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1.  Bacterial Growth at the High Concentrations of Magnesium Sulfate Found in Martian Soils 
Astrobiology  2012;12(2):98-106.
Abstract
The martian surface environment exhibits extremes of salinity, temperature, desiccation, and radiation that would make it difficult for terrestrial microbes to survive. Recent evidence suggests that martian soils contain high concentrations of MgSO4 minerals. Through warming of the soils, meltwater derived from subterranean ice-rich regolith may exist for an extended period of time and thus allow the propagation of terrestrial microbes and create significant bioburden at the near surface of Mars. The current report demonstrates that halotolerant bacteria from the Great Salt Plains (GSP) of Oklahoma are capable of growing at high concentrations of MgSO4 in the form of 2 M solutions of epsomite. The epsotolerance of isolates in the GSP bacterial collection was determined, with 35% growing at 2 M MgSO4. There was a complex physiological response to mixtures of MgSO4 and NaCl coupled with other environmental stressors. Growth also was measured at 1 M concentrations of other magnesium and sulfate salts. The complex responses may be partially explained by the pattern of chaotropicity observed for high-salt solutions as measured by agar gelation temperature. Select isolates could grow at the high salt concentrations and low temperatures found on Mars. Survival during repetitive freeze-thaw or drying-rewetting cycles was used as other measures of potential success on the martian surface. Our results indicate that terrestrial microbes might survive under the high-salt, low-temperature, anaerobic conditions on Mars and present significant potential for forward contamination. Stringent planetary protection requirements are needed for future life-detection missions to Mars. Key Words: Analogue—Mars—Planetary protection—Salts—Life in extreme environments. Astrobiology 12, 98–106.
doi:10.1089/ast.2011.0720
PMCID: PMC3277918  PMID: 22248384
2.  Near-UV Transmittance of Basalt Dust as an Analog of the Martian Regolith: Implications for Sensor Calibration and Astrobiology 
Sensors (Basel, Switzerland)  2006;6(6):688-696.
The Martian regolith is exposed to solar irradiation in the near-UV (200-390 nm). Basalt is one of the main components of the dust on Mars surface. The near-UV irradiation of basalt dust on Mars is simulated experimentally in order to determine the transmittance as a function of the mass and thickness of the dust. This data can serve to quantify the absorption of dust deposited on sensors aiming to measure the UV intensity on Mars surface. The minimum thickness of the dust that corresponds to near-zero-transmittance in the near-UV is measured. Hypothetical Martian microorganisms living on the dusty regolith at deeper layers would be preserved from the damaging solar UV irradiation.
PMCID: PMC3874829
Ultraviolet: solar system; Mars surface; Methods: laboratory; basalt; Instrumentation: photometers; Astrobiology
3.  The transcription factor PHR1 plays a key role in the regulation of sulfate shoot-to-root flux upon phosphate starvation in Arabidopsis 
BMC Plant Biology  2011;11:19.
Background
Sulfate and phosphate are both vital macronutrients required for plant growth and development. Despite evidence for interaction between sulfate and phosphate homeostasis, no transcriptional factor has yet been identified in higher plants that affects, at the gene expression and physiological levels, the response to both elements. This work was aimed at examining whether PHR1, a transcription factor previously shown to participate in the regulation of genes involved in phosphate homeostasis, also contributed to the regulation and activity of genes involved in sulfate inter-organ transport.
Results
Among the genes implicated in sulfate transport in Arabidopsis thaliana, SULTR1;3 and SULTR3;4 showed up-regulation of transcripts in plants grown under phosphate-deficient conditions. The promoter of SULTR1;3 contains a motif that is potentially recognizable by PHR1. Using the phr1 mutant, we showed that SULTR1;3 up-regulation following phosphate deficiency was dependent on PHR1. Furthermore, transcript up-regulation was found in phosphate-deficient shoots of the phr1 mutant for SULTR2;1 and SULTR3;4, indicating that PHR1 played both a positive and negative role on the expression of genes encoding sulfate transporters. Importantly, both phr1 and sultr1;3 mutants displayed a reduction in their sulfate shoot-to-root transfer capacity compared to wild-type plants under phosphate-deficient conditions.
Conclusions
This study reveals that PHR1 plays an important role in sulfate inter-organ transport, in particular on the regulation of the SULTR1;3 gene and its impact on shoot-to-root sulfate transport in phosphate-deficient plants. PHR1 thus contributes to the homeostasis of both sulfate and phosphate in plants under phosphate deficiency. Such a function is also conserved in Chlamydomonas reinhardtii via the PHR1 ortholog PSR1.
