Highly cited researchers of the University of Helsinki in the fields of biology and environmental science.
Highly cited researchers: biology, microbiology and environment
Mar Cabeza (b. 1974), Academy Research Fellow in biology, has brought climate change into conservation planning through her research. When local plant and animal populations change as the climate becomes warmer, nature conservation should be more flexible and dynamic, and less tied to one place.
Originally from Catalonia, Cabeza studied biology in Barcelona, but was unable to find a suitable place to work on her doctoral dissertation after completing her Master’s degree. A professor she knew recommended Helsinki.
In her dissertation articles, Cabeza approached spatial ecology, or the combination of geographical parameters and ecological phenomena. Cabeza suggested a model of conservation areas in which species could move from one area to another in a natural way – something that has since become commonplace in conservation area planning.
Conservation area planning and climate change
After completing her dissertation research, Cabeza wrote an article at the suggestion of the famed Professor Miguel Araújo from Madrid, in which she was the first researcher to ask how the principles of conservation area planning would stand the pressures of climate change. Cabeza and Araújo considered many different kinds of conservation area networks, and tested how they would function when species migrate as the climate changes. They found that no system was sufficient.
This discovery, published in 2004, has defined most of Cabeza’s work since.
Cabeza went to Madrid to join Professor Araújo’s team as a postdoctoral researcher, studying the impact of climate change on biodiversity conservation. She was, however, unhappy in Madrid and frustrated by Spanish bureaucracy, so in 2011 she returned to Helsinki.
Her most cited articles are from her time in Madrid. Including considerations of climate change in nature conservation was a true paradigm shift, and Cabeza and her work were at its forefront, first in Madrid and later in Helsinki.
According to the old paradigm – represented by the Natura 2000 conservation network mandated by EU directives – conservation areas are automatically established on sites where the species listed in the relevant directives is found, regardless of whether the species is likely to stay in the area.
The new paradigm championed by Cabeza is characterised by dynamic conservation. This means accepting change. The Earth’s climate has changed many times during the course of its history, due to factors both related and unrelated to human activity, and species have migrated to new territories as a result.
This is why Cabeza believes we should establish networked conservation areas and examine more closely when and where species migrate. Cabeza does not want to change the location of nature conservation areas, just their administration, funding and goals. In a few decades, the conservation areas’ indigenous species may migrate away and be replaced by others – but the areas may still remain ecologically important.
Because of the warming climate, the conservation network should be positioned roughly on a South to North axis. For Finland, the northward migration of species is fortunate in the sense that most of the country's nature conservation areas are in the sparsely populated north. On the other hand, species native to northern areas will have nowhere to migrate once the climate becomes too warm for them.
In her 2014 article “Multiple dimensions of climate change and their implications for biodiversity”, Cabeza and her colleagues brought additional perspectives to the ongoing research. In addition to the changes in temperature, conservationists should consider the rapidity of the changes and whether the changed climate is historically familiar to the species in the area. For example, average temperatures in Finland have oscillated with the cycle of ice ages, while in tropical rainforests the climate has remained fairly stable.
During her time in Helsinki, Cabeza’s work has become more practical in its focus. She and her team participate in many different tropical conservation projects in Madagascar, Kenya and the Amazon region. She has also included issues from the social sciences, such as the question of what kinds of conservation measures are local people willing to undertake.
While younger, Cabeza was a member of the Spanish national volleyball team, but a back injury thwarted her dreams of becoming a professional athlete. Cabeza chose academia instead – and today, is very happy she did.
Professor of bioinformatics and group leader at the Institute of Biotechnology Liisa Holm (b. 1961) has conducted pioneering research on the developmental history of proteins, and has developed software to help study the subject. Holm’s work has applications in genomics and personalised medicine.
Holm published her most famous software tool, Dali, in 1993 while working as a postdoctoral researcher at the European Molecular Biology Laboratory in Heidelberg.
Dali was the first web-based system to compare protein structures, and to be more effective than the human eye and an expert’s memory combined. The Dali protein database compiles all publicly available three-dimensional protein structures. During its early stages the database had hundreds of such structures; now they number in the hundreds of thousands. Dali is continuously updated in terms of both data and code, and has been in use worldwide for more than 20 years. Dali has also found its way into textbooks in the field.
Dali uses distance matrices to compare a new structure to previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, i.e., that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example from the last common ancestor of humans and bacteria.
