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NYU Abu Dhabi Researchers Unlock the Secrets of Liver Regeneration

Fast facts:

  • The liver is the only solid organ that can regenerate itself in mammals, but what confers this special property to the liver has not been uncovered, despite decades of research.
  • NYU Abu Dhabi researchers suggest that a novel mechanism driven by the epigenome promotes liver regeneration.
  • The epigenome refers to the code that packages the DNA so that some parts can be activated (i.e. genes) and some parts remain in dormant domains – these dormant parts largely contain remnants of old viruses or transposable elements.
  • Epigenetic compensation is when parts of the epigenome that usually have one role – i.e. to suppress genes, are co-opted to do a different job – when another part of the epigenome is missing modifications in the packaging material of the DNA influence how much a genetic program is active or repressed. These modifications do not change the DNA sequence, but instead, affect how cells read genes.
  • This study reports that the primary role of the epigenome is to protect the genome against the activation of genomic parasites (transposable elements).
  • The new findings have been published in the journal Developmental Cell.

In a recent study published in the journal Developmental Cell, NYU Abu Dhabi researchers have reported a new way in which the liver is primed to regenerate itself. They found that by stripping parts of the epigenome, which play a primary role in repressing “jumping genes” (i.e. transposable elements), other epigenetic marks were redistributed.

This newly discovered form of epigenetic compensation protects the genome against transposable elements activation, but takes these compensating epigenetic marks away from their normal job in regulating gene expression. The result is that when these marks are taken away from their normal role, the genes they usually repress are activated early and are sustained during the regenerative response to the surgical removal of part of the liver.

This type of surgery is relevant to humans, as it is used in resection of liver tumors and the regenerative response is essential for the liver to respond to damage. The findings are a significant advance in the understanding of the liver regeneration process, which is unique among the organs of humans, mice, and other mammals.

The researchers from NYU Abu Dhabi’s Sadler Lab, led by Associate Professor of Biology Kirsten Sadler Edepli, removed a key epigenetic regulator, UHRF1 in the mouse liver. They found when they removed part of the liver, the remaining lobes responded more readily by activating pro-regenerative genes activated earlier, and this regeneration program stayed active longer, resulting in enhanced liver regeneration.

The epigenome refers to the code that packages the genome so that some parts can be activated (i.e. genes) and some parts remain in dormant domains – these dormant parts largely contain remnants of old viruses or transposable elements, which were made famous by the 1983 Nobel Prize discovery by Barbara McClintok.

Surprisingly, instead of causing massive activation of transposable elements or an immune response to mitigate the unleashing of transposable elements, as found in previous experiments, they discovered that there is an extra layer of protection by another repressive epigenetic mark (H3K27me3). This mark was redistributed from gene promoters to suppress transposable elements when DNA methylation was missing, thereby compensating for the loss of DNA methylation. When this mark is redistributed, it is removed from its role in repressing genes that promote liver regeneration. Thus, livers lacking UHRF1 are able to regenerate faster.

Shuang Wang, a post-doctoral fellow in the Sadler Edepli laboratory who worked in her group at Icahn School of Medicine at Mount Sinai, led the study in collaboration with members of the lab at NYUAD as well as Emily Bernstein and Amaia Lujambio in NY.

 

This post comes to us from NYU Abu Dhabi and you can find the original here.

New PragueCast Podcast Focuses on our lives Online

The latest PragueCast from NYU Prague is now live and available for a listen here. Launched in 2015 by Prague’s BBC correspondent, Rob Cameron, PragueCast is a podcast with stories of Prague told through the eyes of NYU Prague students. The 20-minute editions, each with a different theme chosen by students, are distributed to an audience beyond NYU Prague. Students write, record, produce, edit, and market the episodes – all as non-credit extracurricular program that meets in the evenings. We hope you’ll enjoy this latest offering!

Leaving a Bright Spot: Practicing Therapeutic Arts with Underserved International Populations

Interns making art with children in Ghana

Interns lead a painting session in Ghana.

Stemming from her own experiences delivering art therapy workshops around the world, Ikuko Acosta, director of NYU Steinhardt’s Graduate Art Therapy program, and clinical associate professor, wanted to offer her students the invaluable experience of practicing art therapy internationally.

More than a decade ago, Acosta established a global internship program at Steinhardt to provide “the opportunity for students to develop racial and cultural self-awareness, work with diverse communities, hone critical thinking skills, and explore the role of art therapy in another culture.” Says alumna Krystal Atwood of her decision to enroll in the internship in Buenos Aires, “I wanted to learn everything I could to provide the most nuanced and culturally fluent art therapy services possible to a range of client populations.”