doi:10.1186/1471-2229-11-19
PMCID: PMC3036608  PMID: 21261953
4.  Searching for signatures of life on Mars: an Fe-isotope perspective 
Recent spacecraft and lander missions to Mars have reinforced previous interpretations that Mars was a wet and warm planet in the geological past. The role of liquid water in shaping many of the surface features on Mars has long been recognized. Since the presence of liquid water is essential for survival of life, conditions on early Mars might have been more favourable for the emergence and evolution of life. Until a sample return mission to Mars, one of the ways of studying the past environmental conditions on Mars is through chemical and isotopic studies of Martian meteorites. Over 35 individual meteorite samples, believed to have originated on Mars, are now available for lab-based studies. Fe is a key element that is present in both primary and secondary minerals in the Martian meteorites. Fe-isotope ratios can be fractionated by low-temperature processes which includes biological activity. Experimental investigations of Fe reduction and oxidation by bacteria have produced large fractionation in Fe-isotope ratios. Hence, it is considered likely that if there is/were any form of life present on Mars then it might be possible to detect its signature by Fe-isotope studies of Martian meteorites. In the present study, we have analysed a number of Martian meteorites for their bulk-Fe-isotope composition. In addition, a set of terrestrial analogue material has also been analysed to compare the results and draw inferences. So far, our studies have not found any measurable Fe-isotopic fractionation in bulk Martian meteorites that can be ascribed to any low-temperature process operative on Mars.
doi:10.1098/rstb.2006.1899
PMCID: PMC1664681  PMID: 17008212
Mars; Martian meteorites; SNC; terrestrial analogues; iron isotopes; life
5.  Potassium ferrate [Fe(VI)] does not mediate self-sterilization of a surrogate mars soil 
BMC Microbiology  2003;3:4.
Background
Martian soil is thought to be enriched with strong oxidants such as peroxides and/or iron in high oxidation states that might destroy biological materials. There is also a high flux of ultraviolet radiation at the surface of Mars. Thus, Mars may be inhospitable to life as we know it on Earth. We examined the hypothesis that if the soil of Mars contains ferrates [Fe(VI)], the strongest of the proposed oxidizing species, and also is exposed to high fluxes of UV radiation, it will be self-sterilizing.
Results
Under ambient conditions (25°C, oxygen and water present) K2FeO4 mixed into sand mineralized some reactive organic molecules to CO2, while less reactive compounds were not degraded. Dried endospores of Bacillus subtilis incubated in a Mars surrogate soil comprised of dry silica sand containing 20% by weight K2FeO4 and under conditions similar to those now on Mars (extreme desiccation, cold, and a CO2-dominated atmosphere) were resistant to killing by the ferrate-enriched sand. Similar results were observed with permanganate. Spores in oxidant-enriched sand exposed to high fluxes of UV light were protected from the sporocidal activity of the radiation below about 5 mm depths.
Conclusion
Based on our data and previously published descriptions of ancient but dormant life forms on Earth, we suggest that if entities resembling bacterial endospores were produced at some point by life forms on Mars, they might still be present and viable, given appropriate germination conditions. Endospores delivered to Mars on spacecraft would possibly survive and potentially compromise life detection experiments.
doi:10.1186/1471-2180-3-4
PMCID: PMC153549  PMID: 12694634
6.  Natural Variants of AtHKT1 Enhance Na+ Accumulation in Two Wild Populations of Arabidopsis 
PLoS Genetics  2006;2(12):e210.
Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomic strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here, we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil. Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that two coastal populations of Arabidopsis collected from Tossa del Mar, Spain, and Tsu, Japan (Ts-1 and Tsu-1, respectively), accumulate higher shoot levels of Na+ than do Col-0 and other accessions. We identify AtHKT1, known to encode a Na+ transporter, as being the causal locus driving elevated shoot Na+ in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence approximately 5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na+. Interestingly, and in contrast to the hkt1–1 null mutant, under NaCl stress conditions, this novel AtHKT1 allele not only does not confer NaCl sensitivity but also cosegregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; http://www.purdue.edu/dp/ionomics). Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the casual locus driving the natural variation in shoot Na+ accumulation we observed in Ts-1 and Tsu-1. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes.
Synopsis
Unlike most animals, plants are sessile and cannot leave a poor-quality environment after germinating. They therefore need to tolerate the particular conditions they encounter to survive. This makes plants an ideal system for the study of adaptive variation, and this is particularly true of Arabidopsis thaliana (Arabidopsis), which shows substantial natural variation and for which numerous genetic tools exist. Using a combination of analytical chemistry, genetics, and genomics, the authors were able to identify the specific genetic alteration that drive the natural variation in shoot sodium (Na+) accumulation capacity observed in Arabidopsis populations from coastal regions of Spain and Japan (Tossa del Mar and Tsu, respectively). They observed that a deletion in the DNA responsible for regulating the expression of HKT1, a gene known to encode for a Na+ transporter, causes reduced expression of AtHKT1 in roots of both the Spanish and Japanese populations. Such altered expression results in the elevated shoot Na+ observed in these two populations. Interestingly, this novel version of the HKT1 genes is also associated genetically with the enhanced NaCl resistance they observe in the Japanese population.
doi:10.1371/journal.pgen.0020210
PMCID: PMC1665649  PMID: 17140289
7.  Natural Variants of AtHKT1 Enhance Na+ Accumulation in Two Wild Populations of Arabidopsis 
PLoS Genetics  2006;2(12):e210.
Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomic strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here, we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil. Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that two coastal populations of Arabidopsis collected from Tossa del Mar, Spain, and Tsu, Japan (Ts-1 and Tsu-1, respectively), accumulate higher shoot levels of Na+ than do Col-0 and other accessions. We identify AtHKT1, known to encode a Na+ transporter, as being the causal locus driving elevated shoot Na+ in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence approximately 5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na+. Interestingly, and in contrast to the hkt1–1 null mutant, under NaCl stress conditions, this novel AtHKT1 allele not only does not confer NaCl sensitivity but also cosegregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; http://www.purdue.edu/dp/ionomics). Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the casual locus driving the natural variation in shoot Na+ accumulation we observed in Ts-1 and Tsu-1. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes.
Synopsis
Unlike most animals, plants are sessile and cannot leave a poor-quality environment after germinating. They therefore need to tolerate the particular conditions they encounter to survive. This makes plants an ideal system for the study of adaptive variation, and this is particularly true of Arabidopsis thaliana (Arabidopsis), which shows substantial natural variation and for which numerous genetic tools exist. Using a combination of analytical chemistry, genetics, and genomics, the authors were able to identify the specific genetic alteration that drive the natural variation in shoot sodium (Na+) accumulation capacity observed in Arabidopsis populations from coastal regions of Spain and Japan (Tossa del Mar and Tsu, respectively). They observed that a deletion in the DNA responsible for regulating the expression of HKT1, a gene known to encode for a Na+ transporter, causes reduced expression of AtHKT1 in roots of both the Spanish and Japanese populations. Such altered expression results in the elevated shoot Na+ observed in these two populations. Interestingly, this novel version of the HKT1 genes is also associated genetically with the enhanced NaCl resistance they observe in the Japanese population.
doi:10.1371/journal.pgen.0020210
PMCID: PMC1665649  PMID: 17140289
8.  Reciprocal regulation among miR395, APS and SULTR2;1 in Arabidopsis thaliana 
Plant Signaling & Behavior  2010;5(10):1257-1259.
Sulfur element plays a pivotal role in plant growth and development. Recently, we have demonstrated that miR395 is crucial for the sulfate homeostasis through regulating the sulfate uptake, transport and assimilation in Arabidopsis thaliana. miR395 controls the sulfate concentration in the shoot by targeting three ATP sulfurylase genes (APS), which encode the first enzymes catalyzing sulfate activation in sulfur assimilation pathway. Furthermore, miR395 also regulates the transport of sulfate between leaves. Under sulfate starvation conditions, upregulated miR395 represses the expression of SULTR2;1, which then confined the transport of sulfate from mature to young leaves. Of note, transcript expression analysis suggested that, unlike APS1 and APS4 mRNA, APS3 and shoot SULTR2;1 is in accordance with miR395 in response to sulfate deprivation. We proposed that the differential regulation of targets by miR395 may be required for adaptation to the sulfate deficiency environment. In addition, our results revealed that there is reciprocal regulation between SULTR2;1 and APS genes through miR395.
doi:10.4161/psb.5.10.12608
PMCID: PMC3115361  PMID: 20935495
sulfate; miR395; APS1; APS3; APS4; SULTR2;1; sulfate transport; sulfate assimilation
9.  Effects of Simulated Mars Conditions on the Survival and Growth of Escherichia coli and Serratia liquefaciens▿  
Escherichia coli and Serratia liquefaciens, two bacterial spacecraft contaminants known to replicate under low atmospheric pressures of 2.5 kPa, were tested for growth and survival under simulated Mars conditions. Environmental stresses of high salinity, low temperature, and low pressure were screened alone and in combination for effects on bacterial survival and replication, and then cells were tested in Mars analog soils under simulated Mars conditions. Survival and replication of E. coli and S. liquefaciens cells in liquid medium were evaluated for 7 days under low temperatures (5, 10, 20, or 30°C) with increasing concentrations (0, 5, 10, or 20%) of three salts (MgCl2, MgSO4, NaCl) reported to be present on the surface of Mars. Moderate to high growth rates were observed for E. coli and S. liquefaciens at 30 or 20°C and in solutions with 0 or 5% salts. In contrast, cell densities of both species generally did not increase above initial inoculum levels under the highest salt concentrations (10 and 20%) and the four temperatures tested, with the exception that moderately higher cell densities were observed for both species at 10% MgSO4 maintained at 20 or 30°C. Growth rates of E. coli and S. liquefaciens in low salt concentrations were robust under all pressures (2.5, 10, or 101.3 kPa), exhibiting a general increase of up to 2.5 orders of magnitude above the initial inoculum levels of the assays. Vegetative E. coli cells were maintained in a Mars analog soil for 7 days under simulated Mars conditions that included temperatures between 20 and −50°C for a day/night diurnal period, UVC irradiation (200 to 280 nm) at 3.6 W m−2 for daytime operations (8 h), pressures held at a constant 0.71 kPa, and a gas composition that included the top five gases found in the martian atmosphere. Cell densities of E. coli failed to increase under simulated Mars conditions, and survival was reduced 1 to 2 orders of magnitude by the interactive effects of desiccation, UV irradiation, high salinity, and low pressure (in decreasing order of importance). Results suggest that E. coli may be able to survive, but not grow, in surficial soils on Mars.
