22 research outputs found
The Gallery 2011
This is a digital copy of the print content produced by the Gallery 2011 team. The Gallery 2011 consists of a box containing a leaflet, four books, and a USB drive. The leaflet lists the works contained on the USB drive in the areas of Time Based Media and Web Design, and provides credits for the Gallery design production team. Content from the USB drive is not included.
The four books contain the artistic works of students in the following genres: Core Studio/Painting, Graphic Design/Illustration, Photography/Printmaking, and Jewelry & Metals/Three Dimensional. Files for individual sections may be viewed on the detailed metadata page by clicking on the book title.https://rdw.rowan.edu/the_gallery/1005/thumbnail.jp
Analysis of Hypoxia and Hypoxia-Like States through Metabolite Profiling
In diverse organisms, adaptation to low oxygen (hypoxia) is mediated through complex gene expression changes that can, in part, be mimicked by exposure to metals such as cobalt. Although much is known about the transcriptional response to hypoxia and cobalt, little is known about the all-important cell metabolism effects that trigger these responses.Herein we use a low molecular weight metabolome profiling approach to identify classes of metabolites in yeast cells that are altered as a consequence of hypoxia or cobalt exposures. Key findings on metabolites were followed-up by measuring expression of relevant proteins and enzyme activities. We find that both hypoxia and cobalt result in a loss of essential sterols and unsaturated fatty acids, but the basis for these changes are disparate. While hypoxia can affect a variety of enzymatic steps requiring oxygen and heme, cobalt specifically interferes with diiron-oxo enzymatic steps for sterol synthesis and fatty acid desaturation. In addition to diiron-oxo enzymes, cobalt but not hypoxia results in loss of labile 4Fe-4S dehydratases in the mitochondria, but has no effect on homologous 4Fe-4S dehydratases in the cytosol. Most striking, hypoxia but not cobalt affected cellular pools of amino acids. Amino acids such as aromatics were elevated whereas leucine and methionine, essential to the strain used here, dramatically decreased due to hypoxia induced down-regulation of amino acid permeases.These studies underscore the notion that cobalt targets a specific class of iron proteins and provide the first evidence for hypoxia effects on amino acid regulation. This research illustrates the power of metabolite profiling for uncovering new adaptations to environmental stress
The Science Performance of JWST as Characterized in Commissioning
This paper characterizes the actual science performance of the James Webb
Space Telescope (JWST), as determined from the six month commissioning period.
We summarize the performance of the spacecraft, telescope, science instruments,
and ground system, with an emphasis on differences from pre-launch
expectations. Commissioning has made clear that JWST is fully capable of
achieving the discoveries for which it was built. Moreover, almost across the
board, the science performance of JWST is better than expected; in most cases,
JWST will go deeper faster than expected. The telescope and instrument suite
have demonstrated the sensitivity, stability, image quality, and spectral range
that are necessary to transform our understanding of the cosmos through
observations spanning from near-earth asteroids to the most distant galaxies.Comment: 5th version as accepted to PASP; 31 pages, 18 figures;
https://iopscience.iop.org/article/10.1088/1538-3873/acb29
The James Webb Space Telescope Mission
Twenty-six years ago a small committee report, building on earlier studies,
expounded a compelling and poetic vision for the future of astronomy, calling
for an infrared-optimized space telescope with an aperture of at least .
