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Interactive tutorials for teaching hypothesis testingChristopher L. Aberson
Department of Psychology; Humboldt State University
The Web Interface for Statistics Education (WISE) provides Internet-based
tutorials that supplement the teaching of core statistical concepts. The project
includes a comprehensive World Wide Web site housing links to electronic journals,
archived discussion lists, datasets, and interactive tutorials (http://wise.cgu.edu).
This poster focuses on two interactive tutorials that supplement undergraduate
instruction on hypothesis testing and statistical power.
The first tutorial examines the logic and mechanics of hypothesis testing.
Students examine hypothesized and actual distributions. The student draws
samples from the actual distribution, using an interactive applet, and draws
conclusions based on each sample. The applet presents a screen that graphs
both distributions (actual and null) and indicates where each sample result
falls. Samples are drawn from three population distributions, each differing
from the hypothesized distribution. One distribution is very different from
the hypothesized distribution, the second is moderately different, and the
third differs only slightly. This tutorial presents the basic logic of hypothesis
testing (i.e., reject null hypothesis if sample result would be unlikely
given that the null is true) and introduces the possibilities of erroneous
hypothesis test conclusions. A series of follow-up questions help the student
relate sample results to theory and application. We typically use this tutorial
as a laboratory assignment during the discussion of the z-test as an introduction
to hypothesis testing. Follow-up questions provide a framework for classroom
discussion of topics related to hypothesis testing.
The second tutorial teaches concepts related to the power of a statistical
test. The power tutorial concentrates on the effects of sample size, effect
size, and alpha level on the ability to reject false hypotheses. This tutorial
again has student draw samples of various compositions and compare results.
Typically, students are instructed to draw samples from a population with
a mean that differs from the null hypothesis. The student examines the sample
mean, the probability of obtaining this result given that the null hypothesis
is true, and the power of the test. After drawing samples, the student indicates
the number of samples that would lead to the rejection of the null hypothesis
when using an alpha value of .05. Next, the student evaluates the same samples
using alpha of .01. The student indicates which case leads to more frequent
rejection of the null hypothesis and the effect of alpha on the power of the
statistical test. The tutorial also contains questions that ask the student
to address issues such as statistical vs. practical significance. We typically
use this tutorial as lab assignment after discussing z and t distributions.
Again, follow-up questions can be used to stimulate classroom discussion.
A Proteomics Study of Quorum Sensing in Escherichia
coliJ. Allen*1, C. Doneanu2, L. Barofsky2, D. Barofsky2, & J. Schineller1
1Department of Chemistry; Humboldt State University, Arcata, CA
2Department of Chemistry; Oregon State University, Corvalis, OR
Background: Quorum sensing bacteria are able to sense the number of other bacteria in the surrounding media by detection of hormone-like secreted compounds. E. coli is known to both secrete an active molecule (inducer), and respond to addition of signal molecules or cell conditioned media. Cellular processes including cell division, transition into stationary phase, and pathogenesis have previously been shown to be regulated or coregulated by quorum sensing mechanisms in E. coli. Study of the proteome provides a link to determine which activities are being affected by quorum sensing.
Methods: Proteins expressed or repressed by addition of n-acylhomoserine lactone or cell conditioned media were visualized on 2D-PAGE (two dimensional polyacrylamide gel electrophoresis) gels.
Results: Spots of interest are being excised from the gels for sequence determination by MALDI-TOF MS (matrix assisted laser desorbtion ionization time of flight mass spectrometry) and or ESI-MS (electrospray ionization mass spectrometry). Proteins that have been identified include a periplasmic oligopeptide-binding protein precursor, dihydrolipoamide dehydrogenase, GDP-E.coli uridine phosphorylase, and 50-S Ribosomal Protein (L9) subunit.
Conclusion: At least five proteins have been identified that are regulated by quorum sensing in E. coli.
Acknowledgements: Funded in part by a HSU-Research and Creative
Activities Grant to J. S. J. Allen received a HHMI summer research scholarship.
