Salinity stress is one of the main challenges for crop growth and production. The estimated loss of crop yield due to salinity stress is up to 20% worldwide each year. Plants have evolved an array of mechanisms to defend themselves against salinity stress. A key aspect of plant responses to salinity stress is the engagement of a nitrosative burst that results in nitric oxide (NO) accumulation. A major mechanism for the transfer of NO bioactivity is S-nitrosylation which is a modification of the reactive thiol group of a rare but highly active cysteine residue within a protein through the addition of a NO moiety to generate an S-nitrosothiol (SNO). S-nitrosylation can result in altered structure, function and cellular localisation of a protein. Our findings suggest that S-nitrosylation is a key regulator of plant responses to salinity stress. Glutathione (GSH), a tripeptide cellular antioxidant, is S-nitrosylated to form S-nitrosoglutathione (GSNO), which functions as a stable store of NO bioactivity. Cellular GSNO levels are directly controlled by S-nitrosoglutathione reductase (GSNOR), thereby, regulating global SNO levels indirectly. The absence of this gene results in high levels of SNOs. In Arabidopsis, previous research has shown that loss-of-function mutation in GSNOR1 results in pathogen susceptibility (Feechan et al., 2005). In our study, we investigated salt tolerance in gsnor1-3 plants. We have found that this line is salt sensitive at various stages of their life cycle. Interestingly, classical salt stress signalling pathways are fully functional in gsnor1-3 plants. We have also explored non-classical pathways involved in salt tolerance. Autophagy is a cellular catabolic process which is involved in the recycling and degradation of unwanted cellular materials under stressed and non-stressed conditions. We have demonstrated that gsnor1-3 plants have impaired autophagy during salt stress. An accumulation of the autophagy marker NBR1 supports the lack of autophagosome formation. We hypothesised that S-nitrosylation might regulate upstream nodes of autophagosome formation. Our study demonstrated that at least one key player involved in autophagosome biogenesis is regulated by S-nitrosylation. ATG7, an E1-like activating enzyme, which regulates ATG8-PE and ATG12-ATG5 ubiquitin like conjugation systems, is S-nitrosylated in vitro and in vivo. S-nitrosylation of ATG7 impairs its function in vitro. We showed that S-nitrosylation of ATG7 is mediated by GSNO. Interestingly, ATG7 is also transnitrosylated by thioredoxin (TRX), another important redox regulatory enzyme. We suggest that similar mechanisms might exist in planta. Finally, work in this study revealed that S-nitrosylation of Cys558 and Cys637 cause the inhibition of ATG7 function. In aggregate, this study revealed a novel mechanism for the redox-based regulation of autophagy during salt stress.

Deep subsurface evaporites are common terrestrial deep subsurface environments found globally. These deposits are known to host communities of halophilic organisms, some of which have been suggested to be millions of years old. The discovery of evaporite minerals on Mars has led to these environments becoming of interest to astrobiology, particularly because the subsurface of Mars represents the best chance of finding more clement conditions conducive to life. Despite this interest, deep subsurface evaporites remain poorly understood and we have little insight into how different salts shape the Earth's biosphere, much of which is underground. This thesis addresses several knowledge gaps present in the literature by sampling a selection of brine seeps and rock salt samples taken from Boulby Potash Mine, UK. The origin and evolution of the brines is determined with geochemical techniques, showing the majority to have been sourced from an aquifer above where they were intersected in the mine. These brines appear to have taken a variety of pathways through the subsurface leading to the presence of a range of different ions dissolved within them. The majority are Na/Cl dominated, whilst one is K/Cl dominated. One brine appears to have a different origin and probably interacted with dolomite becoming very concentrated in Mg. This variety in brine origins and migration pathways has impacted the habitability of the brines. Physicochemical measurements for chaotropicity, water activity and ionic strength, combined with culturing experiments suggest brines from the Sherwood Sandstone were habitable, but the brine from a distinct unknown source was uninhabitable. DNA was successfully extracted from three of the habitable brines and their metagenomes sequenced. These revealed communities largely functionally and phylogenetically similar to surface near saturation brines, indicating that the structure of the communities present in saturated Na/Cl brines are controlled almost exclusively by these ions rather than any other environmental difference between the surface and subsurface. Organisms were also taken from these brines and culturing experiments carried out to determine if any carbon sources were present in ancient salt that might promote growth in the absence of other carbon sources. Controls showed that the geochemical changes to the growth media induced by solving the salts, particularly sylvinite, were responsible for the increases in growth observed, indicating certain salt minerals effectively fertilise the growth of halophiles. Culturing on hydrocarbon seeps collected in the mine suggested they may provide a carbon source periodically to some organisms within the deposit. Work was done to show the presence of dissimilatory sulphate and iron reducing halophiles. Overall this significantly advances our understanding of how salts shape the Earth's biosphere, particularly its deep subsurface component, and what functional capabilities life has to persist in these environments. This work provides a new window on the potential habitability of deep subsurface extraterrestrial environments and how we might go about investigating these environments for habitable conditions.

