Plenary talks

Presenter:  Carmen Gervais
Title: Science career observations from an inside outsider
New technology and cross-disciplinary approaches are enabling scientists to make paradigm-shifting discoveries. Scientists are involved in decision-making at all levels. Research findings have tremendous influence on society. These are exciting times.
But the road to independence trod by postdoctoral fellows is a vulnerable career stage, one which can be derailed by forces often outside of your control. There are ways you can influence your postdoc experience to create opportunities and minimize risks.
I will discuss the role of the postdoc from multiple country perspectives and share my views on what leads to success.

Presenter:  Arsalan Daudi
Title: Improving experimental reproducibility in the lab
The lack of reproducibility in scientific research can be a major problem with significant impact on science policy. One recent study revealed that 54% of materials used in an experiment are not uniquely identifiable across a broad range of the life sciences literature, regardless of field of study, impact factor or journal reporting requirements (PeerJ, 2013). In addition, the materials and methods sections of many research papers are lacking critical details about experimental design or tricks on how to do specific steps of a procedure. Dr. Arsalan Daudi, Executive Editor at Bio-protocol, will explain Bio-protocol’s mission in tackling these and similar problems head on. Bio-protocol is a peer-reviewed, open access protocol-sharing platform established by Stanford researchers. Their goal is to identify the best experimental protocols in the community and work with authors to develop the most reproducible version of their protocols.

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: Mohamed Al-Sayegh
School/Department: Biology
Title: Identifying Genes Associated to the Resistance of Neurodegeneration
Amyotrophic Lateral Sclerosis (ALS) is a common neurodegenerative disease known for impairing motor neurons (MNs), predominantly spinal motor neurons (sMNs). The degeneration of MNs results in patient fatality due to muscle atrophy. Although little is known about the pathology of ALS, few cases (5-10%) have been attributed to genetic mutations. Furthermore, there is a subset of cranial motor neurons (cMNs) that are associated with ALS and survive longer than sMNs. Understanding the developmental nature of sMNs and cMNs at the transcriptome level would potentially give a better view of ALS pathogenesis. In this study, we analyze the transcriptome of two generated embryonic stem cell (ESC) lines carrying different sets of transcription factors (NIL and NIP), which direct differentiation of ESCs to sMNs and cMN, using the deep sequencing approach of RNA-Seq.

Presenter: Eléonore Bouguyon
School/Department: Biology
Title: Multiple mechanisms of nitrate sensing by Arabidopsis nitrate transceptor NRT1.1
In Arabidopsis the plasma membrane nitrate transceptor (trans- porter/receptor) NRT1.1 governs many physiological and devel- opmental responses to nitrate. Alongside facilitating nitrate uptake, NRT1.1 regulates the expression levels of many nitrate assimilation pathway genes, modulates root system architecture, relieves seed dormancy and protects plants from ammonium toxicity. Here, we assess the functional and pheno- typic consequences of point mutations in two key residues of NRT1.1 (P492 and T101).We show that the point mutations dif- ferentially affect several of the NRT1.1-dependent responses to nitrate, namely the repression of lateral root development at low nitrate concentrations, and the short-term upregulation of the nitrate-uptake gene NRT2.1, and its longer-term downregu- lation, at high nitrate concentrations. We also show that these mutations have differential effects on genome-wide gene expression. Our findings indicate that NRT1.1 activates four separate signalling mechanisms, which have independent structural bases in the protein. In particular, we present evi- dence to suggest that the phosphorylated and non-phosphory- lated forms of NRT1.1 at T101 have distinct signalling functions, and that the nitrate-dependent regulation of root development depends on the phosphorylated form. Our findings add to the evidence that NRT1.1 is able to trigger independent signalling pathways in Arabidopsis in response to different environmental conditions. 

Presenter: Martina Bradic
School/Department: Biology
Title: Population genomics of drug resistance in the sexually transmitted human parasite Trichomonas vaginalis
Trichomonas vaginalis is the most prevalent, non-viral, sexually transmitted parasite worldwide. The first T. vaginalis genome sequence, generated using Sanger sequencing technology, revealed massive amplification of many gene families and an unusually high number of transposable elements, making the use of next generation short-read sequencing methods to sequence additional strains problematic. To circumvent this issue, and to characterize the genetic diversity and mechanism of drug resistance we performed ddRAD partial genome sequencing of ∼103 parasite isolates taken from women in five global regions. We identified ~3,900 SNP markers that clustered the T. vaginalis isolates into two “genetic types”, confirming previous studies. We identified multiple SNPs associated with metronidazole resistance, including several missense mutations in genes previously identified in T. vaginalis or other organisms as being potentially involved in resistance. A comparison of changes within several drug resistant lab-derived lines revealed a set of mutations in common between independently evolved lines and also with the clinically resistant parasites. In addition, we establish that copy number variation of some genes (e.g., ferrodoxin 1) also plays an important role in resistance. We also surveyed lab-derived resistant strains of Tritrichomonas foetus, a distantly related species that causes venereal disease in cattle. We observed shared changes between the T. vaginalis and T. foetus parasites, suggesting probable conservation of the genetic pathways through which adaptation occurred. Together, these findings extend our knowledge of drug resistance in T. vaginalis, providing a panel of resistance biomarkers that can be used as a diagnostic tool.