L. G. Ayers, S. R. Hoffman, B. M. Jokinen, M. A. Large, L. M. Roy, D. B. Selway, A. W. Stevens, B. C. Zelenke, G. B. Crawford, and J. C. Borgeld
Department of Oceanography; Humboldt State University
Humboldt Bay comprises two distinct bays (Arcata Bay to the north, South
Bay to the south) which are connected by a long thalweg. Overall, Humboldt
Bay is relatively well-mixed vertically, although horizontal gradients in
water properties are often observed from the ocean to deep within the bay.
Several drifters, drogued at 1.5 m below the surface, were released from sites
north and south of the Humboldt Bay entrance over the course of an ebb tide.
Within one hour of low tide, flow from Arcata Bay was faster than South Bay
by a factor of 2-3, with peak flow speeds reaching 75 cm/s. In addition, drifters
from Arcata Bay were transported across a wide area within the entrance, while
those released from South Bay were held close to the south jetty. This pattern
continued until roughly one hour before low tide, when flows from both bays
became comparable. We suggest the most likely cause for this evolution is
the large difference in tidal prisms for Arcata and South Bay and the location
of the main (dredged) navigational channel, which runs alongside the south
jetty near the bay entrance.
We also attempted to determine whether or not a portion of an ebb plume returned
to the bay on the subsequent flood. To identify and differentiate plume and
ocean waters, several characteristics were measured offshore, at the bay mouth,
and at two sites within the bay. These characteristics included temperature,
salinity, turbidity (as extinction coefficient), total suspended matter, chlorophyll,
ammonium, dissolved oxygen, and nitrate concentrations. Most measurements
were taken within 1 m of the ocean surface; some additional observations were
made at 4 m and just above the bottom. The most promising "tracers"
of bay effluent proved to be turbidity, chlorophyll, and ammonium concentrations.
At the bay entrance, the tracers suggested detectable levels of plume water
returning to the bay during the first three hours of the flood.
F. C. Batista
Departments of Chemistry and Geology; Humboldt State University
G. A. Cutter, L. S. Cutter, and K. H. Johannesson
Department of Ocean, Earth and Atmospheric Sciences; Old Dominion University; Norfolk, Virginia 23529
Arsenic concentrations and speciation were measured in surface water samples collected from the Great Dismal Swamp in southeastern Virginia, USA using selective hydride generation and atomic adsorption spectroscopy. Phosphate concentrations were also determined in these surface waters using the molybdate blue spectrophotometric method. Great Dismal Swamp waters are characterized as blackwaters, having high dissolved organic carbon (DOC) concentrations that range from 445 µM to 6304 µM, with a mean (n = 12) of 3282 ± 2165 µM. The pH ranged from 4.30 to 6.42, with a mean (n = 12) of 5.14 ± 1.04. The inflow waters (Cypress and Pocosin Swamps) reach higher pH values (mean of 6.32 ± 0.10 for n = 5) than Lake Drummond and its immediate inflow and outflow ditches, where the mean pH (n = 7) is 4.30 ± 0.04. Total arsenic concentrations in Great Dismal Swamp waters range from 2.18 nM up to 21.42 nM. Phosphate concentrations range from 0.18 µM to 1.42 µM, but do not correlate with arsenate concentrations (r2 = 0.004). Arsenate typically predominates in oxic, surface waters. However, As(III) was detected at higher concentrations (1 - 17.72 nM, mean value of 8.00 ± 5.80 nM for all samples, n = 10) in half of the samples from the lower part of the watershed (i.e., mainly in Lake Drummond and its outflow, the Feeder Ditch; mean of 12.89 ± 2.89 nM, n = 5). No methylated species were detected in the selected samples analyzed for organoarsenical forms (monomethyl and dimethyl arsenicals). A strong correlation exists between dissolved As(III) concentrations and dissolved organic carbon concentrations (r2 = 0.88), and this correlation is significant at greater than the 99% confidence level. The high abundance of As(III) in comparison to both thermodynamic predictions, and other surface waters, suggests that either there is a strong anoxic source of this form, or that the high DOC concentrations stabilize it via complexation and slower rate of oxidation.
A Computational Study of Stable Helical Structures
in Perfluorinated AlkanesErin M. Brown, William G. Golden, and Robert W. Zoellner
Department of Chemistry; Humboldt State University
Stable conformations of a series of perfluoroalkanes and their hydrocarbon
analogs were analyzed using semi-empirical calculations at the PM3 level (PC
SPARTAN Pro'). It was found that perfluoroalkanes exhibit helical structures
as a significant percentage of their total stable conformations, whereas their
hydrocarbon analogs do not. In the smaller molecules (7 carbons and below),
5-carbon pitch helical structures are found, but these structures are replaced
by 16-carbon pitch structures in 8-carbon and longer perfluoroalkanes. This
effect is essentially non-existent in the analogous saturated alkanes.