Cheng, Chun Chiu. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 164-183). / Abstracts in English and Chinese. / Thesis Committee --- p.i / Statement --- p.ii / Abstract --- p.iii / 摘要 --- p.v / Acknowledgements --- p.vi / General Abbreviations --- p.viii / Abbreviations of Chemicals --- p.xi / List of Figures --- p.xv / List of Tables --- p.xvii / Table of Contents --- p.xix / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Salt stress in plants --- p.1 / Chapter 1.2 --- Overview of the molecular basis of salt tolerance in plants --- p.2 / Chapter 1.2.1 --- Stress perception --- p.3 / Chapter 1.2.2 --- Signal transduction --- p.3 / Chapter 1.2.2.1 --- Protein phosphatases --- p.4 / Chapter 1.2.2.2 --- The SOS pathway for ion homeostasis --- p.4 / Chapter 1.2.3 --- DNA and RNA helicases in post-transcriptional control --- p.6 / Chapter 1.2.4 --- ROS scavengers --- p.7 / Chapter 1.2.5 --- Proteases and proteinase inhibitors --- p.8 / Chapter 1.2.6 --- Heat shock proteins (Hsps) --- p.9 / Chapter 1.2.7 --- Highlights on DnaJ/Hsp40 --- p.9 / Chapter 1.3 --- Review on functional genomics of salt stress responses in plants --- p.11 / Chapter 1.3.1 --- Genomics on model organisms --- p.12 / Chapter 1.3.2 --- Transcriptomics for identifying salt stress responsive genes --- p.12 / Chapter 1.3.2.1 --- Multiple stress transcriptome analysis --- p.13 / Chapter 1.3.2.2 --- Genome-wide transcriptome analysis on molecular crosstalk --- p.14 / Chapter 1.3.2.3 --- Tissue specific transcriptome analysis --- p.16 / Chapter 1.3.2.4 --- Comparative transcriptome analysis --- p.17 / Chapter 1.3.2.5 --- Transcriptome analysis of soybean --- p.24 / Chapter 1.3.3 --- Proteomics in plant salt stress studies --- p.26 / Chapter 1.3.4 --- Beyond the transcriptome and proteome --- p.27 / Chapter 1.4 --- Significance of using soybean germplasms for identifying salt stress responsive genes --- p.28 / Chapter 1.5 --- Objectives --- p.29 / Chapter Chapter 2 --- Materials and Methods --- p.30 / Chapter 2.1 --- Materials --- p.30 / Chapter 2.1.1 --- "Plants, bacterial strains，and vectors" --- p.30 / Chapter 2.1.2 --- Enzymes and major chemicals --- p.33 / Chapter 2.1.3 --- Primers --- p.34 / Chapter 2.1.4 --- Commercial kits --- p.34 / Chapter 2.1.5 --- Equipment and facilities --- p.34 / Chapter 2.1.6 --- "Buffer, solution, gel and medium" --- p.34 / Chapter 2.2 --- Methods --- p.35 / Chapter 2.2.1 --- cDNA microarray analysis --- p.35 / Chapter 2.2.1.1 --- Construction of cDNA subtraction libraries --- p.35 / Chapter 2.2.1.2 --- Assembly of cDNA microarray --- p.36 / Chapter 2.2.1.3 --- External control RNA synthesis --- p.39 / Chapter 2.2.1.4 --- Probe labelling and hybridization --- p.40 / Chapter 2.2.1.5 --- Hybridization signal collection --- p.41 / Chapter 2.2.1.6 --- Image analysis --- p.41 / Chapter 2.2.1.7 --- Data analysis --- p.42 / Chapter 2.2.1.8 --- Selection of salt responsive genes using fold difference in expression --- p.45 / Chapter 2.2.1.9 --- DNA sequencing --- p.46 / Chapter 2.2.1.10 --- Real-time PCR analysis --- p.47 / Chapter 2.2.2 --- Growth conditions and treatments of plants --- p.48 / Chapter 2.2.2.1 --- Soybean for microarray hybridization and real-time PCR --- p.48 / Chapter 2.2.2.2 --- Soybean for the study of GmDNJ1 expression under ABA treatment --- p.48 / Chapter 2.2.2.3 --- Wild-type and transgenic Arabidopsis for functional analysis --- p.49 / Chapter 2.2.2.4 --- Wild-type and transgenic rice for functional analysis --- p.49 / Chapter 2.2.3 --- "DNA, RNA, and protein extraction" --- p.50 / Chapter 2.2.3.1 --- Plasmid DNA extraction from E. coli cells --- p.50 / Chapter 2.2.3.2 --- RNA extraction from plant tissues --- p.51 / Chapter 2.2.3.3 --- Soluble protein extraction from plant tissues --- p.51 / Chapter 2.2.4 --- Blot analysis --- p.51 / Chapter 2.2.4.1 --- Northern blot analysis --- p.52 / Chapter 2.2.4.2 --- Western blot analysis --- p.53 / Chapter 2.2.5 --- Subcloning of GmDNJ1 into pGEX-4T-1 --- p.53 / Chapter 2.2.5.1 --- "Restriction digestion, DNA purification and ligation" --- p.53 / Chapter 2.2.5.2 --- Transformation of competent Escherichia coli (DH5a and BL21) --- p.54 / Chapter 2.2.6 --- Luciferase refolding assay --- p.54 / Chapter 2.2.6.1 --- Culture of E. coli strain BL21 (DE3) --- p.54 / Chapter 2.2.6.2 --- Cell lysis --- p.55 / Chapter 2.2.6.3 --- Purification of the GST-GmDNJ1 fusion protein --- p.55 / Chapter 2.2.6.4 --- Quantitation of protein --- p.55 / Chapter 2.2.6.5 --- Luciferase refolding assay --- p.56 / Chapter Chapter 3 --- Results --- p.57 / Chapter 3.1 --- Overview of cDNA microarray analysis --- p.57 / Chapter 3.2 --- Identification of salt responsive genes in subtraction libraries concerning two contrasting soybean germplasms --- p.61 / Chapter 3.3 --- Data processing before selection of salt stress responsive genes --- p.75 / Chapter 3.3.1 --- M-A plots --- p.75 / Chapter 3.3.2 --- Boxplots --- p.76 / Chapter 3.3.3 --- Scatterplots --- p.76 / Chapter 3.4 --- Selection of salt responsive genes using fold difference in expression --- p.77 / Chapter 3.4.1 --- Selection of genes with differential expression between tolerant and sensitive germplasms --- p.77 / Chapter 3.4.2 --- Selection of genes with differential expression between cultivated and wild germplasms --- p.89 / Chapter 3.4.3 --- Data validation by real-time PCR analysis --- p.91 / Chapter 3.5 --- Selection of salt responsive genes using statistical tools --- p.95 / Chapter 3.5.1 --- Quantitative trait analysis for salt responsive genes --- p.95 / Chapter 3.5.2 --- Identification of salt stress correlation genes --- p.100 / Chapter 3.5.3 --- Cluster analyses --- p.104 / Chapter 3.5.3.1 --- Clustering genes --- p.104 / Chapter 3.5.3.2 --- Clustering samples --- p.108 / Chapter 3.5.4 --- Data validation by real-time PCR analysis --- p.111 / Chapter 3.6 --- Summary of cDNA microarray analysis --- p.112 / Chapter 3.7 --- Studies on GmDNJ1 --- p.120 / Chapter 3.7.1 --- Sequence analysis of GmDNJ1 --- p.120 / Chapter 3.7.2 --- GmDNJ1 was induced by salt stress and ABA treatment in soybean (Glycine max) --- p.127 / Chapter 3.7.3 --- Expressing GmDNJ1 in transgenic Arabidopsis (Arabidopsis thaliana) enhances the tolerance to salt stress and dehydration stress --- p.129 / Chapter 3.7.4 --- Expressing GmDNJ1 in transgenic rice (Oryza sativa) enhances the tolerance to salt stress and dehydration stress --- p.135 / Chapter 3.7.5 --- The GmDNJ1 protein can replace DnaJ in the in vitro luciferase refolding assay --- p.141 / Chapter Chapter 4 --- Discussion --- p.145 / Chapter 4.1 --- Overview of expression profiling of the 20 soybean germplasms --- p.145 / Chapter 4.2 --- Identification of salt responsive genes from subtraction libraries --- p.146 / Chapter 4.3 --- Normalization of data from microarray experiments --- p.148 / Chapter 4.4 --- The