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Undergraduate Research News
Here are some of our undergraduate researchers from 2011, and summaries of their work. The faculty mentor's name is in parentheses after the undergraduate researcher. A recent research report is usually available after the abstract.
Saman Agharahmanian (Boissinot)
Evolution of RTE elements in animals
In this research I examined the genome of all animals with complete genome sequence available for the presence of a transposable element called RTE. This element is believed to have the ability to be transferred horizontally among animals. However, it is not known how frequent horizontal transfer is and which molecular properties allow for the horizontal transmission of the elements. Thus I performed a preliminary analysis of the molecular evolution of the RTE transposon in animals.
Download Saman's research report
Ronveer Chakraborty (Boissinot)
Understanding the Chromosomal Divergence of Baboons in Ethiopia
Baboon research within the genus Papio started fairly early and has remained a primary objective of research. Their relative ubiquity in the African continent, easy visibility, and for some time the idea that it may be a prominent model for human evolutionary reconstruction, have led to an extensive wealth of knowledge over the years. However, not much information exists for these animals at the molecular level. Using molecular techniques, I will be investigating the differences between populations of anubis (olive) baboons, hamadryas baboons, and hybrid baboons (between anubis and hamadryas) at the chromosomal level using fecal collections from different parts of Ethiopia. The fecal samples were put through a DNA extraction protocol, and primers were used to test test their quality. The goal of this project is to check for diversity within X chromosome, which may reveal the different evolutionary factors that might have taken place for the hamadryas and olive Baboons.
Download Ronveer's research report
Kin-Yip Chien (Weinstein)
Regulation of Muscle Fate by Eif4a3
Post-transcriptional, pre-translational RNA processing plays a crucial role in turning genetic information into functional gene products. The exon junction complex (EJC) underlies many of these processing events. The EJC plays a role in destroying defective RNAs. It binds to strands of messenger RNA leaving the cell nucleus for the cytoplasm and targets improperly assembled mRNAs for destruction by a process known as nonsense mediated decay (NMD). Eukaryotic initiation factor 4A3 (Eif4a3) is a core component protein of the EJC. When Eif4a3 function is blocked in embryos of the frog Xenopus laevis, the frogs become paralyzed, have underdeveloped hearts and have a reduced number of pigment cells (melanophores). Similar phenotypes are observed with the knockdown of other “core” EJC components. Nonsense mediated decay (NMD) is triggered by the exon junction complex (EJC) and is an RNA processing mechanism. Learning more about EJC functioning will help us learn more about NMD and diseases involving RNA processing defects, like spinal muscular atrophy. Several muscle related genes expressed at significantly lower levels following knockdown of Eif4A3 were chosen for further study. Reduced expression of these genes may underlie the morphant’s paralysis phenotype.
Download Kim-Yip's research report
Jane Ching (Dennehy)
Migration aids pathogen persistence
Viruses frequently mutate to gain the ability to infect new hosts; however virus emergence (defined as sustained, epidemic infection) is rare in nature. Recent reports suggest that new hosts represent sink habitats for emerging viruses. Here we propose to study effects of migration on a sink population by setting up a simple model of sink and source population that mimic pathogen and host interaction in the real world. We’re trying to see if there is indeed a relationship between greater amounts of migration and its role on pathogen sustainability by calculating absolute fitness at the end of 20 days. Absolute fitness is calculated as Wabs = ln (Nf/Ni) where Ni = 105 and Nf is the total number of progeny produced. Results showing a positive relationship between migration rate and absolute fitness will be construed as support for the hypothesis. This experiment aims at understanding pattern of viral growth on new host population.
Download Jane's research report
Francois Didier Desinor (Hickerson)
BIOCODE Project: Exploring biodiversity in Moorea
Our 3 semester study consists of collecting and analyzing invasive non-microbial species living on artificial surfaces in the island of Moorea located in French Polynesia. The species collected belonged to four main groups of organisms: Ascidians, Bryozoans, Cnidarians and Porifera. We collected our samples by extracting a portion of habitat (such as rocks, coral rubble or tires) from the water. Several locations and different types of habitats were sampled in order to obtain diversity in our species of interest. We extracted tissue samples from each specimen collected, which were then analyzed for DNA barcoding at the Smithsonian Institute of New York. DNA barcoding is an important taxonomic method that uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species. This scientific method has many applications, such as documenting and substantiating species that are known, and it also can help in the discovery of new species. Similar to our research, scientists often sequence Mitochondrial DNA of species, due to its maternal inheritance. An important Mitochondrial DNA is the CO1 gene which is highly conservable throughout the genome. Additionally, the CO1 gene can be isolated in different types of animals. Using a broad range of animal life, this gene has been shown to have distinct CO1 sequences. Using DNA barcoding tools, we can identify and document each species collected and generate a comprehensive database in order to contribute to the Moorea BIOCODE project, which is designed to give an account of the island’s biodiversity and provide the necessary tools for the understanding and overall study of its ecological system.
