Monday, November 25, 2024

 

Scientists recreate mouse from gene older than animal life


New research sheds light on evolutionary origins of stem cells with groundbreaking experiment to create mouse using ancient genetic tools



Queen Mary University of London

Image 1 

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The mouse on the left is a chimeric with dark eyes and patches of black fur, a result of stem cells derived from a choanoflagellate Sox gene. The wildtype mouse on the right has red eyes and all white fur. The colour difference is due to genetic markers used to distinguish the stem cells, not a direct effect of the gene itself.

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Credit: Gao Ya and Alvin Kin Shing Lee, with thanks to the Centre for Comparative Medicine Research (CCMR) for their support.




Published in Nature Communications, an international team of researchers has achieved an unprecedented milestone: the creation of mouse stem cells capable of generating a fully developed mouse using genetic tools from a unicellular organism, with which we share a common ancestor that predates animals. This breakthrough reshapes our understanding of the genetic origins of stem cells, offering a new perspective on the evolutionary ties between animals and their ancient single-celled relatives.

In an experiment that sounds like science fiction, Dr Alex de Mendoza of Queen Mary University of London collaborated with researchers from The University of Hong Kong to use a gene found in choanoflagellates, a single-celled organism related to animals, to create stem cells which they then used to give rise to a living, breathing mouse. Choanoflagellates are the closest living relatives of animals, and their genomes contain versions of the genes Sox and POU, known for driving pluripotency — the cellular potential to develop into any cell type — within mammalian stem cells. This unexpected discovery challenges a longstanding belief that these genes evolved exclusively within animals.

“By successfully creating a mouse using molecular tools derived from our single-celled relatives, we’re witnessing an extraordinary continuity of function across nearly a billion years of evolution,” said Dr de Mendoza. "The study implies that key genes involved in stem cell formation might have originated far earlier than the stem cells themselves, perhaps helping pave the way for the multicellular life we see today."

The 2012 Nobel prize to Shinya Yamanaka demonstrated that it is possible to obtain stem cells from “differentiated” cells just by expressing four factors, including a Sox (Sox2) and a POU (Oct4) gene. In this new research, through a set of experiments conducted in collaboration with Dr Ralf Jauch’s lab in The University of Hong Kong / Centre for Translational Stem Cell Biology, the team introduced choanoflagellate Sox genes into mouse cells, replacing the native Sox2 gene achieving reprogramming towards the pluripotent stem cell state. To validate the efficacy of these reprogrammed cells, they were injected into a developing mouse embryo. The resulting chimeric mouse displayed physical traits from both the donor embryo and the lab induced stem cells, such as black fur patches and dark eyes, confirming that these ancient genes played a crucial role in making stem cells compatible with the animal’s development.

The study traces how early versions of Sox and POU proteins, which bind DNA and regulate other genes, were used by unicellular ancestors for functions that would later become integral to stem cell formation and animal development. "Choanoflagellates don’t have stem cells, they’re single-celled organisms, but they have these genes, likely to control basic cellular processes that multicellular animals probably later repurposed for building complex bodies,” explained Dr de Mendoza.

This novel insight emphasises the evolutionary versatility of genetic tools and offers a glimpse into how early life forms might have harnessed similar mechanisms to drive cellular specialisation, long before true multicellular organisms came into being, and into the importance of recycling in evolution.

This discovery has implications beyond evolutionary biology, potentially informing new advances in regenerative medicine. By deepening our understanding of how stem cell machinery evolved, scientists may identify new ways to optimise stem cell therapies and improve cell reprogramming techniques for treating diseases or repairing damaged tissue.

"Studying the ancient roots of these genetic tools lets us innovate with a clearer view of how pluripotency mechanisms can be tweaked or optimised," Dr Jauch said, noting that advancements could arise from experimenting with synthetic versions of these genes that might perform even better than native animal genes in certain contexts. 