When Holm began to systematically comb through new structures, she also discovered homologies which could not have been detected from the peptide sequence. Structural comparison can reach further into the evolutionary history of proteins than peptide sequencing.
During her time at the European Bioinformatics Institute in Cambridge between 1995 and 2002, Holm focused on developing comparison methods for the peptide sequences of proteins so that traces of the developmental connections between increasingly distant “relatives”, detected by structural comparisons, could be made evident. Together with her research group, Holm developed a method for unsupervised clustering of the entire protein database at the protein domain level. Domains are structurally and functionally independent structures of the protein, which exist in different combinations in different protein families.
Holm has been working since 2002 at the University of Helsinki, with the exception of her one-year researcher visit to Harvard University in 2007–2008. Holm has worked on functional genome annotation, i.e., predicting how a function could connect to a protein encoded by a given gene. For example, the PANNZER program placed highly in the Critical Assessment of Protein Function Annotation competition (CAFA).
In the age of big data, protein databases have grown exponentially, demanding new solutions from their software. Holm has developed a super-fast protein database algorithm which is able to discover homologies in the blink of an eye. This speeds up many bioinformatics applications.
At the moment, Holm is conducting research in personalised medicine and is developing diagnostic algorithms for infections. The algorithms will allow a patient’s sequence data to be analysed quickly enough to determine which bacteria and which resistance factors underlie the infection and to propose a suitable antibiotic.
PANNZER is also still being developed, and it may eventually become a significant tool in the field. Software that produces fast, educated guesses on the functions of proteins is an indispensable tool for many biologists today.
Willem de Vos (b. 1954), Academy professor of microbiology, has been this millennium’s trailblazer in terms of intestinal microflora research. Many research groups at the University of Helsinki have benefitted from the microbiota boom sparked by de Vos moving from Holland to Finland in 2007, first to a FiDiPro professorship funded by Tekes, and later to an Academy professorship.
At the turn of the millennium, de Vos and his colleagues realised that the gut flora of each person is unique, and constitutes the human microbiome. Now an established fact, the discovery was revolutionary at the time, and heralded the beginning of the microbiome research trend.
De Vos’most cited study is the 2010 metagenomic sequencing of the intestinal microbiome. It is the first sequencing of this scale, and resulted in researchers discovering a total of 3.3 million microbial genes in the feces of 124 European test subjects – a figure 150 times the number of human genes in an individual. Approximately 99% of the genes were from bacteria. The researchers estimated that the intestines of the research cohort were home to more than a thousand different species of bacterium, and that the intestines of each individual, to 160, if not more.
Since then, more genes and varieties of bacteria have been identified. The number of individual bacteria in the human intestine is approximately ten times that of human cells in the body.
In his research, de Vos has noted that the human host cooperates with the bacteria, and that the intestinal microbiome has a profound impact on the health of the individual. For example, type 2 diabetes, metabolic syndrome and asthma have been associated with particular microbes linked to susceptibility to these illnesses.
The molecules produced by some intestinal bacteria are the same as those used by the human body as markers, and may thus disrupt normal sugar metabolism and insulin signalling. Additionally, toxins contained in some bacteria, primarily lipopolysaccharide (LPS), cause swelling in many parts of the human body, involving fat cells as well.
In 2012, de Vos and his colleagues established that the insulin resistance of men with metabolic syndrome decreased when their intestines received bacteria from healthy test subjects.
In 2013, de Vos and his team proved that a patient suffering from severe diarrhoea caused by Clostridium difficile could be cured with a fecal transplant – transplanting feces from a person with a healthy intestine into a patient’s colon. This was a significant discovery, as Clostridium difficile is largely resistant to antibiotics.
In many studies, de Vos has found that antibiotics are harmful, as they destroy intestinal bacteria that are beneficial to humans. There are also differences among antibiotics: some are more toxic to the microbiome than others.
Before moving on to intestinal microbes at the turn of the millennium, de Vos studied how bacteria communicate amongst themselves through peptides. The most important peptide message is whether there are few or many bacteria of the same species in the immediate vicinity, as the bacteria’s strategies against pathogens and immune defences vary depending on whether they are solitary or in groups.
During Holland’s economic crisis in the 1980s, de Vos worked briefly for the food industry. He studied lactic acid bacteria and helped make yoghurts and cheeses tastier.
