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News Article | December 12, 2016
Site: www.eurekalert.org

"Through the Installation Grants we encourage some of the best early-career researchers to share their expertise across Europe by setting up laboratories in selected EMBC Member States," explains EMBO Director Maria Leptin. "Each year, we receive applications from outstanding scientists, and it is a pleasure to be able to support them during this challenging career phase in order to establish scientific excellence across the whole continent." EMBO Installation Grants are awarded annually. They are funded primarily by the participating Member States Estonia, Poland, Portugal, Turkey and the Czech Republic. Grantees are selected by a committee of EMBO Members on the basis scientific excellence as the primary selection criterion. Each Installation Grantee receives 50,000 euros annually for three to five years to support the establishment of an independent research group. In addition to financial support, the recipients receive networking opportunities and practical support by becoming part of the EMBO Young Investigator network. Since 2006, EMBO has supported 89 group leaders through Installation Grants. Of the most recent awardees, four will establish laboratories in Turkey, two in Poland, two in Portugal, one in Estonia, and one in the Czech Republic. The next application deadline for EMBO Installation Grants is 15 April 2017. Melih Acar, Hematopoietic stem cell regulation, moving to Bahcesehir University, School of Medicine, Istanbul, TR, from UT Southwestern Medical Center, Dallas, TX, US Jaan-Olle Andressoo, Gene knock-up to treat Parkinson's disease, moving to Tallinn Institute of Technology, EE, from University of Helsinki, FI Claus Maria Azzalin, Telomeres, cancer and aging, moving to Institute of Molecular Medicine, Lisbon, PT, from Institute of Biochemistry, ETH Zurich, CH Murat Alper Cevher, Characterization of mediator-estrogen receptor interaction, moving to Bilkent University, Ankara, TR, from Rockefeller University, NY, US Rafal Ciosk, Cell fate plasticity in development and tissue homeostasis, moving to Institute of Bioorganic Chemistry, Poznan, PL, from Friedrich Miescher Institute for Biomedical Research, Basel, CH Elif Nur Firat-Karalar, Function and regulation of the centrosome/cilium complex, moving to Koç University, Istanbul, TR, from Stanford University, CA, USA Catarina Homem, Temporal and metabolic regulation of stem cells, Chronic Diseases Research Center, moving to Nova Medical School, PT, from Institute of Molecular Biotechnology of Austria, Vienna, AT Abdullah Kahraman, Non-coding cancer driver mutations in isoform networks, moving to Sabanci University, Istanbul, TR, from Institute of Molecular Life Sciences, University of Zurich, CH Vladimír Varga, Construction of the eukaryotic flagellum, moving to Institute of Molecular Genetics of the ASCR, Prague, CZ, from University of Oxford, UK Piotr Ziolkowski, Crossover control in plants, moving to Adam Mickiewicz University, Poznan, PL, from University of Cambridge, Cambridge, UK EMBO is an organization of more than 1700 leading researchers that promotes excellence in the life sciences. The major goals of the organization are to support talented researchers at all stages of their careers, stimulate the exchange of scientific information, and help build a European research environment where scientists can achieve their best work. EMBO helps young scientists to advance their research, promote their international reputations and ensure their mobility. Courses, workshops, conferences and scientific journals disseminate the latest research and offer training in techniques to maintain high standards of excellence in research practice. EMBO helps to shape science and research policy by seeking input and feedback from our community and by following closely the trends in science in Europe. ?For more information: http://www. The European Molecular Biology Conference (EMBC) is an intergovernmental organization comprising 29 Member States. EMBC promotes a strong transnational approach to the life sciences. Within EMBC, Member States pool their resources to improve the quality of research at a national level and to contribute to the advancement of basic research in Europe. For more information: http://www.


