Regulation of the heat shock response by thiol-reactive compounds in the yeast Saccharomyces cerevisiae

Cells govern their activities and modulate their interactions with the environment to achieve homeostasis. The heat shock response (HSR) is one of the most well studied fundamental cellular responses to environmental and physiological challenges, resulting in rapid synthesis of heat shock proteins (HSPs), which serve to protect cellular constituents from the deleterious effects of stress. In addition to its role in cytoprotection, the HSR also influences lifespan and is associated with a variety of human diseases including cancer, aging and neurodegenerative disorders. In most eukaryotes, the HSR is primarily mediated by the highly conserved transcription factor HSF1, which recognizes target hsp genes by binding to heat shock elements (HSEs) in their promoters. In recent years, significant efforts have been made to identify small molecules as potential pharmacological activators of HSF1 that could be used for therapeutic benefit in the treatment of human diseases relevant to protein conformation. However, the detailed mechanisms through which these molecules drive HSR activation remain unclear. In this work, I utilized the baker's yeast Saccharomyces cerevisiae as a model system to identify a group of thiol-reactive molecules including oxidants, transition metals and metalloids, and electrophiles, as potent activators of yeast Hsf1. Using an artificial HSE-lacZ reporter and the glucocorticoid receptor system (GR), these diverse thiol-reactive compounds are shown to activate Hsf1 and inhibit Hsp90 chaperone complex activity in a reciprocal, dose-dependent manner. To further understand whether cells sense these reactive compounds through accumulation of unfolded proteins, the proline analog azetidine-2-carboxylic acid (AZC) and protein cross-linker dithiobis(succinimidyl propionate) (DSP) were used to force misfolding of nascent polypeptides and existing cytosolic proteins, respectively. Both unfolding reagents display kinetic HSP induction profiles dissimilar to those generated by thiol-reactive compounds. Moreover, AZC treatment leads to significant cytotoxicity, which is not observed in the presence of the thiol-reactive compounds at the concentrations sufficient to induce Hsf1. Additionally, DSP treatment has little to no effect on Hsp90 functions. Together with the ultracentrifugation analysis of cell lysates that detected no insoluble protein aggregates, my data suggest that at concentrations sufficient to induce Hsf1, thiol-reactive compounds do not induce the HSR via a mechanism based on accumulation of unfolded cytosolic proteins. Another possibility is that thiol-reactive compounds may influence aspects of the protein quality control system such as the ubiquitin-proteasome system (UPS). To address this hypothesis, β-galactosidase reporter fusions were used as model substrates to demonstrate that thiol-reactive compounds do not inhibit ubiquitin activating enzymes (E1) or proteasome activity. Therefore, thiol-reactive compounds do not activate the HSR by inhibiting UPS-dependent protein degradation. I therefore hypothesized that these molecules may directly inactivate protein chaperones, known as repressors of Hsf1. To address this possibility, a thiol-reactive biotin probe was used to demonstrate in vitro that the yeast cytosolic Hsp70 Ssa1, which partners with Hsp90 to repress Hsf1, is specifically modified. Strikingly, mutation of conserved cysteine residues in Ssa1 renders cells insensitive to Hsf1 activation by cadmium and celastrol but not by heat shock. Conversely, substitution with the sulfinic acid and steric bulk mimic aspartic acid led to constitutive activation of Hsf1. Cysteine 303, located in the nucleotide-binding/ATPase domain of Ssa1, was shown to be modified in vivo by a model organic electrophile using Click chemistry technology, verifying that Ssa1 is a direct target for thiol-reactive compounds through adduct formation. Consistently, cadmium pretreatment promoted cells thermotolerance, which is abolished in cells carrying SSA1 cysteine mutant alleles. Taken together, these findings demonstrate that Hsp70 acts as a sensor to induce the cytoprotective heat shock response in response to environmental or endogenously produced thiol-reactive molecules and can discriminate between two distinct environmental stressors.