doi:10.1128/AEM.02147-09
PMCID: PMC2849189  PMID: 20154104
10.  Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip 
The root functions as the physical anchor of the plant and is the organ responsible for uptake of water and mineral nutrients such as nitrogen, phosphorus, sulfate and trace elements that plants acquire from the soil. If we want to develop sustainable approaches to producing high crop yield, we need to better understand how the root develops, takes up a wide spectrum of nutrients, and interacts with symbiotic and pathogenic organisms. To accomplish these goals, we need to be able to explore roots in microscopic detail over time periods ranging from minutes to days.
We developed the RootChip, a polydimethylsiloxane (PDMS)- based microfluidic device, which allows us to grow and image roots from Arabidopsis seedlings while avoiding any physical stress to roots during preparation for imaging1 (Figure 1). The device contains a bifurcated channel structure featuring micromechanical valves to guide the fluid flow from solution inlets to each of the eight observation chambers2. This perfusion system allows the root microenvironment to be controlled and modified with precision and speed. The volume of the chambers is approximately 400 nl, thus requiring only minimal amounts of test solution.
Here we provide a detailed protocol for studying root biology on the RootChip using imaging-based approaches with real time resolution. Roots can be analyzed over several days using time lapse microscopy. Roots can be perfused with nutrient solutions or inhibitors, and up to eight seedlings can be analyzed in parallel. This system has the potential for a wide range of applications, including analysis of root growth in the presence or absence of chemicals, fluorescence-based analysis of gene expression, and the analysis of biosensors, e.g. FRET nanosensors3.
doi:10.3791/4290
PMCID: PMC3471268  PMID: 22805296
Bioengineering;  Issue 65;  Plant Biology;  Physics;  Plant Physiology;  roots;  microfluidics;  imaging;  hydroponics;  Arabidopsis
11.  Modeling the Reflectance of the Lunar Regolith by a New Method Combining Monte Carlo Ray Tracing and Hapke's Model with Application to Chang'E-1 IIM Data 
The Scientific World Journal  2014;2014:457138.
In this paper, we model the reflectance of the lunar regolith by a new method combining Monte Carlo ray tracing and Hapke's model. The existing modeling methods exploit either a radiative transfer model or a geometric optical model. However, the measured data from an Interference Imaging spectrometer (IIM) on an orbiter were affected not only by the composition of minerals but also by the environmental factors. These factors cannot be well addressed by a single model alone. Our method implemented Monte Carlo ray tracing for simulating the large-scale effects such as the reflection of topography of the lunar soil and Hapke's model for calculating the reflection intensity of the internal scattering effects of particles of the lunar soil. Therefore, both the large-scale and microscale effects are considered in our method, providing a more accurate modeling of the reflectance of the lunar regolith. Simulation results using the Lunar Soil Characterization Consortium (LSCC) data and Chang'E-1 elevation map show that our method is effective and useful. We have also applied our method to Chang'E-1 IIM data for removing the influence of lunar topography to the reflectance of the lunar soil and to generate more realistic visualizations of the lunar surface.
doi:10.1155/2014/457138
PMCID: PMC3913513  PMID: 24526892
12.  Evolutionary Relationships and Functional Diversity of Plant Sulfate Transporters 
Sulfate is an essential nutrient cycled in nature. Ion transporters that specifically facilitate the transport of sulfate across the membranes are found ubiquitously in living organisms. The phylogenetic analysis of known sulfate transporters and their homologous proteins from eukaryotic organisms indicate two evolutionarily distinct groups of sulfate transport systems. One major group named Tribe 1 represents yeast and fungal SUL, plant SULTR, and animal SLC26 families. The evolutionary origin of SULTR family members in land plants and green algae is suggested to be common with yeast and fungal SUL and animal anion exchangers (SLC26). The lineage of plant SULTR family is expanded into four subfamilies (SULTR1–SULTR4) in land plant species. By contrast, the putative SULTR homologs from Chlorophyte green algae are in two separate lineages; one with the subfamily of plant tonoplast-localized sulfate transporters (SULTR4), and the other diverged before the appearance of lineages for SUL, SULTR, and SLC26. There also was a group of yet undefined members of putative sulfate transporters in yeast and fungi divergent from these major lineages in Tribe 1. The other distinct group is Tribe 2, primarily composed of animal sodium-dependent sulfate/carboxylate transporters (SLC13) and plant tonoplast-localized dicarboxylate transporters (TDT). The putative sulfur-sensing protein (SAC1) and SAC1-like transporters (SLT) of Chlorophyte green algae, bryophyte, and lycophyte show low degrees of sequence similarities with SLC13 and TDT. However, the phylogenetic relationship between SAC1/SLT and the other two families, SLC13 and TDT in Tribe 2, is not clearly supported. In addition, the SAC1/SLT family is absent in the angiosperm species analyzed. The present study suggests distinct evolutionary trajectories of sulfate transport systems for land plants and green algae.