Download Francois' research report
Download Francois' poster presentation
Ezra Frager (Waldman)
Species profile of Atlantic silverside (Menidia menidia)
Download Ezra's research report
Stephanie Gampel (Dennehy)
The relative time necessary to gain antibiotic resistance, and the effect of antibiotic resistance on the fitness of bacteria
It has been posited that bacteria interact with one another via social evolution in order to work towards a mechanism of survival. For instance, species such as Streptococcus mutans, found in dental plaque form a biofilm to better ensure survival (Li 1). However, more recent discoveries have found that bacteria will even work to help the greater good even at the expense of themselves. In other words they will self sacrifice for the greater public good since it better ensures the survival of the group. Although these studies show the importance of cooperation, sometimes bacteria can gain a beneficial mutation on its own, which would negate any reason for those bacteria to interact with other bacteria. However, it would be beneficial for the bacteria without that mutation to interact with it. Developing upon this idea, this study hopes to quantify the amount of time it takes for Escherichia coli, or E. coli, of specifically the JJD1 strain, containing different resistance to specific antibiotics to pick up a mutation that codes for resistance to another antibiotic. Additionally the study’s goal is to compare the fitness of a wild type of E. Coli to E. Coli that has obtained resistance in different orders.
Phage infection number in relation to phage number produced in single burst
It has been posited that there is a positive density dependent growth for φ6 at low initial inocula. In this experiment I used titrations, filtrations and cell counts to reconfirm the positive density dependent growth for φ6 on ERA after a single burst assay. My results confirmed a nonlinear relationship between the number of phages and bacteria. Phage productivity, or the average progeny per phage (found via average burst size), seemingly has a directly proportional relationship with multiplicity of infection (MOI), or the ratio of virus to bacteria.
Download Stephanie's research report on antibiotic resistance
Download Stephanie's research report on phage infection number
Kelly T. Garces (Short)
Construction of novel tools for stable transgenesis of Ceratopteris
Ceratopteris richardii is an excellent model plant system because of its unique development properties and its rapid life cycle, which confers an advantage over other ferns. Experimental studies can be conducted in both haploid gametophyte and diploid sporophyte phases, which grow independently. The ability to evaluate large numbers of mutagenized spores in a small space facilitates genetic studies. In addition, the analysis of the gametophyte stage and ability to generate fully homozygous individuals through self-fertilization of hermaphrodites aids isolation and studies of mutations. Moreover, diploid sporophytes can be manipulated to yield diploid spores that will develop into diploid gametophytes; also, the development of haploid sporophytes without the occurrence of fertilization can be achieved in a laboratory. Although Ceratopteris is very useful for genetic studies and manipulation at the cellular level, effects on its development as a response to environmental stimuli, cell maturation, organogenesis, as well as more complex biochemical and physiological processes have not been studied in great detail because of the lack of a reliable transformation system. Molecular manipulation would allow scientists to further investigate Ceratopteris and expand its use as a model fern.
Download Kelly's research report
Tobin George (Short)
Activity of PHY4B gene in the fern Ceratopteris richardii
Ceratopteris richardii is emerging as a model fern to study the process of photomorphogenesis because of its rapid lifecycle and the ability to reduce the expression of targeted genes in dry spores by RNA interference (RNAi). . However, this fern can be used for physiological, genetic, developmental, and molecular studies. In our research, we will be studying the developmental aspects of Ceratopteris, more specifically photomorphogenesis. Five full length phytochrome cDNA and genomic clones have been isolated in Ceratopteris: CrPHY1A, CrPHY1B, CrPHY2, CrPHY4A and CrPHY4B (Bissoondial, T.Y 2006). The goal of our research is to study phytochrome PHY4B in Ceratopteris richardii and determine what its purpose is. The first step in studying PHY4B in is to determine whether it remains in the cytosol as in the lower plants, or whether it enters the nucleus as in the higher plants. Once PHY4B's destination is known, we can then begin to examine which proteins or molecules it may interact with based on its location in either the nucleus or cytosol, and study the effects of over expression of RNAi knockdown of CrPHY4B on growth and development in response to different light regimes.
Download Tobin's research report
Jon Claude Gocheekit (Boissinot)
Variation of the X chromosome in Baboons
Varying levels of diversity in sex chromosomes and autosomes can illuminate the evolutionary history of a primate species. There are five baboon species in Africa and Southern Arabia, these five species (P. ursinus, P. hamadryas, P. anubis, P. papio, P. cynocephalus), have distinct geographic distribution, share a hybrid zone with at least one other baboon, meaning that they can give rise to viable hybrid offspring in these contact areas. In order to determine how this phenomenon is possible we intend to study the genetic diversity of baboon chromosomes so that we can formulate hypotheses about the factors influencing genomic variation. So far we have successfully amplified three regions of the X-chromosome in four baboon species.
Download Jon Claude's research report
Alison Gold (Hickerson)
Analysis of Divergence Times in Fifty-Seven Sister Species
Different sister pairs of birds were analyzed to determine when and how many divergence times occurred. The majority of ancestral speciation, or divergence in species, is believed to occur in the Pleistocene, however there is a counter argument that speciation occurred earlier in the Pliocene. I specifically looked at the Cytochrome B gene in fifty-seven sister pairs to determine the amount of divergence times. Meta-analysis and statistical comparisons was done to the DNA sequence data of the sister species pairs using approximate Bayesian computation. The simulated data sets were generated and compared to the observed data to estimate the number of divergences. That estimate was then used to determine when the speciation occurred. In my research, all of the data sets have not yet simulated and no conclusions or estimations can be made. This approximate Bayesian computation method is being used to infer divergence across 57 sister species pairs of birds.