Presenter: Giuseppe Carluccio
School/Department: School of Medicine, Radiology
Title: Fast Whole-Body Temperature Estimation for Real-Time MRI Safety Assurance
Currently, 10g SAR(Specific Absorption Rate)  is the quantity used most often to assess safety with respect to local tissue heating due to Radiofrequency fields absorption during MRI(Magnetic Resonance Imaging), although by itself SAR is a quantity with limited direct relation to risk. While temperature increase has a much more intuitive and direct relationship to risk, it is typically not calculated at all due to the associated complexity and time requirements. Here we present a method able to dramatically reduce the computation time of temperature increase during an MRI exam, to allow real-time temperature prediction and adjustment of the power levels of the sequences to avoid temperature thresholds. The method takes advantage of the linear nature of the heat equations after characterizing the temperature response to only brief period of heating. This thermal response is then convoluted with the series of power levels applied during the MRI exam. The method includes also variations of core body temperature and corrections through time to allow variation in local perfusion.
The method was applied to predict temperature throughout an actual spine exam: the predicted maximum temperature increase has been within 1% of that with full numerical simulation, with computation time at least 30 times shorter. Much higher accelerations are possible depending on the time step size chosen, with loss in temporal resolution.

Presenter: Irina Depnath
School/Department: School of Medicine
Title: Multifaceted role of transcriptional regulator MrpJ in Proteus mirabilis uropathogenesis
Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (UTIs), a major public health burden worldwide. Two critical aspects of P. mirabilis virulence are fimbria- mediated attachment to the host's urinary tract, and flagella-mediated motility. My research is focused on the major P. mirabilisfimbria-associated transcriptional regulator MrpJ, which modulates the inverse temporal regulation of these two virulence processes during UTI. This helix-turn-helix transcriptional regulator is widely present in both clinical isolates as well as all 14 sequenced strains of Proteus mirabilis. Transcribed at low levels in vitro, the expression of mrpJ is amongst one of the highest elevated genes in vivo during the course of a UTI. To probe MrpJ interactions with DNA in vivo, we used a chromatin immunoprecipitation (ChIP) technique in conjunction with a candidate gene approach. MrpJ-nucleoprotein complexes were evaluated on both a positive as well as on a negative target virulence gene operon (mrp / MR/P fimbrial operon and flhDC/ flagellar master regulator operon, respectively), and we identified in vivo DNA-occupancy on MrpJ-responsive promoter elements of these genes. Binding of MrpJ to the promoters of flhDC and mrp appears to be affected by the native conformation of the chromosome, although both targets share a direct MrpJ binding site proximal to the transcriptional start. Transcriptional analysis by microarray showed that the expression of mrpJ mimicking levels observed during UTI leads to differential regulation of several known and predicted virulence factors indicating a role of MrpJ beyond adherence and motility. Based on this transcriptional analysis, we are now investigating MrpJ regulation of P. mirabilis pathogenesis and innate immune modulation. Our data show that MrpJ is involved in the regulation and virulence contribution of multiple fimbriae. The combinatorial mutations in these fimbrial genes render P. mirabilis unable to compete in a mouse model of UTI. Moreover, our findings also suggest that MrpJ could interface both the cellular as well as the humoral arm of the innate immune effectors in the urinary tract. Altogether, these studies are providing critical molecular insight into how P. mirabilis orchestrates a multifaceted virulence gene network via MrpJ resulting in the discovery of novel virulence genes for future therapeutic targeting. 

