Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization.

IMPORTANCE: Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.

Mars-Analog Calcium Sulfate Veins Record Evidence of Ancient Subsurface Life.

Ancient veins of calcium sulfate minerals (anhydrite, bassanite, and gypsum) deposited by subsurface aqueous fluids crosscut fluviolacustrine sedimentary rocks at multiple localities on Mars. Although these veins have been considered an attractive target for astrobiological investigation, their potential to preserve biosignatures is poorly understood. Here, we report the presence of biogenic authigenic pyrite in a fibrous gypsum vein of probable Cenozoic emplacement age from Permian lacustrine rocks in Northwest England. Pyrite occurs at the vein margins and displays a complex interfingering boundary with the surrounding gypsum suggestive of replacive authigenic growth. Gypsum-entombed carbonaceous material of probable organic origin was also identified by Raman spectroscopic microscopy in close proximity to the pyrite. Spatially resolved ion microprobe (SIMS) measurements reveal that the pyrite sulfur isotope composition is consistently very light (δ34SVCDT = -30.7‰). Comparison with the sulfate in the vein gypsum (δ34SVCDT = +8.5‰) indicates a fractionation too large to be explained by nonbiological (thermochemical) sulfate reduction. We infer that the pyrite was precipitated by microorganisms coupling the reduction of vein-derived sulfate with the oxidation of wall-derived organic matter. This is the first evidence that such veins can incorporate biosignatures that remain stable over geological time, which could be detected in samples returned from Mars.

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks.

Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.

Aeolian abrasion of rocks as a mechanism to produce methane in the Martian atmosphere.

Seasonal changes in methane background levels and methane spikes have been detected in situ a metre above the Martian surface, and larger methane plumes detected via ground-based remote sensing, however their origin have not yet been adequately explained. Proposed methane sources include the UV irradiation of meteoritic-derived organic matter, hydrothermal reactions with olivine, organic breakdown via meteoroid impact, release from gas hydrates, biological production, or the release of methane from fluid inclusions in basalt during aeolian erosion. Here we quantify for the first time the potential importance of aeolian abrasion as a mechanism for releasing trapped methane from within rocks, by coupling estimates of present day surface wind abrasion with the methane contents of a variety of Martian meteorites, analogue terrestrial basalts and analogue terrestrial sedimentary rocks. We demonstrate that the abrasion of basalt under present day Martian rates of aeolian erosion is highly unlikely to produce detectable changes in methane concentrations in the atmosphere. We further show that, although there is a greater potential for methane production from the aeolian abrasion of certain sedimentary rocks, to produce the magnitude of methane concentrations analysed by the Curiosity rover they would have to contain methane in similar concentrations as economic reserved of biogenic/thermogenic deposits on Earth. Therefore we suggest that aeolian abrasion is an unlikely origin of the methane detected in the Martian atmosphere, and that other methane sources are required.

Neoproterozoic copper cycling, and the rise of metazoans.

The rise of animal life is temporally related to the increased availability of oxygen in the hydrosphere and atmosphere during the Neoproterozoic. However, the earliest metazoans probably needed relatively low oxygen concentrations, suggesting additional environmental and/or biochemical developments were involved. Copper was required in the exploitation of oxygen by the evolving animals, through the development of respiratory proteins and the extracellular matrix required for structural support. We synthesize global data demonstrating a marked enrichment of copper in the Earth's crust that coincided with the biological use of oxygen, and this new biological use of copper. The copper enrichment was likely recycled into the surface environment by weathering of basalt and other magmatic rocks, at copper liberation rates up to 300 times that of typical granitic terrain. The weathering of basalts also triggered the Sturtian glaciation, which accelerated erosion. We postulate that the coincidence of a high availability of copper, along with increased oxygen levels, for the first time during the Neoproterozoic supported the critical advances of respiration and structural support in evolving animals.

Assessing Behavioral Styles Among Nurse Managers: Implications for Leading Effective Teams.

Nurse leaders must use behaviors that foster effective teams. The purpose of this study was to determine the behavioral style by 3,396 nurse leaders who attended leadership and communication continuing education courses. Sessions included identifying behavioral style preferences using the DiSC® Personal Profile Instrument. Of the four behavioral dimensions, Dominance, Influence, Steadiness, and Conscientiousness, 73% scored highest in Dominance and Conscientiousness. The remaining 27% scored highest in preferences for Influence and Steadiness. Nursing leaders may benefit from awareness of differences in behavioral style preferences to enhance communication and team effectiveness, as well as improve satisfaction among team members.

From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms.