News Article | March 4, 2016
Site: news.yahoo.com

WASHINGTON — This is your bedbug-size brain on drugs. Researchers at Johns Hopkins University in Baltimore are growing "mini-brains" — smaller than the period at the end of this sentence — that may contain enough human brain cells to be useful in studying drug addiction and other neurological diseases. The mini-brains, grown in a laboratory dish, could one day reduce the need for the use of laboratory animals to conduct this type of research or to test therapeutic drugs, the researchers said. Labs from around the world have been racing to grow these and other organoids — microscopic, yet primitively functional versions of livers, kidneys, hearts and brains grown from real human cells. The version of the mini-brain from Johns Hopkins represents an advance over others reported in the last three years, in that it is quickly reproducible and contains many types of brain cells that interact with each other, just like a real brain, the researchers said. The researchers, led by Dr. Thomas Hartung, director of the Johns Hopkins Center for Alternatives to Animal Testing, reported their progress on Feb. 13 at the annual meeting of the American Association for the Advancement of Science. [11 Body Parts Grown in the Lab] Hartung noted that the mini-brain cannot yet replace animal models in the study of neurological diseases. But he added that the concept, which until quite recently seemed years from maturity, may be realized in as little as 10 months. Growing organoids involves the use of cells called induced pluripotent stem (iPS) cells, a technology developed by Japanese researcher Shinya Yamanaka, who won the Nobel Prize in 2012 for that line of research. With iPS cell technology, scientists can theoretically turn back the clock in any type of mature cell — be it skin, muscle, bone, etc. — and bring it to a near-embryonic state. From there, cells can be coaxed into developing into any of a number of cell types, much in the same way that actual human embryonic cells develop into all the cell types that make up the human body. Several labs are growing mini-brains. The first researchers to accomplish this, in 2013, were Jüergen Knoblich of the Institute of Molecular Biotechnology in Vienna, Austria, and Madeline Lancaster of the MRC Laboratory of Molecular Biology in Cambridge, England. These researchers said they can grow globular mini-brains a few millimeters in diameter in about three months, and that these organoids may be ideal for the study of fetal brain development, including microcephaly, the incomplete brain growth seen in some infants that researchers say may be linked with the Zika virus. Hartung's group has taken a different approach to grow smaller mini-brains, about 350 microns (0.35 millimeters) across, but say their method has easier reproducibility, a greater diversity of brain cell types and takes less time — only 10 weeks. He described them as "Mini Coopers" in that they are small but identical, ideal for comparative studies, as opposed to the hand-crafted, custom-made "luxury cars" made in other labs. "This allows us not to compare different brains but to compare different drivers," Hartung said, referring to different experiments that could be performed on identical brain models. Hartung said his lab's mini-brains have a variety of glia cells (which support neurons) such as astrocytes and Schwann cells, as well as oligodendrocytes, which form the insulating myelin sheaths that enable nerve impulses — all in proportions similar to those found in the human brain. The mini-brains' three-dimensional structure and ability to carry neurotransmitters — chemical messengers such as dopamine that enable communication between neurons — provide a simple but relatively realistic platform to study what goes wrong in the brain in, say, drug addiction and how the problem can be remedied. Hartung said his group accomplishes this by starting with a type of adult skin cell called a fibroblast, inducing those cells back to the state of neural stem cells that give rise to all the cells of the brain and nervous system, and then growing them in a gently rolling, vibrating environment to create the 3D-ball structure. The lab has grown thousands of these mini-brains, each with about 20,000 cells. Missing for now in the mini-brain but present in a real brain, Hartung said, are immune cells, which come from a different line of stem cells. He said he hopes to incorporate these types of cells soon. Hartung said he may have a working mini-brain for laboratory experimentation by the end of 2016, which could be mailed to any laboratory in the world. [Top 3 Techniques for Creating Organs in the Lab] Once the mini-brain model is mature, "no one should have the excuse to still use animal models, which come with tremendous disadvantages for brain studies in particular," Hartung said. "While rodent models have been useful, we are not 150-lb. rats. And even though we are not balls of cells, either, you can often get much better information from these balls of cells than from rodents." Hartung added that upward of 95 percent of therapeutic drugs for neurological orders that look promising in rodent studies fail in humans because of the intrinsic brain differences between the species. The mini-brain model is well-suited for studying brain addiction, in that scientists can study how drugs can destroy glia cells. Such destruction leads to the death of neurons and poorer transmission of neural impulses, Hartung said. Hartung's group is investigating the possibility of using the mini-brain to study the effect of Zika virus on a developing brain. Follow Christopher Wanjek @wanjek for daily tweets on health and science with a humorous edge. Wanjek is the author of "Food at Work" and "Bad Medicine." His column, Bad Medicine, appears regularly on Live Science. 10 Things You Didn't Know About the Brain 6 Foods That Are Good for Your Brain Copyright 2016 LiveScience, a Purch company. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.


