523 Works

Fuels and Materials from Sunlight and Water

Bryan Michael Hunter
The urgency to develop new technologies that harness energy and natural feedstocks in a sustainable fashion has never been more apparent. With global power consumption growing at an exponential rate, only one resource is truly capable of powering the planet: the sun. Sunlight is reliable, clean, and free. Significant resources have been pledged to develop and refine solar energy devices that convert photons into electricity (i.e. photovoltaics), but the sun’s intermittency and the poor overlap...

Localization of tbg-1 mRNAs and GFP::TBG-1 protein in Early C. elegans Embryos

Lauren DeMeyer & Mi Hye Song
tbg-1 encodes gamma-tubulin, a ubiquitous and highly conserved component of centrosomes in eukaryotic cells (Strome et al, 2001). Using smFISH we determined the localization of tbg-1 transcripts (red). tbg-1 transcripts are detected within distinct foci throughout the cytoplasm during both the first (A) and second (B) mitosis. tbg-1 transcripts are not enriched at centrosomes or either blastomere. In contrast, GFP tagged TBG-1 proteins (green signal; arrowheads) localize at centrosomes, as previously shown (Strome et al,...

Reduced pharyngeal pumping rates observed in tph-1 mutants using microfluidic electropharyngeogram (EPG) recordings

Terra Hiebert, Adela Chicas-Cruz & Kathryn McCormick
In Caenorhabditis elegans, serotonin (5-HT) activates and controls pharyngeal pumping in response to food (Horvitz et al., 1982; Sze et al., 2000; Song and Avery 2012). Tryptophan hydroxylase, the enzyme required for serotonin biosynthesis, is encoded by the gene tph-1. Worms with a tph-1 deletion mutation exhibit phenotypes associated with a lack of serotonin-signaling, including reduced pharyngeal pumping (Sze et al., 2000; Avery and Horvitz 1990; Song and Avery 2012). We used a microfluidic electropharyngeogram...

Basal pharyngeal pumping elevated in C. elegans mod-5 mutants

Terra Hiebert, Adela Chicas-Cruz & Kathryn McCormick
In C. elegans, the reuptake of serotonin (5-HT) is facilitated by mod-5, which encodes a 5-HT transporter that is orthologous to a human 5-HT transporter (SLC6A4). mod-5 has been shown to effect both feeding and locomotion in C. elegans (Ranganathan et al., 2001; Jafarau et al. 2011). We obtained and analyzed EPG data using a microfluidic device (NemaMetrix) for mod-5 null mutant strains, mod-5(n3314) (A, Exp 1 n=15; Exp 2 n=32) and mod-5(n822), (B, Exp...

Spectral Exterior Calculus and Its Implementation

Dzhelil Sabahatin Rufat
Preserving geometric, topological and algebraic structures at play in partial differential equations has proven to be a fruitful guiding principle for computational methods in a variety of scientific fields. However, structure-preserving numerical methods have traditionally used spaces of piecewise polynomial basis functions with local support to interpolate differential forms. When solutions are known to be smooth, a spectral treatment is often preferred instead as it brings exponential convergence. While recent works have established spectral variants...

Novel deletion alleles of a C. elegans gene C38D4.9, named as tm4476 and tm4561

Sawako Yoshina, Sayaka Hori, Yuji Suehiro & Shohei Mitani
We report tm4476 and tm4561 as novel alleles of C38D4.9 gene that is an ortholog of human METTL5 (methyltransferase like 5)1. Human METTL5 function has not been reported. The alleles were isolated from the comprehensive screening of gene deletions generated by TMP/UV2. In the screening, both the alleles were detected by nested PCR using the following primer sets, 5’-CCGCCTATATCATGGCGCTT-3’ and 5’-GCTGGTAGTTGCCACCGCAT-3’ for first round PCR and 5’-ACTATCGAAGCCGCGCTTCA-3’ and 5’-AACCCCAACTCCGTCCCATT-3’ for second round PCR. By Sanger...

Prototyping Diverse Synthetic Biological Circuits in a Cell-Free Transcription-Translation System

Shaobin Guo
Synthetic biological circuits are the foundation for the ultimate goals of controlling cells and building artificial cells from the ground up. To get closer to these goals in a more efficient way, we utilize a cell-free transcription-translation system to help perfect biological circuits for the simplicity, freedom, and convenience that the system offers. In this thesis, we demonstrate three distinct aspects of biological circuits in a cell-free transcription-translation system: circuit dynamics, phosphorylation, and membrane proteins....

daf-2 modulates regeneration of mechanosensory neurons II

Zehra C Abay, Michelle Yu-Ying Wong & Brent Neumann
The daf-2 gene encodes an insulin-like growth factor/IGF-1 receptor that regulates C. elegans embryonic and larval development. It has previously been shown that DAF-2 inhibits neurite regeneration of the GABAergic motor neurons and PVD sensory neurons in an age-dependent fashion (Bryne et al., 2014; Kravtsov et al., 2017). Following injury, the posterior lateral microtubule (PLM) neurons are capable of regenerating through axonal fusion, a highly efficient regrowth mechanism in which separated fragments fuse back together...