Novel Imaging-Based Techniques Reveal a Role for PD-1/PD-L1 in Tumor Immune Surveillance in the Lung

The binding of immune inhibitory receptor Programmed Death 1 (PD-1) on T cells to its ligand PD-L1 has been implicated as a major contributor to tumor induced immune suppression. Clinical trials of PD-L1 blockade have proven effective in unleashing therapeutic anti-tumor immune responses in a subset of patients with advanced melanoma, yet current response rates are low for reasons that remain unclear. Hypothesizing that the PD-1/PD-L1 pathway regulates T cell surveillance within the tumor microenvironment, we employed intravital microscopy to investigate the in vivo impact of PD-L1 blocking antibody upon tumor-associated immune cell migration. However, current analytical methods of intravital dynamic microscopy data lack the ability to identify cellular targets of T cell interactions in vivo, a crucial means for discovering which interactions are modulated by therapeutic intervention. By developing novel imaging techniques that allowed us to better analyze tumor progression and T cell dynamics in the microenvironment; we were able to explore the impact of PD-L1 blockade upon the migratory properties of tumor-associated immune cells, including T cells and antigen presenting cells, in lung tumor progression. Our results demonstrate that early changes in tumor morphology may be indicative of responsiveness to anti-PD-L1 therapy. We show that immune cells in the tumor microenvironment as well as tumors themselves express PD-L1, but immune phenotype alone is not a predictive marker of effective anti-tumor responses. Through a novel method in which we quantify T cell interactions, we show that T cells are largely engaged in interactions with dendritic cells in the tumor microenvironment. Additionally, we show that during PD-L1 blockade, non-activated T cells are recruited in greater numbers into the tumor microenvironment and engage more preferentially with dendritic cells. We further show that during PD-L1 blockade, activated T cells engage in more confined, immune synapse-like interactions with dendritic cells, as opposed to more dynamic, kinapse-like interactions with dendritic cells when PD-L1 is free to bind its receptor. By advancing the contextual analysis of anti-tumor immune surveillance in vivo, this study implicates the interaction between T cells and tumor-associated dendritic cells as a possible modulator in targeting PD-L1 for anti-tumor immunotherapy.

Renal Cryoablation: Investigation of Periprocedural Visualization Tools and Treatment Response Quantification

Cryoablation for small renal tumors has demonstrated sufficient clinical efficacy over the past decade as a non-surgical nephron-sparing approach for treating renal masses for patients who are not surgical candidates. Minimally invasive percutaneous cryoablations have been performed with image guidance from CT, ultrasound, and MRI. During the MRI-guided cryoablation procedure, the interventional radiologist visually compares the iceball size on monitoring images with respect to the original tumor on separate planning images. The comparisons made during the monitoring step are time consuming, inefficient and sometimes lack the precision needed for decision making, requiring the radiologist to make further changes later in the procedure. This study sought to mitigate uncertainty in these visual comparisons by quantifying tissue response to cryoablation and providing visualization of the response during the procedure. Based on retrospective analysis of MR-guided cryoablation patient data, registration and segmentation algorithms were investigated and implemented for periprocedural visualization to deliver iceball position/size with respect to planning images registered within 3.3mm with at least 70% overlap and a quantitative logit model was developed to relate perfusion deficit in renal parenchyma visualized in verification images as a result of iceball size visualized in monitoring images. Through retrospective study of 20 patient cases, the relationship between likelihood of perfusion loss in renal parenchyma and distance within iceball was quantified and iteratively fit to a logit curve. Using the parameters from the logit fit, the margin for 95% perfusion loss likelihood was found to be 4.28 mm within the iceball. The observed margin corresponds well with the clinically accepted margin of 3-5mm within the iceball. In order to display the iceball position and perfusion loss likelihood to the radiologist, algorithms were implemented to create a fast segmentation and registration module which executed in under 2 minutes, within the clinically-relevant 3 minute monitoring period. Using 16 patient cases, the average Hausdorff distance was reduced from 10.1mm to 3.21 mm with average DSC increased from 46.6% to 82.6% before and after registration.