News Article | December 20, 2016
Site: www.eurekalert.org

LA JOLLA -- (Dec. 20, 2016) When you build models, whether ships or cars, you want them to be as much like the real deal as possible. This quality is even more crucial for building model organs, because disease treatments developed from these models have to be safe and effective for humans. Now, scientists at the Salk Institute have studied a 3D "mini-brain" grown from human stem cells and found it to be structurally and functionally more similar to real brains than the 2D models in widespread use. The discovery, appearing in the December 20, 2016, issue of Cell Reports, indicates that the new model could better help scientists understand brain development as well as neurological diseases like Alzheimer's or schizophrenia. "Being able to grow human brain cells as miniature three-dimensional organs was a real breakthrough," says senior author Joseph Ecker, a Howard Hughes Medical Institute Investigator and professor and director of Salk's Genomic Analysis Laboratory. "Now that we have a structurally realistic model, we can start to ask whether it is also functionally realistic, by looking at its genetic and epigenetic features." For years, cell biologists have been chemically prompting embryonic stem cells in petri dishes to develop ("differentiate") into various types of brain cells. While researchers are able to glean a tremendous amount of information from these single layers of cells, the obvious limitation is that real brain tissue isn't two-dimensional. In 2013, European investigators developed a method to grow embryonic brain cells in 3D gels, where they begin to differentiate into realistic layers like an actual brain. However, it was unknown how faithfully these lab-grown mini-brains, called cerebral organoids (COs), look and behave like real brains until now. Collaborating with the European lab that developed the protocol for growing COs, Ecker's lab compared COs in early stages of brain development to real brain tissue at the same developmental stage. "Our work demonstrates the remarkable degree to which human brain development can be recapitulated in a dish in cerebral organoids," says Juergen Knoblich, co-senior author of the new paper and head of the European lab. To create COs for analysis, the teams used a human embryonic cell line called H9, adding the right chemicals to induce the cells down a neurodevelopmental pathway for 60 days. They then analyzed the COs' epigenetics, the pattern of chemical markers on DNA responsible for activating or silencing genes. Cells' epigenomes -- which are influenced by environmental factors like diet or stress--have been increasingly tied to development and disease (like schizophrenia). "No one has done epigenome sequencing for cerebral organoids before," says Chongyuan Luo, a Salk research associate and first author of the paper. "This kind of assessment is so important for understanding brain development, especially if we're eventually going to use these tissues for neurological therapies." The team compared their results both to age-matched real tissue from the National Institutes of Health NeuroBioBank and other researchers' 2D brain-model data. They found that COs were much more like real brain tissue than 2D models in the degree of differentiation the cells achieved and in their gene expression; in other words, COs develop along very similar early-developmental timelines as real brains, although they do not mature to the same level. When it came to epigenetics, however, both 3D and 2D models had similar aberrant patterns, which seem to be common to all cells grown in culture versus inside the brain. What this difference means is not entirely clear but, because it is so striking, Ecker suggests it could be a useful measure of how similar a model is to the real brain. "Our findings show that cerebral organoids as a 3D model of brain function are getting closer to a real brain than 2D models, so perhaps by using the epigenetic pattern as a gauge we can get even closer," says Ecker, who also holds the Salk International Council Chair in Genetics. Other authors included: Rosa Castanon and Joseph R. Nery of the Salk Institute, and Madeline A. Lancaster of the Institute of Molecular Biotechnology of the Austrian Academy of Science. The work was funded by the Howard Hughes Medical Institute, the Gordon and Betty Moore Foundation, the Austrian Academy of Sciences, the Austrian Science Fund, the European Research Council, a Marie Curie postdoctoral fellowship and the Medical Research Council. About the Salk Institute for Biological Studies: Every cure has a starting point. The Salk Institute embodies Jonas Salk's mission to dare to make dreams into reality. Its internationally renowned and award-winning scientists explore the very foundations of life, seeking new understandings in neuroscience, genetics, immunology, plant biology and more. The Institute is an independent nonprofit organization and architectural landmark: small by choice, intimate by nature and fearless in the face of any challenge. Be it cancer or Alzheimer's, aging or diabetes, Salk is where cures begin. Learn more at: salk.edu.