A quantitative trait locus for nictation behavior on chromosome V

Jun Kim, Daehan Lee & Junho Lee
Lee et al., 2017 showed that CB4856 has a lower nictation ratio (the number of nictating dauers over the number of moving dauers on a micro-dirt chip) than N2, and that a genetic locus (nict-1) on chromosome IV mediates this phenotype difference. Although this paper had no evidence of any other genetic loci for nictation behavior, we have studied other quantitative trait loci (QTL) using different linkage-based mapping strategies. Here, we report another genetic locus...

Coherent Structures, their Interactions, and their Effects on Passive Scalar Transport and Aero-optic Distortion in a Turbulent Boundary Layer

Theresa Ann Saxton-Fox
This thesis focused on the characterization of coherent structures and their interactions in a turbulent boundary layer using data from particle image velocimetry (PIV) measurements performed at Caltech and from a direct numerical simulation (DNS) of Wu et al. (2017). Connections were identified between instantaneous and statistical descriptions of coherent velocity structures, through the analysis of representative models for their structures derived from the resolvent analysis of McKeon and Sharma (2010). The representative models were...

Discovery and Development of Small-Molecule Modulators for the Sulfation of Glycosaminoglycans and Studying the Role of O-GlcNAc on CREB through Semisynthesis

Sheldon Ting Fong Cheung
Glycosaminoglycans (GAGs) are sulfated polysaccharides that play key roles in many cellular processes, ranging from viral invasion and cancer metastasis to neuronal development. Their diverse biological activities stem from their complex sulfation patterns, which are tightly regulated in vivo. For instance, the GAG chondroitin sulfate (CS) has been shown to undergo regiochemical sulfation during development and after spinal cord injury. However, few tools exist to modulate specific GAG sulfation patterns and study their importance in...

Egospace Motion Planning Representations for Micro Air Vehicles

Anthony Thomas Fragoso
Navigation of micro air vehicles (MAVs) in unknown environments is a complex sensing and trajectory generation task, particularly at high velocities. In this work, we introduce an efficient sense-and-avoid pipeline that compactly represents range measurements from multiple sensors, trajectory generation, and motion planning in a 2.5–dimensional projective data structure called an egospace representation. Egospace coordinates generalize depth image obstacle representations and are a particularly convenient choice for configuration flat mobile robots, which are differentially flat...

nu444 is a novel allele of pkc-1 in C. elegans

Han Wang & Derek Sieburth
Here, we report nu444 as a novel allele of the gene pkc-1 that encodes the protein kinase C-1 in C. elegans. The nu444 allele was originally isolated from a forward genetic screen for mutants that suppressed the “Hic” (Hypersensitivity to Inhibitors of Cholinesterase) phenotype of dgk-1(nu62) mutants, which had increased acetylcholine release at the neuromuscular junction (Sieburth et al., 2007). In this screen, several genes that are important for neuropeptide secretion were recovered, including pkc-1(nu448)...

Screening for C. elegans male copulation-defective mutants by the mating plug phenotype

Katharine Liu, Yvonne Hajdu-Cronin, Ann Chen, Gary Schindelman, Allyson Whittaker, Shahla Gharib & Paul W. Sternberg
We describe an efficient screen for male mating defective mutants in Caenorhabditis elegans. We report the isolation of 20 alleles that confer specific mating defects. In a previously reported screen (Hajdu-Cronin et al, 2017), we isolated 19 Cod (for copulation defective) strains in which morphologically wild-type males fail to mate. Failure to mate could conceivably result from defects in any step of the mating process: response, turning, vulva location, spicule insertion, and sperm transfer. By...