doi:10.3389/fpls.2011.00119
PMCID: PMC3355512  PMID: 22629272
evolution; plant; sulfate; transporter
13.  Root-Associated Bacteria Contribute to Mineral Weathering and to Mineral Nutrition in Trees: a Budgeting Analysis 
The principal nutrient source for forest trees derives from the weathering of soil minerals which results from water circulation and from plant and microbial activity. The main objectives of this work were to quantify the respective effects of plant- and root-associated bacteria on mineral weathering and their consequences on tree seedling growth and nutrition. That is why we carried out two column experiments with a quartz-biotite substrate. The columns were planted with or without pine seedlings and inoculated or not with three ectomycorrhizosphere bacterial strains to quantify biotite weathering and pine growth and to determine how bacteria improve pine growth. We showed that the pine roots significantly increased biotite weathering by a factor of 1.3 for magnesium and 1.7 for potassium. We also demonstrated that the inoculation of Burkholderia glathei PML1(12) significantly increased biotite weathering by a factor of 1.4 for magnesium and 1.5 for potassium in comparison with the pine alone. In addition, we observed a significant positive effect of B. glathei PMB1(7) and PML1(12) on pine growth and on root morphology (number of lateral roots and root hairs). We demonstrated that PML1(12) improved pine growth when the seedlings were supplied with a nutrient solution which did not contain the nutrients present in the biotite. No improvement of pine growth was observed when the seedlings were supplied with all the nutrients necessary for pine growth. We therefore propose that the growth-promoting effect of B. glathei PML1(12) mainly resulted from the improved plant nutrition via increased mineral weathering.
doi:10.1128/AEM.72.2.1258-1266.2006
PMCID: PMC1392890  PMID: 16461674
14.  Nitrogen Regulation of Root Branching 
Annals of Botany  2006;97(5):875-881.
• Background Many plant species can modify their root architecture to enable them to forage for heterogeneously distributed nutrients in the soil. The foraging response normally involves increased proliferation of lateral roots within nutrient-rich soil patches, but much remains to be understood about the signalling mechanisms that enable roots to sense variations in the external concentrations of different mineral nutrients and to modify their patterns of growth and development accordingly.
• Scope In this review we consider different aspects of the way in which the nitrogen supply can modify root branching, focusing on Arabidopsis thaliana. Our current understanding of the mechanism of nitrate stimulation of lateral root growth and the role of the ANR1 gene are summarized. In addition, evidence supporting the possible role of auxin in regulating the systemic inhibition of early lateral root development by high rates of nitrate supply is presented. Finally, we examine recent evidence that an amino acid, l-glutamate, can act as an external signal to elicit complex changes in root growth and development.
• Conclusions It is clear that plants have evolved sophisticated pathways for sensing and responding to changes in different components of the external nitrogen supply as well as their own internal nitrogen status. We speculate on the possibility that the effects elicited by external l-glutamate represent a novel form of foraging response that could potentially enhance a plant's ability to compete with its neighbours and micro-organisms for localized sources of organic nitrogen.
doi:10.1093/aob/mcj601
PMCID: PMC2803407  PMID: 16339770
Arabidopsis thaliana; auxin; dissolved organic nitrogen; foraging; glutamate; lateral roots; MADS box transcription factor; nitrate; nitrogen; root architecture; root development; roots; signalling; Thlaspi caerulescens
15.  The efficacy of magnesium sulfate loading on microalbuminuria following SIRS: One step forward in dosing 
Backgrounds
Magnesium has been known for its antioxidative and antiinflammatory properties in many studies. In this study two dosing regimens of magnesium were compared with a placebo control group in order to investigate safety and efficacy of high doses of intravenous magnesium sulfate infusion on critically ill trauma patients. Inflammatory and oxidative factors were measured in this trial.
Methods
45 trauma patients with systemic inflammatory response syndromes (SIRS) were randomly assigned into 2 treatment and one placebo groups. The high dose group received 15 g MgSO4, low dose group received 7.5 g of MgSO4 over 4 hour infusion, and placebo group received saline alone. The initial and post magnesium sulfate injections levels of tumor necrosis factor alpha (TNF-α), total antioxidant power and lipid peroxidation were measured after 6, 18 and 36 hours. The pre-infusion along with 6 and 36 hour level of microalbuminuria were also determined.
