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IB&B Grad Students

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Michael Bicknell

Michael Bicknell
Advisor: Dr. Tom Langen
Research Interest: Environmental DNA, Ecology, Conservation Biology
The use of environmental DNA (eDNA) is emerging as valuable survey technique for the detection of rare, cryptic, or invasive aquatic species. Species naturally release small amounts of DNA into their environment (within feces, saliva, sloughed skin cells, etc.), which can be detected and amplified from water samples with species specific PCR primers. We currently developing an environmental DNA (eDNA) detection survey for Blanding’s turtle (Emydoidea blandingii). Emydoidea blandingii, is semi-aquatic freshwater turtle of the northern United States and southern Canada that is considered imperiled across most of its range. The species is currently listed as Threatened in New York State with declining populations throughout the Northeast. Current detection methods for E. blandingii (hoop trapping, visual survey) are very labor intensive and yield low and variable detection rates. Due to the low detection rates of traditional survey methods, it requires a large amount of effort to determine if E. blandingii is present in a wetland. An eDNA survey for Blanding’s turtle-if field validated- could provide reliable presence-absence data, which can be used for occupancy modeling, identification of unknown populations, and aid in management decisions of known populations.

           Maurish Bukhari

Maurish Bukhari
Advisor: Dr. Damien Samways
Research Interest: Ion Channels in Drug Transport and Cancer Biology
The core focus of the lab I work in lays in the study of various aspects of ion channels. The projects I am involved with revolve around this core, albeit, in different contexts. One of the directions I am pursuing is exploring transport of different small molecules such as dyes, toxins etc. through ligand gated ion channels, and thereby, investigating the conventional wisdom about the specificity of these channels.  Another project I am working on merges this above attribute of ion channels, and cancer. More specifically, I am exploring the feasibility of delivering certain charged toxins through ligand gated ion channels in cervical cancer as our disease model. So far we have already established such feasibility in 2-D in vitro cultures of cervical cancers derived from various patients. Surprisingly, we found this delivery approach to be selective for cancer cells BUT non-malignant cells are spared. Along the course of this project we have discovered the presence as well as upregulation of a calcium-ctivated potassium channel K Ca 3.1 in cervical cancer; and possibly being the transporter of some of such toxins.  I have recently started working on a spin-off project from the above findings to understand the cell physiological advantages K Ca 3.1 upregulation might confer onto cervical carcinoma. I am currently trying to explore this in the context of some of the hallmarks of cancer such as cell proliferation and invasion etc. on manipulation of this channel activity. Besides these ion channel focused projects, I am also involved in a side project that aims to understand G-protein coupled purinergic signaling (extracellular ATP/UTP) in cervical epithelial cells.

Han Deng

Han Deng
Advisor: Dr. Craig D. Woodworth
Research Interest: Human Papillomavirus and Cervical Cancer
Cervical cancer is one of the leading causes of cancer death in women throughout the world and persistent infection with high-risk human papillomavirus (HPV) is the major risk factor for this disease.  Over 90% of cervical cancers arise from the cervical transformation zone (CTZ), a small anatomic region located between the ectocervix and the endocervix. However, it is unclear why the CTZ is highly susceptible to malignant conversion, and few studies have been performed on cells isolated from this region. We are interested in the mechanisms for increased susceptibility of cells from the CTZ to HPV-16-induced cervical cancer. Our current research focuses on an early stage of malignant development called cellular immortalization and a later stage called dysplastic differentiation. Our results may help to identify important signal pathways or bio-markers that are unique to cells from CTZ and that can be targeted for improved screening, prevention or therapy.

 

Jianlong Li

Jianlong Li
Advisor: Dr. Ken Wallace
Research Interest: Zebrafish as a Model System to Investigate Development of Vertebrate Intestine Zebrafish

(Danio rerio) is a tropical freshwater fish species widely used as an experimental model in biomedical research due to large clutch size, external development, short generation time, as well as easy of rearing in laboratory. The intestinal epithelium is a unique vertebrate tissue that continually renews itself throughout the life of the organism. The intestinal epithelium is organized into crypt and villus regions. Intestinal stem cells are localized in the crypt. Stem cells at the base of crypt interdigitate between Paneth cells. These Paneth cells and fibroblasts surrounding the crypt help maintain stem cells including regulation, lineage specification and maturation through Notch, EGF, Wnt and Noggin signaling pathways. Even though zebrafish epithelium lacks Paneth cells, we have identified a secretory cell that are receiving Notch signal and interdigitating between proliferative cells at the base of the fold. Here we hypothesize that these secretory cells might represent Paneth cells in zebrafish and have a regulatory role during the development of intestinal stem cell compartments. Currently, I am working on the formation and development of these Notch receiving secretory cells (NRSCs), the proliferation pattern of developing ISC compartments and structure of mature ISC compartments, as well as how developing and adult ISC compartments are regulated by NRSCs within zebrafish intestinal epithelium.