 

Transforming marine waste and carbonated water into hydrogels via CO2 release behavior



The study investigates how post-gelation CO₂ release rates affect hydrogel properties, informing medical application development



Tokyo University of Science

CO₂-Based Gelation Process: Mixing Alginate, Calcium Carbonate, and Carbonated Water 

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Carbon dioxide creates the acidic environment necessary for calcium ions to link alginate chains, forming the hydrogel. However, the rapid release of CO₂ after gelation limits calcium ion availability, resulting in reduced crosslinking of the alginate chains.

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Credit: Reproduced from Teshima et al. with permission from the Royal Society of Chemistry Image source: https://doi.org/10.1039/D4MA00257A




Hydrogels, which are soft materials made of water-filled, crosslinked polymer networks, have a wide range of uses, from wound dressings to enhancing soil moisture for plant growth. They are formed through a process called gelation, where polymers in a solution are linked together to form a gel. Biopolymers, such as polysaccharides and proteins, often require the addition of acidic agents for this gelation process. However, these agents can remain in the hydrogel, posing risks for biological applications. To address this issue, a new gelation method uses carbon dioxide (CO₂) instead of acidic agents. CO₂ acts as an acidic agent during gelation but escapes into the atmosphere once the hydrogel forms.

A study led by Professor Hidenori Otsuka and Mr. Ryota Teshima from Tokyo University of Science, Japan, investigated the effect of CO2 release on the properties of hydrogels. Their findings were made available online on June 5, 2024, were published in Issue 16 of the journal Materials Advances on August 21, 2024 and provide valuable insights for synthesizing hydrogels suitable for medical uses.

“The degree of crosslinking in hydrogels is typically controlled by 'pre-gelation parameters,' such as polymer and crosslinker concentrations. However, we demonstrate that the crosslinking degree of hydrogels prepared using carbon dioxide as the acidic agent is also influenced by post-gelation conditions,” says Prof. Otsuka and Mr. Teshima.

The researchers synthesized hydrogels called Alg-gels from alginate, a polymer derived from brown seaweed. They mixed alginate with calcium carbonate (CaCO₃) and added carbonated water, resulting in a porous hydrogel where alginate chains were crosslinked by calcium ions. To control the release of CO₂ from the Alg-gels, two samples were prepared: one incubated in a Petri dish, exposing only its top surface to air, and another on a wire mesh, exposing the entire surface. The rate of CO₂ release was monitored using bromothymol blue (BTB), a pH indicator that changes color with acidity (yellow in acidic conditions, green when neutral, and blue in alkaline conditions).

The gel in the Petri dish gradually turned green (neutral) over 60 minutes, indicating slow CO₂ release, and became fully blue after 5 hours. In contrast, the gel on the wire mesh released CO₂ much faster, turning fully blue by 40 minutes and releasing all the CO₂ in just 90 minutes.

The rapid release of CO₂ immediately after gel formation prevented the calcium carbonate from fully dissolving in the solution, leaving fewer calcium ions available to link the polymer chains. “Rapid release of CO2 from the hydrogel after gelation increased the pH of the system and decreased the degree of crosslinking,” explain Prof. Otsuka and Mr. Teshima. When both samples were subjected to a compression test, the stiffness, breaking stress, and energy required to break the disks were higher for those incubated in the petri dish compared to those on the wire mesh.

This study enhances our understanding of how CO₂ release after gel formation affects the degree of crosslinking and the mechanical properties of hydrogels, providing insights for creating hydrogels using CO₂. Additionally, the use of alginic acid derived from marine waste can transform waste into high-value hydrogels for medical uses such as tissue engineering, including wound healing and organ regeneration.

 

***

 

Reference                    

DOI: 10.1039/D4MA00257A

 

About The Tokyo University of Science
Tokyo University of Science (TUS) is a well-known and respected university, and the largest science-specialized private research university in Japan, with four campuses in central Tokyo and its suburbs and in Hokkaido. Established in 1881, the university has continually contributed to Japan's development in science through inculcating the love for science in researchers, technicians, and educators.

With a mission of “Creating science and technology for the harmonious development of nature, human beings, and society," TUS has undertaken a wide range of research from basic to applied science. TUS has embraced a multidisciplinary approach to research and undertaken intensive study in some of today's most vital fields. TUS is a meritocracy where the best in science is recognized and nurtured. It is the only private university in Japan that has produced a Nobel Prize winner and the only private university in Asia to produce Nobel Prize winners within the natural sciences field.