Download Alison's research report
Johnny Groeling (Fath)
Exploring the use of nanoconstructs to increase bone production by osteoblasts
Collagen, hyaluronic acid and elastin are major components of connective tissue throughout the body. Because of their importance in developing the extracellular matrices within the body, we have explored whether these materials when conjugated to self-assembled nanoparticles containing ellagic acid or kinetin would increase bone production by osteoblasts in vitro. The long-term goal of these studies is to develop new therapeutic tools to increase bone density in the body. We added the various constructs to a human fetal osteoblast cell line growing in culture. We found that the constructs were not cytotoxic and did not alter cell proliferation rates as determined with the cell proliferation reagent WST-1. We next allowed the osteoblasts to differentiate and begin bone production. We assayed for bone production morphologically and quantitatively using the dye Alizarin red, which binds calcium precipitates in bone deposits. We detected no changes in the level of bone production using any of the constructs. We conclude that although these nanoconstructs are biocompatible, they do not increase bone deposition by osteoblasts in vitro.
Brenda Gonzalez (Meléndez)
The molecular and genetic characterization of suppressor of bec-1 (sub-1) induced lethality in C. elegans
Across species autophagy is a vital process for the survival of cells and the organism’s homeostasis. In the nematode C. elegans, a complete loss of function (maternal and zygotic) mutation in bec-1, as in the deletion of o, k691, results in death of the worm, as embryos. Suppressor mutations have been identified that reverse the lethal phenotype of the bec-1 lethality. One such mutation known as sub-1 has been ascertained to be dominant and provides viability of the null mutant as well as the viability of the progeny.
Download Brenda's research report
Bobby Habig (Lahti)
Quantifying behaviors of female African village weaverbirds (Ploceus cucullatus) using a novel method
This paper focuses on the female behaviors of a colony of African Village Weaverbirds (Ploceus cucullatus) where males were attempting to attract females to their nests. A previous study completed by Khan (2011) focused on digitally recording, coding and analyzing the behaviors of male African Village Weaverbirds in Awash National Park in Ethiopia. The purpose of this study, which builds on Khan's previous study, is to monitor the same videos, which consist of twenty-four hours of behavior, and to quantify the behavior of the females after which the information will be joined with existing data on male behavior. Data from both studies will be connected in an effort to determine what behaviors of males are associated with behaviors of females. This study is the first of its kind to use digital video to quantitatively record and analyze behavior in a breeding colony.
Download Bobby's research report
Iosif Kandinov (Fath)
Kinetin nanoconstructs and their biocompatibility
Recently, there has been great interest in research to promote wound healing, allowing damaged tissue to be regrown. Our research focused on kinetin nanoconstructs and their biocompatibility (i.e., cell growth and function will not be hindered with the addition of these nanoconstructs) with chondrocytes, which are the cells found in cartilage. Kinetin is a cytokinin that may protect cells from oxidative damage, and stimulate RNA transcription. The kinetin nanoconstructs act as scaffolds upon which the chondrocytes can proliferate, allowing efficient repair and healing of wounds. Their biocompatibility with the chondrocytes is essential for them to act as a scaffold for new cell growth. In our research we found that the cells associated, and were biocompatible with the kinetin nanoconstructs.
Gallic acid nanoparticles as antibacterial agents
With the rise of antibacterial compound resistant strains emerging, the need for new, effective bactericidal agents is rising. Gallic acid, an organic, phenolic acid found in tree bark and tealeaves has been shown to have antibacterial actions. We wished to determine whether nanoconstructs containing gallic acid and copper (another known antibacterial compound) had greater antibacterial properties than the original compounds in isolation. We self-assembled gallic acid at different pH and the different hydroxyl functional groups substituted with amines. We then used these assemblies as templates for the binding of copper nanoparticles. These nanoconstructs were incubated with the gram positive bacterium Bacillus subtilus (B. subtilis) or the gram positive bacterium Staph aureus (S. aureus). We determined whether the nanoconstructs were bacteriostatic (i.e., inhibit bacteria growth in the continual presence of the additives) and or bacteriocidal (i.e., bacteria killed and will not grow when the compound is removed). In our preliminary results, we found that the nanoassemblies were both bacteriostatic and bacteriocidal, with the highest potency on B. subtilus.
Jordana Lovett (Short)
Elucidation of protein phosphatase pathways involved in Ceratopteris richardii photomorphogenesis.
The regulation of photomorphogenesis in the fern Ceratopteris richardii is likely mediated in part through the interaction of a specific protein phosphatase with one or more phytochromes, as identified through a yeast two-hybrid assay and RNA-interference experiments. To further study the putative role of the CrPP2A protein phosphatase/phytochrome interaction in gametophyte development, pharmacological techniques were employed to test the effects of phosphatase inhibition on photomorphogenesis. Spores were treated with the broad-spectrum phosphatase inhibitor okadaic acid, then incubated in tightly controlled light conditions and examined for differences in morphology and growth from the carrier-treated controls. The non-specificity of okadaic acid, along with its short half-life and ephemeral effects allow for the study of a possible role of one or more phosphatases in early gametophyte photomorphogenesis. Okadaic acid had significant effects on a subset of light-dependent growth and developmental responses. Data gathered in these experiments will direct subsequent studies of long-term CrPP2A knockdown achieved through stable transformation currently being developed.