Results
Repeated measurements illustrated that there was no significant difference in TNF-α, total antioxidant power and lipid peroxidation levels among groups during the period of analysis. The microalbuminuria at 36 hour post infusion of high dose group was lower than that of control group (p = 0.024). Patient’s mortality (28 day) was similar among all treatment groups. Both magnesium infusion groups tolerated the drug without experiencing any complications.
Conclusion
No evidence for antioxidative and antiinflammatory effects of magnesium in traumatic SIRS positive patients was found. Magnesium in high doses may be recommended for traumatic patients with SIRS status to prevent microalbuminuria.
doi:10.1186/2008-2231-20-74
PMCID: PMC3556002  PMID: 23351890
Magnesium; Microalbumin; TNF-α; Oxidative stress; Trauma; Critical care
16.  Spatial Distribution of Total, Ammonia-Oxidizing, and Denitrifying Bacteria in Biological Wastewater Treatment Reactors for Bioregenerative Life Support 
Bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. In this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at Johnson Space Center. The experiment (Lunar-Mars Life Support Test Project—Phase III) consisted of four crew members confined in a test chamber for 91 days. In order to recycle all water during the experiment, an immobilized cell bioreactor (ICB) was employed for organic carbon removal and a trickling filter bioreactor (TFB) was utilized for ammonia removal, followed by physical-chemical treatment. In this study, the spatial distribution of various microorganisms within each bioreactor was analyzed by using biofilm samples taken from four locations in the ICB and three locations in the TFB. Three target genes were used for characterization of bacteria: the 16S rRNA gene for the total bacterial community, the ammonia monooxygenase (amoA) gene for ammonia-oxidizing bacteria, and the nitrous oxide reductase (nosZ) gene for denitrifying bacteria. A combination of terminal restriction fragment length polymorphism (T-RFLP), sequence, and phylogenetic analyses indicated that the microbial community composition in the ICB and the TFB consisted mainly of Proteobacteria, low-G+C gram-positive bacteria, and a Cytophaga-Flexibacter-Bacteroides group. Fifty-seven novel 16S rRNA genes, 8 novel amoA genes, and 12 new nosZ genes were identified in this study. Temporal shifts in the species composition of total bacteria in both the ICB and the TFB and ammonia-oxidizing and denitrifying bacteria in the TFB were also detected when the biofilms were compared with the inocula after 91 days. This result suggests that specific microbial populations were either brought in by the crew or enriched in the reactors during the course of operation.
doi:10.1128/AEM.68.5.2285-2293.2002
PMCID: PMC127532  PMID: 11976099
17.  Verticillium Suppression Is Associated with the Glucosinolate Composition of Arabidopsis thaliana Leaves 
PLoS ONE  2013;8(9):e71877.
The soil-borne fungal pathogen Verticillium longisporum is able to penetrate the root of a number of plant species and spread systemically via the xylem. Fumigation of Verticillium contaminated soil with Brassica green manure is used as an environmentally friendly method for crop protection. Here we present a study focused on the potential role of glucosinolates and their breakdown products of the model plant Arabidopsis thaliana in suppressing growth of V. longisporum. For this purpose we analysed the glucosinolate composition of the leaves and roots of a set of 19 key accessions of A. thaliana. The effect of volatile glucosinolate hydrolysis products on the in vitro growth of the pathogen was tested by exposing the fungus to hydrated lyophilized plant tissue. Volatiles released from leaf tissue were more effective than from root tissue in suppressing mycelial growth of V. longisporum. The accessions varied in their efficacy, with the most effective suppressing mycelial growth by 90%. An analysis of glucosinolate profiles and their enzymatic degradation products revealed a correlation between fungal growth inhibition and the concentration of alkenyl glucosinolates, particularly 2-propenyl (2Prop) glucosinolate, respectively its hydrolysis products. Exposure of the fungus to purified 2Prop glucosinolate revealed that its suppressive activity was correlated with its concentration. Spiking of 2Prop glucosinolate to leaf material of one of the least effective A. thaliana accessions led to fungal growth suppression. It is suggested that much of the inhibitory effect observed for the tested accessions can be explained by the accumulation of 2Prop glucosinolate.
doi:10.1371/journal.pone.0071877
PMCID: PMC3764120  PMID: 24039726
18.  Over-expression of the Arabidopsis proton-pyrophosphatase AVP1 enhances transplant survival, root mass, and fruit development under limiting phosphorus conditions 
Journal of Experimental Botany  2014;65(12):3045-3053.