With the support of their governments in the US, Europe, and Canada, 20,000
people realized that vision as the James Webb Space Telescope. A
generation of astronomers will celebrate their accomplishments for the life of
the mission, potentially as long as 20 years, and beyond. This report and the
scientific discoveries that follow are extended thank-you notes to the 20,000
team members. The telescope is working perfectly, with much better image
quality than expected. In this and accompanying papers, we give a brief
history, describe the observatory, outline its objectives and current observing
program, and discuss the inventions and people who made it possible. We cite
detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space
Telescope Overview, 29 pages, 4 figure
A Double Decarboxylation in Superfolder Green Fluorescent Protein Leads to High Contrast Photoactivation
A photoactivatable
variant of superfolder green fluorescent protein
(GFP) was created by replacing the threonine at position 203 with
aspartic acid. Photoactivation by exposure of this mutant to UV light
resulted in conversion of the fluorophore from the neutral to the
negatively charged form, accompanied by a ∼95-fold increase
in fluorescence under 488 nm excitation. Mass spectrometry before
and after exposure to UV light revealed a change in mass of 88 Da,
attributed to the double decarboxylation of Glu 222 and Asp 203. Kinetics
studies and nonlinear power-dependence of the initial rate of photoconversion
indicated that the double decarboxylation occurred via a multiphoton
absorption process at 254 nm. In addition to providing a photoactivatable
GFP with robust folding properties, a detailed mechanistic understanding
of this double decarboxylation in GFP will lead to a better understanding
of charge transfer in fluorescent proteins
Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding
There is growing interest in using
the nitrile vibrational oscillation
as a site-specific probe of local environment to study dynamics, folding,
and electrostatics in biological molecules such as proteins. Nitrile
probes have been used extensively as reporters of electric field using
vibrational Stark effect spectroscopy. However, the analysis of frequencies
in terms of electric fields is potentially complicated by the large
ground state dipole moment of the nitrile, which may irrevocably perturb
the protein under investigation, and the ability of nitriles to accept
hydrogen bonds, which causes frequency shifts that are not described
by the Stark effect. The consequence of this is that vibrational spectroscopy
of nitriles in biomolecules could be predominately sensitive to their
local hydration status, not electrostatic environment, and have the
potential to be particularly destabilizing to the protein. Here, we
introduce green fluorescent protein (GFP) as a model system for addressing
these concerns using biosynthetically incorporated <i>p</i>-cyanophenylalanine (pCNF) residues in the interior of GFP and measuring
absorption energies of both the intrinsic GFP fluorophore and <i>p</i>CNF residues in response to a series of amino acid mutations.
We show that observed changes in emission energy of GFP due to the
mutations strongly correlate with changes in electric field experienced
by both the nitrile probes and the intrinsic fluorophore. Additionally,
we show that changes in electric field measured from the intrinsic
fluorophore due to amino acid mutations are unperturbed by the addition
of <i>p</i>CNF residues inserted nearby. Finally, we show
that changes in electric field experienced by the vibrational probes
trend monotonically with changes in field experienced by the native
fluorophore even though the nitrile probe is engaged in moderate hydrogen
bonding to nearby water molecules, indicated by the temperature dependence
of the nitrile’s absorption energy. Together these results
demonstrate that even in the presence of hydrogen bonding it is possible
to relate nitrile absorption frequencies to electrostatic environment
by comparing highly similar environments. GFP’s intrinsic linear
sensitivity to electric fields makes it a convenient model system
for studying electrostatics in proteins that offers lessons for proteins
without this visible fluorophore
Quantifying the Effects of Hydrogen Bonding on Nitrile Frequencies in GFP: Beyond Solvent Exposure
Vibrational
spectroscopy is a powerful tool for characterizing
the complex noncovalent interactions that arise in biological systems.
The nitrile stretching frequency has proven to be a particularly convenient
biological probe, but the interpretation of nitrile spectroscopy is
complicated by its sensitivity to local hydrogen bonding interactions.
This often inhibits the straightforward interpretation of nitrile
spectra by requiring knowledge of the molecular-level details of the
local environment surrounding the probe. While the effect of hydrogen
bonds on nitrile frequencies has been well-documented for small molecules
in solution, there have been relatively few studies of these effects
in a complex protein system. To address this, we introduced a nitrile
probe at nine locations throughout green fluorescent protein (GFP)
and compared the mean vibrational frequency of each probe to the specific
hydrogen bonding geometries observed in molecular dynamics (MD) simulations.
We show that a continuum of hydrogen bonding angles is found depending
on the particular location of each nitrile, and that the differences
in these angles account for the differences in the measured nitrile
frequency. We further observed that the temperature dependence of
the nitrile frequencies (measured as a frequency–temperature
line slope, FTLS) was a good indicator of the hydrogen bonding interactions
of the probe, even in scenarios where the nitrile was involved in
complex and restricted hydrogen bonds, both from protein and from
water. While constant offsets to the nitrile frequency to all hydrogen
bonding environments have been applied before to interpret shifts
in nitrile frequency, we show that this is insufficient in systems
where the hydrogen bonds may be restricted by the surrounding medium.
