LCT

Researchers have found that previous studies analyzing the genomes of people with European ancestry may have reported inaccurate results by not fully accounting for population structure. By considering mixed genetic lineages, researchers have demonstrated that previously inferred links between a genomic variant that helps digest lactose and traits such as a person's height and cholesterol level may not be valid. Researchers have found that previous studies analyzing the genomes of people with European ancestry may have reported inaccurate results by not fully accounting for population structure. By considering mixed genetic lineages, researchers at the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, demonstrated that previously inferred links between a genomic variant that helps digest lactose and traits such as a person's height and cholesterol level may not be valid. The study, published in Nature Communications, shows that people with European ancestry, who were previously treated as a genetically homogenous group in large-scale genetic studies, have clear evidence of mixed genetic lineages, known as admixture. As such, the results from previous genome-wide association studies that do not account for admixture in their examinations of people with European ancestry should be re-evaluated. "By reading population genetics papers, we realized that the pattern of genetic makeup in Europe is too detailed to be viewed on a continental level," said Daniel Shriner, Ph.D., staff scientist in the NIH Center for Research on Genomics and Global Health and senior author of the study. "What is clear based on our analysis, is when data from genetic association studies of people of European ancestry are evaluated, researchers should adjust for admixture in the population to uncover true links between genomic variants and traits." To look at European genetic ancestry, the researchers collated data in published genetic association studies and generated a reference panel of genomic data that included 19,000 individuals of European ancestry across 79 populations in Europe and European Americans in the U.S., capturing ancestral diversity not seen in other large catalogs of human genomic variation. As an example, the researchers investigated the lactase gene, which encodes a protein that helps digest lactose and is highly varied across Europe. Using the new reference panel, they analyzed how a genomic variant of the lactase gene is related to traits such as height, body mass index and low-density lipoprotein cholesterol, also known as "bad cholesterol." When the researchers considered the genetic admixture of the European population in their analysis, they found that the genomic variant that gives people the ability to digest lactose is not linked to height or level of low-density lipoprotein cholesterol. In contrast, the same variant does influence body mass index. "The findings of this study highlight the importance of appreciating that the majority of individuals in populations around the world have mixed ancestral backgrounds and that accounting for these complex ancestral backgrounds is critically important in genetic studies and the practice of genomic medicine," says Charles Rotimi, Ph.D., NIH Distinguished Investigator, director of the Center for Research on Genomics and Global Health and senior author of the study. While the lactase gene is one example of a gene that may be incorrectly linked to some traits based on previous analyses, the researchers say it's likely that there are other false associations in the literature and that some true associations are yet to be found. Information about how genomic variants are related to different traits helps researchers estimate polygenic risk scores and may give clues about a person's ability to respond safely to drug treatments. While the differences in any two people's genomes are less than 1%, the small percentage of genomic variation can give clues about where a person's ancestors might have come from and how different families might be related. Information about who a person is biologically descended from, known as genetic ancestry, can give important clues about genetic risks for common diseases. "Finding true genetic associations will help researchers be more efficient and careful with how further research is conducted," said Mateus Gouveia, Ph.D., research fellow in the Center for Research on Genomics and Global Health and first author of the study. "We hope that by accounting for mixed ancestries in future genomic analyses, we can improve the predictive value of polygenic risk scores and facilitate genomic medicine." The reference panel generated in this study is available to the scientific community for use in other studies, with additional information provided in the paper.