Characterization of the MLC box: A conserved {\it cis\/}-acting DNA element present in the chicken MLC1s/1c gene

The slow/cardiac alkali myosin light chain (MLC1s/1c) is a member of a multigene family whose protein products are essential for activation of the myosin ATPase. In the adult, the MLC1s/1c isoform is expressed in both cardiac and slow-twitch skeletal muscles, while it is expressed by all skeletal muscles during development.^ To elucidate the molecular mechanisms that underlie the transcriptional regulation of MLC1s/1c gene expression, the immediate 5$\sp\prime$ flanking region of the gene was isolated and shown to be capable of directing reporter gene expression. Analysis of this region revealed a 110 bp muscle-specific enhancer that includes a myocyte-specific enhancer-binding factor 2 (MEF-2) site, E-boxes, which are potential binding sites for the basic-helix-loop-helix proteins such as MyoD, and a MLC box. The focus of the thesis was to identify the role of the MLC box in expression of the MLC1s/1c gene.^ The MLC box is a member of the family of CArG box containing cis-acting DNA elements. Mutagenesis showed that the MLC box is necessary, but not sufficient, for the expression of a reporter gene linked to the 5$\sp\prime$ flanking region of the MLC1s/1c gene. Linker scanner and site-directed mutagenesis identified a number of potential sites within the 110 bp muscle-specific enhancer that may cooperate with the MLC box. These are the MEF-2 site, the E-box site, and a 10 bp element located upstream of the MEF-2 site that does not have sequence similarity with any known cis-acting element. The MLC box is capable of binding to factors present in muscle nuclear extracts, as well as to human recombinant serum response factor (SRF). Binding of SRF to the MLC box was correlated with the ability of the 5$\sp\prime$ flanking region of the MLC1s/1c gene to drive reporter gene expression. Results suggest a model in which binding of SRF to the MLC box activates expression of the MLC1s/1c gene while binding of the factors present in the nuclear extracts suppresses the expression of the gene. (Abstract shortened with permission of author.) ^

Northwest Iowa On-farm Research Soybean Yield Response to Headline Fungicide

Six years ago the Northwest Iowa On-Farm Research Project was started to cooperate with local farmers to compare crop production methods on a field scale size. Through this project, over 300 replicated comparisons have been done. Beginning in 2012, the Northwest Iowa On-Farm Research project will be recognized as a part of Iowa State University Farmer Assisted Research and Management (FARM) program. This program will also expand to southwest Iowa, north central Iowa, and central Iowa.

Soybean Response to Sulfur Fertilization

The objective of this trial was to investigate response of soybean to sulfur fertilization when grown on irrigated coarse sand soil with low organic matter.

Characterizing Overall Response to Two-shot Vaccination for BVDV Type 2 in Angus Weanling Calves

Vaccination is a management strategy utilized to help reduce prevalence of bovine respiratory disease in feedlots. However, not all animals respond similarly to vaccinations. It is believed that an animal’s genetics control part of the ability to respond to a vaccination protocol. In order to evaluate the genetic control of a new trait such as response to vaccination, it is important to understand the non-genetic factors that affect an animal’s response to vaccination. The objective of this study was to characterize the non-genetic factors affecting overall response to a two-shot vaccination for bovine viral diarrhea virus type 2 (BVDV2) in Angus weanling calves.

Yield Response of Planting Corn in Early April

Corn is planted earlier each year, which is one important component in maximizing grain yield. Earlier planting dates can be attributed to larger farms, less spring tillage, improvements in corn hybrids, improved drainage systems, and better seed treatments. Research conducted at the ISU Northwest Research Farm from 2006 through 2009 showed that the planting window for 98 percent or greater yield potential in northwest Iowa is April 15 to May 9. A 95 percent or greater yield potential can be realized from April 15 to May 18. A study was conducted from 2009 through 2011 at the Northwest Research Farm to determine how corn planted in early April compares with corn planted in the recommended planting window for the area.

Soybean Yield Response to Rhizobium Inoculation on Converted Grass Pasture

Much of the soybean plant's nitrogen requirement is supplied through nitrogen fixation when atmospheric nitrogen is converted into a usable form for the plant. Nitrogen fixation is critical for producing higher yield in soybean. For nitrogen fixation to occur, nitrogen-fixing bacteria (genus Rhizobium) need to be present in the soil. If soils do not already contain a high population of Rhizobium, these bacteria can be added either as a liquid or granular peat inoculant, or as a peat-based powder. The different forms can be seed applied or used in-furrow.

Corn Response to Sulfur Application Rate

Historically, sulfur (S) application has not been recommended on Iowa soils for corn and soybean production. Soils supply, or a combination from sources such as soil organic matter, profile sulfate, manure, and precipitation have met crop S needs. However, over the past few years, S deficiencies in alfalfa and corn have been documented. Large crop yield responses have been measured in some fields containing soils with low organic matter, side-slope landscape position, or coarse soil texture, especially in northeastern Iowa. The objective of this study was to determine S response in corn and soybean in north-central Iowa.

