"The greatest amount of life can be supported by great diversification of structure." Charles Darwin

Wednesday, December 17, 2014

Synthetic chemistry goes green

It goes very unnoticeable how many plant natural products we consume in our daily life. The mint-flavored menthol in toothpaste and mouthwash, aloe extract in soothing moisture lotion, geranium extract in body wash, orange flavor in juice beverages, caffeine in all caffeinated drinks, and vanillin in almost all vanilla-flavored food. You name it. What if these plant natural products are no longer coming from plants? Decades of research in plant metabolism has led to detailed understanding in metabolic pathways that give rise to many plant natural products. Now researchers have started exploiting this knowledge, and implementing these pathways in microbes to produce targeted plant natural products. The idea is very clear. By doing fermentation instead for plantation, harvesting, and extraction, one can get the same final products, hopefully with much higher yield and purity. Natural products produced in such way have already existed on the market. For example, the specific flavor compound nootkatone, a sesquiterpene enriched in grapefruit peels, now can be produced in massive quantity from an engineered yeast strain expressing the terpene synthase that makes this compound in grapefruit (http://www.allylix.com/). Since the final product is exactly the same chemical, the next time when you grab a can of grapefruit-flavored juice, you would never be able to tell whether the flavor is from plants or from the engineered yeast. For some harder-to-get natural products, e. g. flavor compounds from Indian sandalwood, which is highly desirable in the perfume industry, it would be highly profitable and also beneficial to the environment, if one can come up with synthetic ways to produce them in microbes. 

Metabolic engineering of microbes for producing high-value plant natural products is a emerging field both in academic research and industry. I would not be surprised to see more and more commodity natural products currently prepared from plants being replaced by the same molecules produced from engineered bugs.

The same topic was also recently covered on NPR, if you are interested.
Mattheos Koffas (left), a biochemical engineer at Rensselaer Polytechnic Institute, and Andrew Jones, a graduate student in his lab, with a flask of microbe-produced antioxidants.
Mattheos Koffas and his colleagues at Rensselaer Polytechnic Institute have developed E. coli strains that can produce plant anthocyanins, the purple pigment compounds highly enriched in purple cabbage.

Sunday, October 26, 2014

A short video highlighting our research on exploring plant metabolism by genetics and metabolomics approaches

Narrated by: Anastassia Bobokalonova
Produced by: MITK12Videos

Not the regular rhubarb you use for making carrot cake

Rheum nobile, or the Noble rhubarb, is a giant herbaceous plant native to the Himalaya, belonging to the Polygonaceae family. It has such an exotic tower-shape strucutre, so it is hard to believe it is actually related to rhubarb and buckwheat, which are more common plant species in the Polygonaceae family. Rheum nobile are found in the alpine zone at 4000–4800 m altitude, with very few other plants and animals living around.

Rheum nobile has an amazing body plan. Its outer curtain of translucent bracts can pass visible light, creating a greenhouse effect, while blocking ultraviolet radiation. This trait is thought to be a key adaptive feature for Rheum nobile to survive in the harsh high-altitude environment with excessive UV-B radiation and low temperature. Several quercetin flavonoids have been identified in the bracts of Rheum nobile as the major UV protectants in this plant.

A recent study published in the New Phytologist uncovered a secret trick of its lifecycle. Rheum nobile is a selfer, but relies on Bradysia flies for pollination. Seed production resulting from pollination then becomes the food for Bradysia larvae. It also appears that Bradysia flies are particularly attracted by the floral scent emitted from Rheum nobile. This pollinating seed-consuming mutualism represents a remarkable symbiotic adaptation for species to survive in extremely harsh enviroments.

(d) Female and male Bradysia sp. mating outside the bract. (e) A female fly visiting a flower. (f) An ovipositing female fly. (g) A pollinated stigma. (h) A fruit infested by a fly larva. (i) Pupae of fly under litter. Image from Song et al. New Phytol 2014 

Friday, May 23, 2014

Here present the longest-living organism on this planet: It's a plant!

It is somewhat not surprising that plants are among those longest-living organisms. The Hatch Tree (Pinus longaeva) found in White Mountains, California, has a verified age of 5,063 years, and is the longest-living nonclonal organism on Earth. 

Another interesting species, Llareta (Azzorella compacta), a member of the celery family, native to South America can also live up to thousands of years. It is a very slow-growing plant, which grows approximately 1.5 centimeters per year.
File:Azorella compacta close-up.JPG
Why certain plants can live up to thousands of years is a great question posed to modern biologists. Can we learn from these amazing organisms to benefit the well-being of mankind?

Saturday, April 19, 2014

Plants manipulated by their worst enemies

Just came across a new paper published in PLOS Biology "Phytoplasma Effector SAP54 Hijacks Plant Reproduction by Degrading MADS-box Proteins and Promotes Insect Colonization in a RAD23-Dependent Manner" by MacLean et al. It is a remarkable story where specialized bacterial obligate parasites phytoplasma deliver effector protein SAP54 that interactswith a number of transcription factors in plants key for floral development. The he abnormal development of floral parts into leafy structures then make the infected plants more attractable to leafhopper vectors helping the obligate phytoplasmas reproduce and propagate. Plants can be manipulated by their worst enemies in such precision and turned into zombie plants!
File:Phyllody on Coneflower with aster yellows.jpg
Echinacea purpurea flowers undergoing phyllody (the scientific term for the abnormal development of floral parts into leafy structures), induced by phytoplasma infection.

Leafhoppers serve as the veihcles for the transmission of phytoplasma parasites
Phloem tissue infected with phytoplasma

This new discovery is reminiscent of crown gall, which is a well-studied disease in plants caused by the bacterium Agrobacterium tumefaciens. Crown galls are tumor-like structures often found at the base of many woody plants. It happens that Agrobacterium is capable of inserting a piece its own gene, known as T-DNA, into the plant genome. The gene products of the T-DNA will then transform the infected cells as a biosynthetic factory to manufacture opines used as a unique source of nitrogen for A. tumefaciens, but not for most other organisms. We as humans have successfully engineered Agrobacterium tumefaciens and its T-DNA to make any kind of transgenic plants nowadays.
Crown gall on an spindle tree

Sunday, March 2, 2014

Are scientists fooling themselves?

I came across this article recently published on Nature "Statistical errors: P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume" by Regina Nuzzo, and immediately connect to the reproducibility crises in biomedical research in recent years. I still remember that early in my graduate school one professor told me that those best stories do not actually require statistics, because the results are just black and white. I still believe in the power of statistics in biology. However, it should not be used to validate what we want to see at the first place.

Saturday, January 11, 2014

A body map for emotions!

Different emotions are associated with discernible patterns of bodily sensations. (Credit: Image courtesy of Aalto University)

This recent study published on PNAS shows how different emotions affect different parts of our body. The research was carried out using a unique topographical self-report method. See how our cheeks turn red when we feel ashamed or embarrased. It's totally cool!

In traditional Chinese medicine, there is this old philosophy about "Qi", or "natural energy flow" in human body. Drastic emotional swings are thought to disrupt the balance of "Qi" in human body in different ways. For example, anger is often linked to damage in liver, whereas fear is thought to lead to harm in kidneys. This paper indeed connects the abstract concept of "Qi" with some measurable indices in our body.