SPAS-1 expression in neurons and vulva during L4 stage

George Brown & Rachid El Bejjani
spas-1 is the worm homolog of the human spastic paraplegia gene, spastin. Previous work in C. elegans has shown that SPAS-1 disassembles microtubules in an ATP-dependent manner (Matsushita-Ishiodori et al, 2007). Another study shows that SPAS-1 plays a role in synapse remodeling in motor neurons (Kurup et al, 2015). Here we describe the expression of SPAS-1 in L4 hermaphrodite larvae using the transcriptional reporter, axrEx8 [Pspas-1:mCh]: A) Low magnification (10X objective) image of an entire...

sy680 is a novel allele of pkd-2

Allyson Whittaker, Gary Schindelman, Shahla Gharib & Paul W. Sternberg
A new allele of pkd-2 was isolated in a behavioral genetic screen for male mating defects, and found to result in a substitution of Arginine for Glycine in the equivalent of human PKD2 alanine 615. The C. elegans ortholog of polcystin-2 is encoded by pkd-2 (Barr et al., 2001). From an EMS screen of a plg-1; him-5 strain for male mating defective mutants and a secondary behavioral screen for defects in discrete steps of male...

Cell-Selective Chemoproteomics for Biological Discovery

Shannon Elizabeth Stone
Cellular protein synthesis changes rapidly in response to internal and external cues in ways that vary from cell to cell. Global proteomic analyses of microbial communities, tissues, and organisms have provided important insights into the behavior of such systems, but can obscure the diversity of responses characteristic of different cellular subpopulations. Recent advances in cell-specific proteomics—fueled in part by the development of bioorthogonal chemistries, more sensitive mass spectrometers and more advanced mining algorithms—have yielded unprecedented...

New Techniques for Noble Gas Geochronometry and Thermochronometry

Stephen Ellis Cox
Noble gases were among the first species measured by mass spectrometry and interrogated for geochemical information about the solid Earth. The analytical challenge of measuring them has driven technological development in the field, and new applications have in turn followed from new developments. In the first chapter, I present developments that bolster an existing technique, the (U–Th)/Ne system, by verifying the theoretical underpinnings of the method and by exploring its application in several minerals. In...

Hydrodynamics of Insects. Part 1. Jetting of the Dragonfly Larvae. Part 2. Honeybee at the Air-water Interface: Surfing with the Capillary Wave

Chris Roh
This thesis presents the study on the hydrodynamics of two insects commonly known for their aerial adaptation: the dragonfly and the honeybee. Part 1: Anisopteran dragonflies live underwater in their larval stages. The key factor for their aquatic adaptation is the modified hindgut chamber that is used as a pump. The two main functions of this biological pump are jet propulsion and respiration. Both functions involve jetting and refilling of the chamber through an orifice...

Glacial Ocean Dynamics: Insight from Deep-Sea Coral Reconstructions and A Time-Dependent Dynamical Box Model

Sophia Katharine Vizza Hines
Glacial-interglacial cycles, occurring at a period of approximately 100,000 years, have dominated Earth's climate over the past 800,000 years. These cycles involve major changes in land ice, global sea level, ocean circulation, and the carbon cycle. While it is generally agreed that the ultimate driver of global climate is changes in insolation, glacial cycles do not look like insolation forcing. Notably, there is a highly non-linear warming response at 100,000 years to a relatively small...

daf-2 regeneration of mechanosensory neurons: integration

Zehra C Abay, Michelle Yu-Ying Wong & Brent Neumann
We previously established that a critical event for axonal fusion to occur is the exposure of PS ‘save-me’ signals after injury (Neumann et al., 2015), which increase with advancing age (Abay et al., 2017a). To determine if daf-2 is involved in this age-dependent modulation of PS exposure, we visualised and quantified the level of PS exposed after PLM axotomy using a secreted, tagged version of Annexin V (Neumann et al., 2015; Mapes et al., 2012)....

Copulation defective mutants of C. elegans

Yvonne M. Hajdu-Cronin, Katharine S. Liu, Leslie Barber, Helen M. Chamberlin, William Boorstein & Paul W. Sternberg
​Description To identify genes involved in male copulatory behavior, we carried out an F2 clonal screen in a him-5 mutant background. We identified 20 mutations that affect male mating behavior without causing gross defects in morphology. ​ Male mating in C. elegans comprises at least five steps (Liu and Sternberg, 1995). (l) The male responds to the hermaphrodite by backing his tail along the length of the hermaphrodite, (2) he turns over or under her...

Insights on the Formation and Fate of Organic Nitrates in the Atmosphere from Field and Laboratory Observations

Alexander Pai-Chung Teng
Alkenes are oxidized rapidly in the atmosphere by addition of OH and subsequently O2, leading to the formation of peroxy radicals. These peroxy radicals react with NO to form organic nitrates through a minor radical-terminating branching pathway. Over large regions of the continental boundary layer, the formation of organic nitrates control tropospheric ozone and the lifetime of NOx. Laboratory investigations described herein show that the yield of nitrates through this pathway is larger than previously...

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