Okulski H.,Institute of Molecular Biotechnology GmBH | Druck B.,Institute of Molecular Biotechnology GmBH | Druck B.,Hoffmann-La Roche | Bhalerao S.,Institute of Molecular Biotechnology GmBH | And 2 more authors.
Epigenetics and Chromatin | Year: 2011

Background. Polycomb/Trithorax response elements (PREs) are cis-regulatory elements essential for the regulation of several hundred developmentally important genes. However, the precise sequence requirements for PRE function are not fully understood, and it is also unclear whether these elements all function in a similar manner. Drosophila PRE reporter assays typically rely on random integration by P-element insertion, but PREs are extremely sensitive to genomic position. Results. We adapted the ΦC31 site-specific integration tool to enable systematic quantitative comparison of PREs and sequence variants at identical genomic locations. In this adaptation, a miniwhite (mw) reporter in combination with eye-pigment analysis gives a quantitative readout of PRE function. We compared the Hox PRE Frontabdominal-7 (Fab-7) with a PRE from the vestigial (vg) gene at four landing sites. The analysis revealed that the Fab-7 and vg PREs have fundamentally different properties, both in terms of their interaction with the genomic environment at each site and their inherent silencing abilities. Furthermore, we used the ΦC31 tool to examine the effect of deletions and mutations in the vg PRE, identifying a 106 bp region containing a previously predicted motif (GTGT) that is essential for silencing. Conclusions. This analysis showed that different PREs have quantifiably different properties, and that changes in as few as four base pairs have profound effects on PRE function, thus illustrating the power and sensitivity of ΦC31 site-specific integration as a tool for the rapid and quantitative dissection of elements of PRE design. © 2011 Okulski et al; licensee BioMed Central Ltd.


VANCOUVER, British Columbia--(BUSINESS WIRE)--STEMCELL Technologies Inc. has signed an exclusive license agreement with Cincinnati Children’s Hospital Medical Center to commercialize its fundamental technology for generating gastrointestinal organoids from pluripotent stem cells (PSCs). This agreement grants STEMCELL a license to novel methods for generating organoid models and to develop cell culture media and tools that would enable scientists to create organoids from PSCs in their own laboratories. Organoids are three-dimensional structures, or small clusters of cells representing ‘mini-organs’, which are grown in a dish. Organoids more closely mimic the complex structure and physiology of whole organs than standard two-dimensional cell culture models. Generating organoids from PSCs allows for an inexhaustible source of tissue, and opens this field to researchers who may not have access to primary tissues from patient biopsies or other sources. The technology licensed from Cincinnati Children’s describes methods for generating gastrointestinal organoids, including intestinal and stomach, from human PSCs. These discoveries were developed in the laboratory of Dr. James Wells, Director of the Pluripotent Stem Cell Center at Cincinnati Children’s, and are further described in a series of Nature publications (J.R. Spence et al. 2011 and K.W. McCracken et al. 2014). Commenting on the agreement, Dr. Wells said, “There is a tremendous opportunity to use these new organoid models for advancing studies in human development, as well as for applying them in many powerful applications such as disease modeling, drug screening, and for developing therapeutics. I am pleased to partner with STEMCELL given their outstanding reputation for bringing quality research tools to the market.” STEMCELL has previously announced key partnerships with pioneering leaders in the organoid research field. Recently, the company signed an exclusive license with the Hubrecht Organoid Technology Foundation (The HUB) for patented tissue-derived organoid technology generated from the laboratory of Dr. Hans Clevers. Additionally, STEMCELL has exclusively partnered with the Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences to develop cerebral organoids, or ‘mini-brains’, as described by Drs. Jürgen Knoblich and Madeline Lancaster. Dr. Allen Eaves, President and CEO of STEMCELL, commented that “This license with Cincinnati Children’s will enable STEMCELL Technologies to further expand upon our growing portfolio of products supporting organoid studies, including the recently released IntestiCult™ Organoid Growth Medium. STEMCELL Technologies is pleased to be the leading organoid company. We are developing world-class organoid expertise, which we will leverage to deliver important, cutting edge research tools to the scientific community.” As Scientists Helping Scientists, STEMCELL Technologies Inc. is committed to providing high-quality cell culture media, cell isolation products and accessory reagents for life science research. Driven by science and a passion for quality, STEMCELL provides over 2500 products to more than 90 countries worldwide. STEMCELL’s specialty cell culture reagents, instruments and tools are designed to support science along the basic to translational research continuum. To learn more, visit http://www.stemcell.com.


