Post-doc talks
Presenter: Joan Doidy
School/Department: Biology
Title: Nutrient Economics: Uncovering the Pareto optimality of nutrient trade-off in plant biology
A challenge for biological systems is the optimization of processes to achieve maximum performance at the lowest cost, which in turn will increase fitness. However, maximizing performance in one task often comes at the expense of other tasks, causing a “trade-off”. An example of biological and agronomical relevance is the evolutionary strategies of plants to maximize their growth under nutrient-limiting conditions. Our results on 48 natural plant populations show a trade-off between the efficient use of the primary nutrients used in commercial NPK fertilizers, N (nitrogen), P (phosphorous), and K (potassium). The trade-off is that the nutritional conditions that support high biomass under low nutrient inputs (benefit) have a negative effect on plant production under high inputs (cost). In economics, trade-offs have been studied according to the Pareto principle, which defines optimal solutions for multitasking systems. Here, we adopt the economics concept of “Pareto optimality”, which addresses the problem of efficient trade-offs, to our study of nutrient use efficiency (NUE) in plant biology. Specifically, the natural variations of NUE observed for each plant accessions defined as “optimal NUE solutions”, or “Pareto efficient” traits, will be used in genome-wide association mapping studies (GWAS). The developmental and metabolic gene networks underlying evolutionary efficient solutions might be economically important. For instance, they may be used to maximize profit in plant productivity under low nutrient conditions, while minimizing costs at high nutrient inputs. Understanding the molecular basis for this trade-off has broad significance for improving nutrient use in crops, yielding energy, environmental and health benefits.
Presenter: Georg Wolf
School/Department: Physics
Title: Orthogonal spin transfer magnetic random access memory (OST-MRAM)
Combining high density, low power consumption, long term storage capabilities and fast operation speed is the key challenge for future data storage devices. Orthogonal spin transfer magnetic random access memory (OST-MRAM), a concept invented at New York University [1], combines the features of a non-volatile magnetic memory with fast write times in the nanosecond or even sub-nanosecond regime. The magnetic state of nanometer sized element is changed by applying a short spin-polarized current pulse to the structure. The spin-polarized current exerts a torque on the magnetization, referred to as spin transfer torque, which causes the magnetization to reverse.
This presentation covers fundamental aspects of the current induced magnetization reversal as well as technological aspects of the development of this new type of memory device. A special focus of this research lies in understanding the mechanism of magnetization reversal under the influence of the spin transfer torque. This is a key aspect to the development of a reliable memory device. Thermal fluctuations at room temperature introduce a stochastic variance to the problem. By measuring thousands of individual reversal processes in real time using a high bandwidth oscilloscope we can not only characterize the statistical properties of the reversal process, but also measure the state of the magnetization each point in time while the current is applied. This ultimately feeds back into more advanced physical modeling and helps to improve performance such a memory cell.
[1] A. D. Kent, B. Özyilmaz and E. del Barco, Appl. Phys. Lett. 84, 3897 (2004).
Presenter: Emily Miraldi
School/Department: Biology
Title: Developing a quantitative understanding of the gut immune-microbial ecosystem
Approximately 5-8% of Americans suffer from autoimmune diseases, yet even the most prevalent autoimmune diseases have no cure and require costly lifelong immune-suppressive therapies. Recent studies highlight a crucial role for gut mucosal immunity in both gut-proximal autoimmune diseases (Inflammatory Bowel Disease (IBD)) and in those involving extraintestinal compartments (rheumatoid arthritis and multiple sclerosis). The development of autoimmune disease involves the coordination of multiple gut-resident cell types and the gut microbiome. On the host side, immune cells and intestinal epithelium orchestrate gut microbial homeostasis via secretion of effector cytokines, antimicrobial peptides, and other molecules. Microbiota are also important modulators of immune responses, influencing the differentiation and function of immune cell populations. Here, we use a combined experimental-computational design to develop an understanding of (1) how defects in immune signaling pathways genetically associated with IBD alter gut immune and microbial populations and (2) how pathobionts, when introduced into environments with compromised immune signaling, interact with other gut microbes and immune populations to bring about expansion of colitis-associated immune lineages. Here, these questions are addressed in parallel, from an ecological perspective, using population-level measurements of immune-lineages and microbiota to build ecological models of the gut, and, from a molecular perspective, through construction of gene regulatory models from transcriptional and other genomics measurements in key immune cell populations.
