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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 18 March 2002