However, the strength of the observed correlation between nitrile
frequency and hydrogen bonding angle suggests that it may be possible
to disentangle electrostatic effects and effects of the orientation
of hydrogen bonding on the nitrile stretching frequency. Meanwhile,
the experimental measurement of the FTLS of the nitrile is an excellent
tool to identify changes in the hydrogen bonding interactions for
a particular probe
Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and p<i>K</i><sub>a</sub> Shifts Provide a Unique Benchmark for Electrostatics Models
Measurement
of the magnitude, direction, and functional importance
of electric fields in biomolecules has been a long-standing experimental
challenge. p<i>K</i><sub>a</sub> shifts of titratable residues
have been the most widely implemented measurements of the local electrostatic
environment around the labile proton, and experimental data sets of
p<i>K</i><sub>a</sub> shifts in a variety of systems have
been used to test and refine computational prediction capabilities
of protein electrostatic fields. A more direct and increasingly popular
technique to measure electric fields in proteins is Stark effect spectroscopy,
where the change in absorption energy of a chromophore relative to
a reference state is related to the change in electric field felt
by the chromophore. While there are merits to both of these methods
and they are both reporters of local electrostatic environment, they
are fundamentally different measurements, and to our knowledge there
has been no direct comparison of these two approaches in a single
protein. We have recently demonstrated that green fluorescent protein
(GFP) is an ideal model system for measuring changes in electric fields
in a protein interior caused by amino acid mutations using both electronic
and vibrational Stark effect chromophores. Here we report the changes
in p<i>K</i><sub>a</sub> of the GFP fluorophore in response
to the same mutations and show that they are in excellent agreement
with Stark effect measurements. This agreement in the results of orthogonal
experiments reinforces our confidence in the experimental results
of both Stark effect and p<i>K</i><sub>a</sub> measurements
and provides an excellent target data set to benchmark diverse protein
electrostatics calculations. We used this experimental data set to
test the p<i>K</i><sub>a</sub> prediction ability of the
adaptive Poisson–Boltzmann solver (APBS) and found that a simple
continuum dielectric model of the GFP interior is insufficient to
accurately capture the measured p<i>K</i><sub>a</sub> and
Stark effect shifts. We discuss some of the limitations of this continuum-based
model in this system and offer this experimentally self-consistent
data set as a target benchmark for electrostatics models, which could
allow for a more rigorous test of p<i>K</i><sub>a</sub> prediction
techniques due to the unique environment of the water-filled GFP barrel
compared to traditional globular proteins
Design, prototyping, and evaluation of a collapsible device for single-operator sheathing of ultrasound probes
During interventional ultrasound-guided procedures, sterility is maintained by covering the transducer head and cord with a sterile sheath. The current sheathing technique is cumbersome, requires an assistant to complete, and poses a risk of tangling the probe cord and breaching the sterile barrier. This paper presents the design, proof-of-concept prototyping, and evaluation of a probe holder and cartridge-style, single-use applicator that enables faster, more reliable, single-user sheathing of ultrasound probes, with a decreased risk of compromising sterility.Center for Integration of Medicine and Innovative Technology (US Army Medical Research Acquisition Activity Agreement W81XWH-09-2-0001
A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase
Transcarbamylases catalyze the transfer of the carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate such as aspartate, ornithine, or putrescine. Previously, structural determination of a transcarbamylase from Xanthomonas campestris led to the discovery of a novel N-acetylornithine transcarbamylase (AOTCase) that catalyzes the carbamylation of N-acetylornithine. Recently, a novel N-succinylornithine transcarbamylase (SOTCase) from Bacteroides fragilis was identified. Structural comparisons of AOTCase from X. campestris and SOTCase from B. fragilis revealed that residue Glu92 (X. campestris numbering) plays a critical role in distinguishing AOTCase from SOTCase. Enzymatic assays of E92P, E92S, E92V, and E92A mutants of AOTCase demonstrate that each of these mutations converts the AOTCase to an SOTCase. Similarly, the P90E mutation in B. fragilis SOTCase (equivalent to E92 in X. campestris AOTCase) converts the SOTCase to AOTCase. Hence, a single amino acid substitution is sufficient to swap the substrate specificities of AOTCase and SOTCase. X-ray crystal structures of these mutants in complexes with CP and N-acetyl-L-norvaline (an analog of N-acetyl-L-ornithine) or N-succinyl-L-norvaline (an analog of N-succinyl-L-ornithine) substantiate this conversion. In addition to Glu92 (X. campestris numbering), other residues such as Asn185 and Lys30 in AOTCase, which are involved in binding substrates through bridging water molecules, help to define the substrate specificity of AOTCase. These results provide the correct annotation (AOTCase or SOTCase) for a set of the transcarbamylase-like proteins that have been erroneously annotated as ornithine transcarbamylase (OTCase, EC 2.1.3.3)