Presenter: Tara Mandalaywala
School/Department: Psychology
Title: Relationships between essentialist beliefs and racial prejudice among White and Black American adults
Psychological essentialism is a cognitive bias that leads people to view members of a category as sharing an underlying, inherent nature that causes them to be fundamentally similar. Although essentialist beliefs can be beneficial, allowing people to view the social world as stable, these beliefs are also thought to underlie the development of prejudice. However, the mechanisms underlying the latter relationship have rarely been examined. Essentialism could contribute to prejudice by leading people to view essentialized out-groups as highly dissimilar to the self, in which case both lower and higher status individuals would have more negative attitudes towards out-groups. Alternately, essentialism could contribute to beliefs that the social world reflects objective, natural structure, thus both lower and higher status individuals would devalue low status groups. We found that racial essentialism (i.e. beliefs that race is a meaningful, biologically-based category) was associated with increased explicit prejudice towards Blacks among both White (n = 151; r=0.59, p<0.001) and Black (n = 141; r=0.42, p<0.001) participants (recruited via Amazon Mechanical Turk). Among White participants only, racial essentialism was also weakly associated with more negative implicit attitudes towards Blacks (r=0.16, p=0.045). That essentialism led to increased prejudice towards Blacks among both Black and White participants indicates that it did so by leading participants to view the social world as reflecting objective, natural structure and to devalue lower status groups, and not by increasing prejudice toward racial outgroups. Thus, the link between essentialism and prejudice appears rooted in conceptions of social hierarchies and group status.
Presenter: Kwami Coleman
School/Department: Gallatin School of Individualized Study
Title: The “New Thing” and the “Blue Thing”? Experimentalism and Tradition in 1960s Jazz
In March of 1965, a young trumpeter from Philadelphia named Ted Curson entered a recording studio in New York City to complete an album for Atlantic Records titled _The New Thing & The Blue Thing_. Its elliptical title works to situate Curson at vanguard of musical innovation (the “new thing”) and at the heart of the jazz tradition (the blues), and freer improvisatory techniques are juxtaposed with more conventional forms across the album’s six tracks. Recorded at the height of the backlash against the “new thing,” when critics, musicians, and record-buyers dismissed avant-gardists as radicals destroying the jazz tradition, Curson’s album strikes a mitigating tone between both sides. The possibility that improvising musicians in the 1960s considered experimentalism a part of tradition has been largely overlooked in jazz studies—an oversight abetted by the hostile reception of the jazz avant-garde in the trade media of the decade. This paper takes Curson’s evocative title as an invitation to reexamine the jazz avant-garde from within his proposed nexus space. I focus on individual tracks on Curson’s album, the recording’s tepid critical reception in _Down Beat_ magazine, and a revealing critical debate on the jazz avant-garde printed in the magazine that same year to show how notions of experimentalism and tradition were made both congruous and contentious by different factions in the jazz field. By considering the aesthetic positions articulated by musicians, discursively and sonically, I demonstrate how experimentalism was a pervading trope among improvising musicians in this defining period in jazz history.
Presenter: Amandine Alard
School/Department: Microbiology (School of Medicine)
Title: DAP5, a regulator of lung metastasis in breast cancer
During their journey to colonize a distant organ, cancer cells undergo wide varieties of stresses that shut down their cap-dependent protein synthesis machinery. Then, the disseminated cells rely on an alternative translation mechanism, typically through non cap-dependent means such as internal ribosome entry (IRES).
DAP5 is a poorly studied translation initiation factor that mediates IRES-driven translation of cellular mRNAs which include factors involved in stress responses. Therefore, we hypothesized that DAP5 is crucial for the survival and expression of the metastatic cell proteome.
We engineered highly metastatic murine 4T1 cancer cells to express a doxycycline inducible shRNA system to silence DAP5. These cells and the control cells were grown s.c. in immunocompetent syngeneic mice.
While no significant effect was observed on cell proliferation in vitro, silencing DAP5 significantly decreased primary tumor growth and lung colonization. Importantly, when the same tumor study was performed in immunodeficient animals the inhibition of tumor growth with DAP5 silencing was completely abolished. This suggested that DAP5 likely enables cancer cells to evade the immune response. However in this model, DAP5 silencing significantly decreased the number of lung metastases, implying that at least one of the mechanisms by which DAP5 prevents metastasis is immune system-independent.
Our results suggest that the translation initiation factor DAP5 likely plays a critical role in breast cancer metastasis and provides new concepts for therapeutic strategies involving translational regulation and immunotherapeutics. Indeed, inhibiting DAP5 might be a powerful approach, as it impacts the whole proteome of disseminated cancer cells.