Website: https://www.tus.ac.jp/en/mediarelations/

 

About Professor Hidenori Otsuka from Tokyo University of Science
Prof. Hidenori Otsuka completed his Ph.D. from the Department of Chemistry, Tokyo University of Science (TUS) Graduate School, and currently heads his own laboratory at TUS. With more than 100 research publications to his credit, his research focuses mainly on the basics and applications of physical chemistry, especially colloid and surface chemistry.

 

Funding information
This work was supported by Grants-in-Aid for Research Activities from the Masason Foundation [grant numbers: GD14469, GD9675, and GD2825] and Grants-in-Aid for Extracurricular Activities for Students at Tokyo University of Science Parents Associations (Kouyoukai) [grant number: 2019-15].

 

The MIT Press releases workshop report on the future of open access publishing and policy



The MIT Press
Open Access at the MIT Press 

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Open Access at the MIT Press 

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Credit: The MIT Press, 2024.




Cambridge, MA (November 18, 2024) – Today, the MIT Press is releasing a comprehensive report that addresses how open access policies shape research and what is needed to maximize their positive impact on the research ecosystem.

The report, entitled "Access to Science & Scholarship 2024: Building an Evidence Base to Support the Future of Open Research Policy," is the outcome of a National Science Foundation-funded workshop held at the D.C. headquarters of the American Association for the Advancement of Science on September 20, 2024.

While open access aims to democratize knowledge, its implementation has been a factor in the consolidation of the academic publishing industry, an explosion in published articles with inconsistent review and quality control, and new costs that may be hard for researchers and universities to bear, with less affluent schools and regions facing the greatest risk. The workshop examined how open access and other open science policies may affect research and researchers in the future, how to measure their impact, and how to address emerging challenges.

The event brought together leading experts to discuss critical issues in open scientific and scholarly publishing. These issues include:

  • The impact of open access policies on the research ecosystem
  • The enduring role of peer review in ensuring research quality
  • The challenges and opportunities of data sharing and curation
  • The evolving landscape of scholarly communications infrastructure

The report identifies key research questions in order to advance open science and scholarship. These include:

  • How can we better model and anticipate the consequences of government policies on public access to science and scholarship?
  • How can research funders support experimentation with new and more equitable business models for scientific publishing?
  • If the dissemination of scholarship is decoupled from peer review and evaluation, who is best suited to perform that evaluation, and how should that process be managed and funded?

“This workshop report is a crucial step in building a data-driven roadmap for the future of open science publishing and policy,” said Dr. Phillip Sharp, Institute Professor and Professor of Biology Emeritus at MIT and faculty lead of the working group behind the workshop and the report. “By identifying key research questions around infrastructure, training, technology, and business models, we aim to ensure that open science practices are sustainable and that they contribute to the highest quality research.”

The full report is available for download here, along with video recordings of the workshop.

About The MIT Press:

The MIT Press is a leading academic publisher committed to advancing knowledge and innovation. It publishes significant books and journals across a wide range of disciplines spanning science, technology, design, humanities, and social science.

For more information, please contact Nick Lindsay at nlindsay@mit.edu.

 

Purdue launches institute to help farmers commercialize new value-added products

USDA-funded effort targets economic development in rural communities

Grant and Award Announcement

Purdue University

Food institute director 

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Dharmendra Mishra, associate professor of food science at Purdue University. Mishra also directs Purdue’s new Institute for Food Product Innovation and Commercialization.

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Credit: Purdue Agricultural Communications / Joshua Clark

WEST LAFAYETTE, Ind. — A newly formed institute at Purdue University is offering training and development support to agriculture producers with novel food and beverage product ideas. The new Institute for Food Product Innovation and Commercialization is funded by a $1.5 million grant from the U.S. Department of Agriculture Rural Development.

“This grant is focused on farmers who want to add value to their product,” said Dharmendra Mishra, institute director and associate professor of food science. Entrepreneurs face many steps and challenges in converting commodity crops into new products for retail sales. “We want to remove those hurdles for farmer-entrepreneurs,” he said. 