A Computational Investigation of the Structure
and Properties of MonocarbonylironIan T. Clark, Robert W. Zoellner, and William G. Golden
Department of Chemistry; Humboldt State University
This project initiates the computational modeling of the interactions of carbon monoxide (CO) with iron atoms or clusters. The simplest such system, a single iron atom bound to a single carbon monoxide (carbonyl) ligand, has been completed and the results will be reported. In order to establish the accuracy of the methods used, comprehensive testing on carbon monoxide was first carried out using each of the method and basis set combinations available in Gaussian 98W. Because experimental dipole moments and vibrational frequencies are notoriously difficult to absolutely determine computationally, these properties were used as the criteria for choosing the computational methods appropriate for monocarbonyliron (FeCO). The CO calculations revealed that density functional methods were superior to Hartree-Fock methods. All calculations were carried out individually on FeCO with multiplicities of 1 (no unpaired electrons), 3 (two unpaired electrons), or 5 (four unpaired electrons) and with bond angles varied from 90-180 degrees. All calculations supported the experimental linear structure for FeCO and generally reproduced experimental vibrational frequencies. However, the effect of multiplicity on the calculated frequency and bond lengths raised interesting questions regarding the actual electronic configuration of FeCO in the gas phase and in low temperature matrices.
M. A. de Angelis, M. Torres and J. McManus
Department of Oceanography; Humboldt State University
Methane oxidation activity within marine sediments during an Alvin cruise
in 2000 was measured at various locations associated with cold seeps of the
San Clemente Escarpment. The Navy Fan, a 100 to 200 m section that overlies
older San Clemente strata, is characterized by the presence of distinct sand
layers ranging from 3 to 5 cm in thickness that provide discrete pathways
for migration of fluids at high lateral advective rates. The San Clemente
fault cuts through the Navy Fan deposits and exposes migration pathways on
a 60 m high scarp wall with fluid discharge sites along the escarpment zone
demarked by chemosynthetic communities and barite deposits. Sediments collected
at seep sites on the scarp exhibited elevated methane turnover times ranging
from 2 to 45 days within the upper 10 cm. Methane oxidation rate maxima within
the sediment were observed at depths corresponding to porewater anomalies
of dissolved metabolites indicative of lateral flow of methane-rich fluids
within the sediment. Seep sites located at the base of the scarp are characterized
by vertical fluid flow along high permeability conduits of the San Clemente
fault. Sediments collected at these sites exhibited methane turnover times
of 8 days to 27 years in the upper 10 cm with the majority of oxidative activity
confined to the upper 0.5 cm. Nearby background (non-seep) sediments characterized
by diffusive flow had relatively longer methane turnover times of 42 days
in surface sediments and greater than 300 years below 2 cm depth. Methane
turnover times for San Clemente seep sediments supplied by lateral flow of
methane-enriched fluids were significantly higher than those observed elsewhere
in methane-saturated sediments characterized by disruptive gas bubble flows
driven by decomposing methane hydrates. Fluid flow characteristics appeared
to be a more important controlling parameter of methane turnover times in
marine sediments than methane porewater concentrations except in surficial
sediments directly in contact with bottom seawater.
A Computational Investigation of the Structures
and Properties of Derivatives of Methylphenidate and Cocaine with Comparisons
to Experimental Activity DataLaura A. Duckworth, Gary W. Van Horn, and Robert W. Zoellner
Department of Chemistry; Humboldt State University
Methylphenidate (Ritalin®) is a commonly prescribed pharmaceutical used
to minimize the symptoms of attention deficit hyperactivity disorder (ADHD).