Phosphorus (P), an element required for plant growth, fruit set, fruit development, and fruit ripening, can be deficient or unavailable in agricultural soils. Previously, it was shown that over-expression of a proton-pyrophosphatase gene AVP1/AVP1D (AVP1DOX) in Arabidopsis, rice, and tomato resulted in the enhancement of root branching and overall mass with the result of increased mineral P acquisition. However, although AVP1 over-expression also increased shoot biomass in Arabidopsis, this effect was not observed in tomato under phosphate-sufficient conditions. AVP1DOX tomato plants exhibited increased rootward auxin transport and root acidification compared with control plants. AVP1DOX tomato plants were analysed in detail under limiting P conditions in greenhouse and field trials. AVP1DOX plants produced 25% (P=0.001) more marketable ripened fruit per plant under P-deficient conditions compared with the controls. Further, under low phosphate conditions, AVP1DOX plants displayed increased phosphate transport from leaf (source) to fruit (sink) compared to controls. AVP1DOX plants also showed an 11% increase in transplant survival (P<0.01) in both greenhouse and field trials compared with the control plants. These results suggest that selection of tomato cultivars for increased proton pyrophosphatase gene expression could be useful when selecting for cultivars to be grown on marginal soils.
doi:10.1093/jxb/eru149
PMCID: PMC4071825  PMID: 24723407
Fruit development; H+-pyrophosphatase; phosphorus; root development; tomato; transplant efficiency.
19.  EFFECT OF SODIUM SULFATE AND MAGNESIUM SULFATE ON HETEROPOLYSACCHARIDE SYNTHESIS IN GRAM-NEGATIVE SOIL BACTERIA 
Journal of Bacteriology  1962;83(3):483-489.
Markovitz, Alvin (University of Chicago, Chicago, Ill.) and Susan Sylvan. Effect of sodium sulfate and magnesium sulfate on heteropolysaccharide synthesis in gram-negative soil bacteria. J. Bacteriol. 83:483–489. 1962.—The effect of Na2SO4 and MgSO4 on heteropolysaccharide biosynthesis has been investigated in gram-negative bacteria isolated from soil. These bacteria may be divided into three arbitrary groups on the basis of the effect of Na2SO4 and MgSO4 on heteropolysaccharide synthesis: group 1, synthesis of polysaccharides containing uronic acid is inhibited by increasing the concentration of sulfate ion; group 2, synthesis of polysaccharides containing uronic acid is stimulated by sulfate ions; group 3, synthesis of polysaccharide not containing uronic acid is stimulated minimally by Na2SO4.
PMCID: PMC279300  PMID: 14470034
20.  Raman Spectroscopic Analysis of Geological and Biogeological Specimens of Relevance to the ExoMars Mission 
Astrobiology  2013;13(6):543-549.
Abstract
A novel miniaturized Raman spectrometer is scheduled to fly as part of the analytical instrumentation package on an ESA remote robotic lander in the ESA/Roscosmos ExoMars mission to search for evidence for extant or extinct life on Mars in 2018. The Raman spectrometer will be part of the first-pass analytical stage of the sampling procedure, following detailed surface examination by the PanCam scanning camera unit on the ExoMars rover vehicle. The requirements of the analytical protocol are stringent and critical; this study represents a laboratory blind interrogation of specimens that form a list of materials that are of relevance to martian exploration and at this stage simulates a test of current laboratory instrumentation to highlight the Raman technique strengths and possible weaknesses that may be encountered in practice on the martian surface and from which future studies could be formulated. In this preliminary exercise, some 10 samples that are considered terrestrial representatives of the mineralogy and possible biogeologically modified structures that may be identified on Mars have been examined with Raman spectroscopy, and conclusions have been drawn about the viability of the unambiguous spectral identification of biomolecular life signatures. It is concluded that the Raman spectroscopic technique does indeed demonstrate the capability to identify biomolecular signatures and the mineralogy in real-world terrestrial samples with a very high degree of success without any preconception being made about their origin and classification. Key Words: Biosignatures—Mars Exploration Rovers—Raman spectroscopy—Search for life (biosignatures)—Planetary instrumentation. Astrobiology 13, 543–549.
doi:10.1089/ast.2012.0872
PMCID: PMC3689185  PMID: 23758166
21.  Influence of Incubation Solution on the Rate of Recovery of Pratylenchus brachyurus from Cotton Roots 
Journal of Nematology  1971;3(4):378-385.
The rate of recovery of Pratylenchus brachyurus from cotton roots was enhanced when the tissue was incubated in solutions containing 10 ppm ethoxyethyl mercuric chloride, 50 ppm dihydrostreptomycin sulfate, 50, 100, or 1,000 ppm diisobutylphenoxethyl dimethyl benzyl ammonium chloride, or mixtures of these compounds. Incubation in 10 or 100 ppm zinc sulfate, zinc chloride, or magnesium chloride also enhanced the rate of recovery. Incubation solutions containing 1 or 1,000 ppm zinc chloride or magnesium chloride had no influence on this phenomenon, whereas, 10,000 ppm zinc sulfate, zinc chloride, or magnesium chloride retarded the rate of recovery. A t all incubation intervals during the first 21 days after the roots were removed from soil, the P. brachyurus population consisted of approximately 25% second-stage juveniles, 44% third and fourth-stage juveniles, and 31% females. At least 88% of the second-stage juveniles and 51% of the third and fourth-stage juveniles passed through a single 325-mesh sieve, whereas, 84% of the females collected were retained on a sieve of this mesh.