A new study has found evidence of cheesemaking, using milk from multiple animals in Late Neolithic Poland. A new study has found evidence of cheesemaking, using milk from multiple animals in Late Neolithic Poland. The research suggests that early farmers reduced the lactose content in milk by making it into cheese or other dairy products like yoghurt, and used dairy products from a number of different animals, such as cows, sheep or goats. Lactose intolerance was a common condition in almost everyone in Europe during the Neolithic and until the Late Bronze Age when the genetic mutation became widespread, enabling adults to produce lactase, the enzyme which breaks down lactose in the body. Researchers looked at the practice of dairy processing in the Late Neolithic, identifying high curd-content residues in pottery indicating cheesemaking, and revealing that multiple dairy species were utilised. Dr Harry Robson, from the Department of Archaeology at the University of York, said: "These results contribute significantly to our understanding of the use of dairy products by some of the earliest farmers of Central Europe. "Whilst previous research has shown that dairy products were widely available in some European regions during this period, here, for the first time, we have clear evidence for a diversified dairy herd, including cattle, sheep and goats, from the analysis of ceramics." The scientists and archaeologists from the Universities of York, Cambridge, Toru? and Kraków used a multi-stranded proteomic and lipid-analysis approach to investigate ceramics and deposits on their surface, from the site of S?aw?cinek in central Poland. The new development provides evidence that cheesemaking (and other curd-enriching dairy processing) can be directly detected by scrutinising the proportion of curd proteins, by comparing proteomic data. The results are also the first of their kind in Europe. Despite widespread lactose intolerance in the period, there is evidence of dairy being consumed during the Neolithic, such as animal bones with kill patterns expected for dairy herds, dairy lipids in ceramic vessels, and dairy proteins in ancient dental calculus or plaque. Lead author, Miranda Evans, PhD student at Cambridge's Department of Archaeology, said: "The proteomic results showed that the ancient residues closely resembled both the modern cheesemaking residues and cheese itself and not whole milk. This reveals that the people of S?aw?cinek practised cheesemaking or another form of curd-enriching dairy processing." Evidence of multiple species used for cheesemaking was backed up by the presence of both cow and sheep or goat bones on the site." Dr Jasmine Lundy from the Department of Archaeology, said: "This study highlights how complementary lipid and proteomic analyses are, particularly in understanding the use of the ceramic vessel over time. From this, for example, we could see that not only did some techniques waterproof or seal the ceramics but also what foods were being produced in them.

Researchers demonstrate the implementation of a remote laboratory activity to teach students about enzyme kinetics. The COVID-19 pandemic forced teachers across the globe to embrace remote learning. Although adapting existing materials was relatively easy for lecture-based courses that revolved around theory, teaching laboratory classes remotely presented a formidable challenge. In a new paper, researchers from the Department of Bioengineering demonstrate the implementation of a remote laboratory activity to teach students about enzyme kinetics. "A significant challenge for online learning is the delivery of hands-on lab coursework. During the COVID-19 pandemic, we developed and shipped kits with supplies and reagents to provide lab experience to remote students," said Karin Jensen, a Teaching Assistant Professor of Bioengineering. "We wanted to help students practice techniques and perform experiments remotely using protocols that do not require large and expensive equipment that students normally have access to in our instructional lab." Previously, the researchers had developed remote exercises to teach students how to use micropipettes using at-home kits. Now, they are focusing on how to teach undergraduate students about enzyme kinetics, which looks at how quickly an enzyme breaks down its target to form a product. To do so, the team has developed an at-home enzyme kinetics kit that can be used as an alternative to traditional techniques that are performed in a laboratory setting. "While other instructors have developed lab kits in the past, none of those were focused on teaching enzyme kinetics, which is particularly challenging given the specialized equipment normally required to accurately measure the products of the enzymatic reactions" said Pablo Perez-Pinera (ACPP), an associate professor of bioengineering. "We used very basic and affordable equipment to teach students how to perform simple experiments and rapidly collect data to study enzyme kinetics." The students were studying how the enzyme lactase converts lactose to glucose. The kit included micropipettes; scales; lactose; lactase pills; and a glucose meter. In the weeks prior to the exercise, the students were trained remotely to use micropipettes and were taught to record data in electronic lab notebooks. After watching a prerecorded lecture on enzymes, they were provided with instructions on how to carry out the experiments. Eileen Johnson, a graduate student teaching assistant in bioengineering who taught the remote lab sections, engaged students in the activity by creating a friendly competition for students to design and conduct their own experiments. After meeting with the instructors and learning the basics of the experiment, the students were asked to investigate how different perturbations changed the kinetics of the reaction: do different brands of lactase make a difference, does boiling the lactase change anything, and does freezing the enzyme change the outcome? After introducing such variables, the students met with the instructors and presented their results. "Several students reported that the enzyme kinetics lab was one of their favorite parts of the course," said Abhishek Bhattacharjee, an undergraduate student in the Department of Bioengineering and lead course lab assistant who developed and optimized the protocols. "Our main limitation was the small number of students who provided feedback. Our future work will include additional and formal assessment of student feedback." The need for such at-home kits will remain long after the pandemic. For example, students who cannot attend in-person labs, those in summer camps, or participants of online programs may still require remote lab learning opportunities. The researchers hope that similar lab activities will also help in increasing access to STEM education.