The primary mode of action of this medication is thought to be through binding
to an active site on the dopamine transporter. When abused, methylphenidate
exhibits physiological effects similar to those of cocaine, most notably dopamine
re-uptake inhibition. Because both methylphenidate and cocaine appear to bind
to similar sites on the dopamine transporter, and because methylphenidate
is a cocaine antagonist, it is may be feasible to use derivatives of methylphenidate
to treat cocaine abuse. Semiempirical (PM3) methods have been used to calculate
the structures and properties of approximately fifty derivatives of methylphenidate
and fifty derivatives of cocaine in order to establish correlations between
experimental binding affinities and calculated electronic and molecular orbital
properties. Calculated properties that appear to correlate strongly with binding
affinities will be discussed and methods to enhance binding affinity will
be inferred for both methylphenidate and cocaine.
Predictors of Clinical Use of Nonerotic Touch in
PsychotherapyJames L. Dupree and Lura T. Reddick
Department of Psychology; Humboldt State University
The therapeutic and ethical implications of the use of nonerotic touch in
psychotherapy sessions is currently argued in both the theoretical and data-based
literature. Opinions abound but research is scant and findings are inconsistent.
This study was conducted to investigate whether or not gender of therapist,
theoretical orientation, or academic training is related to attitudes about,
and usage of, such nonerotic touch. Nonerotic touch was defined in the study
as "touch that is not intended to give or elicit sexual feelings and
is not culturally a form of touch considered sexual." Examples are touching
the client's hand, knee, back, arm, or giving a hug.
A questionnaire specifically designed for this study was developed. It contained
four demographic variables: gender, age, license status, and therapeutic orientation.
Respondents were asked to identify their theoretical orientation as Psychodynamic/Object
relations, Humanistic/Existential, Behavioral/Cognitive, Systemic, or Other.
A total of 43 items were gleaned from the literature. Items were virtually
quotes from theoretical discussions and opinions expressed in the literature
or from phrases used to describe results. Responses were measured on a five-point
Likert-type scale. The items were
grouped into three areas of investigation with eight subscales.
a) Overall Attitude toward Nonerotic Touch: General Attitude, Assists in Bonding,
Creates Misunderstandings, Communicates Caring, Depends on Content of Session.
b) Training Received regarding Nonerotic Touch: Whether Training was Received,
Attitude Taught During that Training.
c) The actual Usage of Nonerotic Touch in present therapy.
The questionnaire was mailed to 167 mental health professionals in a northern
California county. Seventy-seven professionals returned the questionnaire,
with a return rate of almost 50%. Respondents included 51 females and 26 males.
License status included psychiatrists, licensed psychologists, licensed clinical
social workers, marriage and family therapists, interns, and trainees.
One-way Analysis of Variance (ANOVA) was performed to measure most of the
results. Pearson Product-moment Correlations were conducted as appropriate.
Results were as follows:
1) No significant gender differences were found on any of the eight subscales,
however there were differences on two individual items: the males scored higher
than females on two items about caution in using touch ("The only touch
that is permissable is a handshake before or after a session" F(1,75)
= 7.148, p < .01, and "Most therapists use touch too much," F(1,75)
= 4.362, p < .05).
2) Surprisingly, there was no difference among different therapeutic orientations
regarding attitude or usage of nonerotic touch with one exception. Those identifying
as Humanistic were more apt than others to endorse the statement, "I
wish we had more training or discussion of the use of touch in therapy,"
F(4,72) = 2.25, p < .05.
3) Generally therapists reported a lack of training in the use of nonerotic
touch, that they wished they had had more training on the topic, and that
what little training they did receive discouraged the use of touch. However,
those therapists who were taught that touch is a positive influence continue
to view it that way (r = .228, p < .05) and to use it in practice (r =
.411, p < .001).
4) Older therapists tended to report receiving more training about nonerotic
touch and that the attitude they were given in training toward such touch
was positive r(75) = .242, p < .05 and r(75) = .232, p < .05.
The most endorsed (M > 4.0, "true" or "very true")
items were: "Generally it is best not to touch clients." "Generally
I do not use touch very often in therapy." "The use of nonerotic
touch was not part of my training." "Failure to use touch in therapy
can give off the message of being distant and aloof."
The least popular or most rejected (M < 2.0, "false" or "very
false") items were:
"It is often helpful to touch a client when there is a history of physical
punishment or abuse." "From my training I have learned that touch
is very helpful with most clients."
"In my graduate training I was taught that touch is a necessary part
of most therapy."