News Article | November 11, 2016
Site: www.sciencedaily.com

Researchers at the Institute of Molecular Biotechnology in Vienna have unravelled how a tiny microRNA molecule controls growth and differentiation of brain cells. It is mind-boggling to imagine how our brain develops from just a handful of cells at the early embryo into a highly convoluted biochemical and bioelectric system comprising more than 100 billion neurons in adults. Scientists at the Institute of Molecular Biotechnology (IMBA) in Vienna have published new research in EMBO Journal, in which they reveal how cells are instructed by a small RNA molecule to shape the complex layered structures of developing mouse brains. When stem cells divide to form new tissues and organs, they have to position their cell division apparatus in a specific orientation to position their daughter cells at sites where they experience different fate cues defining their subsequent function. The newly formed cells may then go on to take a specialised function -- in the brain, for example, they can become various types of neurons to generate and transmit electrical impulses -- or stay stem cells that will keep dividing to generate more cells. Failure to correctly induce fate decisions leads to multiple developmental brain disorders. Dr Juan Pablo Fededa, a postdoctoral scientist at IMBA and first author of the study, explains his findings: "Our research focused on understanding what controls the orientation of the mitotic spindles. We already knew that if the spindles are not in the correct orientation, then cells divide irregularly, and in the brain this can lead to neurodevelopmental disorders. We also knew that molecules called microRNAs might be important in this process, but we didn't know exactly how." From microscopy-based screening to the study of mouse brains Tiny 'micro-RNA' molecules can interfere with the expression of genes -- turning them on, turning them off, or causing them to function differently. Led by principal investigator Dr Daniel Gerlich, Dr Fededa and the IMBA team used cultured cells in a dish to test the function of all micro-RNAs expressed during brain cell division. Fededa describes the approach: "By visualizing the spindle of the cells with a fluorescent marker in live cells, we observed that a family of six microRNAs called miR-34/449 influenced the spindle orientation during cell division. We then tested whether these micro-RNAs could also influence the orientation of mitotic spindles in developing mouse brains, using methodology established in Jürgen Knoblich's laboratory at IMBA. Indeed, we found that after deletion of miR-34/449 genes, mice developed smaller brains and these contained a larger proportion of stem cells called radial glial cells. This showed us that radial glial cells can grow relatively normally, but suggested that they are unable to further differentiate into more complex cells. We therefore concluded that miR-34/449 microRNAs must be required for normal brain development." miR-34/449 regulates the orientation of the mitotic spindle The scientists at IMBA compared the gene expression patterns in cells with or without miR-34/449 and discovered a difference in the expression of a protein called JAM-A. This protein was interesting, as it was previously shown to have a role in orienting the mitotic spindle in other tissues. By engineering a JAM-A gene version that is insensitive to miR-34/449, the team at IMBA was able to pinpoint its relevance for mitotic spindle orientation. "Our findings show that in developing mouse brains, miR-34/449 regulates JAM-A to ensure the correct orientation of dividing cells and accurate formation of brain layers" concludes Daniel Gerlich. "The current research provides insights into the role of micro-RNAs in brain development, but similar mechanisms might be at place in other organs."