Presenter: Fang-Ke Huang
School/Department: School of Medicine 
Title: Phosphoproteomic Analysis of BDNF Signaling in Cortical Neurons
Brain-derived neurotrophic factor (BDNF) regulates many important aspects of neural function including cell survival, cell fate decisions, axonal and dendritic growth, long-term potentiation and synaptic plasticity. Decreased BDNF levels have been linked with disease pathology and symptoms, and replacement strategies are considered as potential therapeutics for neurodegenerative diseases such as Parkinson’s, Alzheimer’s, and Huntington’s diseases. While BDNF signaling events have been characterized extensively after a short term treatment (3 to 15 min), it is not known what changes in protein phosphorylation occur when primary neurons are exposed to BDNF for 2 hours. We used stable isotope labeling by amino acids in cell cultures (SILAC) in primary cortical neurons to assess changes in the neuronal phosphoproteome after BDNF treatment. A total of 20058 phosphorylation sites were identified in this analysis. 8220 out of 20058 were quantified in two biological replicates with site localization probability over 75%. Seventy phosphorylation sites (corresponding to 62 proteins) showed consistent and significant (FDR = 0.01) SILAC ratio changes upon BDNF treatment. Among 8252 proteins identified in this analysis, 5392 were quantified in both biological replicates. Only one protein (Dual specificity protein phosphatase 4) showed consistent and significant SILAC ratio changes upon BDNF treatment, indicating protein levels were not significantly affected by BDNF within 2 hours. Among proteins harboring regulated phosphorylation sites, some were well-known BDNF effectors such as TrkB, TrkC, jun-B, Gab2, and calmodulin. This confirmed that by applying the presented approach we were able to detect previously confirmed and biologically relevant BDNF target proteins. We report, for the first time, phosphorylation of protein kinases, Srpk2 and Brsk1 that are induced by BDNF. In addition, we observed BDNF-induced phosphorylation of proteins regulating transcription and translation, such as nuclear cap-binding protein subunit 1(Ncbp1) and eukaryotic translation initiation factor 3 subunit B (Eif3b). Network analysis revealed an enrichment of cytoskeleton reorganization that could be important in neurite outgrowth induced by BNDF. To our knowledge, this study represents the first comprehensive SILAC phosphoproteomic analysis in primary cortical neurons after 2h BDNF treatment. Our findings expand the understanding of BDNF-mediated signaling events and have the potential to provide novel therapeutic targets in diseases where dysregulation of BDNF is observed.

Presenter: Dan Hupalo
School/Department: Biology
Title: Population Genomics of a Global Sample of 200 Plasmodium vivax Malaria Parasites 
The parasite Plasmodium vivax, implicated in less virulent but longer lasting cases of malaria, is a major public health concern, causing the majority of malaria infections each year outside Africa. Here we describe the collection and sequencing of more than 170 clinical isolates of P. vivax sampled from eight regions around the world, including New World isolates from Central and South America as well as Old World isolates from East Asia, Southeast Asia and Melanesia. Using a method called hybrid selection, we enriched parasite DNA from clinical samples displaying a diversity of parasite densities. We used the resulting high coverage genome sequences to identify over 150,000 SNPs and generate the first global genome wide polymorphism profile for P. vivax. Using this panel of variation we identified strong population structure within P. vivax, including a genetically distinct population from Papua New Guinea, and the likely European origin of new world P. vivax populations. We also evaluated diversity across all P. vivax genes, identifying divergent regions in antigen genes between and within populations. Lastly, we investigated several known genes of interest, including the human host Duffy antigen genotype, using in silico and molecular biology techniques. Our analyses highlight the utility of generating a global dataset of genomes for an infectious disease, which can help clarify demographic history and adaptation within the species, in addition to providing new paths towards answering long standing biological questions.

Presenter: Lakshmanan Jagannathan 
School/Department: Environmental Medicine
Title: Ambient oxygen levels induce NF-kB1/RelA mediated inflammatory response in human lung epithelial cells in vitro
Oxygen (O2) levels in cell culture conditions are typically 2-5 fold higher than the physiological O2 levels that most tissues experience in vivo. The ambient atmospheric O2 (21%) is known to induce cell proliferation defects and cellular senescence in stem cell and primary cell cultures. Therefore, culturing these cells under lower O2 levels (2-9%) are currently a standard practice. However, the non-cancerous immortalized cells and cancer cells, which evade cellular senescence are normally cultured at 21% O2 and the effects of higher O2 on these cells are not fully understood. Here we addressed this problem by culturing immortalized human bronchial epithelial (BEAS-2B) cells at ambient 21% O2 and lower 10% O2. BEAS-2B cells were subject to increased oxidative stress at 21% O2. Our results show NF-κB/RelA mediated activation of pro-inflammatory cytokines as a major outcome of cells being cultured 21% O2. Moreover, we demonstrate increased RelA binding at the NF-κB1/RelA target gene promoters at 21% O2. Interestingly, contrary to cells cultured at 21% O2, external stress induced by H2O2 exposure did not induce inflammatory response in cells grown at 10% O2, suggesting increased ability to handle external stress in cells cultured at lower O2 levels.

