The Rutger Scholar

Editorial

Susan G. Forman — 2004-10-31

Thoughts on undergraduate research

True understanding of the academic disciplines and professions on which the modern university is based requires understanding of the methods those disciplines or professions use to generate and evaluate knowledge. For Rutgers undergraduates, undergraduate research is the gateway to developing an understanding of how knowledge is created. It is the means through which advanced understanding of a discipline or profession can be derived.

Scientific literature on learning tells us that "hands-on" experiences enhance the acquisition of new information and skills. Through an undergraduate research experience, Rutgers students go beyond reading and hearing about the process of discovery in their courses, to engaging in it and experiencing it for themselves. The results can be seen in this volume of undergraduate student work in which students, alongside their faculty mentors, tackle scholarly and scientific issues with the hope of advancing knowledge and improving individual lives and society.

Susan G. Forman
October, 2004
Piscataway, NJ

Parting words

With this, the 6th publication of the Rutgers Scholar, I step down as editor. It has been fun and interesting to work on "articles" from disciplines not my own, articles that have run the gamut of formats from traditional plaintext to video and audio clips. I like to think that the process of creating the articles has been useful for both the Rutgers Undergraduate Research Fellows who were the authors, and for unknown surfers of the web, who came to the Rutgers Scholar searching for information or were just browsing through.

I would like to thank all those who have supported the production of the journal and especially Susan Forman, our former Vice President for Undergraduate Education and Sam McDonald, who has been our web editor for the last two years.

Gregory Herzog
New Brunswick
October, 2004

The crossroads of theory of mind and moral reasoning: intention†

Adam Cohen — 2004-10-31

What is the relationship between moral judgment and the child's "theory of mind?" The present studies address whether preschool children can attribute the mental state, caring/not caring, and judge whether the consequences of an act were intended or not, as a function of the moral valence of the consequence. Pilot data suggested that younger children might not understand "not caring." Experiment 1 examined whether children, 3- to 5-years-old, could predict the affective state of someone who either cared or did not care about a food object or a person under different circumstances. Regarding objects, the results showed that 3-, 4-, and 5-year olds have adult-like intuitions regarding caring about objects and not caring about objects. The pattern of data was similar across the three age groups, but with strengthening effects across age. The "caring about people" results indicated that children were more likely to say that a person would feel happy or sad if someone they cared about was happy or sad. On the other hand, children tended to say that a person would feel neutral if someone else was happy or sad if the person did not care about the other person. These results demonstrate an understanding of both caring and not caring about people.

Experiment 2 explored how caring/not caring interacts with a judgment of "on purpose" in moral contexts. Adults have recently been shown to make asymmetric judgments of intention depending on whether a consequence of an action, that a protagonist does not care about, is beneficial or harmful to others. If the not-cared-about side effectside effect is beneficial, adults judge that the actor did not intend it. If the side effectside effect is harmful then the actor is judged to have brought it about intentionally. Preschool children, 3-, 4-, and 5-years-old were tested on scenarios in which an actor knew about, but did not care about, a side effectside effect of one of their actions. A control question screened for an understanding of "not caring that [someone would be harmed…]." A test question then required the subject to judge whether the side effectside effect of the action was brought about "on purpose." The results showed that for those children who failed the control "do not care that…" question, there was an overall bias to answer, "yes" to the "on purpose" question. However, the majority of children (aged 5 years), who passed the "not care" control question, showed the adult-like asymmetry, judging the side effectside effect to have been brought about intentionally when harmful, and to have been unintentional when beneficial. This is the first study to examine the relationship between developing 'theory of mind' and moral judgment in preschoolers.

†Based closely on a thesis submitted in fulfillment of the requirements of The Henry Rutgers Scholars Program and written under the direction of Dr. Alan Leslie, April 2004.

Functional genomics study in Arabidopsis thaliana of histidine biosynthesis

Christopher DeFraia — 2004-10-31

This study was aimed at analyzing the function of a gene thought to be required for histidine biosynthesis in the vascular plant Arabidopsis thaliana. A DNA insertion mutant of locus At2g36230 was isolated. Based on homology with the Saccharomyces cerevisiae His6 gene, At2g36230 was predicted to encode phosphoribosylformimino-5-aminoimidazole carboximide ribotide isomerase. Individual plants heterozygous for the AtHis6::TDNA insertion allele produced siliques in which approximately 25% of the seeds were aborted during early embryo development. The vegetative phenotype of the heterozygous plants was normal. When histidine was applied exogenously to the heterozygous plants the frequency of embryo-abortion was reduced to approximately 5%. The fact that the homozygous mutant seeds fail to grow while the maternal plant thrives suggests that histidine, unlike other amino acids, cannot be transported from the maternal plant to developing embryos.

