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Showcase Marilyn Reed

Phenotyping tree architecture using proximal and remote sensing techniques

Phenotyping tree architecture using proximal and remote sensing techniques

Primary author: Chongyuan Zhang
Co-author(s): Juan José Quirós Vargas; Sara Serra; Stefano Musacch; Worasit Sangjan; Sindhuja Sankaran
Faculty sponsor: Dr. Sindhuja Sankaran

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Tree architecture optimizes the light interception and improves tree growth, fruit quality, and yield with the goal of simplify orchard management and harvest. However, currently tree architectural traits are measured manually by researchers or growers. In this study, both proximal and remote sensing techniques were evaluated to phenotype critical architectural traits with the final goal to assist tree fruit breeders, physiologists and growers in collecting architectural traits easily and efficiently. A red-green-blue (RGB) camera was used to collect proximal side-images of apple tree, while an unmanned aerial system integrated with RGB camera was programmed to image tree canopy at 15 m above ground level. The data were processed to extract architectural features from 2D images (proximal) and 3D digital surface model (remote sensing). The sensing data were compared to ground reference data that have three training systems (Spindle, V-trellis, Bi-axis), two rootstocks (‘WA38’ trees grafted on G41 and M9-Nic29) and two pruning methods (Bending and Click). The results from proximal sensing indicated that there was a significant (P < 0.0001) difference in box-counting fractal dimension (DBs) between Spindle and V-trellis training systems, and correlations between DBs with tree height (r = 0.78) and total yield per unit area in Mton/hectare (r = 0.70) was significant (P < 0.05). Moreover, correlations between average or total tree row volume and ground reference data, such as trunk area, total fruit yield per tree, were significant (P < 0.05). This study demonstrated the potential of sensing or phenotyping techniques in detecting tree architectural traits.

Development of Simplified Soil Microbial Consortia and Activity-Based Probes to Characterize the Activity of Chitin Degrading Enzymes

Development of Simplified Soil Microbial Consortia and Activity-Based Probes to Characterize the Activity of Chitin Degrading Enzymes

Primary author: Elias Zegeye
Faculty sponsor: Dr. Aaron Wright

Primary college/unit: Voiland College of Engineering and Architecture
Campus: Pacific Northwest National Laboratory (PNNL)

Abstract:

We investigated the succession, selectivity and dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer in a soil matrix and liquid environment. We hypothesized that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant consortia over time. We found that the lower initial richness stabilizes rapidly, and the resulting community composition differed greatly in soil than liquid medium. The reduced and stable consortia found in this study will aid in the discovery of functionally active chitin-degrading microbes using Activity-Based Probes (ABP). Chitin-derived ABPs (i.e. N-acetyl glucosamine and chitotriose) were developed including 1) a moiety that will covalently label an enzyme upon glycosidic bond hydrolysis, and 2) a chemical handle for isolation of labeled enzymes. The ABPs were first tested on a sample harvested from Cellvibrio japonicus, a soil bacterium with well-characterized chitinolytic enzyme machinery, that have grown on different carbon sources. As a result, the ABPs showed the induction and activities of the chitinase enzyme depend on the carbon sources and the time course of bacterial growth. Additionally, the application of this small chemical probe will be extended to identify and measure the activity of chitinase enzymes in simplified soil consortia. Generally, ABPs can be used to broaden our functional understanding of chitin breakdown and to characterize the soil consortia’s metabolic potential for chitin degradation.

