas are best served at room temperature. This can be made a day ahead and stashed in the refrigerator to allow the flavors to meld.

IMG_4063

I served the dolmas with dollops of Lebanese yogurt or labneh, sprinkled with za’atar and a side of grilled halloumi cheese. Rescue the sliced potatoes and lemons- they taste great too!

IMG_4065.JPG

Although I don’t grow grape vines in my Maryland backyard, here are some red fall berries from the heavenly bamboo Nandina, as an ode to the anthocyanins.

IMG_3822

 

 

 

 

 

 

 

 

 

Posted in FOOD, Garden, Middle Eastern, science, Spices, Vegetarian | Tagged , , , , , | 2 Comments

Owl Be Seeing You

Owl Be Seeing You

It’s time for the #SuperbOwl and #ScienceSunday ! 

Did you know that the eyes of an owl are 5% of its body weight? Imagine Peyton Manning with eyes the size of a baseball.. errr…football. Their large pupils dilate at night, harvesting more light to be captured by an abundance of rods, specialized for night vision. Their eyes don’t have as many cone cells as we do, so their color vision is not that great. But they can see up to 100 times better than the Broncos at night! 

How does the owl rotate its head without wringing its neck? An owl has twice as many vertebrae compared to the 7 in humans, giving it a 270 degree flexibility, without tearing the delicate blood vessels in their necks and heads, and cutting off blood supply to their brains.. That’s because unlike human vertebrae, the vertebrae of the owl have large cavities, about ten times the diameter of the vertebral artery that goes through, allowing for plenty of slack. The artery also enters the cervical vertebrae at a higher point, for more freedom of movement. It is heavily networked so that blood supply to the brain and eyes is not interrupted by twisting of the neck even if one route is blocked. Astonishingly, the blood vessels at the neck became wider as they branched, in contrast to that of mere humans, where they get smaller and narrower. 

Read More: http://goo.gl/hFUq2 Research by Michael Habib  and colleagues at Johns Hopkins University on the mystery of the Owl’s neck. This award winning study was featured in Science magazine and may be the first use of angiography, CT scans and medical illustrations to unravel the mystery of the magnificent owl. 

For rare avis  who wanted to know about the #SuperbOwl 🙂

Image Source: Northern Hawk Owls  https://vimeo.com/17355313

Posted in Rajini Rao | Tagged , | 107 Comments

Why are there “dew drops” at the tips of leaf veins?

Why are there “dew drops” at the tips of leaf veins?

❦ Have you ever seen clear orbs of water glisten along a leaf edge? You may have mistaken them for dew drops, which are caused by moisture from the air condensing on cool surfaces. But these drops are only found at the edges of leaves and if you look around- they won’t be found on dead leaves. So what are they?

❦ Plants use a plumbing system of xylem tubes to move water and nutrients. During the day, transpiration (water evaporation) from leaves creates a vacuum that pulls the column of water up from the roots to the leaves. At night, the stomata (leaf pores) close, transpiration stops and salts accumulate in the xylem of roots, drawing in water from the surrounding soil by osmosis. The excess water rises up the xylem tubes and is forced out at the leaf tips through openings called hydathodes. This exudation of plant sap is known rather inelegantly as guttation, and only happens at night. The water pressure is not strong enough to rise beyond 3 feet, so guttation is not seen on tree leaves. The thermal image (inset) taken by infrared photography shows the cooler temperature (blue) in the guttation droplets.

❦ When the drops dry, they sometimes leave behind a residue of salts and minerals. This is not a problem, unless the soil is over-fertilized resulting in fertilizer burn of leaf tips. In the same way, guttation droplets in corn seedlings were shown to have high levels of neonicotinoid compounds, used as pesticidal coatings on the seed. These concentrations could be a lethal dose for honey bees that sip on guttation drops as a water source. While shedding toxins through guttation drops protects the plant, it may have repercussions – both beneficial and harmful, on insects and other animals. 

Inset of thermal image: http://thermal-imaging-blog.com/index.php/page/13/#.Vq1LIvkrLcs

REF on neonicotinoids in guttation droplets #openaccess: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284396/

Posted in Rajini Rao | Tagged | 166 Comments

The Flight of the Hummingbird

The Flight of the Hummingbird

A route of evanescence

With a revolving wheel

A resonance of emerald,

A rush of cochineal

With these words, the poet Emily Dickinson summed up the fleeting magic of the hummingbird.  

Hummingbirds are the only vertebrates capable of hovering in place. In addition to flying forwards, they can also fly backward and upside down! They are tiny: the smallest bee hummingbird of Cuba weighs less than 2 grams, less than a penny! Add to this their speed- they can clock up to 45 mph, and stamina- they can fly 18 straight hours, and you may appreciate their unusual metabolism. In fact, they have the highest metabolic rate of any warm blooded animal. 

With a heart beat of 1,200/min and wing beat of 200/sec during flight, hummingbirds generate a tremendous amount of heat. Because their muscles are only ~10% efficient, much of the energy they consume is released as heat. But their thick plumage of feathers keeps in the heat: useful when the bird wants to conserve body heat, but a problem during flight. 

Using infrared thermal photography, scientists have found that hummingbirds (and probably most birds) lose body heat from three areas seen as bright white spots in the gif below: the region around the eyes, at the shoulder where the wings meet the body, and the feet, which they can dangle downward to dissipate even more heat. 