Download Jordana's research report
Chris Ludvik (Hickerson)
Research for the Moorea BIOCODE project
The main focus of our research was to collect sessile marine species living on man-made structures around the island of Moorea. The species collected consisted of four main groups: Ascidians, Bryozoans, Cnidarians, and Porifera. Compound mircoscopes and digital photographic tools were used to observe and record all the data collected. DNA extraction of each sample was obtained and sent to the smithsonian institute for sequencing. In total we collected 376 samples for genetic marker (CO1 gene) analysis. The data we collect will help to characterize and better understand the biodiversity of sessile organisms living on man-made structures in a tropical island ecosystem.
Download Chris's research report
Download Chris's poster presentation
Alishba Maira (Holtzmann)
The drug FK506 disturbs morphology in young age zebrafish embryo
The drug FK 506 (Tacrolimus) is one of the drugs that interrupt angiogenesis. Blood vessels development disturbance in zebrafish embryo would cause its irregular growth and appearance (phenotype). In fact, improper blood vessels developments may results inadequate blood supply to embryo; therefore, zebrafishes embryos physical appearance changes than its normal shape. It is assuming that angiogenesis interruption may impact on heart morphology; thus, there might be interaction between endocardium and myocardium.
Download Alishba's research report
Omer Naseer (Short)
Isolation and characterization of the constitutive photomorphogenic 1 (COP1) gene from Ceratopteris richardii
The COP1 gene is responsible for the suppression of light-mediated development in plants in the absence of light. The purpose of this project was to isolate this gene from Ceratopteris richardii and to compare it to the known sequences of COP1 of other plant species. The effects of various light wavelengths on the extent of expression of this gene will also be observed, as well as the protein’s light-mediated translocation from the nucleus to the cytosol. Total RNA was isolated from Ceratopteris richardii and used it to prepare cDNA and G-cap-dependent adapters ligated to the 5’ end of intact mRNA. Gene-specific primers and adapter primers were used to amplify the 5’ end of the gene. A product of about 350 bp was isolated and the DNA will be sequenced. A related method using nested PCR reactions for the 3’ end will allow determination of the complete sequence of COP1 transcript.
Download Omer's research report
Maureen Pereyra (Lahti)
Developmental trajectories of trill rate of songs in the swamp sparrow Melospiza georgiana
Song development in the swamp sparrow, Melospiza georgiana, can be divided into two phases: a sensitive phase, when a young swamp sparrow memorizes tutor songs, and a motor phase, when the male practices them. It was suggested that the swamp sparrow actively adjusts the model songs to his vocal abilities prior to full crystallization of his song repertoire. The male does not accurately copy too challenging or too easy model songs. In the case when a model song is too difficult to produce, the bird simplifies it. On the other hand, when the male is trained with a nonchallenging song, he improves its quality. In this paper, I analyzed a period of 35 days before the crystallization of the song repertoire in order to decipher the pattern of trill rate changes. In this study, I used three copied song types of one male swamp sparrow. The male was trained with slowed trill rate models and according to the hypothesis, he should have improved his song repertoire. However, during the song ontogeny, he progressively elevated the trill rate of one song type and decreased of two others. Further, in the crystallized song, he dropped the most complex song type, preserving only the simpler ones. In conclusion, the degree
and direction of the song trill rates were not the same for all copied song types.
Download Maureen's research report
Surei Quintana (Boissinot)
Genetic drift between marine and freshwater populations of Gasterosteus aculeatus
The threespine stickleback (Gasterosteus aculeatus) is a small fish found in both ocean and freshwater habitats. Freshwater populations of the threespine stickleback have evolved different anatomical traits than ocean stickleback. Thus it is believed that the freshwater stickleback fish originally descended from the oceanic stickleback and were likely deposited in bodies of fresh water after glacial melting approximately 20,000 years ago. To study the genetic variation between oceanic and freshwater stickleback, ten neutral regions of DNA were selected from a genomic database. These sequences were tested and verified to exist in several lake populations in Alaska. In the future my research focus will be to analyze the data collected in order to discover the evolutionary relationships between the populations.
Download Surei's research report
Xie Xiaoou (Hickerson)
Validation of accuracy of hyper-parameters estimation from MTML-msBayes
The divergence time of bird species has long been argued. Using the set of COI genes in mtDNA sequences of birds, which are published on NCBI, we inferred the two general time of speciation, either about 2 million years ago or 20,000 years ago. In this program, we collected the COI genes in 71 sister species pairs from 3 datasets, created an observed dataset (real data) by aligning them, used msBayes to estimate them with Approximate Bayesians Computation Theory, and finally got estimates of the parameters given the data. The result of the comparison of the two sets of data can show the divergence time patterns across the 71 sister species pairs of birds. To verify our conclusion, we estimated the data using the given divergence times as a new parameter and compared it with the observed data again.
Download Xie's research report
Kristina Zabierek (Baker)
Olfactory response of the Colorado potato beetle (Leptinotarsa decemlineata)
Resistance to pesticides can have negative deleterious effects which can affect olfaction. The olfactory response of the Colorado potato beetle (Leptinotarsa decemilineata) was tested using a Y-maze olfactometer with various concentrations of potato plant (Solanum tuberosum) odors. Initial tests were performed on the susceptible New Jersey populations and the results were inconclusive; the beetles did not perform better than random. A comparison was made with resistant Mac populations, and again, the results were no better than random. Plant concentration, length of time starved, and age did not affect choice significantly.