The embryo's genomic integrity is monitored and safeguarded by the fertilized egg cells within 24 hours of fertilization, reports a recent study. The DNA present in the sperm and egg cells are the genetic blueprints of the zygote, the single-cell embryo. After fertilization, the male parental DNA initiates the modification of its "epigenetic memory" of its sperm state. In the meantime, the fertilized egg that comes into play provide proteins to erase this memory to a large extent and helps in generation of a totipotent embryo, which paves way for rise of a new individual. Though the reprogramming of fertilized egg to totipotent embryo is an important process of fertilization, it has not been studied in detail by far. Kikuë Tachibana-Konwalski, the study's senior author from Institute of Molecular Biotechnology, noted that it takes weeks for cell cultures to be reprogrammed into induced pluripotent cells. On the contrary, the zygotes are reprogrammed to totipotent cells in just 24 hours. Furthermore, it is noted that the fertilized eggs don't just participate in the reprogramming process of male DNA but also closely monitor and protect the genetic integrity of the material. As soon as the sperm enters the ovum, the tightly packed male chromatin is unraveled and arranged around the histone protein scaffolds, noted Sabrina Ladstätter, the study's first author. It is found in the mice study that as soon as the sperm enters the egg the reprogramming of the sperm DNA begins. The fertilized egg triggers demethylation of sperm DNA and erases the epigenetic memory inherited from the father, thereby paving way for creation of new epigenetic memory. The process of demethylation could cause damage to the genetic material which could result in embryo loss, chromosome fragmentation and infertility. However, the fertilized egg cells surprisingly do more than just reprogramming. In addition to initiating and monitoring the reprogramming of epigenetic memory, the egg cells also fix the damages caused during demethylation. The lesions caused in the parental DNA triggers the activation of check points in the zygote that stops cell division until the damages are completely rectified. Eventually, the lesions are fixed and reprogramming is done in just 24 hours, say in one cell cycle, making sure the epigenetic memory is intact. That being the case, there are possibilities that the fertilization taking place in vitro may not undergo such processes as efficiently as in natural conditions. "It will be exciting to explore how cell culture conditions enhance the zygote's intrinsic surveillance and repair mechanisms, thus leading to better quality embryos and potentially more successful pregnancies," noted Tachibana-Konwalski in a press release. The study is published in the journal Cell. © 2017 Tech Times, All rights reserved. Do not reproduce without permission.