"Touch is often the best way to show concern when a client is tearful."
"The use of nonerotic touch was well covered in my training." "Touch
is needed to create a sense of safety." "Touch encourages clients
to go deeper into therapy."
The overriding conclusions are that despite a variety of opinions and research
implications, gender of therapist, theoretical orientation, or academic training
appear to have limited impact on whether the clinician uses nonerotic touch.
Furthermore, nonerotic touch was seen by most respondents as not necessary
to effective psychotherapy and perhaps even inappropriate. Nonerotic touch
appears to be a complicated and multifaceted issue and this study highlights
the need for increased training and research regarding such touch.
J. L. Graham, and J. O. Reiss
Department of Biological Sciences; Humboldt State University
There are two distinct classes of odorant receptors (OR). Class I ORs are
thought to be responsible for olfaction in water, while Class II ORs are for
olfaction in air. Most fish possess only Class I ORs, while mammals possess
only Class II ORs. Since amphibians undergo metamorphosis to change from an
aquatic larva to a terrestrial adult, it is important for them to have both
classes of ORs.
The broad objectives of this project are to reveal the molecular characteristics
of the amphibian nose that allows it to functionally transition from smelling
substances in water to smelling in air. This will be done by isolating genes
from Class I and Class II odorant receptors and determining when and where
they are being expressed in the nose at all stages of development in Ascaphus
truei.
To isolate Class I and II odorant receptor genes, genomic DNA was first isolated
from muscle tissue of A. truei tadpoles. Gene regions were then amplified
by PCR using degenerate primers based on conserved regions of olfactory receptors
in other species. PCR products were then cloned into a T-vector system and
screened using blue/white selection. A second PCR was then done to determine
which clones contained the appropriate size fragment, and these clones were
sequenced with Li-Cor Sequencer. Sequences were then run through BLASTx program
to determine which were odorant receptors, and in which Class the ORs belong.
To examine expression of these genes, in situ hybridization was performed
by using digoxygenin-labeled RNA probes to cryo-sections of frog nose. Hybrid
molecules can be visualized by a colorimetric reaction.
I have successfully isolated a novel Class II odorant receptor from A.
truei and have designated it pJENN101. Some potential Class I odorant
receptor genes have been isolated, but more analysis must be performed before
absolute identity can be established.
The in situ hybridization procedure of pJENN101 to nasal sections of
A. truei has thus far been unsuccessful. Modifications to the protocol
and a set of positive and negative controls are being made in order to increase
success of hybridization and visualization.
As only a few potential odorant receptors have been isolated and in situ
hybridization techniques have been ineffective, more data is essential
before accurate conclusions can be made regarding evolution of the molecular
features of amphibian olfaction.
Funding for this project has been provided by HHMI and NSF.
Effects of Three Insecticides on Survival, Growth,
and Metamorphosis of Three Amphibian SpeciesShannon E. Julian
Department of Biology, Frostburg State University
James E. Howard
College of Natural Resources and Sciences, Humboldt State University
Concern over the decline of amphibian populations has prompted studies of the effects of pesticides on amphibians. Because many amphibians breed in water associated with agricultural areas, testing the sublethal effects of pesticide exposure throughout larval development may be especially relevant. We investigated the effects of pulsed exposure to three insecticides (carbaryl, chlorpyrifos, and imidacloprid) on survival, growth, and time to metamorphosis of three amphibian species (Pseudacris triseriata, Bufo americanus, and Rana sphenocephala). Tadpoles were raised from two weeks post-hatching to metamorphosis in 20-gallon aquaria containing one of three dosages of a pesticide. Survival to metamorphosis of tadpoles in high concentrations of all three pesticides was significantly decreased for all species. As a result, subsequent analysis on sublethal effects was only performed on medium, low, and control concentrations. Growth of R. sphenocephala tadpoles was significantly decreased by exposure to medium concentrations of all three pesticides, however growth of B. americanus tadpoles was decreased by medium concentrations of carbaryl and chlorpyrifos only. Growth of P. triseriata in all pesticide treatments was not significantly different from controls. Time to metamorphosis of tadpoles of all three species was significantly increased by medium concentrations of all three pesticides. Sublethal effects on time to metamorphosis and growth would be expected to have negative impacts on population persistence.
