Volume 16, Issue 2, 2012
Save or Destroy
The history of Berkeley Scientific Journal at Cal starts at 1996, when several undergraduates involved in research who wanted to create a new avenue to publish their research. The first faculty sponsor was Professor Caroline Kane, whose passionate support of undergraduate education through the Biology Fellows Program earned her the College of Letters and Science Award for Distinguished Research Mentoring of Undergraduates in 2002. She earned her PhD from UC Berkeley and has studied the mechanisms of genetic expression and regulation. Although she is retired, she is an active emerita who facilitatated BSJ's transition to a DeCal course in the MCB department by signing on as the faculty sponsor.
After graduating from Berkeley with a PhD in sociology, Leah Carroll returned to UC Berkeley in 2001 as the director of the Haas Scholars Program. Like Professor Kane, Leah became involved with Berkeley Scientific Journal through the undergraduate research programs in the Office of Undergraduate Research. She has guided BSJ since then and served as the staff advisor. Her experience in research and undergraduate education has been an invaluable asset, and her new position as the Director of the Office of Undergraduate Research is a testament to that. Leah’s new book, “Violent Democratization: Social Movements, Elites, and Politics in Columbia’s Rural War Zones,” shows her all-encompassing involvement in research, both in a mentoring and in pursuing her own fields of interest.
Interview with Robert Knight and Brian Pasley: Brain-Machine Interfaces: Neural Prosthetics and Patient Care
Professor Robert Knight served as the Director of the Helen Wills Neuroscience Institute from 2001 to 2011 and has run a lab in human neuroscience within that institute since 1998. Using electrophysiological techniques, the Knight lab studies the role of the prefrontal cortex in human cognition. After graduating with a BS in Physics from the Illinois Institute of Technology, he earned his MD from Northwestern University, completed his neurology training at UC San Diego, and finished his post-doctoral work at the Salk Institute for Biological Studies. In 2010, Professor Knight helped found the Center for Neural Engineering and Prosthesis, a joint program between UC Berkeley and UCSF focused on brain-machine interfaces.
Brian Pasley, a post-doctoral student in Dr. Knight’s lab since 2010, conceived the lab’s latest publication, which announced the possibility for scientists to reconstruct human speech from recorded brain activity. Both Pasley and Knight hope the research will lead to advances in neural prosthetics for patients with neurological disorders.
One of the visual system’s many tasks is to be able to distinguish objects from the background. The ability to do this is limited and affected by the relationship between the object (or stimulus) of interest and the background. Adaptation in retinal neurons is the process of changing the cell’s response to a stimulus according to that stimulus’s background. When the stimulus is hard to discern from the background, the retina adapts by improving its sensitivity to low contrast. The large response range maintained by adaptation comes at a cost, however. Adaptation complicates neural coding by making the brain interpret identical stimuli as different based on differences in background. In order to further our understanding of adaptation, this study modified the background to be in terms of time and space rather than light intensity as is the norm. By changing the interval between two circular stimuli (inter-stimuli interval; IsI) of the same diameter, and by changing the diameter over a common IsI, we measured a ganglion cell’s output for one stimulus relative to another stimulus. the results show saturation (loss of output to the 2nd stimulus) of stimuli at lower IsIs. Also, the degree of saturation for a given IsI depends on the diameter of the stimulus. These combinations of results illustrate the temporal and spatial dependence of adaptation on ganglion cells. A larger-diameter stimulus involves multiple neurons surrounding the ganglion cell being recorded so various pathways most likely influence that cell’s ultimate output. Rapid stimuli (low IsI) can be defined as having large mean luminosity that directly affects ganglion cell output.
Identification of Burseraceae trees from Peru: a comparison of the nuclear DNA marker ITS and the plastid DNA marker rbcL for DNA barcoding
The immense plant diversity that is characteristic of tropical rain forests often makes it difficult for ecological and conservation studies to identify individual plant species and measure biodiversity. DNA barcoding is a species identification technique that utilizes standard, short dnA sequences to distinguish between species when traditional taxonomic identification is not practical. Accurate identification of animals with DNA barcoding has been well established, but a universally accepted DNA barcode for plants still does not exist. The use of nuclear DNA markers and plastid DNA markers from the chloroplast are the two contending approaches to DNA barcoding. This study compares the utility of the nuclear DNA marker ItS and the plastid DNA marker rbcL as DNA barcodes among 35 Burseraceae tree species from the Peruvian Amazon. I found that the proposed DNA barcode rbcL greatly underperformed the nuclear marker ItS as a DNA barcode. While both markers exhibited greater than 90% amplification success ItS demonstrated a mean pairwise percentage sequence divergence of 5.4% while rbcL demonstrated 0.83%. Additionally, at 1% sequence divergence resolution ItS discriminated between 99% of species-pairs while rbcL only discriminated between 26%. The results of my study suggest that ItS should not be completely discounted from the plant DNA barcode debate and rbcL be reevaluated as a proposed universal barcode.
Algerian ivy is an invasive non-native vine that limits native plant biodiversity. In this study I examined three removal techniques for managing Algerian ivy: manual removal, foliar herbicide application (round up® Pro), and cut-stem herbicide application. I hypothesized that cut-stem herbicide application would be the most effective removal technique and that both herbicide applications would not affect native seedling growth. I measured plots monthly for ivy and native seedling growth and analyzed results using a random complete block design, tukey-Kramer analysis, and Simpson’s diversity Index (SdI). I found no significant difference in ivy re-growth among treatments and no significant difference in native seedling growth between plots. However, manual removal plots had an SdI double that of other treatments (0.7652). Based on these results, I recommend that further use of herbicides be ceased until investigations into the effects of herbicide on native plant diversity have been completed.
Peripheral benzodiazepine receptor protein expression in cells treated with alcohol and cytokines; a study on alcoholism
Alcoholism is a complex disease that impacts the cnS through tolerance, dependence, brain damage and neurological and cognitive deficits. chronic exposure to ethanol brings neurodegeneration and an increase in the level of an outer mitochondrial membrane protein, called the peripheral benzodiazepine receptor, PBr for short. In this study, western blotting and immunocytochemical methods were used to detect the effects of ethanol and cytokine treatments on astrocytes, astrocytomas, and microglia. Although ethanol seemed to have led to a decrease in PBr in the astrocytes and microglia, it did produce an increase in astrocytomas. Additionally, LPS and cytokine mix seemed to have at least physically altered the appearance of these ethanol-exposed cells.