Presenter: Jeremie Barral
School/Department: Center for Neural Science
Title: Propagation of synchronous input in reconstituted feedforward networks
The sequence of action potentials produced by neurons defines a coding strategy to transduce information in neuronal networks. Information may either be represented as the average number of action potentials per unit time (rate coding) or by the precise timing of action potentials (temporal coding). The nervous system utilizes both strategies and there appears to be a continuum between these two extremes. A rudimentary feature of most neural networks consists of several neurons’ pools arranged in a feedforward manner, like the multiple sheets in the cortex. The feedforward network model provides a useful and minimal framework for studying information processing in the brain and has been investigated by computer simulations. They revealed that the number of neurons and their probabilities of connections are critical parameters for the propagation of rate and temporal information. However, experimental support is lacking to test this hypothesis. Here, we studied experimentally how the connection pattern shapes the computing properties of neuronal networks. We reconstructed in vitro neuronal networks by culturing neurons in microfabricated environment to control both the density of neurons and the connection probability from one layer to the next. Neurons of the first layer were activated optogenetically by a packet of pulses whose spread and number were the control parameters. We identified the conditions of network architecture to transmit the input and showed that spike synchrony faithfully propagates only if the packet of stimulation is sufficiently precise. Finally, we determined the role of network state in opening a gate to transmit synchronous input.
Presenter: Enrico Fonda
School/Department: Physics
Title: Creative Turbulence: Experiments in Art and Physics
Effective communication of basic research to non-experts is necessary to inspire the public and to justify support for science by the taxpayers. The creative power of art is particularly important to engage an adult audience, who otherwise might not be receptive to standard didactic material. Interdisciplinarity defines new trends in research, and works at the intersection of art and science are growing in popularity, even though they are often isolated experiments.
We present a public-facing collaboration between physicists/engineers performing research in fluid dynamics and condensed matter, and audiovisual artists working in cutting-edge media installation and performance. The project, funded by the American Physical Society, is in collaboration with scientists from leading research universities, and with Pioneer Works, an innovative arts exhibition space in Red Hook, Brooklyn. The project team based at NYU will organize a public call for works for artists collaborating with the researchers. A jury composed by curators of the art space as well as scientists, will commission 5 artists for an exhibition. We discuss the science of classical fluids and quantum turbulence phenomena proposed as inspiration for the artists, with possible ideas for installations based on similar work, future developments and directions.
Presenter: Joan Doidy
School/Department: Biology
Title: Nutrient Economics: Uncovering the Pareto optimality of nutrient trade-off in plant biology
A challenge for biological systems is the optimization of processes to achieve maximum performance at the lowest cost, which in turn will increase fitness. However, maximizing performance in one task often comes at the expense of other tasks, causing a “trade-off”. An example of biological and agronomical relevance is the evolutionary strategies of plants to maximize their growth under nutrient-limiting conditions. Our results on 48 natural plant populations show a trade-off between the efficient use of the primary nutrients used in commercial NPK fertilizers, N (nitrogen), P (phosphorous), and K (potassium). The trade-off is that the nutritional conditions that support high biomass under low nutrient inputs (benefit) have a negative effect on plant production under high inputs (cost). In economics, trade-offs have been studied according to the Pareto principle, which defines optimal solutions for multitasking systems. Here, we adopt the economics concept of “Pareto optimality”, which addresses the problem of efficient trade-offs, to our study of nutrient use efficiency (NUE) in plant biology. Specifically, the natural variations of NUE observed for each plant accessions defined as “optimal NUE solutions”, or “Pareto efficient” traits, will be used in genome-wide association mapping studies (GWAS). The developmental and metabolic gene networks underlying evolutionary efficient solutions might be economically important. For instance, they may be used to maximize profit in plant productivity under low nutrient conditions, while minimizing costs at high nutrient inputs. Understanding the molecular basis for this trade-off has broad significance for improving nutrient use in crops, yielding energy, environmental and health benefits.
Presenter: Georg Wolf
School/Department: Physics
Title: Orthogonal spin transfer magnetic random access memory (OST-MRAM)
Combining high density, low power consumption, long term storage capabilities and fast operation speed is the key challenge for future data storage devices. Orthogonal spin transfer magnetic random access memory (OST-MRAM), a concept invented at New York University [1], combines the features of a non-volatile magnetic memory with fast write times in the nanosecond or even sub-nanosecond regime. The magnetic state of nanometer sized element is changed by applying a short spin-polarized current pulse to the structure. The spin-polarized current exerts a torque on the magnetization, referred to as spin transfer torque, which causes the magnetization to reverse.