Download Kristina's research report
Here are some of our undergraduate researchers from 2010, and summaries of their work. The faculty mentor's name is in parentheses after the undergraduate researcher. A recent research report is available after each abstract.
Aida Abbasiazam (Fjerdingstad)
Recognition of US Lasius niger as an outgroup of European L. niger
Lasius niger has been known to inhabit a wide range of regions (from northern Spain to Ireland, over central Europe to southern Fennoscandinavia and across Russia to Mongolia) (Fjerdingstad, 2002). The goal of the experiment was to determine whether L. Niger in the United States is a possible outgroup of the European species which is a model system for mating system research (Fjerdingstad, 2003). In order to test the degree to which populations are genetically differentiated, we used allele size and mtDNA sequences to provide clues about genetic differentiation of populations (European and United States). DNA was extracted from ants in western North America (Arizona, Utah and Nevada) using the Qiagen DNA extraction kit and the sequences were amplified with PCR. The study of the different populations was done by investigating the sequence variability of the mtDNA and microsatellite allele sizes which allows for phylogenetic reconstruction in closely related species. The mtDNA cytochrome oxidase I (COI, about 1250 bp) was examined for sequence substitutions between EU and US L. niger. The presence of deletions and/or mutations indicates the genetic distance between the American and European species. We were not able to obtain sequences of the US mtDNA except for a short fragment (about 480) due to contamination problems. The microsatellite DNA study of the ants revealed the sizes of the alleles at different loci which were compared to the alleles in the loci of the European populations. The US L. niger tended to have smaller alleles specially at the La33-b locus and larger alleles were present in the L10-53 locus which was not in the size range of the European species. The locus L10-53 was also duplicated in the US L.niger ( 1 locus L10-53 in EU and 2 L10-53 in US), with larger alleles not in the size range of the European species.
Download Aida's Research Report
Seema Choudhary (Lahti)
Ethnobotany in The Gambia, West Africa
This study examines ethnobotany and traditional medicine in The Gambia, West Africa. The aim of the research project as to identify medicinal herbs used and systemize them while trying to figure out whether they do contain the properties listed and if they are used in other areas. The scientific names of each of the local plants used are also identified. This was done through the analysis of a video, photographs, and an interview transcript collected on-site in Janjangbureh, The Gambia. With this, we hope to better understand the role of traditional medicine in The Gambia in terms of effectiveness and potency in curing. We also hope to see where it stands with relation to biomedicine.
Download Seema's Research Report
Kazi Hossain (Baker)
Imidacloprid effect on resistant Colorado potato beetle
The Colorado potato beetle, Leptinotarsa decemlineata, is widely regarded as the most important and destructive insect pest of potatoes. The potato Beetle can reproduce at a very fast rate; just within 5-6 weeks a new generation can be made. So, they can become resistant to pesticides very quickly over as little as 2 generations. Even though these beetles can become resistant to pesticides quickly, there is often a cost to it. One cost is that their development time in different stages is longer, thus more susceptible to predatory attack, and also it can lead to the reduction of the number of generations that can come out every year. Studying the development time for susceptible vs. resistant beetle on pesticide-treated plants can give us some clues on how to control these pests. Hatchlings were put onto plants treated with 1/4 tsp of Marathon 1% Imidacloprid Granular (Olympic Horticultural products) at planting. At this pesticide concentration, even resistant beetles had a low survival rate. All the susceptible beetles died within 4-7 days. Some resistant beetles went to pupation, but only 1 survived to adulthood.
Download Kazi's Research Report
Stephanie Kandasami (Lahti)
Characterizing the moral system of the Wolof people of West Africa
Cultures vary in their predominant moral teachings or beliefs, but also vary in other ways including prevailing climate, geography, population size, and social organization. Our aim is to determine whether diverse ecological features might explain some of the moral diversity we observe between cultures. I am focusing on the Wolof people of Western Africa. Using the Human Relations Area Files (HRAF), I characterized the moral prohibitions of the Wolof culture, producing an extensive list of moral taboos and restrictions that are current in the Wolof culture. The next step is to continue collecting data on the Wolof culture, categorize the prohibitions, and code them in a quantitative manner. Combined with similar data from other cultures, we can determine what areas enforce certain prohibitions or taboos as compared to other locations. Being able to determine what prohibitions are associated with which parts of the world can bring us closer to understanding the moral diversity of cultures based on ecological factors.
Download Stephanie's Research Report
Khaleda Khan (Lahti)
Temporal and spatial changes in house finch song
House finches from southern California were introduced to New York in the 1940s. Since then they have migrated throughout eastern and central North America. House finch colonization of different regions has resulted in geographic variation in male song. For instance, eastern populations have smaller song repertoires than the ancestral western populations. Birds in eastern populations also tend to share more of their songs with their neighbors than do western house finches. I have recorded the songs of male house finches around New York City. I plan to compare these and other recordings to songs of western house finches in order to see how the song of the eastern house finch has changed since it was introduced. The purpose of this study is to determine how learned traits such as bird song are culturally transmitted through a population and change through time and space.