A study of thermal crosslinking hydrogel with coaxial needle for manufacturing tubular shape structure

A study of thermal crosslinking hydrogel with coaxial needle for manufacturing tubular shape structure

Primary author: Ilhan Yu
Co-author(s): Luiz Longo
Faculty sponsor: Chen, Roland

Primary college/unit: Voiland College of Engineering and Architecture
Campus: Pullman

Abstract:

Extrusion using a coaxial needle to create tubular shapes has become a popular method in tissue engineering and drug delivery. Chemical crosslinking hydrogels were the most popular materials used to manufacture tubular shapes with coaxial needles, but because of fast gelation times, non-uniform gelation, and low strength and toughness have been pointed out as drawbacks. Thus, in this study, we investigated the feasibility of using a thermal crosslinking hydrogel with coaxial needle to get the tubular shape. Gellan Gum (GG), a thermal crosslinking material, was used and extruded via the outer needle. Phosphate-buffered saline (PBS) was extruded through the inner needle. First, we analyzed the delay and response time of the system due to heat exchange of the two fluids computationally. Second, we determined the hydrogel extrusion condition and its influence on the structural geometry of shapes structure both computationally and experimentally. Various flow rates of the inner needle and outer needle was tested, and the resulting wall thickness of the structure was measured. Results show that there is a delay of transition for thermal hydrogels due to the heat exchange between two fluids. The response time of system when the flow rate of PBS changes from steady state and how long does it takes to become steady state. In the second part of the experiment, we observed that it is possible to control the wall thickness of tubular shape by changing inner fluid with certain boundary.

Among the Remnants: Josh Gortler’s Journey, as told to Gigi Yellen

Among the Remnants: Josh Gortler’s Journey, as told to Gigi Yellen

Primary author: Gigi Yellen

Primary college/unit: Edward R. Murrow College of Communication
Campus: Pullman

Abstract:

The home page of the Edward R. Murrow College of Communication posts a link to “The Murrow Legacy.” That legacy includes Murrow’s own tribute to the WSU teacher who sparked his career: she “taught me to love good books, good music….”
My part-time staff position at Murrow College is that of classical music host on Northwest Public Broadcasting. Based at NWPB’s Lakewood studios, I do not often have the chance to engage in person with the college community, or, of course, with radio audiences.
In the other part of my time, I am the “as-told-to” coauthor on a memoir, Among the Remnants, to be published in 2020. The author is Dr. Joshua Gortler, honored by Washington State House Resolution 2019-4633 not only as a leader in the field of elder care but also as an educator/speaker about his European childhood during the era known as the Holocaust.
On the Edward R. Murrow page of its website, the US Holocaust Memorial Museum asks, “How does the media, in any form, impact public understanding and/or will to action?” At Murrow College, I aim for understanding: I encourage listeners to meet unknown people, across time and geography, through music.
If the legacy of WW2’s displaced persons is as yet unknown to many of my listeners, I hope to ease them into this knowledge, as they recognize on the cover of this book the familiar name of their evening radio host.

YAZZ Band: Fun Sized Edition

YAZZ Band: Fun Sized Edition

Primary author: Gregory Yasinitsky

Primary college/unit: Arts and Sciences
Campus: Pullman

Abstract:

Greg Yasinitsky, WSU Regents Professor of Music, received a 2019-2020 CAS Arts and Humanities Fellowship to produce a recording project of big band jazz for his ensemble YAZZ Band, composed by and featuring saxophone performances by Yasinitsky. The music is scored for “little big band,” a big band with the reduced instrumentation of four saxophones, two trumpets, trombone, piano, bass and drums. At this writing, five pieces have been composed, arranged, recorded and mixed and are essentially ready to be released. The recordings were made in the WSU Recording Studio and feature some of the finest musicians in the country. Two or three additional pieces will be orchestrated, recorded and mixed and when completed, the entire project will be released internationally streaming sites, including Spotify and Apple Music, and download sites including iTunes and Amazon. Physical compact discs will also be made available. The sheet music for all of the pieces will be published by Walrus Music, a top firm specializing in jazz. Yasinitsky’s big band music is performed in over forty countries around the world. His previous big band CD: YAZZ Band, was featured for fourteen weeks on national radio play lists and received numerous positive reviews around the world. YAZZ Band was named one of the top Big Band CDs of the year by BeBop Spoken Here in the United Kingdom. Because this new project is for a smaller ensemble, Yasinitsky’s new recording is called YAZZ Band: Fun Sized Edition.