*Effects of three insecticides on survival, growth and time
to metamorphosis of three amphibian species. (20th Annual Meetings of the
Society of Environmental Toxicology and Chemistry Pennylvania Convention
Center, Philadelphia, PA. November 17, 1999.)
Senqi Hu
Department of Psychology; Humboldt State University
The purpose of the present study was to investigate the facial EMG activities
while the subjects were voluntarily acting four types of facial muscle contractions.
Thirty-six subjects were asked to voluntarily perform four types of facial
muscular actions, such as "pull your eyebrows down and together",
"raise your upper eyelids and tighten your lower eyelids", "narrow
your lips and press them together", or "slightly open your mouth
and raise your cheek muscles" for 64 seconds while their EMGs were recorded.
It was expected that these four sentences would make the muscular movements
that have been found universally for the emotions of anger, fear, disgust,
and happiness. Results indicated that the subjects generated the highest ratios
of EMG spectral power between muscular acting of happiness and baseline periods
at the zygomatic region, followed by the levator labii region,
the corrugator region, and the frontalis region. The subjects
generated the highest ratios of EMG spectral power between muscular acting
of anger and baseline periods at the corrugator region, followed by
the frontalis region, the zygomatic region, and the levator
labii region. The subjects generated the highest ratios of EMG spectral
power between muscular acting of fear and baseline periods at the corrugator
region, followed by the frontalis region, the zygomatic region,
and the levator labii region. The subjects generated the highest ratios
of EMG spectral power between muscular acting of disgust and baseline periods
at the levator labii region, followed by the corrugator region,
the zygomatic region, and the frontalis region. It is concluded
that voluntarily performing muscular actions generating distinctive facial
expressions reflect four main emotions: happiness, anger, fear, and disgust,
and that happiness was associated with increased EMG power mainly at the zygomatic
muscles, that disgust was associated with increased EMG power mainly at the
levator labii muscles, and that anger and fear were associated with
increased EMG power mainly at the corrugator muscles.
A Method for Quantifying Asymmetries in Flocculent
Disk GalaxiesDavid A. Kornreich
Department of Physics and Physical Science; Humboldt State University
Martha P. Haynes, and Richard V. E. Lovelace
Cornell University
A photometric method for quantifying deviations from axisymmetry in optical
images of disk galaxies is applied to a sample of 32 face-on and nearly face-on
spirals. The method involves comparing the relative fluxes contained within
trapezoidal sectors arranged symmetrically about the galaxy center of light.
Application of this "method of sectors" to R-band images of 32 disk
galaxies indicates that about 30% of spirals show deviations from axisymmetry
at the 5 sigma level. Thus, in agreement with prior studies (Rix and Zaritsky
1995, Zaritsky and Rix 1997, and Conselice 1997) we find that disk galaxies
in the field do not universally exhibit undisturbed morphology. These results
are ill-explained by the conventional hypothesis of a tidally-induced perturbation
in the disk.
Superconducting Mixed State Phase Diagram of k-(ET)2Cu(NCS)2M. M. Mola
Department of Physics and Physical Science; Humboldt State University
S. Hill
Department of Physics; University of Florida; Gainesville, FL 32611
J. S. Qualls
Department of Physics; Wake Forest University; Winston-Salem, NC 27109
We have explored the superconducting, mixed state phase diagram of the layered organic superconductor k-(ET)2Cu(NCS)2. In particular, the melting of the quasi-two dimensional (Q2D) vortex lattice is investigated throughout a wide range of the available field and temperature parameter space. At moderate magnetic fields (0.01 2 T) and temperatures (1.5 10 K), a cavity perturbation technique is used to study the Josephson plasma resonance. By investigating this phenomenon over a wide frequency, field, and temperature range, we have determined the line in the phase diagram that corresponds to either a flux lattice melting or a depinning transition. For higher fields (2 20 T) and lower temperatures (0.025 0.300 K), cantilever beam torque magnetometry is used to determine the melting of the Q2D flux lattice. In this regime, it is shown that this transition is due to quantum fluctuations in the positions of the vortices. From the results of these two experiments, one can piece together the mixed state phase diagram. Upon doing so, it is seen that the Q2D flux solid and the vortex liquid states dominate the majority of the phase diagram.
