Coffee is the perfect blend of caffeine, smell and taste.

Researchers have sequenced coffee's genome, revealing the evolution of caffeine in the plant and providing insights into the popular drink's flavor and aroma. The genome sequence also gives scientists a tool to quickly locate specific genes on specific coffee chromosomes, a resource that could help them improve coffee breeding, accelerate the development of new coffee varieties and increase the plant's response to environmental stresses such as climate change and pests. Frances Denoeud and colleagues used advanced sequencing techniques to obtain a draft genome of medium-fruit coffee, commonly known as Robusta coffee, which accounts for about 30 percent of coffee production worldwide. Medium fruit coffee is one of the two most important types of coffee commercially available, the other being Arabica coffee, which accounts for most of the rest of the world's coffee production because of its lighter acidity (a result of its lower caffeine concentration). To identify the unique gene family of Coffea arabica, Denoeud et al. ran comparative genomics software on protein sequences from coffee, grape, tomato, and Arabidopsis. They identified more than 16,000 genes in these plants that originated from a single gene from a last common ancestor. Further analysis revealed valuable adaptations unique to coffee genes, including in disease-resistant genes and caffeine-producing genes; enzymes involved in caffeine production in coffee underwent adaptations independent of those in cocoa and tea, the researchers said. In contrast to Arabidopsis thaliana, which has a gene for linoleic acid, an important contributor to aroma and taste, coffee has six genes for linoleic acid. DaniZamir highlighted the importance of transforming the coffee genome into a new tool for coffee cultivation, especially at a time when diversity in coffee plants is declining globally.

As part of this process, Zamir said, scientists must share phenotypic data (for traits like aromas and flavors) so that gene sequences can be clearly linked to the phenotype behind their desired. Zamir said the effort is critical to ensuring that variation persists in coffee plant varieties, which in turn will help mitigate the effects of unstable weather and plant diseases on the crop.

A soft, shape-changing new material formulation

By placing liquid crystals on soft, deformable liquid containers or vesicles, researchers have designed a new, shape-changing material that mimics the very complex properties of a living organism. Their findings demonstrate that topological constraints such as liquid crystals placed on active substances can accommodate internal defects that drift and self-align spontaneously, resulting in structures and dynamics not available in traditional equilibrium systems. Felix Keber and colleagues coated lipid vesicles with liquid crystals containing microtubules, kinesin dynamos, or the polymer polyethylene glycol (PEG) and found that coordinated movement of defects in these crystals resulted in a wide range of interactions between the two materials. For example, when researchers wrapped a spherical vesicle in a kinesin-doped liquid crystal film, they found that the system oscillated back and forth between planar and tetrahedral configurations. The timescale of these physical changes can be controlled by the size of the sphere and the protein engine that drives it, they say. Keber and his colleagues also found that deflating or reducing the diameter of the vesicle caused four filiform foot-like projections to grow at the defect site. When the vesicles inflate back and have an expansion in diameter, the bumps decrease in size and eventually disappear, they say. Together, their findings demonstrate that topological constraints can be used to control the nonequilibrium dynamics of reactive substances such as liquid crystals.

How marine microbes respond to limited nutrients

Two new studies advance understanding of how nutrient availability affects protein production by marine microbes. Depending on the concentration of nutrients available in the surface waters of the ocean, marine organisms such as phytoplankton produce proteins that play a role in important processes in the ocean, for example, they act as catalysts for nutrient cycling reactions. So far, scientists have not been able to figure out how a single nutrient limits marine microbial growth. However, thanks to recent advances in mass spectrometry, they are beginning to be able to detect microbial proteins in their natural environment (as substitutes for nutrient scarcity). Using this technique, MakSaito and colleagues have shown for the first time that they can accurately detect the amount of specific proteins from specific marine microbial species at different locations in the ocean. Saito et al. collected samples along a 2500-mile stretch of the Pacific Ocean. Their work spans regions with widely varying nutrient concentrations, from those rich in iron to those with low iron but rich in phosphorus and nitrogen. Back in the lab, they used mass spectrometers to distinguish and detect specific proteins and identify them by their peptide sequences. While previous field studies have been based on the idea that microbial growth is controlled by a single most scarce nutrient, here Saito and colleagues show how multiple scarce nutrients can work together to affect marine microbial communities.

In a second study, Shee Yong et al. provided new insights into the need for trace metals by marine plankton to extract phosphorus from a low-phosphorus marine environment. Normally, plankton use an enzyme that binds zinc to do this, but Yong et al. show here that instead a phosphatase is structured to bind iron. Depending on the relative availability of iron or zinc in the ocean, plankton can thus choose between the two phosphatases. Together, these studies reveal how marine microbes respond to limited nutrients by regulating the abundance of specific proteins.