Evaluation of ENSO Impact on Hydroclimatic Variability

Evaluation of ENSO Impact on Hydroclimatic Variability

Primary author: Chen Xu
Co-author(s): Mingliang Liu; Jennifer Adam; John Abatzoglou; Kirti Rajagopalan
Faculty sponsor: Jennifer Adam, Kirti Rajagopalan

Primary college/unit: Voiland College of Engineering and Architecture
Campus: Pullman

Abstract:

Superposed epoch analysis is performed to 1) quantify the effects of ENSO phase on the distribution of hydroclimatologic anomalies across the PNW, and 2) identify where these anomalies are statistically significant. Annual and seasonal precipitation and temperature anomalies are analyzed using gridded observations from the gridMET product, while runoff, evapotranspiration and soil moisture anomalies are obtained through VIC-CropSyst simulations (a coupled macroscale hydrologic and cropping system model). Results reveal strong precipitation anomalies over the mountainous regions, although not with a consistent sign for all mountain ranges. El Niño (La Niña) years are drier (wetter) than normal over the North Cascades, Bitterroots, and Northern Rockies; while the opposite effect is experienced by the Olympic Mountains. Outside of mountainous areas, precipitation anomalies are smaller and heterogeneous but with generally more (less) rainfall during El Niño (La Niña) years. Runoff, evapotranspiration and soil moisture anomalies are found to be generally consistent with the precipitation anomalies. There are, however, limited variables and areas with statistically significant anomalies, including El Niño precipitation and runoff in northern Idaho, and La Niña evapotranspiration in western Washington. Given that the skill of seasonal forecasts (with lead time of 1 to 7 months) has been associated with the ENSO signal, this study has the potential to provide insights in building institutional decision support capacity through a forecast system. It helps such a system prioritize meteorological, hydrological and agriculture relevant variables with sufficient forecast skill in a region-specific manner, and inform agricultural and water resources decisions in a meaningful way.

Occam’s Razor Cuts Out Low Mass Stars

Occam’s Razor Cuts Out Low Mass Stars

Primary author: Guy Worthey
Co-author(s): Xiang Shi; Islam Khan

Primary college/unit: Arts and Sciences
Campus: Pullman

Abstract:

A galaxy’s light is a composite of the various stars that make it up. Both giant stars and dwarf stars contribute to the total light output. The giants are cool, luminous, about one solar mass, and rare. The dwarfs are cool, faint, about 0.1 solar masses, and numerous. Most of the stellar mass of a galaxy is in these dwarf stars.

Some features in the red optical spectrum respond to dwarf/giant status in stars. Comparison of galaxy spectra to plausible mixtures of dwarf and giant light leads to the conclusion that the hugest galaxies have more dwarfs than galaxies like the Milky Way. The current picture is that these huge galaxies were formed from mergers of smaller galaxies. This leads to a paradox. If a huge galaxy is the sum of several smaller ones, why is the stellar content different?

We posit that the apparent enhancement in the number of dwarf stars in huge galaxies is an illusion. The increased heavy element content in huge galaxies causes in turn a decrease in the number of viable giant stars. The decrease in number of giants has been misinterpreted as an increase in the number of dwarfs. The trend we see in the spectrum is therefore naturally explained without generating new puzzles.

Cheating Detection in Tests: A Systematic Review

Cheating Detection in Tests: A Systematic Review

Primary author: Tarid Wongvorachan
Faculty aponsor: Chad Gotch

Primary college/unit: College of Education
Campus: Pullman

Abstract:

High-stakes testing is significant in education across the world. Unfortunately, widespread cheating undermines the interpretations and uses of test results. When test-takers cheat, other test-takers, testing programs, and test users can suffer substantial negative consequences. Educational measurement professionals have developed numerous cheating detection methods to counter these potential consequences, but to-date no research has undertaken a comprehensive inventory of the field. The purpose of this systematic review is to document current trends and identify needs for further research, in order to improve the security of high-stakes testing programs. From an exhaustive library database search, I selected 62 primary studies for the in-depth review. Each study was reviewed for both general (e.g., authorship) and specific level characteristics (e.g., application of empirical data and type-I error). This review produced 27 variables that were synthesized to portray characteristics of the field as a whole.