Download Khaleda's Research Report
Cathy Le (Savage-Dunn)
Worm Length in Daf-2; Dbl-1 Double Mutants
Growth is a vital property of organisms that must be regulated to ensure normal organismal function. The misregulation of growth contributes to a variety of diseases such as cancer and obesity. We are using C. elegans as a model organism to understand the growth regulating pathways. In C. elegans, there are two TGF-b signaling pathways, one called Sma/Mab pathway, regulating body size and male tail phenotype, the other is called dauer pathway, regulating the entrance and exit of dauer stage. The mechanism underlying the two pathways mentioned above is not yet known. To address this question, daf-2; dbl-1 double mutant are constructed. Worm length is measured and data are analyzed. From the data, we can find that the double mutant is not different in length from dbl-1 alone. Thus, we can conclude that dbl-1 is epistatic to daf-2 for body length. This data suggests that in a growth regulating pathway, dbl-1 is downstream from daf-2. It can also suggest that in growth regulation, dbl-1 strain plays a more primary role than daf-2.
Download Cathy's Research Report
Rivka Lederman (Fath)
Jasmonates As Antibacterial Agents
Jasmonates are a group of plant hormones that regulate the response to stress and wounding. Because of their effects on plants, they were explored as possible anticancer agents and found to carry great potential due especially to their selective cytotoxicity. We studied their effect at the nano-scale on both gram negative and gram positive bacteria. We treated 200μl of bacteria with 5μl of jasmonic acid samples prepared in various solvents and assayed for growth by measuring their increase in turbidity. The jasmonic acid was found to inhibit bacterial growth. We also treated bacteria with nanoparticles of jasmonic acid associated with CdS quantum dots. These exhibited a greater inhibitory effect on bacterial growth than unassociated jasmonic acid. We increased the concentration of jasmonic acid to 13μl to see if it would cause an increase in inhibition. Increasing the concentration did not appear to increase the inhibitory effects. We treated bacteria with 1 μl and 2 μl of Jasmonic Acid +CdS to see if there would be an effect. There was a 10% decrease in inhibition of bacterial growth. Our studies demonstrated that jasmonic acid has bacteriostatic effects.
Download Rivka's Research Report
Chenell Livingston (Holtzman)
Profiling the expression of endothelial genes in the endocardium
Vascular endothelial (VE)-cadherin is an adhesive transmembrane protein specifically expressed at interendothelial junctions. Its extracellular domain exhibits Ca2+-dependent homophilic reactivity, promoting cell-cell recognition. Cdh5-expressing cells are first visible by 12 hpf in bilateral patches at the edge of anterior and trunk mesoderm. We have profiled the expression of this gene in 17hpf zebrafish embryos through in situ hybridization.Download Chenell's Research Report
Tanya Mack (Short)
Ceratopteris richardii and its use in studying light signal transduction and photomorphogenesis
In higher plants many of the functions of phytochromes have been molecularly characterized; however the molecular biology of phytochromes of ferns have been relatively shrouded due to its long lifecycle and the lack of specific tools to knockdown or knockout specific target genes (Bissoondial, 2005). Ceratopteris richardii has recently emerged as a model fern to study the process of photomorphogenesis. It has a rapid lifecycle; and is susceptible to RNA interference (RNAi) of targeted genes by uptake of dsRNA as dry spores imbibe (Bissoondial, 2005). Five full length phytochrome cDNA and genomic clones have been isolated in Ceratopteris: CrPHY1A, CrPHY1B, CrPHY2, CrPHY4A and CrPHY4B. By isolating the Ceratopteris richardii phytochrome sequences and their likely signaling intermediates, we will be able to examine their light-regulatory signaling pathways through a series of physiological, biochemical, and molecular approaches, as well as be able to systematically decrease the expression of those gene products by RNAi (Bissoondial, 2005). This project is focused on producing and expressing a fusion of CrPhy2 with green fluorescent protein (CrPHY2::GFP) using Gateway technology. Over- and under-expression of CrPHY2will allow us to observe important effects of phytochrome activation on cell division, cell growth, tissue morphology, sexual differentiation, and gene expression. Additionally, we are currently in the process of developing new techniques for the integration of genetic constructs into the Ceratopteris genome.
Download Tanya's Research Report
Bushra Meraj (Fjerdingstad)
Evolution of mating strategies in European Lasius niger populations: a microsatellite based study
Numerous studies have been conducted on the evolution of mating strategies in the ant Lasius niger. It has previously been established that in most northern European populations, queens practice single mating while in most southern populations, they have been found to practice multiple mating (Fjerdingstad and Corley et al in review). However, it remains unknown whether single/multiple mating has evolved once and then spread to other populations through co-ancestory and gene flow (Dornisthorpe 1927) or whether each population has individually evolved its mating strategy to better fit its local environment. To better answer this, we conducted a microsatellite study in which we amplified the DNA of 200 worker ants (taken from 20 colonies in each of 10 different European countries). The DNA was amplified at 4 different, highly variable regions (loci) within the ant genome using PCR. The resulting PCR fragments were then analyzed using an automated sequencing machine. The results were presented in the form of peak diagrams, one for each individual, using which we assigned alleles to each ant at all 4 loci. The results revealed genetic similarity between geographically close populations, which if combined with more supporting evidence, can lead us to believe that L. niger populations either shared a recent co-ancestor or are engaged in constant gene flow through outbreeding and migration. However, as the geographic distance between populations grew, allelic variation grew (the trend was that cold, northern populations had different alleles than hotter, southern populations). This may mean that geographically close populations have similar mating strategies due to coancestry and only few evolutionary events led to each population’s local adaptation to its local habitat. When combined with Fjerdingstad’s mtDNA and haplotype based research, our microsatellite study can allow us to make more decisive conclusions about evolution of mating strategies in European L. niger populations.