Presenter: Sophie Léran
School/Department: Biology
Title: A protein regulatory network links calcium signaling to nitrate transport and sensing in Arabidopsis
Transmembrane transport of nitrogen forms is a key step of the life cycle in all living organisms. In plants, NPF (NRT1/PTR Family) (members transport diverse substrates: nitrate, nitrite, dipeptides, amino-acids, auxin, abscisic acid, gibberellin and glucosinolates. 
The NPF6.3 protein (previously named NRT1.1/CHL1) (1) is involved in nitrate transport and sensing in Arabidopsis thaliana: beside its role in root nitrate uptake, NPF6.3 triggers specific signaling pathways governing molecular, physiological and developmental responses to nitrate availability. 
A protein regulatory network (PRN) including the transceptor NPF6.3, a kinase, CIPK23 and a calcium sensor, CBL9, has been identified to be crucial for nitrate sensing. Using a functional screen in Xenopus oocytes and in planta characterization, we identified here two additional components of this PRN: the calcium sensor, CBL1 and the phosphatase ABI2. ABI2 physically interacts and dephosphorylates CIPK23 and CBL1 leading to enhanced transport and sensing activities of NPF6.3. These findings identify an important functional link between nitrate transport, nitrate sensing and calcium signaling in plants. 

Presenter: Bin Lin
School/Department: School of Medicine, Leon H. Charney Division of Cardiology
Title: Using a metabolism method to purify pluripotent stem cell-derived cardiomyocytes
With rising advances in stem cell technology, it is becoming increasingly efficient to differentiate pluripotent stem cells into cardiomyocytes. These cardiomyocytes are powerful tools that can be used to study the mechanism of cardiovascular disease, for drug screen/drug toxicology, and for developing promising cardiac-regenerative therapy techniques. However, the lack of robust methods to acquire abundant mature cardiomyocytes still hinders these applications. Recently, it was reported that using glucose-depleted culture medium supplemented with lactate can obtain high purity pluripotent stem cell (PSC)-derived cardiomyocytes. Here, we present that using fatty acid as a glucose replacement has a similar purification effect as the lactate-supplemented condition. Moreover, glucose-depleted culture medium supplemented with fatty acid (FA) and Tri-iodo-L-thyronine (T3) can promote maturation while purifying the PSC-derived cardiomyocytes. The FA and T3 treated cardiomyocytes have an enhanced action potential, as shown by a significant increase in dVmax/dt, maximum negative potential, action potential amplitude (APA), action potential duration at 50% (APD50) and action potential duration at 90% (APD90) compared to untreated control cells. The expression of major cardiac ion channel genes and cardiac index genes are elevated. The proportion of cardiomyocytes with organized sarcomeres also increases after FA and T3 treatment. We anticipate that this method can obtain cells with high purity while promoting maturation of pluripotent stem cell-derived cardiomyocytes.

Presenter: Gungor Ozer
School/Department: Chemistry
Title: Computational modeling of chromatin organization at the mesoscale level
In eukaryotic cells, the 2 meters long DNA is stored in the micron-size nucleus in the form of a nucleoprotein complex called chromatin. Double-stranded DNA interacts with various histone proteins to achieve such enormous compaction. The first level of compact chromatin organization involves the formation of nucleosome where ~1.7 turns of DNA is wrapped around the histone octamer (two copies of H2A, H2B, H3, and H4). Multiple nucleosomes come together to form chromatin fibers. At this higher organization, the chromatin fibers can be loosely compacted into a 10-nm wide beads-on-a-string structure (euchromatin) or densely compacted into a 30-nm wide structure (heterochromatin) to regulate DNA accessibility. The instantaneous fold of chromatin fibers depends on many structural and physiological factors such as the length of linker DNAs connecting nucleosomes, the presence/absence of linker histones, and the ionic conditions of the medium. We have developed a mesoscale chromatin model to investigate the structure and dynamics of oligonucleosomes using Monte Carlo simulations. Our mesoscale model consists of the nucleosome that is treated as an irregularly shaped body of 300 uniformly distributed Debye-Huckel charges with exclusively defined core-histone tails, linker DNA, linker histones, and monovalent/divalent ions. By varying the linker DNA length, concentration of linker histones, and salt conditions, our model can produce many experimentally observed properties of chromatin fibers such as fiber length/width, packing ratio, internucleosomal interaction patterns, and force-extension dependence. Here we present some of our recent findings, discuss relevant biological implications, and propose future directions to the computational modeling of chromatin.