This presentation covers fundamental aspects of the current induced magnetization reversal as well as technological aspects of the development of this new type of memory device. A special focus of this research lies in understanding the mechanism of magnetization reversal under the influence of the spin transfer torque. This is a key aspect to the development of a reliable memory device. Thermal fluctuations at room temperature introduce a stochastic variance to the problem. By measuring thousands of individual reversal processes in real time using a high bandwidth oscilloscope we can not only characterize the statistical properties of the reversal process, but also measure the state of the magnetization each point in time while the current is applied. This ultimately feeds back into more advanced physical modeling and helps to improve performance such a memory cell.
[1] A. D. Kent, B. Özyilmaz and E. del Barco, Appl. Phys. Lett. 84, 3897 (2004).
Presenter: Emily Miraldi
School/Department: Biology
Title: Developing a quantitative understanding of the gut immune-microbial ecosystem
Approximately 5-8% of Americans suffer from autoimmune diseases, yet even the most prevalent autoimmune diseases have no cure and require costly lifelong immune-suppressive therapies. Recent studies highlight a crucial role for gut mucosal immunity in both gut-proximal autoimmune diseases (Inflammatory Bowel Disease (IBD)) and in those involving extraintestinal compartments (rheumatoid arthritis and multiple sclerosis). The development of autoimmune disease involves the coordination of multiple gut-resident cell types and the gut microbiome. On the host side, immune cells and intestinal epithelium orchestrate gut microbial homeostasis via secretion of effector cytokines, antimicrobial peptides, and other molecules. Microbiota are also important modulators of immune responses, influencing the differentiation and function of immune cell populations. Here, we use a combined experimental-computational design to develop an understanding of (1) how defects in immune signaling pathways genetically associated with IBD alter gut immune and microbial populations and (2) how pathobionts, when introduced into environments with compromised immune signaling, interact with other gut microbes and immune populations to bring about expansion of colitis-associated immune lineages. Here, these questions are addressed in parallel, from an ecological perspective, using population-level measurements of immune-lineages and microbiota to build ecological models of the gut, and, from a molecular perspective, through construction of gene regulatory models from transcriptional and other genomics measurements in key immune cell populations.
Presenter: Tara Mandalaywala
School/Department: Psychology
Title: Relationships between essentialist beliefs and racial prejudice among White and Black American adults
Psychological essentialism is a cognitive bias that leads people to view members of a category as sharing an underlying, inherent nature that causes them to be fundamentally similar. Although essentialist beliefs can be beneficial, allowing people to view the social world as stable, these beliefs are also thought to underlie the development of prejudice. However, the mechanisms underlying the latter relationship have rarely been examined. Essentialism could contribute to prejudice by leading people to view essentialized out-groups as highly dissimilar to the self, in which case both lower and higher status individuals would have more negative attitudes towards out-groups. Alternately, essentialism could contribute to beliefs that the social world reflects objective, natural structure, thus both lower and higher status individuals would devalue low status groups. We found that racial essentialism (i.e. beliefs that race is a meaningful, biologically-based category) was associated with increased explicit prejudice towards Blacks among both White (n = 151; r=0.59, p<0.001) and Black (n = 141; r=0.42, p<0.001) participants (recruited via Amazon Mechanical Turk). Among White participants only, racial essentialism was also weakly associated with more negative implicit attitudes towards Blacks (r=0.16, p=0.045). That essentialism led to increased prejudice towards Blacks among both Black and White participants indicates that it did so by leading participants to view the social world as reflecting objective, natural structure and to devalue lower status groups, and not by increasing prejudice toward racial outgroups. Thus, the link between essentialism and prejudice appears rooted in conceptions of social hierarchies and group status.
Presenter: Kwami Coleman
School/Department: Gallatin School of Individualized Study
Title: The “New Thing” and the “Blue Thing”? Experimentalism and Tradition in 1960s Jazz
In March of 1965, a young trumpeter from Philadelphia named Ted Curson entered a recording studio in New York City to complete an album for Atlantic Records titled _The New Thing & The Blue Thing_. Its elliptical title works to situate Curson at vanguard of musical innovation (the “new thing”) and at the heart of the jazz tradition (the blues), and freer improvisatory techniques are juxtaposed with more conventional forms across the album’s six tracks. Recorded at the height of the backlash against the “new thing,” when critics, musicians, and record-buyers dismissed avant-gardists as radicals destroying the jazz tradition, Curson’s album strikes a mitigating tone between both sides. The possibility that improvising musicians in the 1960s considered experimentalism a part of tradition has been largely overlooked in jazz studies—an oversight abetted by the hostile reception of the jazz avant-garde in the trade media of the decade. This paper takes Curson’s evocative title as an invitation to reexamine the jazz avant-garde from within his proposed nexus space. I focus on individual tracks on Curson’s album, the recording’s tepid critical reception in _Down Beat_ magazine, and a revealing critical debate on the jazz avant-garde printed in the magazine that same year to show how notions of experimentalism and tradition were made both congruous and contentious by different factions in the jazz field. By considering the aesthetic positions articulated by musicians, discursively and sonically, I demonstrate how experimentalism was a pervading trope among improvising musicians in this defining period in jazz history.