Investigations of Environmental and Microbial Diversity
in High Temperature, Low pH Geothermal Features at Lassen Volcanic National
ParkPatricia Siering and Mark S. Wilson
Department of Biological Sciences; Humboldt State University
The hot springs, steaming fumaroles, boiling mudpots, and sulfurous vents of Lassen Volcanic National Park (LVNP) in northern California represent some of the most extreme life-supporting environments on earth with temperatures ranging from 50°C to greater than 115°C, and pH from 0-3 being common. We recently initiated a long-term project to investigate the environmental and microbial diversity in several of these environments. No microbiological work has previously been done at LVNP. Field measurements for temperature and pH were obtained from several thermal features within the park. Water, underlying sediment, and mudpot samples were aseptically obtained from 34 sites (ranging from 55°C -95°C, pH 1-3), and each was processed for total nucleic acid extraction and acridine orange direct counts (AODC). Most of the water samples were also processed for geochemical analyses (cation, anion, and sulfur speciation). The AODCs are on the order of 106-108 cells/mL (or cells/gm) for all samples studied thus far. Electrophoresis of nucleic acid extracts from many of the sediment and mudpot samples reveals abundant rRNA suggesting the existence of active microbial communities. Using universal primers, portions of the 16S rRNA genes were PCR amplified from extracts obtained from a hotspring sediment (55°C, pH 1.2), a mudpot (82°C, pH 1.2), and a fumarole-charged hotspring (93.5°C, pH 1.2). Amplicons were cloned and sequenced using standard procedures. Based on similarity to sequences available in the public databases, clones from the high temperature mudpot were identified as belonging to the Group 1 Crenarchaeota. Many of these sequences appear unrelated to previously isolated organisms or identified sequences, having ~85% RDP similarity with closest cultured isolate (Crenarchaea) sequence. Both Bacterial and Archaeal domains were detected in the moderate temperature sediment, with the Archaeal sequences again appearing unrelated to previously isolated organisms or identified sequences (~85% RDP similarity with closest cultured isolate (Eurarchaea) sequence). Sequences retrieved from DK-12 were 91-95% similar to Crenarchaea sequences in the RDP. Ultimately, we wish to correlate differences in geochemistry, temperature and pH with differences in microbial inhabitants to investigate the role of biotic processes (and population dynamics) in the geochemistry of these systems.
A Single Molecule DiodeJoshua R. Smith
Department of Chemistry, Humboldt State University
Josef Michl
Department of Chemistry and Biochemistry, University of Colorado, Boulder
With Moore's Law looming over the computer chip industry a large interest is underway to develop new microchip technology. One direction this is going is to make computer chips, and chip components, out of molecules. The design, synthesis, and testing of a single molecule diode, an important microchip component, will be presented.
Darcy A. Walden and William F. Wood
Department of Chemistry; Humboldt State University
There is a steady demand for new compounds that can be synthesized for medical treatment. Bacteria and fungi develop resistance to antimicrobial agents in current use, and therefore new bioactive compounds must be discovered. An undeveloped source of new medicines comes from marine algae, which are under constant attack by marine bacteria and fungi. The three species of marine algae that were included in this study are Ulva californica, Egregia menziessi and Porphyra perforata. The extracts from these species were screened for antimicrobial activity using a suspension assay with Trichophyton mentagrophytes (Athlete's Foot fungus). The minimum inhibitory concentration (MIC) of the active extracts/fractions was determined using a serial broth dilution assay. The dichloromethane extract of P. perforata was found to be most active (MIC = 12.5 µg/mL); extracts of the other species showed lesser activity.
The Development of Amino Alcohols as Acyl Transfer
CatalystsKjirsten A. Wayman
Department of Chemistry; Humboldt State University
Tarek Sammakia
Department of Chemistry and Biochemistry, University of Colorado, Boulder
We have developed two amino-alcohol systems as nucleophilic oxygen catalysts
for acyl transfer reactions. These molecules bear an alcohol and a base in
close proximity to facilitate the acylation and subsequent deacylation of
the catalyst oxygen. Initial studies focused on 4-dialkylaminopyridines as
the basic unit, with substitution at both the 2- and 6-positions in order
to sterically deactivate the nucleophilic pyridine nitrogen. A second system
was based on an ortho disubstituted benzene, consisting of a pyrrolidinomethyl
substituent at one site and a hydroxyalkyl group at the other. A variety of
catalysts of these types were prepared with varying acidities due to the presence
of electron-withdrawing and electron-donating alkyl groups geminal to the
hydroxyl group.