Isolation and characterization of a thermophilic, chemolithotrophic nitrate-reducing bacterium from deep-sea hydrothermal vents

Susan Ellor — 2004-10-31

The nitrogen cycle at deep-sea hydrothermal vents has yet to be thoroughly studied. Novel thermophilic microorganisms that couple autotrophic CO₂ fixation with the reduction of nitrate to ammonia have been suggested in recent studies to be important for primary production and nitrogen cycling in marine geothermal environments (Blochl, et al. 1997, Alain, et al. 2002b, Huber, et al. 2002, Miroshnichenko, et al. 2004, Vetriani, et al. 2004). In the summer of 2001, hydrothermal samples were collected from the Rainbow deep-sea vent field on the Mid-Atlantic Ridge (MAR), and several novel thermophilic organisms were obtained in pure culture. Among these novel isolates, cells of strain TB-1 were found to be Gram-negative rods with optimal growth occurring at 55°C, slightly acidic pH, and a salt concentration lower than that of seawater. This bacterium was capable of chemolithoautotrophic growth by coupling H₂-oxidation to NO₃^- reduction, which was reduced to ammonium. Under these conditions the generation time of TB-1 was about 50 minutes.

Isolate TB-1 is phylogenetically related to the epsilon-proteobacteria (genus Caminibacter). The ecological significance of such deep-sea hydrothermal vent bacteria is twofold: 1) these organisms contribute to the primary productivity by fixing CO₂, and 2) their nitrate respiratory metabolism (namely, the reduction of NO₃^- to NH₄⁺) implicates that nitrogen is conserved and recycled within the vent system.

Synthesis and characterization of recyclable porous materials

Sean P. Kelly — 2004-10-31

Zeolites are solid materials that contain rigid frameworks and accessible internal channels or cages. They have been used in many applications in areas of catalysis and phase separation.[1] Recent work has shown that porous metal organic materials have properties that mimic and sometimes are superior to those of zeolites.[2] Novel metal organic framework structures with specific functionality can be designed and rationally synthesized, by selecting suitable organic ligands and metal centers. In this paper, we describe our recent study of a group of organic framework structures based on the metal cobalt and the organic ligands biphenyldicarboxylate (bpdc) and bipyridine (bpy), RPMs (Rutgers Recyclable Porous Materials) that are porous and recyclable.[3] This remarkable structural recyclability makes these systems highly promising for use as host materials in ship-in-bottle catalysis.

Shortcut to mycothiol analogues

Spencer Knapp — 2004-10-31

The synthesis of a simplified thioglycosidic analogue (2) of mycothiol (1) is described. Evaluation of 2 against mycothiol S-conjugate amidase from Mycobacterium tuberculosis reveals good specific activity (7500 nmol min^-1 mg-protein^-1, vs 14 200 for 1), indicating that 2 can serve as a starting point for antitubercular drug design.

Asymptotics of a Nonlinear Fibonacci Recurrence†

Thomas D. Peters — 2004-10-31

^† This project was carried out under the supervision of Prof. Stephen Greenfield, Department of Mathematics, Rutgers University.

Molecular Modeling as a visualization tool in design of DNA crosslinked polyacrylamide

Karin Rafaels — 2004-10-31

Since DNA-crosslinked gels are likely to find a range of applications it is important to know how to tailor the gel composition for a particular application. In this study, polyacrylamide gel crosslinked with DNA has been assayed with respect to conformational energy and linker size using AMBER 7.0 software [1]. The molecular models generated in AMBER make it possible to estimate the mechanical properties of the gel as a function of crosslinker density, polyacrylamide density, and crosslinker length. The structure of an equilibrium state is computed using an explicitly solvated model, in which water was the solvent Visual inspection of the model determines other mechanical properties of the gel and helps predict chemical interactions. A long-term goal of this work is to use computer assisted modeling techniques to guide the experiments, to predict linker stiffness, and to examine other mechanical properties of the DNA crosslinker.