fold difference analysis --- p.149 / Chapter 4.4.1 --- Response to stress --- p.149 / Chapter 4.4.2 --- Gene expression --- p.150 / Chapter 4.4.3 --- Molecular function --- p.150 / Chapter 4.4.4 --- Metabolic activity --- p.151 / Chapter 4.4.5 --- Cellular component --- p.152 / Chapter 4.4.6 --- Genes with 2.5-fold difference in expression between cultivated and wild germplasms --- p.153 / Chapter 4.5 --- Selection of salt responsive genes using statistical tools --- p.153 / Chapter 4.5.1 --- Quantitative trait analysis --- p.153 / Chapter 4.5.2 --- Cluster analyses --- p.154 / Chapter 4.6 --- Studies on GmDNJ1 --- p.157 / Chapter 4.6.1 --- GmDNJ1 is a good candidate for gene studies --- p.157 / Chapter 4.6.2 --- Sequence analysis of GmDNJ1 suggested it to be a DnaJ/Hsp40 homologue in soybean --- p.158 / Chapter 4.6.3 --- GmDNJ1 was induced by salt stress and ABA treatment --- p.158 / Chapter 4.6.4 --- GmDNJ1 has a higher expression in salt tolerant soybean germplasms over sensitive ones --- p.159 / Chapter 4.6.5 --- Ectopic expression of GmDNJ1 enhanced the tolerance to salt stress and dehydration stress in transgenic Arabidopsis --- p.159 / Chapter 4.6.6 --- Ectopic expression of GmDNJ1 enhanced the tolerance to salt stress and dehydration stress in transgenic rice --- p.160 / Chapter 4.6.7 --- Luciferase activity assay showed that GmDNJ 1 functioned as a DnaJ/Hsp40 in vitro --- p.161 / Chapter Chapter 5 --- Conclusion --- p.162 / References --- p.164 / Appendix I - Enzymes and major chemicals --- p.184 / Appendix II - Primers --- p.188 / Appendix III - Major commercial kits --- p.192 / Appendix IV - Major equipment and facilities --- p.193 / "Appendix V - Formulation of buffer, solution, gel, and medium" --- p.194 / Appendix VI - Plots in microarray experiments --- p.198 / Appendix VII - Clones with differential expression (>2.5-fold or >1.8-fold) between germplasms --- p.208 / Appendix VIII - Salt responsive genes revealed by quantitative trait analysis --- p.216 / Appendix IX - Supplementary data in real-time PCR analysis --- p.221 / Appendix X - Supplementary data in functional analyses --- p.233

Exploring uses of two-phase mixtures as a way to store peak solar energy for off-peak usage is a novel approach that has been gaining attention in recent years to address the issues tied to solid fuel dependence. This research explores a “solar salt” mixture (40%wt KNO3 and 60%wt NaNO3) in an aluminum enclosure under two test conditions: conduction enhancement and no conduction enhancement. The central aim is to develop an understanding of thermal distributions and melt developments as the system moves from room temperature to 300 oC. Thermal pattern development is explored by experimentally observing a 2-D temperature field at 8 co-planar points, comprised of 3 radial positions with complementary circumferential measurements, using thermocouples. The instrument array is traversed to three different axial positions where collected data is compared with results from a numerical solver. Results find three important details. First, the melt pattern of the fin experiments show quicker rates of melting after the onset of melt at the bottom of the enclosure. Second, the spatial effects of the instrumentation influence the presence of thermal phenomena. Lastly, approximations of the salts behavior using numerical simulations are supported in identifying phases of melt development.