News Article | November 16, 2016
Site: www.sciencedaily.com

PIWI-interacting RNAs, or piRNAs for short, are a class of 'small regulatory RNAs' -- tiny pieces of nucleic acid just 22-30 nucleotides in length. They may be small, but with their associated Argonaute proteins, piRNAs have the power to 'silence' transposable elements, so called egoistic genes found in the genomes of plants, fungi, and animals. piRNA-guided silencing can act on chromatin to block transposon transcription, or by destroying transposon mRNAs in order to block their translation into proteins. Although scientists understand quite well how piRNAs repress gene expression, until now, it has been much less clear how piRNAs are actually made. In a milestone research paper published in Nature, scientists from the Institute of Molecular Biotechnology in Austria (IMBA) have painstakingly unravelled the sequence of events that generate piRNAs with a defined length and sequence, a central requirement to define the target spectrum of the silencing system. Julius Brennecke, one of the paper's senior authors, explained: "We already knew that piRNAs are formed from longer RNA species that are chopped up into pieces by Argonaute proteins or a protein called Zucchini. This forms the 5' ends of so-called pre-piRNAs, which are loaded into Argonaute proteins and subsequently trimmed and modified to yield mature piRNAs. As we had a fairly good understanding of the generation of piRNA 5' ends, our group focused on the 3' ends, a process that was not understood for nearly ten years." Using the common fruit fly Drosophila melanogaster, a major genetic model organism, IMBA scientists Rippei Hayashi and Jakob Schnabl -- both first authors of the article -- revealed that piRNA 3' end formation in fact follows one of two parallel pathways. "Once biogenesis is initiated, some piRNA 3' ends are actually generated by Zucchini, the endonuclease that is primarily known to generate piRNA 5' ends," said last author Stefan Ameres. "But Zucchini explains the biogenesis of only a subset of piRNAs. We then discovered that the exonuclease Nibbler is a second key-enzyme that can form piRNA 3' ends and realized that two genetically separated pathways act in parallel in the cell. This was a true deja vu as we also found Nibbler to mature some microRNAs, yet another class of small RNA molecules, during my postdoctoral work." Beyond unravelling these pathways, their place of action, and their implications for downstream gene regulatory mechanisms, the team also made some interesting observations that might provide clues as to the evolution of small RNA biogenesis. "The nucleases we've identified in this study have homologs in animals ranging from sponges to human. Interestingly, some notable exceptions are apparent. Nematode worms, for example, have lost the Zucchini enzyme, and mosquitos from the Anopheles genus have lost Nibbler. Whether here other piRNA trimming mechanisms exist or whether in these species the two-pathway model is reduced to one, is unclear. Remarkably, upon simultaneous ablation of Zucchini and Nibbler in Drosophila, piRNAs can still be generated, in this case by closely spaced piRNA-guided Argonaute cleavage events. This Argonaute-only pathway might be the ancient piRNA generating system, onto which sophisticated nucleases like Zucchini and Nibbler were added later to enhance efficiency and accuracy of piRNA biogenesis," concludes Julius Brennecke.


News Article | November 17, 2016
Site: phys.org

PIWI-interacting RNAs, or piRNAs for short, are a class of 'small regulatory RNAs'—tiny pieces of nucleic acid just 22–30 nucleotides in length. They may be small, but with their associated Argonaute proteins, piRNAs have the power to 'silence' transposable elements, so called egoistic genes found in the genomes of plants, fungi, and animals. piRNA-guided silencing can act on chromatin to block transposon transcription, or by destroying transposon mRNAs in order to block their translation into proteins. Although scientists understand quite well how piRNAs repress gene expression, until now, it has been much less clear how piRNAs are actually made. In a milestone research paper published in Nature, scientists from the Institute of Molecular Biotechnology in Austria (IMBA) have painstakingly unravelled the sequence of events that generate piRNAs with a defined length and sequence, a central requirement to define the target spectrum of the silencing system. Julius Brennecke, one of the paper's senior authors, explained: "We already knew that piRNAs are formed from longer RNA species that are chopped up into pieces by Argonaute proteins or a protein called Zucchini. This forms the 5' ends of so-called pre-piRNAs, which are loaded into Argonaute proteins and subsequently trimmed and modified to yield mature piRNAs. As we had a fairly good understanding of the generation of piRNA 5' ends, our group focused on the 3' ends, a process that was not understood for nearly ten years." Using the common fruit fly Drosophila melanogaster, a major genetic model organism, IMBA scientists Rippei Hayashi and Jakob Schnabl—both first authors of the article—revealed that piRNA 3' end formation in fact follows one of two parallel pathways. "Once biogenesis is initiated, some piRNA 3' ends are actually generated by Zucchini, the endonuclease that is primarily known to generate piRNA 5' ends", said last author Stefan Ameres. "But Zucchini explains the biogenesis of only a subset of piRNAs. We then discovered that the exonuclease Nibbler is a second key-enzyme that can form piRNA 3' ends and realized that two genetically separated pathways act in parallel in the cell. This was a true deja vu as we also found Nibbler to mature some microRNAs, yet another class of small RNA molecules, during my postdoctoral work." Beyond unravelling these pathways, their place of action, and their implications for downstream gene regulatory mechanisms, the team also made some interesting observations that might provide clues as to the evolution of small RNA biogenesis. "The nucleases we've identified in this study have homologs in animals ranging from sponges to human. Interestingly, some notable exceptions are apparent. Nematode worms, for example, have lost the Zucchini enzyme, and mosquitos from the Anopheles genus have lost Nibbler. Whether here other piRNA trimming mechanisms exist or whether in these species the two-pathway model is reduced to one, is unclear. Remarkably, upon simultaneous ablation of Zucchini and Nibbler in Drosophila, piRNAs can still be generated, in this case by closely spaced piRNA-guided Argonaute cleavage events. This Argonaute-only pathway might be the ancient piRNA generating system, onto which sophisticated nucleases like Zucchini and Nibbler were added later to enhance efficiency and accuracy of piRNA biogenesis," concludes Julius Brennecke. More information: Rippei Hayashi et al. Genetic and mechanistic diversity of piRNA 3′-end formation, Nature (2016). DOI: 10.1038/nature20162