Kangning Li

Kangning Li
Advisor: Dr. Thomas Lufkin
Research Interest: Evaluating Gene Expression Patterns In the Adult Bovine Intervertebral Disc (IVD) Via RNA Section In Situ Hybridization (SISH)

Low back pain (LBP) is one of today’s most prevalent health problems worldwide. At some point in their lives, over 75% of the population will be affected by LBP. In the USA the annual expenditures related to LBP can surpass $100 billion in terms of medical health care costs and the reduction in productivity from lost workdays. This exceeds the combined costs of coronary artery disease, stroke, rheumatoid disease, diabetes and respiratory infection and imposes an enormous socio-economic burden. Intervertebral disc (IVD) degeneration is considered a major cause of LBP, resulting from injury or the natural aging process of IVD cells. The field of regenerative medicine (RM) aims to restore the function of defective tissues or entire organs via cell-based approaches. However if a cell-based approach is envisaged for degenerated IVD treatment, it is crucial to know whether the therapeutic cells are taking on the fate of IVD cells. Thus, in order to develop a safe and robust RM approach to treat degenerative disc disease my project aims to identify a set of biomarkers that are unique to the two major cell types of the IVD, namely the nucleus pulposus (NP) and the annulus fibrosus (AF). We have previously established the bovine IVD as suitable human-like model organism and my project is using RNA section in situ hybridization (SISH) and proteomics to validate and quantify the gene expression of an array of potential biomarkers. Our data point to several NP- and AF-specific biomarkers. Furthermore our data indicate a cellular heterogeneity among the populations of NP and AF cells that cannot simply be explained with existing data from mouse genetic models. This requires a refinement of the existing model for IVD development and cellular composition in higher vertebrates in order to develop effective RM strategies to reverse IVD degeneration. Our work will benefit the future application of RM and tissue engineering studies in humans.

 

Morgan Prochaska

Morgan Prochaska
Advisor: Dr. Ken Wallace
Research Interest: Zebrafish as a Model System to Investigate Development of Vertebrate Intestine

I have been investigating aspects of two different research projects. One is working on characterization of the role of secretory cells in formation of the developing stem cell compartment within the intestinal epithelium. We are disrupting formation of secretory cells through addition of small molecule inhibitors, transgenics, and mutants. The secretory cells modify proliferation and we are currently characterizing patterns of proliferation in embryo and juvenile phase. The other project involves investigation of the effects of nanoparticle and additive components of Chemical Mechanical Planarization (CMP) slurry on the developing zebrafish embryo. In my experiments, I am investigating whether CMP components result in localized inflammation using a transgenic line allowing me to visualize altered migration of macrophages to determine whether there is localized damage within the developing embryo.

Antonio Rockwell

Antonio Rockwell
Advisor: Dr. Cintia Hongay
Research Interests: Role of Dm ime4 in Spermatogenesis of Drosophila melanogaster ion)

I want to spend the next phase of my life working in the lab and using the scientific process to answer biological questions.  Analyzing cellular mechanisms is what interests me.  Analyzing genes and proteins provides us with evolutionary insight into their function within the cell.  Answering or developing ideas on these functional roles help further our understanding of biology, from cells to organisms.  Overall, the technology that is nowadays driving the fast-pace growth in cell and molecular biology allows new questions to arise constantly and their answers to be possible in our lifetime.  I have chosen to pursue my PhD degree in Dr. Hongay’s laboratory primarily because of her scientific pedigree and because she has pioneered the investigation of mRNA N6A-methylation (a ubiquitous mRNA modification by the evolutionarily conserved IME4 enzyme) in the development of metazoans.  After her studies of IME4 in yeast, Dr. Hongay continued her research in Drosophila, and has established collaborations to move the research up the evolutionary tree to sea urchin and zebrafish.  Using Drosophila melanogaster as the model organism, I will answer many questions that, because of the conservation of this enzyme from yeast to humans, will inform of its function in higher-order vertebrates (like us, humans).  The field of methylomics and epitranscriptomics has come to the front stage of science recently, after decades of being found in obscure journals given the difficulty to study non-editing modifications.  Because the excitement of the newly rediscovered field of study and Dr. Hongay’s pioneer role in this field, I would like to contribute to her work as her graduate student.  In addition, she has established herself as a very good mentor, and knows about being a minority in the sciences from her own experience as a Hispanic woman.  I am certain she would have a significant impact in my life as a research scientist and will prepare me to be a role model for the scientific community. 

 

Angela Ross

Angela Ross
Advisor: Dr. Tom Langen
Research Interests:  The conservation and recovery of a New York State – endangered bird species, the Spruce Grouse.

Angie Ross (B.S., SUNY Potsdam; M.S., SUNY ESF) is a graduate student in Prof. Tom Langen’s lab as well as an Endangered Species Biologist for the New York State Department of Environmental Conservation.  Her thesis research focuses on the conservation and recovery of a New York State – endangered bird species, the Spruce Grouse, which is emblematic of the lowland boreal forest of the Adirondack Mountains. Ms. Ross is monitoring forest management practices that can potentially help grouse populations recover. She is also conducting a population supplementation study, releasing birds from Ontario and Maine into the Adirondacks within the historical range of the Spruce Grouse, with the goals of increasing genetic diversity in existing populations and repopulating areas that have appropriate habitat where Spruce Grouse no longer occur.

Darren Sipes

Darren Sipes
Advisor: Dr. Shantanu Sur
Research Interests: Cellular Mechanisms at work in Hypoxia
Hypoxia is a common issue that is the cause of much of the damage seen in common health issues such as diabetes, cerebral and cardiac ischemias, as well as cancers. Although this is categorized clinically on the scale of tissue loss, the cellular mechanisms that are occurring during hypoxia are still relatively unknown. Working in the Cell-Material Interactions lab at Clarkson University has allowed me to pursue my research goals of creating an in vitro model that allows monitoring of acute hypoxic stress at a level before cell death occurs, elucidating the cellular mechanisms at work throughout hypoxia that lead to cell death, and exploring possible treatments to alleviate hypoxic damage.