“Much of what we understand about the known two per cent of the genome that codes for proteins comes from looking for long strands of protein-coding nucleotide sequences, or long open reading frames,” explained computational biologist Dr Sonia Chothani, a research fellow with Duke-NUS’ Cardiovascular and Metabolic Disorders (CVMD) Programme and first author of the study. “Recently, however, scientists have discovered small open reading frames (smORFs) that can also be translated from RNA into small peptides, which have roles in DNA repair, muscle formation and genetic regulation.”

Scientists have been trying to identify smORFs and the small peptides they code for, since disruption in these smORFs can cause disease. However, currently available approaches are very limited.

“Much of the current datasets do not provide information that is detailed enough to identify smORFs in RNA,” added Dr Chothani. “The majority also comes from analyses of immortalised human cells that are propagated — sometimes for decades — to study cell physiology, function and disease. However, these cell lines aren’t always accurate representations of human physiology.”

Publishing in Molecular Cell, Chothani and her colleagues in Singapore, Germany, the UK and Australia describe a methodology they developed to address these issues. They screened currently available ribosome profiling datasets for short strands of RNA with periodic three-base sections, covering more than 60 per cent of the RNA’s length. They then conducted their own RNA sequencing and Ribosome profiling to generate a combined data resource of six types of cells and five types of tissue, such as from the heart and the brain, derived from hundreds of patients.

Analyses of these data identified nearly 8,000 smORFs. Interestingly, they were highly specific to the tissues that they were found in, meaning that these smORFs may perform a function specific to their environment. The team also identified 603 microproteins coded by some of these smORFs.

“The genome is littered with smORFs,” said Assistant Professor Owen Rackham, senior author of the study from the CVMD Programme. “Our comprehensive and spatially resolved map of human smORFs highlights overlooked functional components of the genome, pinpoints new players in health and disease and provides a resource for the scientific community as a platform to accelerate discoveries.”

Professor Patrick Casey, Senior Vice-Dean of Research at Duke-NUS, said, “With the healthcare system evolving to not only treat diseases but also prevent them, identifying potential new targets for disease research and drug development could open avenues to new solutions. This research by Dr Chothani and her team, published as a resource for the scientific community, brings important insights to the field.”

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The researchers will present their results today at the fall meeting of the American Chemical Society (ACS).

“Plant-based milk alternatives have been growing in popularity, but there’s not a lot known about the mineral content of these products, especially in the U.S.,” says Ben Redan, Ph.D., research chemist at the U.S. Food and Drug Administration (FDA), who is the principal investigator on the project. “Although they can be voluntarily declared, from a regulatory perspective, these minerals are not always required to be on the Nutrition Facts label.”

Made from base ingredients such as soy, almonds or oats, these products provide an alternative to dairy milk for people with allergies or intolerances, or who choose dairy-free diets. Although non-dairy options are increasing in variety and availability, the nutritional content of certain minerals in each type largely remains unknown — with dietary health implications for those who use them as a dairy substitute.

Redan and his colleague Lauren Jackson, Ph.D., performed the study, and they are both at the Institute for Food Safety and Health, a research consortium that includes the Illinois Institute of Technology, FDA and the food industry.

Redan and Jackson chose to measure the amount of magnesium, phosphorus, zinc and selenium in plant-based milk alternatives because these essential minerals are not required on the Nutrition Facts label and are components of dairy milk. In fact, dairy milk is a key contributor of these micronutrients in American diets, and people’s bodies can’t make them. Because people must instead consume foods and beverages with these minerals in them, it’s important to know how much is provided by various milk alternatives.

The researchers analyzed a selection of locally available plant-based beverages that were sold under a variety of brand names. Each product was made from a single base ingredient, such as almond, cashew, coconut, hemp, oat, pea, rice or soy. A technique called inductively coupled-mass spectrometry quantified the minerals present in a total of 85 samples. Using statistical analyses, the team found that the mineral content varied significantly across different product types — for example, soy-based versus almond-based drinks — and even between brands of the same type of product. When considering the amount of each specific mineral, they found that pea-based drinks had the most phosphorus, zinc and selenium, while soy drinks had the highest amounts of magnesium, on average.

Of all the samples analyzed, only pea- and soy-based drinks had higher levels of the four essential minerals than cow’s milk, with pea-based drinks containing about 50% higher levels of phosphorus, zinc and selenium. “These plant-based milk alternatives could be important sources of these micronutrients if you’re trying to reach the recommended dietary allowances for them,” Redan says. “That’s why these data points are important to get out to the public.”

In the end, the researchers hope that their data about essential minerals will help consumers make informed dietary decisions about non-dairy plant-based drink products.

The researchers acknowledge support and funding from FDA.

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The researchers will present their results at the fall meeting of the American Chemical Society (ACS).

“Vanilla is the second-most expensive spice in the world,” says Diana Paola Forero-Arcila, Ph.D., who is presenting this work at the meeting. “One of the reasons it’s so expensive is because its flavor is developed during a curing process that takes up to nine months.”