Coordinated in collaboration with several of NYU’s global sites, Acosta’s interns have practiced therapeutic arts in a wide array of foreign settings, including Florence, which welcomes its third cohort in July 2019. Some of this year’s group will serve a geriatric population that has worked with two different intern cohorts. Acosta recalled that this population was especially receptive to engagement in creative activities, noting “their facial expressions became cheerful, moods were boosted, and their social interactions improved.” In Accra, Ghana, students have worked at a rehabilitation center for young men with mental, cognitive and physical disabilities. A grouping, Acosta said, that contrasts with “facilities in the US where patients are usually separated based on the nature of their disabilities.” The men are also provided with “job training and various types of skills to survive in society” explained Acosta. During the three weeks that the men worked with interns, she emphasized that “they are not treated in a clinical sense, yet a very positive change can be seen in their self-esteem due to their increased ability to express themselves freely without being judged. Their general attitudes became more positive.”

Returning to NYU’s global sites offers faculty the opportunity to observe the long-term impacts of programs. In Ghana, when the van entered the driveway to the rehabilitation center one year later, Acosta and her students were greeted by shouts of “art therapy!” “And,” she added, “the young men went right back into making art as if they had done so yesterday.” When returning to the geriatric facility in Florence two years later, the demeanor of the residents immediately became “uplifted,” and they “even remembered the names of some interns from prior years,” providing “evidence,” that the “experiences were etched in their memories.” Acosta says that “while what we do may be little, at a basic human level, the experience leaves a bright and memorable spot in their minds.”

“There is an amazing resilience that each location reveals. The internship leads to a questioning of one’s values in a way that can’t be gained inside a classroom.”

Professor Ikuko Acosta

Indeed, Acosta notes that “the program is not geared toward addressing mental illness directly” and that “it would be unrealistic to treat a patient in three weeks.” Furthermore, she explained that “applying a western concept of art therapy to non-western societies can create tension with local attitudes around mental illness. And therapeutic techniques that are not adapted to the culture situate the therapist as a colonialist.” But while mental illness is viewed in various ways around the world, she emphasized that “the symptoms and behavioral manifestations of mental and psychological disturbances are very similar.  What differs are cultural attitudes and treatment.” Yet she has observed that art therapy brings together commonalities in international settings. “Art is universal and so too is human suffering.”

Regardless of location, Acosta says, art therapy students work to build a “human connection.” In every country in which the course has been held, Acosta has seen “students establish relationships despite not speaking the local language. They learn to become highly receptive and attuned to the subtleties of body language and other non-verbal cues.” She added that her students “thoroughly enjoy getting to know each client’s personality beyond his/her disability through creative communication.” Inevitably, explained Acosta, “basic human bonds are formed during experiences that are not bound by a singular form of expression. Connecting in this way is a universal phenomenon.”

Other skills that students quickly acquire, said Acosta, are “flexibility and adaptability, because their clinical training does not translate directly in foreign locations.” She went on to say that “outside of the US, concepts of boundaries between patient and client are much different, particularly those that are physical – it is common and natural for patients to openly and physically express affection to their therapists in many cultural contexts. Another example is corporal punishment, which seems to be an acceptable form of discipline in some countries.” Therapists in the US, Acosta explained, are trained to report signs of “abuse,” so it can be “difficult to set aside feelings of confusion about roles and responsibilities during the internship.”

Reflecting on her experiences in Buenos Aires, Atwood explained that she “felt humbled by the grace and dignity with which Dr. Acosta acknowledged our interpersonal struggles while maintaining hope for all of the involved parties and, ultimately, guiding the student interns toward providing life-changing art therapy services to the clients.” The level of care delivered by the interns is possible, says Acosta, because they “very quickly, learn to take a humanistic perspective and adapt to local mores.” “Interns observe, learn, and respect the host country and are not there to negate or impose their cultural norms,” she explained, and added that “after we leave, they resume their own lives, yet are instilled with memories of the brief but undeniable human connections that we all shared.”

A boy paints a cardboard puppet in Florence.

Creating stick puppets in Florence.

“Students also learn to adapt their planning process for clinical sessions,” said Acosta, as “they develop activities appropriate to the population […] and seek out locally available art materials.” During an early iteration of the program in India, coordinated by Cross-Cultural Solutions, a New York-based non-profit that provides volunteer service to communities around the world, Acosta said her students “found beautiful textiles with which they made dolls with women at a shelter for victims of domestic violence. They also collected many found objects from the streets, which they incorporated into a piece of artwork.” In Florence, a capital of the art world, “students find low cost materials at art stores and unusual items from junk shops.” Acosta elaborated that “these experiences too contribute to students’ creative growth and help them to become more flexible and less confined in their practice of art therapy.”