Ref: http://rsos.royalsocietypublishing.org/content/2/12/150598

Video: https://www.youtube.com/watch?v=btuu_hDU7B4

Posted in science | Tagged | 59 Comments

Gene Drives: Green Signal or Back Seat?

Should we use Gene Drive engineered mosquitoes to fight Malaria? Poll results: 972 votes on Google Plus, 11/2015

What is the deadliest animal on earth? If you’re thinking of the great white shark or a venomous snake, you could be wrong. Counting human deaths, it is the innocently named (Spanish for “little fly”) mosquito. Millions, mostly children in third world countries, are killed or sickened each year by malaria, dengue, yellow fever and encephalitis caused by parasites and viruses that are transmitted by mosquito bites. This happens despite billions of dollars spent, years of research and potential cures ranging from vaccines and drugs to public health management. 

Stop or Go, that is the Question: Imagine if the mosquito could kill the parasite before it has the chance to spread to its human victims. For example, the mosquito could be engineered to make antibodies against Plasmodium, killing the parasite soon after it enters the mosquito after a blood meal. Just like a vaccination, nearly all mosquitoes would need to carry this new trait to be effective. There is a way to do this and it is not a new idea. What used to be theory, however, has just become a reality. A new paper published in the journal PNAS has now changed the question from Can we do this? to Should we do this?

What are Gene Drives?: Normally, the chance that any gene trait is passed from parent to offspring is 50%, since only one of a chromosome pair is inherited from that parent. But some selfish genes can copy themselves so that both chromosomes carry the trait, which now affects 100% offspring. A gene drive consists of DNA sequences that provides the technical ability to do this. With the new CRISPR/Cas9 tool that precisely cuts and inserts any gene of interest, the gene drive has become a reality. 

Can Gene Drives work on Humans? Gene drives work best in fast reproducing species, like mosquitoes, that can be released in large numbers. For this reason, they are not going to be effective in spreading inadvertently through humans, or even commercial crops and animals which are bred by controlled processes like artificial pollination and insemination.  

Gene Drives are Natural: For example, a gene called P element swept through all fruit flies in the wild, but is not found in lab strains that were isolated before it spread. 

Gene Drives can be Reversed: For each gene drive that spreads a trait, a reverse gene drive can undo the genetic changes in the original strain. Such reversal drives should be tested in advance, and could be released to stop the spread of any unintended consequences.

What else can Gene Drives do? Besides targeting mosquitoes, gene drives could be used to eradicate invasive species, or reverse resistance to herbicides and pesticides. 

Take the Poll: A public conversation based on sound scientific information, weighing pros and cons, must be the starting point for developing policy. Engineered mosquitoes that could rapidly spread in the wild and eradicate the malarial parasite have been made. Here is the question: Should we use Gene Drive engineered mosquitoes to fight Malaria? 

FAQ on Gene Drives: http://goo.gl/V3Jmz1

Image: Matt Panuska

Pop Science Read: http://goo.gl/oROVBG

Advanced Read: http://goo.gl/uTN47v

Posted in science | Tagged | 84 Comments

I am really worried about priorities..

I am really worried about priorities..

❖ On a recent science post about the evolution of land plants, a community member worried: “what about poverty?? people are dying in hunger, lack of medical support, clean water and other simple things which can be fixed… but without fixing something for them we are trying to find water in Mars. I’m really worried about the priorities..”

❖ A similar comment lamented the cost of curiosity in the search for earth-like planets (http://goo.gl/9OUM0D). Physics professor Robert McNees had an awesome response:

❝ You posted your comment using technology that exists only because of a chain of discoveries and insights that began with fascination-driven research in the late 19th century.❞

❝ If Balmer hadn’t studied spectral lines, Planck may not have proposed the quantum. Then Bohr may not have conceived his model of the atom, which means Heisenberg and Schrödinger wouldn’t have developed their formulations of quantum mechanics. That would have left Bloch without the tools he needed to understand the nature of conduction in metals, and then how would Schottky have figured out semiconductors? It’s hard to imagine, then, how Bardeen, Brattain, and Schockley would have developed transistors. And without transistors, Noyce and Kilbey couldn’t have produced integrated circuits.❞

❝ Almost every major technological advance of the 20th and 21st centuries originated with basic research that presented no obvious or immediate economic benefit. That means no profit motive, and hence no reason for the private sector to adequately fund it. Basic research isn’t a waste of tax dollars; it’s a more reliable long-term investment than anything else in the Federal government’s portfolio.❞

GIF: Johns Hopkins professor Andy Feinberg spent several days on NASA’s zero gravity aircraft (known as “vomit comet”) trying out different pipetting techniques for future experiments in space. It wasn’t that easy with flying pipet tips and tubes! Andy did eventually figure out the best technique (using positive displacement pipets, seen in the second video in this link http://goo.gl/AFpnJq). Feinberg is leading one of ten experiments in NASA’s Twin Study to examine epigenetics and other biological changes that affect astronauts in space. Samples from Scott Kelly, who is spending a year onboard the ISS, will be compared with those from his twin on earth, Mark. Feinberg credits NASA for funding this study. He says, “They’re very curious people. They really want to know.”

Who knows, one day we may even grow potatoes on Mars! 🙂

Share your favorite example of the unexpected benefits of basic research! 

Shout out to Gnotic Pasta  who made the GIF. Thanks, Dan! 

Posted in Rajini Rao | 89 Comments