A joint effort of Purdue’s departments of Food Science and Agricultural Economics, the institute is part of the USDA Agriculture Innovation Center Program. 

“It’s bringing together the technical expertise on food manufacturing and food safety from food science, and the marketing, entrepreneurship and business management strengths of ag econ,” said Kenneth Foster, the institute’s assistant director and professor of agricultural economics.

Dairy farmers might want to produce ice cream or high-protein beverages. Growers of tomatoes and jalapenos might want to market a salsa. Or a beekeeper who sells honey may wish to develop a syrup as well. 

Whatever the value-added product, the new institute can help train rural entrepreneurs in developing a recipe, making their product, educating them about the safety factors they need to control, and assessing their potential market.

“There’s only so much agricultural commodity you can produce,” said Foster, who runs a beekeeping and honey business as his grandfather and father did before him. And that commodity likewise has value limits.

“We put it on a truck, barge, train or plane and we ship it somewhere else and people add value to it,” Foster said. “What can we do to support value-adding at the local level so more of that stays in the local community where the product is produced?"

A key element of the new program is the Food Entrepreneurship and Manufacturing Institute (FEMI) established in 2021 while Foster served as interim head of the food science department. Like the new institute, FEMI is a collaboration of Purdue’s food science and agricultural economics departments.

When Purdue established FEMI, “the idea was to drive economic growth in Indiana and help entrepreneurs struggling with commercializing their food products,” Foster said. Another idea was to reduce the region’s dependence on the national and global supply chain that caused so many problems during the COVID pandemic.

Purdue’s recent history in product development includes introducing Boiler Chips ice cream and Boilermaker Hot Sauce Black and Gold Editions. The students and faculty members involved in these projects benefited from access to the food science department’s Skidmore Food Product Development Laboratory, as will the farmers who participate in the new USDA program at Purdue.

Also providing resources to the new institute is the food science department’s Pilot Plant. After entrepreneurs develop their recipe, they need a pilot test before they begin full-scale commercial production.

“That’s where our Pilot Plant is important,” Mishra said. “We can create or simulate a commercial process in our Pilot Plant to know how this is going to behave in a larger-scale manufacturing environment.”

Agricultural economists at the Purdue Institute for Family Business and the Center for Food Demand Analysis and Sustainability will lend further expertise to the endeavor. They will help develop marketing and business plans, along with insights about consumer demand for food and related products.

The program has three phases. Phase 1 consists of six online training courses that introduce participants to the basics of food product design, food safety and business planning. Once participants pass the online training, they can proceed to Phase 2 for a one-day on-campus workshop on the food product life cycle. In Phase 3, program participants receive intensive on-campus, personalized feedback and assessments of their ideas.

Serving on the institute’s board of directors are representatives from Indiana Farm Bureau, Indiana Grown, Indiana State Department of Agriculture, Indiana Dairy Producers, Indiana Vegetable Growers Association, Indiana Nut and Fruit Growers Association, Indiana Corn Marketing Council, and Indiana Soybean Alliance.

In addition to benefiting the economic well-being of the region, “we also want to create impact for the farmer participants and our students as well as the broader program of FEMI,” Mishra said. “At any given time, we have many undergraduate students and graduate students working on real-life projects.”


Dharmenda Mishra, director of Purdue University’s Institute for Food Product Innovation and Commercialization, adjusts equipment in Purdue’s Pilot Plant. The Pilot Plant allows manufacturers to see how a process works before committing to full production.

Credit

Purdue Agricultural Communications / Joshua Clark



Cups of Purdue’s ice cream Boiler Chips and One Giant Scoop, developed in 2023 by the Food Entrepreneurship and Manufacturing Institute (FEMI). 

Credit

Purdue Agricultural Communications/Jessica Kerkhoff

Students and staff part of the Food Entrepreneurship and Manufacturing Institute (FEMI) at Purdue University work with Boilermaker Gold hot sauce in preparation for bottling.