Examination of these variables showed that cheating detection methods are in an emerging stage. Future research needs to expand beyond the current focus on western countries, employ more real test data (vs. simulated), and use more varied data sets. The field also needs a single standard to assess proposed detection methods. Further, machine learning could be a viable addition to the predominant statistical approaches observed in the literature. Expansion of the research base in these directions could help strengthen the security of high-stake testing in education, and ultimately support valid interpretations and uses of test scores.

Trace element chracteristics of the Columbia River Basalts

Trace element chracteristics of the Columbia River Basalts

Primary author: John Wolff
Co-author(s): Arron Steiner

Primary college/unit: Agricultural, Human and Natural Resource Sciences
Campus: Pullman

Abstract:

Investigations in the Peter Hooper GeoAnalytical Laboratory (School of the Environment) are leading to a new and radical model for the origin of the Miocene (~16 million years ago) Columbia River flood basalts of the inland PNW. The flood basalts erupted from fissures mostly located in eastern WA and northeatern OR, and flowed westwards from there to create the Columbia and Oregon plateaux. The fissures were fed by magma-filled dikes at depth. Traditionally, these dikes were thought to directly tap sources of magma deep within Earth’s mantle. Our observations and geochemical analyses, especially of trace elements in the basalt lavas, point instead to a new interpretation where the dikes are feeding magma northwards from a volcanic hyper-system located around Vale, OR. This system extended 8 km depth down to the base of the crust and fed lava super-eruptions continuously and copiously for about 700,000 years. Towards the end of that time, activity gradually shifted to even more deadly explosive rhyolitic super-eruptions such as produced the Mascall tephra, which we have identified as far away as New Mexico. After a further 1 million years, volcanism reverted to basaltic to produce the youngest Columbia River lavas. These later lavas have unusual trace element features that suggest the new magmas re-occupied the old hyper-system, melting and re-cycling it. Our poster presents the evidence for (1) a centralized source for basalt magma, (2) its depth range, (3) switching between basaltic and explosive rhyolitic volcanism, and (4) rejuvenation of the system.

Naturally derived peptides enhance killing efficiency of colistin against colistin-resistant bacteria

Naturally derived peptides enhance killing efficiency of colistin against colistin-resistant bacteria

Primary author: Kaitlin Witherell
Faculty sponsor: Dr. Douglas Call

Primary college/unit: College of Veterinary Medicine
Campus: Pullman

Abstract:

Colistin is a “last-line” antibiotic that is used to treat multidrug-resistant, Gram-negative bacteria, but colistin resistance has emerged. In susceptible bacteria, colistin binds lipid A and destroys the bacterial membrane. MCR (encoded by mcr-1 and others) is a phosphoethanolamine transferase that modifies lipid A resulting in decreased affinity for colistin. We are investigating two cysteine-dense peptides (CDPs), “B03” and “B11” that appear to kill bacteria by interacting with the bacterial membrane. We propose that using CDPs in combination with colistin we can kill colistin- and multidrug-resistant bacteria at lower concentrations and more quickly compared to colistin alone. We have shown B03 and B11 are able to reduce the colistin resistance profile of mcr-1 harboring and multidrug-resistant Escherichia coli AR Bank #0346. By adding 100 µg/ml of peptide B03 we are able to significantly reduce the minimum inhibitory concentration (MIC) of colistin from 1.25 µg/ml to 0.063 µg/ml. When 50 µg/ml of peptide B11 is added the MIC of colistin is reduced to less than 0.0005 µg/ml. We also found that by adding either peptide, 346 is killed faster and at lower concentrations compared to using colistin alone. We are determining the mechanism of action of these peptides by performing membrane potential assays and employing scanning electron microscopy.