“Through exposure to how others survive amidst adversity,” Acosta noted, “with very limited resources and significant hardship, students gain a sense of humbleness.” For Atwood, her work with refugees and asylum seekers in Buenos Aires provided a glimpse into individuals’ experiences – many had fled war and violence, and struggled to live with uncertainty in the confines of refugee centers. During the internship, explained Krystal, she saw increases in “self-efficacy and a reduction of isolation as they connected with other refugees and asylum seekers in art therapy groups.”

“There is an amazing resilience that each location reveals,” said Acosta. “The internship leads to a questioning of one’s values in a way that can’t be gained inside a classroom. And that is essential as a therapist because personal value systems can’t be brought into clinical sessions.”

A Lab for Pedagogical Innovation: Doctoral Masterclasses at NYU Paris

Galichon teaching the masterclass

Galichon delivering a coding session.

Paris hosted its first-ever master class, math+econ+code Masterclass on Optimal Transport, Choice and Matching Models, delivered by Alfred Galichon, NYU Paris site director, and professor, Department of Economics and Mathematics, Courant Institute, in late June.

Interdisciplinary in nature, the five-day course focused on “models of demand, matching models, and optimal transport methods, with various applications pertaining to labor markets, the economics of marriage, industrial organization, matching platforms, networks, and international trade from the crossed perspectives of theory, empirics and computation.”

Interestingly, it is Paris’ world renowned cooking schools, such as Le Cordon Bleu and L’Atelier des Chefs, that inspired Galichon to take a new approach to the delivery of coding lessons. Galichon says his approach was informed by “scientific-context-based learning principles, where theoretical tools are introduced just in time, as needed, at the point in time when they are called for by the specific application.” Under this model, much as culinary students would in a kitchen, Galichon’s students essentially take on the role of apprentices, and over time, move from their position at the periphery of a learning community to the center as they build their expertise.

Galichon explained that the course starts with a presentation of “the raw ingredients to the student, which in this case, means the data, such as the characteristics of consumers and of products.” Following this, he describes to the class “what we will cook, which in this case means the type of matching or pricing problems we will solve.” To make this delivery format possible, Galichon emphasized that “[t]he time-consuming data preparations” – the tasks of the sous chef – “have been done off-line. I show the ideas on the whiteboard, and then I cook/code them myself in front of the students,” explains Galichon. “The students then code themselves, inspired by what they saw.”

Galichon grounds his pedagogy in “a ‘learning-by-coding’ philosophy,” which involves creating code “in front of the students rather than showing them lines of pre-written code.” In this way, students actively learn in-situ, rather than via a scripted method that relies heavily on the passive visualization of code and other course content. Delivering immersive courses, he says, has allowed him to be “quite creative and test new pedagogical ideas that may apply to other courses of this type.”

The curriculum, said Galichon, was constructed to serve the needs of two core groups of doctoral candidates. “There is a big demand from students in economics who look to acquire coding skills, and who want to develop a deeper understanding of the mathematical structure behind the economic models,” he said, “and at the same time from students in math/computer students who seek to understand better the economic applications of their tools.” Crafted around these requirements, the “course provides students with the conceptual tools and coding skills in an apprenticeship philosophy.”

The masterclass quickly attracted “a wonderful mix of students,” said Galichon, from quantitative disciplines, including economics, math, computer science, and engineering. In addition to students from NYU, the inaugural cohort comprised international enrollees from Faculté des sciences de Tunis, and Harvard as well as others from “very strong [local] institutions” such as Sciences Po, and Ecole Polytechnique/Ensae.

The international nature of the masterclass is also part of the linguistic aspects of learning to code. The course presents several different types of coding languages simultaneously, lending to a sense of multiliteracy within the learning environment. This is accomplished, Galichon explained, with “the presence of ‘veteran students’ who, after the lectures, present the course material coded in other programming languages than the one I am presenting.” He added that “These are among the novel ideas that I will test in Paris, which will thus serve as a lab for pedagogical innovation.”

Czech Republic’s Second Female Conductor, Miriam Nemcova, Teaching at NYU Prague

The Czech Republic has one of Europe’s strongest music education programs, and children as young as 15 can start learning to conduct at the conservatory (students in the USA don’t start learning to be conductors until much later, usually after they have completed a BA degree). This semester NYU Prague’s music students can take a new course on conducting taught by Miriam Nemcova, who is the second Czech woman to become a professional conductor.  

The first professional Czech female conductor was Vitezslava Kapralova who was also the first woman to earn a conducting degree from the Janacek Academy in 1935.  She had a very successful early career, conducting the Czech Philharmonic in 1937 and the BBC Symphony Orchestra in 1938.  Tragically she died of tuberculosis at the age of 35.