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Jacqueline Milander (Waldman)
Morphological significance in the clam shrimp, Caenestheriella gynecia: ring number in relation to carapace size
The following paper will discuss the morphological significance of a newly discovered branchiopod Caenestheriella gynecia. The organism is found in shallow pools which undergo alternate exposure to shade and sunlight. The main objective of the research by Jonelle Orridge, City University of New York PhD candidate, is to determine the correct taxonomic identity of the newly discovered species via morphology and genetic analysis. Specimens were dissected and properly catalogued. The main focus on this report is to determine if a relationship exists between the number of rings and the size of the carapace. Our preliminary results do show a significant relationship.
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Olivier Noel (Holtzman)
Immunosuppressant drug Tacrolimus induces endocardial defects in zebrafish
Immunosuppressant drugs are being used more and more in the scientific world for treatment of diseases and mostly to prevent the rejection of transplanted organs in subjects after surgeries. Very often, unpredicted side effects are associated with their use. In this study, we show how the immunosuppressant Tacrolimus also called FK-506 can affect endocardial formation. This observed side effect might lead to more serious heart defects in an organism throughout its development. We use zebrafish as a model organism to study FK-506 effect on the heart because of their specific characteristics. They have external fertilization and rapid development that allows us to collect offspring and perform experiments at different stages during a relatively short period of time. The zebrafish heart can easily be observed at the different stages of its development. Additionally, target cells such as heart cells can be labeled by green fluorescent protein (GFP) and observed with great details under the fluorescent microscope. Zebrafish also allow us to use a variety of drugs that can affect specific genes and allow for more in-depth study.
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Yeong Mi Shin (Short)
Molecular determination of Phy4A phytochrome gene in the fern Ceratopteris richardii
The phytochromes are red/far-red light receptor proteins that have been shown to regulate development, germination and growth in plants. Ceratopteris richardii is an annual fern that is an emerging model system for genetic and molecular based studies. The goal of this research is to determine the molecular photobiology of the phy4A phytochrome gene in the fern C. richardii. The Phy4A gene is among the six phytochrome genes recently isolated from C. richardii which has been sequenced. Although as a member of the phytochrome gene family, phy4A shares sequence homology with other phytochrome members, Phy4A is missing motifs at the N-terminus and is truncated at the C-terminus. The C-terminal ends of the phytochrome proteins are thought to be regulatory binding regions, and the absence of this region from Phy4A may be an indication of a regulatory function of this gene, representing a functional departure from the other phytochromes. We are using the Gateway vector system to insert the phy4A gene into destination vectors with Green fluorescent protein tags (GFP) at either the 5' or 3' end. The tagged gene will be introduced into developing C. richardii gametophytes through particle bombardment and treated under experimental light conditions. The GFP tags will allow us to observe the expression or lack of expression of the phy4A gene under different light conditions. The tags will also allow us to determine whether the phy4A gene product translocates to the nucleus in a light-dependent manner and thus may function as a transcriptional regulator as it does in angiosperms or is limited to protein-binding signaling interactions in the cytosol.
Download Yeong Mi's Research Report
Luis Vega, Jr. (Boissinot)
Molecular evolution of the Dnmt3L gene in primates
Dnmt3L is a gene belonging to the cytosine methyltransferase family. These enzymes silence and regulate gene expression by methylating their promoter. Among other genetic elements, the L1 family of retrotransposons is a prime candidate for this form of regulation. In mice, periods of Dnmt3L activity have been correlated with the silencing of L1 activity during the development of the germ line. This relationship, coupled with L1’s rapid rate of evolution, and the host-parasite model between L1 and its host genome, heavily implies the presence of an evolutionary arms-race between L1 and Dnmt3L. Our investigation of this matter entails the full sequencing of the Dnmt3L gene among primates, in order to trace its evolutionary history, and compare its rate of evolution with that of L1. This, combined with biochemical advances elucidating the mechanism by which Dnmt3L silences L1, will allow us to determine whether or not these selective pressures have resulted in coevolution between the two.
Download Luis' Research Report
Here are some of our undergraduate researchers from 2009, and summaries of their work. The faculty mentor's name is in parentheses after the undergraduate researcher.
Sung Kim (Baker)
Direct fitness of cannibalism in Colorado potato beetles (Leptinotarsa decemlineata)
The Colorado potato beetle(Leptinotarsa decemlineata) is cannibalistic within clutches. Newly hatched beetles eat their unhatched siblings in their own clutch. Since this cannibalism leads to a loss of indirect fitness due to eating their siblings, we hypothesized that there must be direct fitness gains for cannibalism to be maintained. This experiment aimed at discovering these direct benefits. Individual beetle hatchlings were provided 0, 1, or 2 eggs. Timing of development stage, weight, and size of emerging beetle were analyzed as a function of egg consumption. Individual beetle data were recorded daily. Beetles that ate one or two eggs gained more weight and developed more quickly than beetles that were not provided eggs, establishing a direct benefit to cannibalism.