Potato Response to Boron and Sulfur Fertilization

This trial was conducted to investigate how potatoes respond to boron and sulfur fertilization when grown on coarse sand soil with low organic matter.

Geochemistry, physical properties, diatom abundance and datums of ODP Site 186-1150 and Hole 186-1151A

Detection of climate response to orbital forcing during Cenozoic long-term global cooling is a key to understanding the behavior of Earth's icehouse climate. Sedimentary rhythm, which is a rhythmic or cyclic variation in the sequence of sediments and sedimentary rocks, is useful for quantitative reconstruction of Earth's evolution during geological time. In this study, we attempt to (1) identify sources of natural gamma ray (NGR) emissions of core recovered during Ocean Drilling Program (ODP) Leg 186 by analyses of physical properties, major element concentrations, diatom abundances, and total organic carbon contents, (2) integrate whole-core NGR intensity of recovered core with wireline logging NGR measurements in order to construct a continuous sedimentary sequence, and (3) discuss changes in the NGR signal in the time domain. This attempt gives us preliminary information to discuss climate stability in relation to orbital forcing thorough geologic time. NGR values are obtained mainly by indirectly measuring the amount of terrigenous minerals including potassium and related elements in the sediments. NGR intensity is also affected by high porosity, which in these sediments was related to the amount of diatom valves. NGR signals might be a proxy of the intensity of the East Asian monsoon off Sanriku. A continuous sedimentary record was constructed by integration of the whole-core NGR intensity measured in sediments obtained from the drilled holes with that measured directly in the borehole by wireline logging, then using a stratigraphic age model to convert to a time series covering 1.3-9.7 Ma with a short break at ~5 Ma. High sedimentation rate (H) stages were identified in the sequence, related to intervals of low-amplitude precession and eccentricity variations. The transition of the dominant periodicities through the four H stages may correlate to major shifts in the climate system, including the onset of major Northern Hemisphere glaciation, the initial stage of the East Asian monsoon intensification, and the onset of the East Asian monsoon with uplift of the Himalayas and the Tibetan Plateau.

Response of marine palynomorphs to Neogene climate cooling in the Iceland Sea, ODP Hole 151-907A

The present study on ODP Leg 151 Hole 907A combines a detailed analysis of marine palynomorphs (dinoflagellate cysts, prasinophytes, and acritarchs) and a low-resolution alkenone-based sea-surface temperature (SST) record for the interval between 14.5 and 2.5 Ma, and allows to investigate the relationship between palynomorph assemblages and the paleoenvironmental evolution of the Iceland Sea. A high marine productivity is indicated in the Middle Miocene, and palynomorphs and SSTs both mirror the subsequent long-term Neogene climate deterioration. The diverse Middle Miocene palynomorph assemblages clearly diminish towards the impoverished assemblages of the Late Pliocene; parallel with a somewhat gradual decrease of SSTs being as high as 20 °C at ~13.5 Ma to around 8 °C at ~3 Ma. Superimposed, palynomorph assemblages not only reflect Middle to Late Miocene climate variability partly coinciding with the short-lived global Miocene isotope events (Mi-events), but also the initiation of a proto-thermohaline circulation across the Middle Miocene Climate Transition, which led to increased meridionality in the Nordic Seas. Last occurrences of species cluster during three events in the Late Miocene to Early Pliocene and are ascribed to the progressive strengthening and freshening of the proto-East Greenland Current towards modern conditions. A significant high latitude cooling between 6.5 and 6 Ma is depicted by the supraregional "Decahedrella event" coeval with lowest Miocene productivity and a SST decline. In the Early Pliocene, a transient warming is accompanied by surface water stratification and increased productivity that likely reflects a high latitude response to the global biogenic bloom. The succeeding crash in palynomorph accumulation, and a subsequent interval virtually barren of marine palynomorphs may be attributed to enhanced bottom water oxygenation and substantial sea ice cover, and indicates that conditions seriously affecting marine productivity in the Iceland Sea were already established well before the marked expansion of the Greenland Ice Sheet at 3.3 Ma.