Presenter: Amandine Alard
School/Department: Microbiology (School of Medicine)
Title: DAP5, a regulator of lung metastasis in breast cancer
During their journey to colonize a distant organ, cancer cells undergo wide varieties of stresses that shut down their cap-dependent protein synthesis machinery. Then, the disseminated cells rely on an alternative translation mechanism, typically through non cap-dependent means such as internal ribosome entry (IRES).
DAP5 is a poorly studied translation initiation factor that mediates IRES-driven translation of cellular mRNAs which include factors involved in stress responses. Therefore, we hypothesized that DAP5 is crucial for the survival and expression of the metastatic cell proteome.
We engineered highly metastatic murine 4T1 cancer cells to express a doxycycline inducible shRNA system to silence DAP5. These cells and the control cells were grown s.c. in immunocompetent syngeneic mice.
While no significant effect was observed on cell proliferation in vitro, silencing DAP5 significantly decreased primary tumor growth and lung colonization. Importantly, when the same tumor study was performed in immunodeficient animals the inhibition of tumor growth with DAP5 silencing was completely abolished. This suggested that DAP5 likely enables cancer cells to evade the immune response. However in this model, DAP5 silencing significantly decreased the number of lung metastases, implying that at least one of the mechanisms by which DAP5 prevents metastasis is immune system-independent.
Our results suggest that the translation initiation factor DAP5 likely plays a critical role in breast cancer metastasis and provides new concepts for therapeutic strategies involving translational regulation and immunotherapeutics. Indeed, inhibiting DAP5 might be a powerful approach, as it impacts the whole proteome of disseminated cancer cells.
Presenter: Jeremie Barral
School/Department: Center for Neural Science
Title: Propagation of synchronous input in reconstituted feedforward networks
The sequence of action potentials produced by neurons defines a coding strategy to transduce information in neuronal networks. Information may either be represented as the average number of action potentials per unit time (rate coding) or by the precise timing of action potentials (temporal coding). The nervous system utilizes both strategies and there appears to be a continuum between these two extremes. A rudimentary feature of most neural networks consists of several neurons’ pools arranged in a feedforward manner, like the multiple sheets in the cortex. The feedforward network model provides a useful and minimal framework for studying information processing in the brain and has been investigated by computer simulations. They revealed that the number of neurons and their probabilities of connections are critical parameters for the propagation of rate and temporal information. However, experimental support is lacking to test this hypothesis. Here, we studied experimentally how the connection pattern shapes the computing properties of neuronal networks. We reconstructed in vitro neuronal networks by culturing neurons in microfabricated environment to control both the density of neurons and the connection probability from one layer to the next. Neurons of the first layer were activated optogenetically by a packet of pulses whose spread and number were the control parameters. We identified the conditions of network architecture to transmit the input and showed that spike synchrony faithfully propagates only if the packet of stimulation is sufficiently precise. Finally, we determined the role of network state in opening a gate to transmit synchronous input.
Presenter: Enrico Fonda
School/Department: Physics
Title: Creative Turbulence: Experiments in Art and Physics
Effective communication of basic research to non-experts is necessary to inspire the public and to justify support for science by the taxpayers. The creative power of art is particularly important to engage an adult audience, who otherwise might not be receptive to standard didactic material. Interdisciplinarity defines new trends in research, and works at the intersection of art and science are growing in popularity, even though they are often isolated experiments.
We present a public-facing collaboration between physicists/engineers performing research in fluid dynamics and condensed matter, and audiovisual artists working in cutting-edge media installation and performance. The project, funded by the American Physical Society, is in collaboration with scientists from leading research universities, and with Pioneer Works, an innovative arts exhibition space in Red Hook, Brooklyn. The project team based at NYU will organize a public call for works for artists collaborating with the researchers. A jury composed by curators of the art space as well as scientists, will commission 5 artists for an exhibition. We discuss the science of classical fluids and quantum turbulence phenomena proposed as inspiration for the artists, with possible ideas for installations based on similar work, future developments and directions.