News Article | November 11, 2016
Site: phys.org

It is mind-boggling to imagine how our brain develops from just a handful of cells at the early embryo into a highly convoluted biochemical and bioelectric system comprising more than 100 billion neurons in adults. Scientists at the Institute of Molecular Biotechnology (IMBA) in Vienna have published new research in EMBO Journal, in which they reveal how cells are instructed by a small RNA molecule to shape the complex layered structures of developing mouse brains. When stem cells divide to form new tissues and organs, they have to position their cell division apparatus in a specific orientation to position their daughter cells at sites where they experience different fate cues defining their subsequent function. The newly formed cells may then go on to take a specialised function – in the brain, for example, they can become various types of neurons to generate and transmit electrical impulses – or stay stem cells that will keep dividing to generate more cells. Failure to correctly induce fate decisions leads to multiple developmental brain disorders. Dr Juan Pablo Fededa, a postdoctoral scientist at IMBA and first author of the study, explains his findings: "Our research focused on understanding what controls the orientation of the mitotic spindles. We already knew that if the spindles are not in the correct orientation, then cells divide irregularly, and in the brain this can lead to neurodevelopmental disorders. We also knew that molecules called microRNAs might be important in this process, but we didn't know exactly how." From microscopy-based screening to the study of mouse brains Tiny 'micro-RNA' molecules can interfere with the expression of genes – turning them on, turning them off, or causing them to function differently. Led by principal investigator Dr Daniel Gerlich, Dr Fededa and the IMBA team used cultured cells in a dish to test the function of all micro-RNAs expressed during brain cell division. Fededa describes the approach: "By visualizing the spindle of the cells with a fluorescent marker in live cells, we observed that a family of six microRNAs called miR-34/449 influenced the spindle orientation during cell division. We then tested whether these micro-RNAs could also influence the orientation of mitotic spindles in developing mouse brains, using methodology established in Jürgen Knoblich's laboratory at IMBA. Indeed, we found that after deletion of miR-34/449 genes, mice developed smaller brains and these contained a larger proportion of stem cells called radial glial cells. This showed us that radial glial cells can grow relatively normally, but suggested that they are unable to further differentiate into more complex cells. We therefore concluded that miR-34/449 microRNAs must be required for normal brain development." miR-34/449 regulates the orientation of the mitotic spindle The scientists at IMBA compared the gene expression patterns in cells with or without miR-34/449 and discovered a difference in the expression of a protein called JAM-A. This protein was interesting, as it was previously shown to have a role in orienting the mitotic spindle in other tissues. By engineering a JAM-A gene version that is insensitive to miR-34/449, the team at IMBA was able to pinpoint its relevance for mitotic spindle orientation. "Our findings show that in developing mouse brains, miR-34/449 regulates JAM-A to ensure the correct orientation of dividing cells and accurate formation of brain layers" concludes Daniel Gerlich. "The current research provides insights into the role of micro-RNAs in brain development, but similar mechanisms might be at place in other organs." Explore further: Schizophrenic stem cells do not differentiate properly into neurons More information: Juan Pablo Fededa et al. MicroRNA‐34/449 controls mitotic spindle orientation during mammalian cortex development, The EMBO Journal (2016). DOI: 10.15252/embj.201694056

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