Download Sung Kim's Poster
Olivier Noel (Holtzman)
FK-506 (Tacrolimus) is a drug that has been demonstrated to prevent angiogenesis in the zebrafish at 15 to 18 somite (16- 18 hours post fertilization), causing edema in the embryos. As a first step in my study, I attempted to repeat the published work with limited success. I then looked at its effects on the endocardium population. In all trials, it provoked cardiac morphologic defect, edema and blood pull at 48 hpf. Multiple drug tests were also performed on the embryos at younger stages and the obtained results attested to the disruptive action of FK-506 to the endocardial cells. My next step will be to study the migration of the heart cells population in treated embryos. These experiments fall within the study of the specific interaction between the endocardium and the myocardium populations of the heart. The Holtzman laboratory, having already proven that a signal coming from the endocardium is necessary for the proper formation of the myocardium, my experiment will add on to this found and will give us more insight in term of when and how the cells migrate during that process.
Samira Rabbanifar (Fath)
The development of antibiotic resistant strains of bacteria has increased in recent years, resulting in widespread effort being put towards finding new antimicrobial agents that are not harmful to humans. For centuries, many forms of copper have been used for hygienic purposes because of their antimicrobial properties. Within the past several years it has been discovered that metal nanoparticles have bactericidal properties. We are exploring whether copper-based nanoparticles posses more effective antibacterial properties than the solid copper surfaces used in the past. We have found that nanoparticles made from copper or composites of copper-nickel have potent antibacterial properties which have inhibited the growth of six different gram-positive and gram-negative bacteria that we have tested. Our current research is now focused on understanding the mechanisms involved in copper’s antibacterial properties, specifically if the bound particles are killing the bacteria due to compromising the cell membrane. These nanoparticles are not harmful to mammalian cells in culture and therefore express the potential for being useful in medical applications.
Luis Vega (Boissinot)
I work in Dr. Boissinot's molecular evolution lab. This semester I have continued and solidified my preliminary research into the evolution of the de novo methyltransferase 3-like gene in primates. My focus is to compare its rate of evolution with that of the L1 family of retrotransposons, to determine whether or not a correlation, possibly implying co-evolution, has taken place between the two. Having spent a summer in the lab performing PCRs and preparing samples of dnmt3l from various primates for sequencing, this semester was spent more in conjunction with my graduate student mini-adviser, developing the rationale behind why we are looking into their relationship. This was done in addition to participation in the HMNS and MARC programs, both of which required presentations on my research that incorporated all these preliminary investigations.
Tanya Mack (Short)
This past fall semester, I have been working in Dr. Short's laboratory, where my hypothesis has been that the molecular mechanisms of the phytochrome 2 (CrPHY2) photoreceptor action in the fern Ceratopteris richardii is similar to that of higher plants. Based on phylogenetic analyses and physiological studies, phytochrome responses in ferns show some limited similarities to those controlled by phyA and phyB of angiosperms. In higher plants, phytochromes have been shown to be localized to the nucleus after exposure to light in vivo. Taking the CrPHY2 gene in the pGEM vector and subcloning it into a Gateway© vector containing GFP fused in frame, I will attempt to transform Ceratopteris richardii and observe the effect of red and far red light on CrPHY2::GFP localization in dark-adapted plants to determine if it behaves like angiosperm phytochromes. These observations will indicate whether phytochrome activity of the fern Ceratopteris richardii represents a mechanism of action in common with higher plants, where light-dependent intracellular redistribution is one of the major regulatory steps in photomorphogenesis, and whether this mechanism was likely present in a common ancestor since the seed plants diverged from ferns approximately 400 million years ago.
Download Tanya Mack's resume
Emmanuel Datan (Zakeri)
My research interest and experience at Dr. Zahra Zakeri’s lab has focused on host-pathogen (i.e. influenza, dengue and modoc virus) interactions. Major goals of my research has been to understand how influenza A virus interacts with the host cell’s proteolytic components and how this knowledge can enable predicting outcomes during infection, enhance cellular antiviral responses and intervene during the critical periods of infection. Influenza induces a form of cell death that has been classified as program cell death 1 or apoptosis. When cells die in an apoptotic manner the cell undergoes an orchestrated process of structural and biochemical changes like DNA and nuclear fragmentation, cellular blebbing (pinching of the cell into droplets) and activation of proteases called caspases. It seems that influenza triggers the apoptotic process in order to minimize if not halt host antiviral responses like macroautophagy. We have shown by upregulating autophagy and using cells with knock-out and knock-down of key autophagy components, like ATG 5 or Beclin-1, that macroautophagy needs limits viral induced death and viral production. In our recent publication mitochondria associated proteins Bax and Bak were identified as key proteins for influenza induced apoptosis. We are also finding new roles for other forms of autophagy like Chaperone Mediated Autophagy in addition to identifying key signaling mechanisms behind cell death and viral production during infection. Our work on dengue and modoc, both belonging to the family Flaviviridae, takes a different spin since it focuses on how these viruses utilize key processes in host cells like autophagy for it’s benefit. We are taking a whole virus and viral gene approach in studying these host-pathogen interactions.
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