Students and staff in the Food Entrepreneurship and Manufacturing Institute (FEMI) at Purdue University prepare to bottle a hot sauce developed as a part of a Food Science semester long class project.

 

Credit

Purdue Agricultural Communications/Tom Campbell

About Purdue Agriculture

Purdue University’s College of Agriculture is one of the world’s leading colleges of agricultural, food, life and natural resource sciences. The college is committed to preparing students to make a difference in whatever careers they pursue; stretching the frontiers of science to discover solutions to some of our most pressing global, regional and local challenges; and, through Purdue Extension and other engagement programs, educating the people of Indiana, the nation and the world to improve their lives and livelihoods. To learn more about Purdue Agriculture, visit this site.

About Purdue University  

Purdue University is a public research institution demonstrating excellence at scale. Ranked among top 10 public universities and with two colleges in the top four in the United States, Purdue discovers and disseminates knowledge with a quality and at a scale second to none. More than 105,000 students study at Purdue across modalities and locations, including nearly 50,000 in person on the West Lafayette campus. Committed to affordability and accessibility, Purdue’s main campus has frozen tuition 13 years in a row. See how Purdue never stops in the persistent pursuit of the next giant leap — including its first comprehensive urban campus in Indianapolis, the Mitch Daniels School of Business, Purdue Computes and the One Health initiative — at https://www.purdue.edu/president/strategic-initiatives.

Writer: Steve Koppes

Media contact: Devyn Ashlea Raver, draver@purdue.edu

Sources: Dharmendra Mishra, mishradh@purdue.edu; Ken Foster, kfoster@purdue.edu.

 

 

 

Emory researchers launch investigation into why air pollution impacts Alzheimer’s disease risk




Emory University

Emory researchers launch investigation into why air pollution impacts Alzheimer’s disease risk 

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Rollins researchers Anke Huels, PhD and Donghai Liang, PhD are studying why and how specific toxic components in air pollution increase the risk of developing Alzheimer’s disease and related dementias.

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Credit: Emory University


Researchers from Emory University recently received two separate grants, totaling $15 million, from the National Institutes of Health (NIH) to lead a first-of-its-kindmultifaceted study into why specific types of air pollution increase the risk of Alzheimer’s disease and related dementias. 

Previous studies have linked Alzheimer’s disease and related dementias to air pollution­—specifically exposure to fine particulate matter <2.5 micrometers (PM2.5), a common class of particles and gases—but it is not known how specific concentrations of this mixture of toxins impact the brain.

The researchers from the Rollins School of Public Health and Emory School of Medicine are partnering with investigators from The University of California, DavisThe University of British Columbia; and Georgia Institute of Technology to gain a more nuanced understanding of why and how specific toxic components in air pollution increase the risk of developing Alzheimer’s disease and related dementias.

For the first time, the study is measuring the components of PM2.5 particles in the blood and cerebral spinal fluid of a diverse range of study participants from the Goizueta Alzheimer’s Disease Research Center, including both cognitively healthy adults and adults with a previous dementia diagnosis. They will also measure PM2.5 in brain tissue samples from the center’s brain bank.

“Changes in the early biomarkers of cognitive function can be seen more than a decade before someone develops Alzheimer’s disease,” says Anke Huels, PhD, assistant professor of epidemiology and principal investigator of the two NIH awards. “By measuring the biological response to air pollution, we have a really unique opportunity to find out what is causing the effects of PM2.5on Alzheimer’s disease risk. This could give us a better understanding of why some people develop Alzheimer’s disease and others do not, but also identify potential intervention and prevention strategies to make a difference on a policy level.”

As part of this effort, the researchers are developing improved air pollution models to measure PM2.5components in the Atlanta area and assign air pollution estimates to the study participants based on their address. They are conducting metabolomics, proteomics, epigenomics, and genomics analyses to better understand the biological response to air pollution.

“We are using cutting-edge methods to unravel the thousands of environmental chemicals that exist in PM2.5 and assess their individual and joint effects on our brain health,” says Donghai Liang, PhD, associate professor of environmental health and principal investigator of the two NIH awards. “And in the future, other scientists will have a much better understanding of the toxic components of PM2.5that are responsible for an increased risk of developing Alzheimer’s disease.”