PMCID: PMC2619902  PMID: 19322395
Gossypium hirsutum; Extraction; Incubation
22.  Plant nutrition for sustainable development and global health 
Annals of Botany  2010;105(7):1073-1080.
Background
Plants require at least 14 mineral elements for their nutrition. These include the macronutrients nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and sulphur (S) and the micronutrients chlorine (Cl), boron (B), iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), nickel (Ni) and molybdenum (Mo). These are generally obtained from the soil. Crop production is often limited by low phytoavailability of essential mineral elements and/or the presence of excessive concentrations of potentially toxic mineral elements, such as sodium (Na), Cl, B, Fe, Mn and aluminium (Al), in the soil solution.
Scope
This article provides the context for a Special Issue of the Annals of Botany on ‘Plant Nutrition for Sustainable Development and Global Health’. It provides an introduction to plant mineral nutrition and explains how mineral elements are taken up by roots and distributed within plants. It introduces the concept of the ionome (the elemental composition of a subcellular structure, cell, tissue or organism), and observes that the activities of key transport proteins determine species-specific, tissue and cellular ionomes. It then describes how current research is addressing the problems of mineral toxicities in agricultural soils to provide food security and the optimization of fertilizer applications for economic and environmental sustainability. It concludes with a perspective on how agriculture can produce edible crops that contribute sufficient mineral elements for adequate animal and human nutrition.
doi:10.1093/aob/mcq085
PMCID: PMC2887071  PMID: 20430785
Biofortification; fertilizer use efficiency; mineral nutrition; pollution; toxicity; transport protein
23.  Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana 
PLoS ONE  2012;7(4):e35121.
In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org.
doi:10.1371/journal.pone.0035121
PMCID: PMC3338729  PMID: 22558123
24.  Sultr4;1 mutant seeds of Arabidopsis have an enhanced sulphate content and modified proteome suggesting metabolic adaptations to altered sulphate compartmentalization 
BMC Plant Biology  2010;10:78.
Background
Sulphur is an essential macronutrient needed for the synthesis of many cellular components. Sulphur containing amino acids and stress response-related compounds, such as glutathione, are derived from reduction of root-absorbed sulphate. Sulphate distribution in cell compartments necessitates specific transport systems. The low-affinity sulphate transporters SULTR4;1 and SULTR4;2 have been localized to the vacuolar membrane, where they may facilitate sulphate efflux from the vacuole.
Results
In the present study, we demonstrated that the Sultr4;1 gene is expressed in developing Arabidopsis seeds to a level over 10-fold higher than the Sultr4;2 gene. A characterization of dry mature seeds from a Sultr4;1 T-DNA mutant revealed a higher sulphate content, implying a function for this transporter in developing seeds. A fine dissection of the Sultr4;1 seed proteome identified 29 spots whose abundance varied compared to wild-type. Specific metabolic features characteristic of an adaptive response were revealed, such as an up-accumulation of various proteins involved in sugar metabolism and in detoxification processes.
Conclusions
This study revealed a role for SULTR4;1 in determining sulphate content of mature Arabidopsis seeds. Moreover, the adaptive response of sultr4;1 mutant seeds as revealed by proteomics suggests a function of SULTR4;1 in redox homeostasis, a mechanism that has to be tightly controlled during development of orthodox seeds.
doi:10.1186/1471-2229-10-78
PMCID: PMC3095352  PMID: 20426829
25.  Perchlorate Radiolysis on Mars and the Origin of Martian Soil Reactivity 
Astrobiology  2013;13(6):515-520.
Abstract
Results from the Viking biology experiments indicate the presence of reactive oxidants in martian soils that have previously been attributed to peroxide and superoxide. Instruments on the Mars Phoenix Lander and the Mars Science Laboratory detected perchlorate in martian soil, which is nonreactive under the conditions of the Viking biology experiments. We show that calcium perchlorate exposed to gamma rays decomposes in a CO2 atmosphere to form hypochlorite (ClO−), trapped oxygen (O2), and chlorine dioxide (ClO2). Our results show that the release of trapped O2 (g) from radiation-damaged perchlorate salts and the reaction of ClO− with amino acids that were added to the martian soils can explain the results of the Viking biology experiments. We conclude that neither hydrogen peroxide nor superoxide is required to explain the results of the Viking biology experiments. Key Words: Mars—Radiolysis—Organic degradation—in situ measurement—Planetary habitability and biosignatures. Astrobiology 13, 515–520.
doi:10.1089/ast.2013.0999
PMCID: PMC3691774  PMID: 23746165

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