It took sixty years for another female conductor to appear on the Czech music scene.  It hasn’t been easy. The first time Nemcova applied to the conducting program at the Prague Music Academy in 1983 she wasn’t accepted.  Not only was she female, but she was also religious, and the Communist regime was in control of the educational system. She was criticized for wearing a cross when she conducted an orchestra for a concert that took place just before her audition for school.  Nemcova persevered, and she was accepted the following year. Throughout her studies and early in her career colleagues and teachers told her that they didn’t think women have the authority necessary to conduct an orchestra. Nemcova, whose mother was a well-known opera singer, ignored the criticism, believing that when you conduct, you shouldn’t display either female or male attributes.   

A few years after graduation Nemcova was offered the prestigious position of conductor and choir master of the State Opera in Prague where she worked for several years.  She later spent six years in Italy, conducting choirs and orchestras around the country, and she has recorded CDs with the Hradec Kralove Philharmonic Orchestra and conducted film music for many Czech and international productions.

Nemcova is optimistic that the prejudices against women are slowly disappearing in her field, in part because of her own role at the music academy where she has taught for over twenty years, mentoring her female students.   “I have trained at least ten females to be conductors. Still, after graduation not very many of them work professionally. Being a female conductor is complicated. It’s difficult in terms of time but also difficult physically, especially when you have a family and children.  A lot depends on having support from your family and also your financial situation.”

Recently Nemcova conducted a concert of Dvorak and Smetana with the Cairo Symphony Orchestra in Egypt at an event organized by the Czech Embassy.  She was a bit nervous approaching them as a woman. “But the musicians respected my position – hierarchy was more important than gender to them. A maestro is a maestro – doesn’t matter if that maestro is a woman or man.”

Conversations Podcast Hosted by NYU President Andy Hamilton

In this new podcast, President Andy Hamilton interviews NYU faculty, students, and alumni who are using their intellectual gifts, determination, and creativity to make a profound difference in our world. With each guest, he pulls back the curtain to learn the origins of their inspiration, the current focus of their work, and their vision for the future. His first guest is Rubén Blades(Fear The Walking Dead)— Steinhardt’s scholar in residence.

NYU Researchers Find Answer to How Fish & Birds Hang Together without Colliding

Fish and birds are able to move in groups, without separating or colliding, due to a newly discovered dynamic: the followers interact with the wake left behind by the leaders. 

The findings, by a team of researchers including NYU Shanghai Professor of Physics and Mathematics Jun Zhang, offer new insights into animal locomotion and point to potential ways to harness energy from natural resources, such as rivers or wind.  

“Air or water flows naturally generated during flight or swimming can prevent collisions and separations, allowing even individuals with different flapping motions to travel together,” explains Joel Newbolt, a doctoral candidate in New York University’s Department of Physics and the lead author of the research, which appears in the Proceedings of the National Academy of Sciences. “Notably, this phenomenon allows slower followers to keep up with faster-flapping leaders by surfing on their wake.”

More broadly, the study opens possibilities for better capturing natural resources to generate energy from wind and water.

“While we currently use wind and water to help meet our energy needs, our work offers new ways to more efficiently leverage them as we seek new methods for enhancing sustainable practices,” observes Leif Ristroph, one of the paper’s co-authors and an assistant professor in NYU’s Courant Institute of Mathematical Sciences.

It’s well known that animals such as fish and birds often travel in groups, but the details of these interactions in schools and flocks are not fully understood.

In order to study the effects of flapping motions and flow interactions on the movement of members in a group, the researchers conducted a series of experiments in the Courant Institute’s Applied Math Lab. Here, they designed a robotic “school” of two hydrofoils, which simulate wings and fins, that flap up and down and swim forward. The flapping motion of each foil was driven by a motor, while the forward swimming motions were free and result from the pressure of the water on the foils as they flap.

The researchers varied the speed of the flapping motions to represent faster and slower swimmers and fliers.

The process may be viewed here. (credit: video courtesy of Joel Newbolt, NYU’s Courant Institute of Mathematical Sciences).

Their results showed that a pair of foils with different flapping motions, which would swim or fly at different speeds when alone, can, in fact, move together without separating or colliding due to the interaction of the follower with the wake left behind by the leader.

Specifically, the follower “surfs” in distinct ways on the wake left by the leader. If trailing behind, the follower experiences a “push” forward by this wake; if moving too fast, however, a follower is “repelled” by the leader’s wake.

“These mechanisms create a few ‘sweet spots’ for a follower when sitting behind a leader,” observes Zhang.

Original article first appeared as an NYU news release: How Do Fish & Birds Hang Together without Colliding? Researchers Find the Answer is a Wake with Purpose

Read additional coverage of the research by PBS/NOVA here.