Presenter: Karsten Pilones
School/Department: School of Medicine, Radiation Oncology
Title: Cooperative effects of PD-1 blockade and radiotherapy in a model of poorly immunogenic breast cancer
We have previously shown that radiation therapy (RT) converts poorly immunogenic tumors resistant to antibodies (mAbs) against the checkpoint receptor CTLA-4 into susceptible ones. Importantly, RT induced the upregulation of PDL-1 and PDL-2 on the tumor cells and infiltrating myeloid cells in the TSA mouse breast cancer, suggesting that PD-1 ligands may limit rejection of the irradiated tumor by T cells. PD-1 is a checkpoint receptor upregulated on T cells shortly after activation and expressed at high levels on exhausted T cells. To test the hypothesis PD-1 blockade can promote the ability of RT to induce effective anti-tumor immunity we employed BALB/c mice inoculated s.c. with the syngeneic poorly immunogenic  TSA breast cancer cells. When tumors became palpable mice were randomly assigned to one of 4 treatment groups (N=6-7): (1) control, (2) RT, (3) anti-PD-1 mAb and (4) RT+anti-PD-1 mAb. RT was delivered exclusively to the primary tumor in 8 Gy fractions on days 13, 14 and 15 post tumor inoculation. PD-1 blocking mAb RMP1-14 was given on day 15 and every 4 days thereafter, and mice were followed for tumor growth. In a separate experiment, mice were euthanized on day 20 to characterize tumor-infiltrating lymphocytes  (TILs) and development of CD8+ T cells specific for the tumor epitope AH1 by pentamer analysis. 
TSA tumors were resistant to PD-1 blockade. RT significantly delayed tumor growth (p<0.01), but tumor regression was seen only in 1 of 6 mice.  In contrast, when RT was combined with anti-PD-1 mAb, all of the mice completely rejected tumors by day 25. AH1-specific CD8+ T-cells were markedly increased  (5.5%) in the spleen of mice treated with RT+anti-PD-1 compared to control (1.7%) and anti-PD-1 (1.9%) or RT (3.7%) treated mice (p<0.01). Analysis of TILs showed a significant increase in mice treated with RT compared to control in CD8+ T cells expressing high levels of PD-1 (CD8+PD-1hi) (67% versus 36%, p<0.01), as detected by a mAb non-cross-reactive with RMP1-14. Interestingly, in mice receiving anti-PD-1 mAb there was a significant decrease in CD8+PD-1hi (14% RMP1-14 versus 36% control, p<0.01; and   30% RT+RMP1-14 versus 67% RT, p<0.01). In contrast, CD8+ T cells expressing activation markers CD69 and CD137 and low levels of PD-1 were increased significantly in the tumors of mice treated with RT (64%) compared to control (42%) (p<0.001) irrespective of the treatment with anti-PD-1.   
Overall, data suggest that the IgG2a anti-PD-1 mAb RMP1-14 selectively depletes CD8+PD-1hi TILs, possibly by ADCC, while enhancing the RT-elicited priming and activation of tumor-specific CD8+ T cells. We propose that this represents a novel mechanism of anti-tumor activity of anti-PD-1 mAb and supports testing its combination with radiotherapy. 

Presenter: Anne Plessis
School/Department: Biology
Title: A modeling method to analyze “real-life” experiments in plant biology
Although plants have evolved to respond to complex fluctuating conditions, most studies that aim to connect molecular biology to environmental effects on plants are conducted in controlled laboratory settings, where the effect of only one or a few drastic changes is measured. This preponderance of experimental designs in artificial environments inhibits the translation of insights from molecular biology into improved resistance to adverse conditions, as they often overlook the fact that stresses happen gradually and interact with each other.
To address this issue, we have developed an approach to analyze gene expression under naturally varying conditions, isolating the effect of specific environmental components on gene expression in rice growing in two types of field (rainfed and irrigated). Our method relies on a modeling strategy to relate the main variations in global gene expression to variations in climatic factors like temperature and humidity, and detect differences in climatic response between the two field environments.
We found that groups of genes involved in photosynthesis and development responded differently to weather conditions depending on the type of field the plant is growing in. We showed that the variations in expression of a group of stress response genes could be interpreted as resulting from additive effects of short-term heat/light stress and long-term drought stress. We identified functionally relevant genes with a strong response to climatic conditions as good candidate for the regulation of environmental responses. Our results illustrate how using modern computing methods in biology can help fill the lab-field gap.