Two shortcuts are currently used to get around this long, drawn-out curing process. One is to speed it up with quick-curing methods that attempt to recreate the luscious natural vanilla flavor in a fraction of the time. Another is to make artificial vanilla, familiar to consumers as a less pricey alternative to the real thing.

But these types of products fall flat in terms of flavor because they both focus on vanillin, Forero-Arcila explains. Quick curing attempts to maximize the amount of vanillin in the cured bean, whereas artificial vanilla contains only one flavoring agent — lab-made vanillin. Though vanillin is an important part of a vanilla bean’s flavor, the alternative products are missing many other flavor compounds that develop during the long, traditional curing process and that are essential to the distinctive vanilla taste. “It’s very important that we understand the complexity of vanilla’s flavor and try to identify the compounds that are behind that complexity,” says Forero-Arcila.

To capture that complexity, Forero-Arcila, who is a postdoc at The Ohio State University, used an approach called untargeted flavoromics to pinpoint which chemicals in vanilla bean extracts are the most important for the overall aroma and taste. The researchers first made extracts from 15 beans they sourced from various countries and that were cured differently. They then constructed a chemical profile of each type of bean and identified which compounds were present. To find out how people reacted to the extracts, the team asked more than 100 individuals to taste the samples and rate whether they liked or disliked the flavors.

By connecting the dots between the chemical profiles and the taste ratings, the researchers identified 20 compounds that are the main drivers behind whether a person likes the flavor of a vanilla extract. Of these compounds, some, like vanillin, were expected. “Some of the compounds we identified are well-known vanilla components; however, this is the first report of them impacting consumer acceptability,” says Forero-Arcila. And several compounds important for the flavor were completely unknown, says Devin Peterson, Ph.D., the project’s principal investigator. The researchers are still analyzing these novel vanilla compounds to determine the final structures, but they have observed that the compounds have phenolic and aglycone parts. They also identified some compounds present in the extracts that made people dislike the flavor. One example is anisaldehyde, which has a floral aroma. Forero-Arcila found that anisaldehyde is produced during the curing process from a previously unknown precursor.

With this new profile of compounds, the researchers plan to share what they’ve learned with others in the food and agricultural industries. They think that the profile could help producers and farmers identify high-quality, valuable extracts, and price those extracts to match their quality. “The more you understand about how to make the materials more valuable, the more that value should flow through the whole system,” says Peterson. In the future, vanilla breeding programs and curing methods could focus on selectively producing the optimum compound profile for good flavor in vanilla plants.

The researchers acknowledge support and funding from the Flavor Research and Education Center at The Ohio State University.

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The researchers will present their results today at the fall meeting of the American Chemical Society (ACS). 

“The idea for this project initially came about because I was interested in what happens when laser light is used to remove tattoos,” says John Swierk, Ph.D., the project’s principal investigator. “But then I realized that very little is actually known about the composition of tattoo inks, so we started analyzing popular brands.”

Swierk and undergraduates in his laboratory interviewed tattoo artists to see what they knew about the inks they use on their customers. The artists could quickly identify a brand they preferred, but they didn’t know much about its contents. “Surprisingly, no dye shop makes pigment specific for tattoo ink,” Swierk explains. “Big companies manufacture pigments for everything, such as paint and textiles. These same pigments are used in tattoo inks.” He also notes that tattoo artists must be licensed in the locales where they operate for safety reasons, yet no federal or local agency regulates the contents of the inks themselves.

Tattoo inks contain two parts: a pigment and a carrier solution. The pigment could be a molecular compound such as a blue pigment; a solid compound such as titanium dioxide, which is white; or a combination of the two compound types such as light blue ink, which contains both the molecular blue pigment and titanium dioxide. The carrier solution transports the pigment to the middle layer of skin and typically helps make the pigment more soluble. It can also control the viscosity of the ink solution and sometimes includes an anti-inflammatory ingredient.

Swierk’s team at Binghamton University (State University of New York) has been investigating the particle size and molecular composition of tattoo pigments using a variety of techniques, such as Raman spectroscopy, nuclear magnetic resonance spectroscopy and electron microscopy. From these analyses, they have confirmed the presence of ingredients that aren’t listed on some labels. For example, in one case ethanol was not listed, but the chemical analysis showed it was present in the ink. The team has also been able to identify what specific pigments are present in some inks.

“Every time we looked at one of the inks, we found something that gave me pause,” Swierk says. “For example, 23 of 56 different inks analyzed to date suggest an azo-containing dye is present.” Although many azo pigments do not cause health concerns when they are chemically intact, bacteria or ultraviolet light can degrade them into another nitrogen-based compound that is a potential carcinogen, according to the Joint Research Centre, which provides independent scientific advice to the European Union.

In addition, the team has analyzed 16 inks using electron microscopy, and about half contained particles smaller than 100 nm. “That’s a concerning size range,” says Swierk. “Particles of this size can get through the cell membrane and potentially cause harm.”

After the researchers run a few more tests and have the data peer reviewed, they will add the information to their website “What’s in My Ink?” “With these data, we want consumers and artists to make informed decisions and understand how accurate the provided information is,” says Swierk.

The researchers acknowledge support and funding from Binghamton University (State University of New York).

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