The importance of the hydroxyl group for catalytic activity has been established
by blocking the hydroxyl group as the methyl ether. The methyl ethers of both
the pyridine-derived and benzene-derived systems were found to be 94 and 930
times less active than the corresponding alcohol derivatives, respectively.
The inductive effect of the alkyl group plays a significant role in the reactivity
of this class of catalysts. An electron-withdrawing group renders the hydroxyl
group more acidic, more readily deprotonated and more reactive towards acylation,
and a better leaving group for deacylation. As a result, trifluoromethyl substituted
catalysts were found to proceed 4 and 40 times faster than the methyl substituted
derivatives of the pyridine and benzene-derived systems, respectively.
The mechanism of this process is further revealed by the following observations.
Immediately after the reaction is initiated, the NMR spectra (used to monitor
the reaction progress) show the rapid decrease in the concentration of the
catalyst and the appearance of a new set of signals corresponding to the acylated
catalyst. The acylated catalyst remains as the predominant species until the
reaction nears completion and the catalyst reverts to its original unacylated
state. The system displays zero order kinetics with respect to the p-nitrophenyl
methoxyacetate throughout the majority of the reaction, suggesting a rate-limiting
deacylation of a steady state concentration of the acyl-catalyst intermediate.
The reaction is first order in catalyst, as expected. We are confident that
the dominant catalytic pathway proceeds via acylation-deacylation of the catalyst
oxygen.
William F. Wood
Department of Chemistry; Humboldt State University
Todd M. Palmer
Department of Environmental Horticulture; University of CaliforniaDavis;
Davis, California 95616
Maureen L. Stanton
Section of Evolution and Ecology; Division of Biological Sciences;
University of CaliforniaDavis; Davis, California 95616
Gas chromatographicmass spectral (GCMS) analyses of dichloromethane extracts of the mandibular glands from three coexisting Crematogaster species, C. mimosae, C. nigriceps, and C. sjostedti, showed distinct differences in the 28 volatile compounds that were identified. The variations of gland components in these ant species may facilitate species identification and lead to species-specific alarm and defense responses that influence their competitive interactions. The compounds 3-Hexanol, 3-methylbutanoic acid, 2-methylbutanoic acid, 3-octanone, 3-octanol, phenylacetaldehyde, 2-phenylpropenal, and 3-decanone were found in all three species. The mandibular glands of C. nigriceps contain seven compounds not detected in the two other species: 3-methyl-2-pentanone, 3-methyl-2-pentanol, and 3- and 2-methylheptanoic acid. The mandibular gland secretion of C. sjostedti also contains seven compounds not detected in the other two species: butanoic acid, 3-heptanol, 2-methylpentanoic acid, glycerol, 6-methyl-3-octanol, 2-pyrrolidinone and 3-nonanol. Nonanal was the only compound detected solely in extracts of C. mimosae.
2-Pyrrolidinone, a Putative Alerting Pheromone
in Pronghorn Rump GlandsWilliam F. Wood and James T. Welsh
Departments of Chemistry and Biological Sciences; Humboldt State University
When alarmed, the pronghorn (Antilocapra americana) erect the hair
on their rump glands and release an odor reminiscent of buttered popcorn.
This odor has frequently been observed by humans 20 to 30 meters downwind.
Because this scent is only released by alarmed animals, it has been long been
suggested that this scent functions as an alerting or alarm pheromone. Gas
chromatographic-mass spectral (GCMS) analyses were done on dichloromethane
extracts of the rump gland secretion. They showed one major and four
minor components that were not found in extracts of a non-glandular control
sample. The major compound, 2-pyrrolidinone and the minor compounds, 3-pyrrolin-2-one,
4-pyrrolin-2-one, succinimide, and 2-piperidone were identified by comparison
with authentic samples. Of the five compounds, only 2-pyrrolidinone had a
popcorn-like odor. Further behavioral studies are needed for confirmation
that any of these compounds act as an alarm pheromone for pronghorn.
last modified 09/08/2008
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