Fluvial and lacustrine sediments of great thickness accumulated in the intermountain basins of the western United States during Tertiary time. The Salt Lake group in northern Utah and parts of surrounding states is a conspicuous stratigraphic unit of these basins. The "beds of light color" in Morgan Valley in the Wasatch Mountains of northern Utah were named the "Salt Lake group" by Hayden (1869) because of similar occurrences in Salt Lake Valley and because he reasoned that the succession could be divided into formations. Similar rocks crop out in Ogden Valley, north of Morgan Valley, and in Cache Valley, Utah and Idaho. Cache Valley is bounded by the Wasatch and Malad Ranges to the west and the Bear River Range to the east (Fig. 1). It extends from the divide between Ogden and Cache valleys about 18 miles south of Los an. Utah. to Red Rock Pass. about 19 miles northwest of Preston. Idaho. The Bear River enters Cache Valley northeast of Preston. Idaho. and leaves through the Bear River Narrows west of Logan. Utah. at a point between the northern end of the Wasatch Range and the Malad Range. Red Rock Pass, northwest of Preston, Idaho, was the outlet of Lake Bonneville.

Bile salts are supramolecules with amphiphilic properties. Bile salts form aggregates in aqueous solutions. The primary aggregates of bile salts are hydrophobic and the secondary aggregates which form at higher concentrations are relatively hydrophilic. Among bile salts, sodium deoxycholate (NaDC) has been known to form hydrogels at pHs close to the neutral pH and within a certain concentration range. The aim of this work was to provide insight into the properties of a NaDC hydrogel as a supramolecular gel system through three different projects. Pyrene is a hydrophobic polycyclic aromatic compound which was used as a fluorescent probe and the guest for these projects. 1,1’-dioctadecyl-3,3,3’,3’-tetramethylindodicarbocyanine perchlorate (DiD) is another fluorescent compound which was used as another guest. The objective of the first project was to understand the mobility of a small guest molecule in NaDC gel in the presence of cucurbit[6]uril (CB[6]) compound as an additive for the gel. Cucurbit[n]urils are macrocyclic compounds with a hydrophobic cavity and two hydrophilic portals. The presence of CB[6] provides another binding site for pyrene in addition to the primary aggregates of the bile salts. The results showed that the mobility of the guest from water and CB[6] to the bile salts network happens when the temperature is raised. The release of the guest back into the water happens when the gel is cooled. The objective of the second project was to investigate the effect of surfaces with different hydrophilicity on the NaDC gel properties. The results of fluorescence correlation spectroscopy (FCS) experiments revealed that either the hydrophilicity of the surface does not affect the NaDC gel network or the FCS is insensitive to the structural changes induced by the hydrophilicity of the surface. These experiments depicted that the aggregates involved in the gel’s network are the same as those formed in the aqueous solutions. Moreover, results of the steady-state and time-resolved fluorescence experiments showed that the bulk gel properties are not affected by the hydrophilicity of the surface. The objective of the last project was to determine the effect of ions on NaDC gel properties. The results showed that cations with different charge density have different effects on the gel formation and properties. The presence of inorganic salts with a monovalent cation leads to the formation of a kinetically favored gel sample within a few hours after sample preparation. The extension of the network occurs overtime and a thermodynamically stable gel forms a couple of days after sample preparation. / Graduate / 2020-10-20

Art, for all its apparent simplicity is anything but straightforward. I admire and strive to make work that, when first introduced is both comfortable and exciting. I aim for work that is true to its medium. I want my work to be approachable, inviting, though questioning and introspective just the same. I think art should make the world a better place. I admire the technicality that is inherent to minimalism. I think at the least, an acceptable piece of art should be an insight into the world of the viewer.