Presenter: Christine Ponder 
School/Department: Office of Postdoctoral Affairs
Title: NYU STEP Program IDP course effectiveness
The New York University Scientific Training Enhancement Program (NYU-STEP) is funded by a five-year BEST (Broadening Experiences in Scientific Training) grant from the National Institutes of Health (NIH). The program uses a three-phase structure to 1. Introduce the variety of careers available to PhD trained scientists and encourage self-assessment to identify career goals; 2. Develop broad and specific skills to prepare PhDs for the job after postdoc or grad student; 3. Support the job search and career transition. Phase 1 consists of an 8-week course on the Individual Development Plan (IDP). This course has been twice per academic year at each the Med Center and Washington Square campuses for two years. Course participants are surveyed twice, before the course begins and after the last session. 163 individuals completed the initial survey, however for this analysis we included only entry data when it could be matched to an exit survey from the same individual, reducing the sample size to 53. The IDP course increased participant knowledge about where to look for jobs in their desired field (from 28% to 72%) and knowledge about how candidates in that field are evaluated (from 22% to 67%). The ultimate goal of the NYU-STEP program is to reduce time in training and move NYU PhDs into careers more quickly. We do not yet have sufficient data to test the effectiveness of this program in that goal, but we feel the increase in knowledge about available careers is a strong step in the right direction.

Presenter: Charlotte Proudhon
School/Department: School of Medicine, Pathology
Title: Enhancer-mediated long-range regulation during lymphocyte development
The adaptive immune system is composed of B and T lymphocytes, development of which is driven by V(D)J recombination. This process involves the introduction of multiple double strand breaks within antigen receptor (AgR) loci to rearrange their coding segments and generate a vast repertoire of antigen receptor genes. Tight regulation of this rearrangement is required to preserve genome integrity and prevent translocation events that could lead to lymphoma. One key aspect of this regulation is ensuring that the appropriate loci are rearranged in the appropriate lineage (T versus B lymphocytes) and at the appropriate developmental stage. Several studies including numerous ones from the Skok lab have shown that nuclear dynamics is involved in this regulation. Our lab previously showed that communication between AgR loci happen through long-range physical interactions, ensuring that breaks are introduces on only one allele and locus at a time. Enhancers associated to AgR loci are one driving component of this communication. To identify the enhancer-mediated regulatory networks that underpin differentiation of developing lymphocytes, we performed a combination of genome-wide studies to survey chromatin organization, accessibility and transcriptome profiles in lymphocytes undergoing rearrangement. We studied 3 enhancers, Eβ and MiEκ and 3'Eκ, associated with AgR loci, Tcrb and Igk respectively, and used enhancer deletions to determine their individual roles in controlling nuclear organization, gene expression and rearrangement. We discovered that both Tcrb and Igk enhancers control developing T-cell gene expression programs and revealed a new enhancer-mediated crosstalk between Tcrb and Igk which promotes Tcrb rearrangement.

Presenter: Pavitra Rao
School/Department: Biology
Title: Next Generation Sequencing to Study Antimalarial Drug Resistance in India 
Resistance to antimalarial drugs continues to be an important factor in hindering malaria control. As we head towards elimination of this disease, next-generation sequencing methods have become especially relevant in facilitating surveillance of emerging drug resistance, since they provide high resolution, scalability and sensitivity. We have established an amplicon sequencing protocol on the Ion Torrent PGM platform for targeted re-sequencing of multiple loci in clinical isolates. Our initial panel includes a number of genes from the malarial parasite Plasmodium falciparum that are implicated in resistance to various antimalarials (e.g. K13, dhfr, dhps). Preliminary experiments using reference strains show promising results. We are now scaling this method for multiplexed sequencing of clinical isolates as part of an NIH-funded International Center of Excellence for Malaria Research in India. We have collected P. falciparum-infected patient samples from three epidemiologically diverse sites in India. Analysis of the amplicon sequencing results in conjunction with clinical data associated with these isolates can help us identify novel genetic mutations that could impact drug susceptibility or disease phenotype.

Presenter: Brendon Richbourgh
School/Department: School of Medicine, Orthopaedic Surgery
Title: The synergistic effects of PGRN and LIPUS on chondrocyte metabolism
Osteoarthritis (OA) is a degenerative disease of the joints with no cure. Progranulin (PGRN) a pleiotropic growth factor, binds directly to tumor necrosis factor receptors (TNFR), and can disturb the TNFα/TNFR interaction and protect cartilage matrix proteins from degradation. Low intensity pulsed ultrasound (LIPUS) is an acoustic pressure wave capable of providing localized mechanical stimulation to chondrocytes. It has been published that LIPUS also increases levels of Collagen II, Collagen X and Aggrecan in chondrocytes in vtiro cultures. 
An acoustic device was used for LIPUS stimulations, at a frequency of 1Mhz, pulse duration of 200μs, with repetitive frequency of 100 Hz at an intensity of 30mW/cm2 for 20 min per day. We analysed ex vivo explants from human patients (IRB#12758) and C2812 cell line for the Migration Assay and BMP2 adenovirus infected C3H10T1/2 cells to evaluate Differentiation. 
LIPUS significantly increases migration in chondrocytes. LIPUS treated cells show 80% confluency relative to 40% in control samples at 48hrs. LIPUS neutralizes IL-1beta effects (10% confluency) by restoring chondrocyte migration to approximately 25% at 48 hr . LIPUS significantly increased the expression of Runx2, Col II, Sox 9 and Col X in BMP2 infected C3H10T1/2 cells.  IL-1beta significantly reduced chondrogenesis, which was rescued by LIPUS. Quantitative PCR analysis of MMP13, ADAMTS4, ADAMTS5, Col 11, Aggrecan and Comp showed that LIPUS regulates chondrocytes metabolism by enhancing anabolism and suppressing expression of catabolic enzymes. Furthermore, application of LIPUS neutralizes the catabolic effects of IL-1beta in human primary chondrocytes. 

Presenter: Jawed Siddiqui
School/Department: College of Dentistry, Basic Science and Craniofacial Biology
Title: Monocyte Chemoattactant protein-1: A Mediator of Parathyroid Hormone’s Actions in Bone
Parathyroid hormone is an essential regulator of calcium homeostasis and now the only osteo-anabolic hormone available for treating osteoporosis. The mechanism for PTH’s anabolic effects is still poorly understood. Our microarrays of bone from rats injected with PTH-(1-34) daily for 14 days showed a number of cytokines and chemokines were highly induced, in particular, RANKL, IL-6, CXCL1 and CCL2 (Monocyte Chemoattractant Protein-1, MCP-1). The chemokine, MCP-1, was the most highly stimulated gene from 14-day intermittent hPTH-(1-34) administration. MCP-1 is a potent pro-inflammatory member of the CC motif chemokine family. We have performed both in vivo and in vitro studies to look more closely at MCP-1 as a mediator of PTH. We have found that MCP-1 increases multinucleate osteoclasts in culture and with daily injections of PTH in animal models, there is an increase in macrophages, bone growth, and serum MCP-1 levels. MCP-1, secreted by cells of the osteoblast lineage in response to PTH stimulation, is necessary for the recruitment of monocytes and preosteoclastic cells and assists in the formation of mature osteoclasts. The transient increase in osteoclastic activity leads to a subsequent increase in bone formation, resulting in a net increase in bone mass. The absence of MCP-1 eliminates PTH-induced osteoclast formation and bone resorption. Thus, the anabolic effect of PTH is attenuated. The overall goal of our studies is to look closely at the signaling pathway for MCP-1, the cells that might be producing it, and to investigate its role in the anabolic versus catabolic effects of PTH.

Presenter: Gustavo Silva
School/Department: Biology
Title: The ubiquitous Ubiquitin and its role in the protection of life
Ubiquitin is one of most conserved proteins throughout evolution and yet, we recently discovered an unexpected function for this protein in cellular defense against oxidative injuries. Oxidation is a widespread challenge that all cells are subjected to on a daily basis due to the action of pollutants, chemicals in foods and drinks, UV radiation, and many more. Therefore, cells - from yeast to humans - have evolved a plethora of mechanisms to counteract oxidative damage and also to repair damaged biomolecules such as DNA, proteins and lipids. Ubiquitin is mostly known for its role as a tag for protein destruction, but researchers have recently characterized many other functions for this well-known protein. Ubiquitin can form different types of chains when attached to a protein and we recently found that one of these chains - instead of promoting destruction - increases the stability of the protein synthesis machinery in response to stress. Our findings show that ubiquitin has multiples roles in cellular defense against oxidative stress, promoting destruction of damaged components but also fostering the production of new molecules to combat the stress. Our work developed in yeast and neuronal cells provides new insights into molecular mechanisms of cellular defense against oxidative stress. The results are relevant for the understanding of several nervous system diseases as Parkinson’s and Alzheimer’s in which increasing oxidative stress and accumulation of damaged proteins play a pivotal role.

Presenter: Viji Subramanian
School/Department: Biology
Title: Meiotic Chromosomes Choreograph Recombination
Meiosis is a specialized cell division that results in the formation of eggs or sperm in humans. During this process, recombination between the parental chromosomes not only creates genetic diversity but also assists in proper chromosome assortment. Several mechanisms promote this recombination during meiosis, but less is known about how recombination is restricted in due course to prevent mutations. We found that, as meiosis progresses, dynamic changes in chromosome structural proteins transmit a chromosome-wide signal to tune-down recombination. Utilizing a powerful conditional depletion strategy to remove these structural proteins from the chromosomes, we found that the meiotic chromosomes utilize progressive chromosome-structure assembly as a built-in negative feedback mechanism to restrict excessive recombination.

Presenter: Mei San Tang
School/Department: School of Medicine, Microbiology
Title: Differential regulation of alternative M2 macrophage activation for monocyte derived and tissue resident macrophages
Different immune cell types are activated distinctly when exposed to various external stimuli. Elucidating these activation mechanisms are important to complete our understanding of disease pathogenesis and to harness the potential of immune cells for therapeutic purposes. 
The activation mechanism of macrophages is conventionally conceptualized as an M1-M2 polarization framework. The classical M1 activation pathway is driven by Th1 cytokines (such as interferon-gamma) and engagement of TLRs; exemplified by immune response in bacterial infections, while the alternative M2 activation pathway is driven by Type 2 cytokines (interleukin-4 and interleukin 13) and is exemplified by immune response to helminth infections. M2-activated macrophages can be derived from monocyte-derived macrophages and tissue resident macrophages. These macrophages of differing origins respond to IL-4 stimulation with different gene expression profiles. IL-4-induced genes in monocyte-derived macrophages are predominantly involved in immune-related functions, while IL-4-induced genes in tissue resident macrophages are predominantly involved in metabolic functions. 
Characterizing the genomic regulatory elements in both populations of macrophages may provide insight into the mechanisms underlying the differences in IL-4 response. Therefore, we performed ATAC-Seq to profile the accessible chromatin regions that are induced by IL-4 in both monocyte and tissue derived macrophages, as accessible genomic regions have been associated with regulatory DNA elements. Our findings demonstrate that tissue-resident and monocyte-derived macrophages have very different IL-4 induced accessible genomic regions. We are also able to identify transcription factor (TF) binding motifs in these accessible genomic regions and subsequently identify candidate TFs for experimental validation of their importance in M2 macrophage activation. 
Presenter: Swapna Uplekar
School/Department: Biology
Title: Using next-generation sequencing to detect early signs of drug failure in multi-clonal malaria infections
A major obstacle in malaria drug surveillance is the early and rapid detection of drug-resistant parasites. As malaria infections typically consist of more than one parasite clone, the presence of both drug-sensitive and drug-resistant parasites is common. Competitive release is characterized by the removal of susceptible parasites in a mixed infection by aggressive drug treatment, thus enabling the resistant parasite population to expand and obtain transmission opportunities. Therefore, clonal variation in response to chemotherapy can be determined by tracking individual clone frequencies before and shortly after treatment. Next generation sequencing methods provide the high resolution and sensitivity required to examine the within-host diversity of malaria infections. Our goal is to use amplicon sequencing of clone-specific markers in order to quantify relative parasite population sizes in the host and track changes in their frequencies during the course of drug treatment. As a proof-of-principle we have assessed the efficacy of the amplicon sequencing approach using a rodent malaria experimental system. We sequenced mixtures of genetically distinct Plasmodium chabaudi clones from infected mice in order to determine the relative proportion of each clone in the mixture. Upon comparison of sequencing data from technical and biological replicates we observed that the results were reproducible. We also obtained independent estimates of the relative abundance of different clones using quantitative PCR, which correlated well with the amplicon sequencing results.

Presenter: Viviana Volta
School/Department: School of Medicine, Microbiology
Title: mTOR inhibition favors the differentiation of human in vitro-induced regulatory T cell through selective protein synthesis
Human regulatory T cells (Tregs) suppress immune cell function, thus maintaining immune system homeostasis and promoting peripheral tolerance. They prevent autoimmune diseases and are involved in tumor escape from the immune surveillance.
Studies in mice and humans show that Treg development is promoted by mTOR inhibition. mTOR is a kinase that forms two complexes in the cell, mTORC1 and mTORC2, regulating multiple metabolic processes. mTORC1 is inhibited by rapamycin and is the best-known regulator of protein synthesis. The mechanism by which mTOR down regulation in activity induces Tregs is unknown. Our hypothesis is that mTOR absence alters lymphocyte gene expression by favoring protein synthesis of specific mRNAs required for Treg differentiation.
Our work shows that human in vitro-induced Tregs (iTregs) are generated by mTORC1 inhibition (by RAD001, an improved version of rapamycin), and not by mTORC1/2 dual inhibition (by PP242). Proliferation of highly suppressive iTregs requires co-treatment of RAD001 and the cytokine TGFβ. Protein synthesis analysis in double-treated (RAD001+TGFβ), control-treated, RAD001- and TGFβ-treated cells shows that translation is inhibited in the double-treated cells. Only selective specific mRNAs are translated in the iTreg population, as shown by genome-wide profiling of mRNAs associated with actively translating ribosomes in double-treated iTregs compared with control-treated effector lymphocytes. 
By applying an emerging understanding of protein synthesis control to the field of immunology, this interdisciplinary work shows how iTreg development is driven by selective translation of specific genes. This knowledge can be used to prevent autoimmune diseases, avoid transplant rejection, and understand Tregs-cancer relationship.