Rare earth element data for sediments from ODP Leg 127

The relative effects of paleoceanographic and paleogeographic variations, sediment lithology, and diagenetic processes on the recorded rare earth element (REE) chemistry of Japan Sea sediments are evaluated by investigating REE total abundances and relative fractionations in 59 samples from Ocean Drilling Program Leg 127. REE total abundances (Sum REE) in the Japan Sea are strongly dependent upon the paleoceanographic position of a given site with respect to terrigenous and biogenic sources. REE concentrations at Site 794 (Yamato Basin) overall correspond well to aluminosilicate chemical indices and are strongly diluted by SiO2 within the late Miocene-Pliocene diatomaceous sequence. Eu/Eu* values at Site 794 reach a maximum through the diatomaceous interval as well, most likely suggesting an association of Eu/Eu* with the siliceous component, or reflecting slight incorporation of a detrital feldspar phase. Sum REE at Site 795 (Japan Basin) also is affiliated strongly with aluminosilicate phases, yet is diluted only slightly by siliceous input. At Site 797 (Yamato Basin), REE is not as clearly associated with the aluminosilicate fraction, is correlated moderately to siliceous input, and may be sporadically influenced by detrital heavy minerals originating from the nearby rifted continental fragment composing the Yamato Rise. The biogenic influence is largest at Site 794, moderately developed at Site 797, and of only minor importance at Site 795, reflecting basinal contrasts in productivity such that the Yamato Basin records greater biogenic input than the Japan Basin, while the most productive waters overlie the easternmost sequence of Site 794. Ce/Ce* profiles at all three sites increase monotonically with depth, and record progressive diagenetic LREE fractionation. The observed Ce/Ce* record does not respond to changes in oxygenation state of the overlying water, and Ce/Ce* correlates slightly better with depth than with age. The downhole increase in Ce/Ce* at Site 794 and Site 797 is a passive response to diagenetic transfer of LREE (except Ce) from sediment to interstitial water. At Site 795, the overall lack of correlation between Ce/Ce* and La_n/Yb_n suggests that other processes are occurring which mask the diagenetic behavior of all LREEs. First-order calculations of the Ce budget in Japan Sea waters and sediment indicate that ~20% of the excess Ce adsorbed by settling particles is recycled within the water column, and that an additional ~38% is recycled at or near the seafloor (data from Masuzawa and Koyama, 1989). Thus, because the remaining excess Ce is only ~10% of the total Ce, there is not a large source of Ce to the deeply buried sediment, further suggesting that the downhole increase in Ce/Ce* is a passive response to diagenetic behavior of the other LREEs. The REE chemistry of Japan Sea sediment therefore predicts successive downhole addition of LREEs to deeply-buried interstitial waters.

Chemical element concentrations in sediments from DSDP Holes 60-458 and 60-459

The development of laser ablation-inductively coupled plasma-mass spectrometry has revolutionized the analysis of tephras by providing (1) an efficient and precise method for determining abundances of a wide variety of trace elements at low concentrations in individual glass shards and (2) assessment of geochemical heterogeneities within individual ash horizons. This development is important for petrogenetic studies of intraoceanic arc systems, where tephras provide the most complete temporal record of magmatism. Results from the Izu-Bonin and Mariana arc systems indicate that despite close geographical proximity and similar tectonic evolution, they contrast strongly in terms of geochemical evolution since 35 Ma. Whereas the Mariana tephras have exceptional compositional diversity, ranging from low-K (Oligocene), to high-K (Miocene), and subsequently medium-K compositions (Pliocene-Quaternary), the Izu-Bonin arc has been dominated by low-K compositions throughout. The Mariana increases in K are paralleled by increases in abundances of incompatible trace elements and by increased values of diagnostic ratios (e.g., Nb/yb and Th/yb) regarded as monitors of potential mantle-source fertility. The relative uniformity of Nb/yb and Nb/Zr ratios in Izu-Bonin tephras indicates that cyclic processes of backarc basin development and mantle depletion do not necessarily induce large-scale temporal geochemical variations in the associated arc. Temporal variability within the Mariana arc, and its divergence from the Izu-Bonin arc ca. 13 Ma, can be traced to a major injection of subducted sediment in the Mariana system at this time.