When most omnivores and herbivores become sodium depleted they engage in the motivated behavior of sodium appetite (AKA salt appetite), or the seeking out and ingestion of salty substances. Sodium appetite is associated with psychological processes that serve to enhance the incentive and rewarding value of salty substances in order to attract animals to salty substances and reinforce the ingestion of them. The experience of sodium depletion also produces long-lasting changes in behavior; one of the most apparent changes being a seemingly life-long increase in hypertonic salt intake which indicates sodium appetite is sensitized. Two neural circuits have been implicated in the sensitization of sodium appetite: 1) a forebrain neural circuit that regulates body fluid homeostasis, and 2) the mesolimbic dopamine system which mediates motivated behaviors. This dissertation has three aims that serve the overall purpose of providing a better understanding of the neurobiological mechanisms that mediate the sensitization of sodium appetite. The first aim is to develop a model of sodium depletion that is amenable to pharmacological manipulation in order to determine whether the -blockade of N-methyl-d-aspartate receptors, which are critical for neural plasticity, will prevent the sensitization of sodium appetite. The second aim is to determine whether sensitization is associated with relatively long-term molecular changes in forebrain areas that regulate body fluid homeostasis. The third aim is to identify how forebrain areas involved in body fluid homeostasis may connect to and influence activity in the mesolimbic dopamine system.

Halogeton (Halogeton glomeratus) is a halophytic, invasive species that displaces Gardner’s saltbush (Atriplex gardneri) on saline rangelands. Forage kochia (Bassia prostrata) is a potential species to rehabilitate these ecosystems. This study compared the salinity tolerance of these species and tall wheatgrass (Thinopyrum ponticum) and alfalfa (Medicago sativa). Plants were evaluated for 28 days in hydroponics where they were maintained at 0, 150, 200, 300, 400, 600, and 800 mM NaCl. Shoot growth and ion accumulation were determined. Alfalfa and tall wheatgrass were severely affected by salt with both species’ shoot mass just 32% of control at 150 mM NaCl. Alfalfa did not survive above 300 mM NaCl, while, tall wheatgrass did not survive at salt levels above 400 mM NaCl. In contrast, forage kochia survived to 600 mM, but produced little shoot mass at that level. Halogeton exhibited ‘halophytic’ shoot growth, reaching maximum mass at 141 mM, and not less mass than the control until salinity reached 400 mM. Gardner’s saltbush did not show a dramatic decrease in dry mass produced until it reached salt levels of 600 and 800 mM NaCl. Forage kochia yielded high amounts of dry mass in the absence of salt, but also managed to survive up to 600 mM NaCl. Salt tolerance ranking (GR50 = 50% reduction in shoot mass) was Gardner’s saltbush=halogeton>forage kochia> alfalfa>tall wheatgrass. Both halogeton and Gardner’s saltbush actively accumulated sodium in shoots, indicating that Na+ was the principle ion in osmotic adjustment. In contrast, forage kochia exhibited a linear increase (e.g. passive uptake) in Na+ accumulation as salinity increased. This study confirmed that halogeton is a halophytic species and thus well adapted to salt-desert shrubland ecosystems. Gardner’s saltbush, also a halophyte, was equally salt tolerant, suggesting other factors are responsible for halogeton displacement of Gardner’s saltbush. Forage kochia is a halophytic species that can survive salinity equal to seawater, but is not as salt tolerant as Gardner’s saltbush and halogeton.

The reciprocal effects of vegetation and soils have long been a subject of speculation and conjecture. In the management of any natural land area the problem of interpreting vegetational expression is especially important. The effects of native vegetation on soils and the effects of the soil on the vegetation have been studied and observed for many years. The arid-desert range lands have been studied and observed for many years. The arid-desert range lands have been studied least and as a result are not well understood. As human populations increase there will be additional need for agricultural production, and these lands may be put to higher use, perhaps even to irrigated crop production. Basic to increasing the productivity of these lands is an understanding of the vegetation they are now supporting, what they supported prior to their use by domestic livestock, and why the present vegetation grows to the exclusion of other vegetation types.