Before moving to Helsinki in 2007, de Vos had already forged an illustrious career in Holland. For example, at the University of Wageningen he worked as the professor of bacterial genetics and microbiology, as the director of the Department of Biomolecular Sciences, as the programme director for a centre of excellence at the Centre for Food Sciences, and as a director of international business.
De Vos continues to hold a secondary post at the University of Wageningen, which he visits regularly to check on follow-up studies and other developments from his earlier research projects.
De Vos has supervised more than a hundred dissertations in Holland and Finland.
In the 1980s, de Vos played an offensive position for a team in the highest Dutch field hockey league. He continued to play in the senior leagues until he was 40.
Academy Professor Juha Merilä (b. 1965) is mainly cited for the review articles in which he analyses whether climate change has caused evolution.
Particularly in previous years it was widely thought that the changes caused by climate change in animal populations, such as smaller average size of individuals, are evolutionary adaptations to climate change.
However, Merilä's genetic analyses indicate that this is usually not the case. The appearance of the populations may have reacted to changes in their environment, but the underlying genetics have remained largely the same.
This was a new observation, as ecologists and geneticists traditionally work separate from one another. Meanwhile, Merilä is among the first researchers to bring genetic methods to the study of how populations adapt to changing environments and how new species are created.
Merilä has done many case studies around the world on the adaptations of a variety of vertebrate species. In his studies, Merilä examines whether the change derives from genes or the environment. Approximately forty of these review and case study articles have been cited more than one hundred times.
For example, the reduction in the average size of the silver gulls in New Zealand would have traditionally been interpreted as an adaptation to a warming climate, but the genetic analyses conducted by Merilä’s group reveal that the change was not genetic in nature. It is more likely that the silver gulls have become smaller as the marine ecosystem has begun to produce less of the food they need.
Merilä has also questioned the theory that fishing causes “genetic dwarfism”, i.e., that selective fishing would automatically generate genetically smaller fish which reach sexual maturity earlier. The theory seems logical, but the lack of genetic proof makes it difficult to rule out alternative explanations.
Merilä's large citation figures are partially explained by the fact that his discoveries are interesting to researchers from several fields - climate change, ecology and genetics.
Merilä defended his doctoral dissertation on animal ecology at the University of Uppsala in 1996 and worked there as an assistant professor until being appointed professor of population genetics at the University of Helsinki in 2001. During his free time, Merilä plays squash competitively and fishes for salmon.
Jaakko Kangasjärvi (b. 1960), professor of plant biology, has built his career around reactive oxygen species (ROS), such as hydroxyl radicals and hydrogen peroxide. Kangasjärvi was among the first scholars to establish that ROS compounds are also beneficial to plant cells in transmitting signals. He is ranked as the 13th most cited among the world's botanists and zoologists.
ROS compounds have traditionally been thought to be unfortunate by-products of energy production, harmful to cells which must neutralise them with antioxidants.
At the beginning of his career in the 1990s, Kangasjärvi’s research group studied the harmful effects of ozone on plants. The leaves of birch trees, for example, begin to die when the air has a high concentration of ozone. This damage was thought to be physical in nature.
The truth, however, proved to be more complex. Kangasjärvi discovered that the ROS compounds created when ozone degrades trigger a suicide mechanism in the plant cell. The plant cell interprets the presence of an ROS compound as a sign that pathogens are nearby. One form of defence against pathogens is that the cell destroys itself so that the pathogen cannot spread.
This means that ozone damage is the result of both gene function and metabolism - and that ROS compounds have a signalling function. After making this discovery, Kangasjärvi has focused on the many signalling functions and mechanisms of ROS compounds by studying the Arabidopsis, a common model plant in plant biology.
When plants are exposed to pathogenic microbes they begin to produce ROS compounds to signal that action is needed. Similarly, when plants are exposed to bright light after long periods in the shade they begin to produce ROS compounds, after which the plant is quick to adapt to its new circumstances.
During his career, Kangasjärvi has also conducted a great deal of genome sequencing, for example on the Populus trichocarpa, Arabidopsis and Petula bendula. Even though Kangasjärvi studies genes and molecular biology, his work has a basis in evolutionary biology, as he has been trying to determine what concrete benefit can particular gene functions yield to the plant as it strives to adapt to its environment.