Emory researchers launch inves [VIDEO] | 


Study of paper wasps shows that body size is larger in habitats nearer the equator


An analysis of 429 specimens belonging to 39 species representative of the diversity of Polistes in the Americas confirmed the inverse of Bergmann’s rule by pointing to larger body size for species occurring in or near the tropics.



Fundação de Amparo à Pesquisa do Estado de São Paulo

Study of paper wasps shows that body size is larger in habitats nearer the equator 

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Variation in body size of paper wasps (Polistes) analyzed in the study. Each individual in the image represents a different species 

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Credit: Alexandre Somavilla




A study of the correlation between environmental variables such as latitude and body size in paper wasps (genus Polistes) by a group of Brazilian researchers concludes that the nearer the habitat of a species to the equator, the larger its body size. The genus is widely distributed around the world and serves as a model for sociobiological and ecological studies.

An article on the study is published in the Biological Journal of the Linnean Society. The findings refute for these insects a nineteenth-century theory that predicts larger body size at higher latitudes or in colder regions of the planet.

“If you examine wasp collections worldwide, you notice that body size varies considerably from one species to another. We analyzed many specimens from a representative number of species and concluded that latitude is the key determinant of these differences,” said André Rodrigues de Souza, first author of the article and a researcher at the University of São Paulo’s Ribeirão Preto School of Philosophy, Science and Letters (FFCLRP-USP) with a Young Investigator Grant from FAPESP. 

The researchers found that species living in warmer, less seasonal habitats closer to the equator tend to be larger than species living at higher latitudes, where temperatures are lower. This is the opposite of what is predicted by Bergmann’s rule.

Named for German biologist Carl Bergmann, who proposed it in 1847, the rule states that species with larger body sizes are found at high latitudes or in cold environments. A large body is an advantage for survival in a cold habitat: with less surface area in proportion to volume, they radiate less heat and can maintain a stable body temperature.

The article argues for the converse Bergmann’s rule, a twentieth-century theory proposed by scientists who observed that many ectothermic organisms inhabiting warmer regions tend to have larger body sizes than those in colder habitats. Ectotherms rely primarily on the external environment to regulate body temperature.

“A possible explanation for the converse Bergmann’s rule in this case is that at high latitudes and in more seasonal environments with low temperatures, the foraging period for wasps is very short and they become smaller adults as a result. Individuals that develop faster have an advantage, but at the cost of a smaller body size,” Souza said.

In temperate regions the favorable season for wasps lasts three to four months, while in the tropics it lasts about nine months, allowing more time for their young to forage and grow.

Collections

The researchers analyzed 429 well-preserved adult Polistes wasps belonging to species that occur throughout the Americas from Canada to Argentina. The specimens were sent to Brazil from museum collections in different countries or analyzed at the institutions holding the collections abroad. In all, 37 species were represented by females and 28 also by males; two were represented only by males, giving a total of 39 species investigated. The analysis included the use of statistical tools showing a direct correlation between latitude and body size.

Polistes species inhabiting the Americas were chosen because the phylogeny of this group on the continent is well-resolved: all species descend from the same ancestor, which is not known to be the case in other regions of the planet. Moreover, the diversity of the genus is greatest in the Americas, with around 90 species. The sample was therefore considered sufficient to validate the theory that body size is significantly influenced by environmental conditions.

previous study by Souza and other collaborators showed that regulation of body temperature in paper wasps is not the main determinant of body size, as predicted by Bergmann’s rule. The authors conclude that darker insects have an advantage in colder environments because they can heat faster than lighter ones.

“Studies like these contribute to a broader picture of the evolution of paper wasps, helping us understand their diversity in tropical regions better and emphasizing the importance of conserving their habitats,” Souza said.

Furthermore, he added, the studies highlight the importance of preserving entomological collections, which provide material for ongoing research on the many species of paper wasps and the relationships among them.

The authors of the latest study also include researchers at the Federal University of the Minas Triangle (UFTM), the Federal University of Viçosa (UFV), and the National Institute of Amazon Research (INPA).

About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe.