Cohort Two Projects
1. Studying the Pharmacokinetics of PHLIP with in vitro and in silico Models | Read more
2. Biogeochemical Transformation and Transfer Mechanisms of Reactive Nitrogen and Metal Species in Roadside Ecosystems | Read more
3. Statistical Analysis of Genes Affecting Female Re-mating in Fruit Flies | Read more
4. P53 Binding to DNA in Nanofluidic Devices | Read more
5. Glutamate Transport and Nociception | Read more
6. Applications of Statistical Learning Theory to Recurrent Lung Cancer | Read more
7. Ancient Microorganisms in Fluid Inclusions | Read more
8. The Transmission, Risk, and Emergence of Lyme disease in the Northeast United States| Read more
9. Characterization of Multiple Species Biofilms by Quantifying their Spatial Properties | Read more
10. Development of a Computer Program for Mass Spectrometry-Based Peptide Identification | Read more
11. Activity Profiling of Proteases using Peptide Nucleic Acids as Molecular Recognition Tools | Read More
12. Characterization of the Mechanism of Biofilm Dispersion in Pseudomonas aerugina | Read more
13. Image Stitching of a Devonian Fossil Forest| Read more
14. Wireless Communication and Tracking of American Crows | Read more
1. Studying the Pharmacokinetics of PHLIP with in vitro and in silico Models
One of the characteristics of cancer is the growth of tumors at a much lower pH than the rest of the body. This is caused by rapid cell proliferation, poor circulation, and the subsequent buildup of waste products. The pH-low insertion peptide, or pHLIP is water soluble, binds reversibly to cell surfaces at biological pH (7.4), and inserts across cell membranes at low pH (5.5). Because of these unique properties, pHLIP can be conjugated to drug molecules for targeted treatment of low-pH cells, or conjugated to fluorescent dyes in order to create detailed images of these areas.
Unfortunately, the kidney is naturally quite acidic and may also be targeted by pHLIP. The objective of this project is to better understand how pHLIP interacts with human tissues and cells within the body, including those of the kidney.
Faculty Mentors: Dr. Gretchen Mahler (Bioengineering) and Dr. Ming An (Chemistry)
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Graduate Mentors: Joab Onyango (Bioengineering) and Courtney Sakolish (Chemistry)
2. Biogeochemical Transformation and Transfer Mechanisms of Reactive Nitrogen and Metal Species in Roadside Ecosystems
The ultimate goal of our project is to determine the movement and retention of reactive forms of nitrogen (NH4+ and NOx) and metals (Zn, Cu, Cd etc.) in roadside ecosystems. We will examine the Lake Lieberman (LL) wetland located in the Fuller Hollow Creek Watershed near Binghamton University's Newing Dormitories as well as a similar wetland ecosystem located near Broome Community College (BCC). LL and BCC sites act as storm water retention ponds, receiving water from surface runoff and groundwater sources. We will contrast these results to sites adjacent to roadways that do not have retention ponds (the I-81 and Route 434 sites).
A study performed by Binghamton University's Center for Integrated Watershed Studies proposed that storm water runoff and deicing salt applied to the roads caused higher levels of trace metals and nitrogen in urban ecosystems. The precise biogeochemical interactions within the environment are not well defined. We will examine the pollutants' spatial distribution and retention of these nitrogenous and metallic pollutants via sediment cores, particulate matter, and plant material within these ecosystems.
Faculty Mentors: Dr. Joseph Graney (Geology), Dr. John Titus (Biology) and Dr. Weixing Zhu (Biology)
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Graduate Mentors: Jonathon Schmitkons (Geology) and Stephanie Craig (Biology)
3. Statistical Analysis of Genes Affecting Female Re-mating in Fruit Flies
Female Drosophila are polyandrous which means that they mate with several different males during a mating season. Some females are found to re-mate more with certain types of males over others. The goal of this project is to determine which genes control and influence the female re-mating rate. A number of factors affect the female re-mating rate such as sperm count from male fruit flies, genotype of female and genotype of the males she has mated with. Throughout the course of the research, we will be focusing on male fruit flies from two different classes. In class 1 the male fruit flies have the ability to make the female fruit fly less likely to re-mate. In class 2 the male fruit fly does not have the ability to make the female fruit fly less likely to re-mate.
Faculty Mentors: Dr. Anthony Fiumera (Biology) and Dr. Xingye Qiao (Mathematics)
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Graduate Mentor: Wenyu Du (Mathematics)
4. P53 Binding to DNA in Nanofluidic Devices
Our project is focused on visualizing p53 binding to specific DNA sequences using nanofluidic devices and immunofluorescence. P53 is a tumor suppressor that regulates genes in response to an array of cellular stress, including UV radiation, ionizing radiation, and hypoxia, that induce DNA damage. The protein functions by binding to the promoter DNA sequence causing the expression of genes involved in cell cycle arrest, DNA repair, and cell death. There are many questions regarding the mechanisms by which the p53 protein binds specific DNA sequences.
Faculty Mentors: Dr. Stephen Levy (Physics) and Dr. Susannah Gal (Biology)
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Graduate Mentor: Steven Button (Physics)
5. Glutamate Transport and Nociception
Numerous studies on alcohol's effects in the brain have been carried out over the years due to the severe problems that alcohol poses to human health. Specifically, alcohol abuse during adolescence may lead to neurological deficits including problems with memory. When a person engages in binge-drinking over an extended period of time, many brain-related effects of alcohol remain even after the person stops drinking altogether. In order to better understand the effects of ethanol in the brain, our research will utilize a rat model of binge-like ethanol exposure so we can study its effects on behavior and learning in adolescence and adulthood.
Faculty Mentors: Dr. Jilla Sabeti (Psychology) and Dr. Christof Grewer (Chemistry)
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Graduate Mentor: Rose Tanui (Chemistry)
6. Applications of Statistical Learning Theory to Recurrent Lung Cancer
This summer our team has been assembled to develop and validate a model that can be used to better predict non-small cell lung cancer recurrence in patients. This research is crucial as the medical community currently lacks a tool to help oncologists distinguish between a patient whose cancer may come back and one whose cancer will remain defeated. As a result, doctors resort to treating most patients with chemotherapy that takes a physical, emotional and monetary toll, in order to prevent the cancer from coming back. It is our hope that development of a model will eliminate the use of chemotherapeutic treatments on patients not likely to experience recurrence, which would spare them the awful barrage of side effects and allow doctors to make more informed decisions on how aggressive the cancer treatment should be.
Faculty Mentors: Dr. Walker Land (Bioengineering), Dr. David Schaffer (Bioengineering) and Dr. Xingye Qiao (Mathematics)
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Graduate Mentors: Jin Woo Park (Bioengineering) and Qiyi Lu (Mathematics)
7. Ancient Microorganisms in Fluid Inclusions
Evaporites, such as halite (NaCl) and gypsum (CaSO4·2H2O), form in hypersaline environments, including deep perennial basins, shallow perennial lakes, and dry saline pans. During their formation, the salt crystals trap the parent brine, along with the microbial community in them, within tiny droplets known as "fluid inclusions". Our goals are to investigate the biomaterials inside the fluid inclusions using microscopy and to analyze the diversity, distribution, and survival of these trapped microorganisms. We will be studying both modern and ancient samples in order to fully understand the environments from which they came from and the extent to which they have changed over time.
Faculty Mentors: Dr. Tim Lowenstein (Geology/Environ. Sciences and Dr. J. Koji Lum (Anthropology/Biology)
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Graduate Mentors: Sarah Feiner (Geology) and Krithivas Sankaranarayanan (Anthropology)
8. The Transmission, Risk, and Emergence of Lyme disease in the Northeast United States
We propose investigating the factors involved in the quickly evolving emergence of acute Lyme disease in Upstate New York and other areas of the Northeast, in order to ultimately establish a comprehensive and convenient algorithm of risk to illustrate the epidemic and aid in clinician diagnosis.
The investigation aims to focus on five strategic areas that are designed to address the factors influencing Lyme disease emergence in human populations in Upstate NY and other northeast areas.
Faculty Mentors: Dr. Ralph Garruto (Anthropology) and Dr. Hiroki Sayama (Bioengineering)
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Graduate Mentors: John Darcy (Anthropology) and Jeff Schmidt (Bioengineering)
9. Characterization of Multiple Species Biofilms by Quantifying their Spatial Properties
The proposed research will investigate the dynamics of the multi species biofilm populations within Eukaryotic epithelial cell lines. Microbial infections, including nosocomial infections are mainly caused by multi-species bacterial populations. However, the available treatments are based on studies of single species bacterial populations. Currently not much is known about the initial stages of infection and how several bacterial species interact and eventually develop into biofilm within a Eukaryotic cell. Understanding the development of mixed species biofilms within epithelial cells could lead to a significant improvement on the efficacy of the treatment of infections.
Faculty Mentors: Dr. Claudia Marques (Biology) and Dr. Scott Craver (Electrical Engineering)
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Graduate Mentors: Diana Amari (Biology) and Alireza Baroughi (Electrical Engineering)
10. Development of a Computer Program for Mass Spectrometry-Based Peptide Identification
In global studies of the changes in protein levels that accompany processes in living cells and organisms, the ability to identify proteins based on mass spectrometry data is crucial. Up to a few years ago, database matching was the main strategy for correlating the masses of peptide fragments to peptide, and by inference, to proteins. Our project is focused on a second strategy – de novo sequencing – to work with mass spectrometry data that does not lead to peptide identification by database matching.
Faculty Mentors: Dr. Patrick Madden (Computer Science) and Dr. Anna Tan-Wilson (Biology)
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Graduate Mentor: Jason Gallia (Computer Science)
11. Activity Profiling of Proteases using Peptide Nucleic Acids as Molecular Recognition Tools
In this project, peptide nucleic acid (PNA) probes will be synthesized for a new approach to activity-based protein profiling (ABPP). Peptide nucleic acids are DNA analogs with a peptide backbone, which replaces the negatively charged phosphate backbone of DNA. In ABPP, proteins are labeled with small molecules called probes in order to determine the activity of proteins expressed by a genome. We will be probing active proteases, enzymes that cut proteins at particular amino acid residues. To compare the efficiency of commercially available probes to PNA probes, they will be tested on the cysteine protease papain and a cysteine protease from soybeans, both of which have been characterized.
Dr. Karl Wilson (Biology), Dr. Eriks Rozners (Chemistry) and Dr. Anna Tan-Wilson (Biology)
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Graduate Mentors: Yuanyuan Wang (Biology) and Thomas Zengeya (Chemistry)
12. Characterization of the Mechanism of Biofilm Dispersion in Pseudomonas aerugina
Our project is mainly about the characterization of the biofilm dispersion in Pseudomonas aeruginosa and using conjugated fluorescence chemosensor to investigate the related heme-binding protein. Biofilms are communities of surface associated bacteria, while dispersion is characterized by bacteria actively dislodging from the biofilm. Dispersion can be induced by the sudden increase in the medium carbon and ammonium chloride concentration as well as upon exposure to nitric oxide. The Pseudomonas aeruginosa sensory protein BdlA is central to the dispersion response as a mutant harboring a deletion in the bdlA gene is seen to be impaired in biofilm dispersion. BdlA is a heme binding protein and its central iron is believed to cycle between the Fe2+ and Fe3+ state during the biofilm dispersion response. To detect changes in the redox state during biofilm formation and biofilm dispersion, this project will make use of fluorescent polymeric organic/inorganic hybrid chemosensors.
Faculty Mentors: Dr. Wayne Jones (Chemistry) and Dr. Karin Sauer (Biology)
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Graduate Mentors: Tatyana Boyko (Biology) and Megan Fegley (Chemistry)
13. Image Stitching of a Devonian Fossil Forest
Scientists need high-resolution images to make good, empirical observations. Often, they take multiple close-ups of some object or region of interest. But having many separate images isn't as effective as a single, seamless, Google Maps-like panorama. Our goal is to stitch together a particular set of scientific images—high-resolution photos of a Devonian fossil forest—using image stitching techniques.
Faculty Mentors: Dr. Lijun Yin and Dr. William Stein
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Graduate Mentor: Xing Zhang
14. Wireless Communication and Tracking of American Crows
This project's goal is to provide energy-efficient solutions for small devices that fit the goals of tracking movements and social networks of individual birds, specifically American crows. Traditional radio-transmitter-based technology for tracking the location of birds requires that people physically follow and triangulate FM signals to estimate the bird's location. Such transmitters provide no information on previous locations or behavior and their longevity is limited because battery weight must be very low for flying birds. For highly social, long-lived birds such as crows, an ideal tag would weigh only 8-10 gram maximum, record GPS location and the close presence of other tag-carrying birds, transmit this data without having to recover bird or tag, and last at least a year.
Solutions to the weight, longevity and data transmission problems lie in environmental energy harvesting and in designs of energy efficient low-duty cycle data transmission other than FM radio waves. The highly unpredictable pattern of the bird's behavior introduces a big challenge. Therefore, different energy harvesting (i.e., solar panels) and energy storage (i.e., ultra-capacitors) strategies will be investigated. The extremely energy efficient low-duty cycle data exchange and routing protocols will be studied. Once the basic designs are established, further research will be done to evaluate the efficiency of our design through both simulation and potential on-site experiments.
Faculty Mentors: Dr. Ting Zhu (Computer Science) and Dr. Anne Clark (Biology)
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Graduate Mentor: Jie Piao (Computer Science)