Any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. Microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. This paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. In addition, we review some of the most effective microbial products on the market today, explore the reasons for their success and outline some of the major challenges involved in industrial production and commercialization of beneficial strains for widespread agricultural application. General processes associated with commercializing viable microbial products are discussed in two broad categories, biofertility inoculants and biocontrol products. Specifically, we address what farmers desire in potential microbial products, how mode of action informs decisions on product applications, the influence of variation in laboratory and field study data, challenges with scaling for mass production, and the importance of consistent efficacy, product stability and quality. In order to make a significant impact on global sustainable agriculture, the implementation of plant beneficial microorganisms will require a more seamless transition between laboratory and farm application. Early attention to the challenges presented here will improve the likelihood of developing effective microbial products to improve crop yields, decrease disease severity, and help to feed an increasingly hungry planet.

Asphaltene detection using surface enhanced Raman scattering (SERS).

Surface enhanced Raman spectroscopy using a gold substrate and excitation at 514 nm can detect sub parts per million quantities of asphaltene and thereby petroleum. This simple format and sensitivity make it transformative for applications including sample triage, flow assurance, environmental protection and analysis of unique one of a kind materials.

Raman spectroscopy on Mars: identification of geological and bio-geological signatures in Martian analogues using miniaturized Raman spectrometers.

The first Raman spectrometers to be used for in situ analysis of planetary material will be launched as part of powerful, rover-based analytical laboratories within the next 6 years. There are a number of significant challenges associated with building spectrometers for space applications, including limited volume, power and mass budgets, the need to operate in harsh environments and the need to operate independently and intelligently for long periods of time (due to communication limitations). Here, we give an overview of the technical capabilities of the Raman instruments planned for future planetary missions and give a review of the preparatory work being pursued to ensure that such instruments are operated successfully and optimally. This includes analysis of extremophile samples containing pigments associated with biological processes, synthetic materials which incorporate biological material within a mineral matrix, planetary analogues containing low levels of reduced carbon and samples coated with desert varnish that incorporate both geo-markers and biomarkers. We discuss the scientific importance of each sample type and the challenges using portable/flight-prototype instrumentation. We also report on technical development work undertaken to enable the next generation of Raman instruments to reach higher levels of sensitivity and operational efficiency.

Effect of a dairy- and calcium-rich diet on weight loss and appetite during energy restriction in overweight and obese adults: a randomized trial.

BACKGROUND/OBJECTIVES: A diet rich in dairy and calcium (Ca) has been variably associated with improvements in body composition and decreased risk of type 2 diabetes. Our objective was to determine if a dietary pattern high in dairy and Ca improves weight loss and subjective appetite to a greater extent than a low dairy/Ca diet during energy restriction in overweight and obese adults with metabolic syndrome. SUBJECTS/METHODS: A total of 49 participants were randomized to one of two treatment groups: Control (low dairy, ≈ 700 mg/day Ca, -500 kcal/day) or Dairy/Ca (high dairy, ≈ 1400 mg/day Ca, -500 kcal/day) for 12 weeks. Body composition, subjective ratings of appetite, food intake, plasma satiety hormones, glycemic response and inflammatory cytokines were measured. RESULTS: Control (-2.2 ± 0.5 kg) and Dairy/Ca (-3.3 ± 0.6 kg) had similar weight loss. Based on self-reported energy intake, the percentage of expected weight loss achieved was higher with Dairy/Ca (82.1 ± 19.4%) than Control (32.2 ± 7.7%; P=0.03). Subjects in the Dairy/Ca group reported feeling more satisfied (P=0.01) and had lower dietary fat intake (P=0.02) over 12 weeks compared with Control. Compared with Control, Dairy/Ca had higher plasma levels of peptide tyrosine tyrosine (PYY, P=0.01) during the meal tolerance test at week 12. Monocyte chemoattractant protein-1 was reduced at 30 min with Dairy/Ca compared with Control (P=0.04). CONCLUSIONS: In conclusion, a dairy- and Ca-rich diet was not associated with greater weight loss than control. Modest increases in plasma PYY concentrations with increased dairy/Ca intake, however, may contribute to enhanced sensations of satisfaction and reduced dietary fat intake during energy restriction.

Elevated expression of artemis in human fibroblast cells is associated with cellular radiosensitivity and increased apoptosis.

BACKGROUND: The objective of this study was to determine the molecular mechanisms responsible for cellular radiosensitivity in two human fibroblast cell lines 84BR and 175BR derived from two cancer patients. METHODS: Clonogenic assays were performed following exposure to increasing doses of gamma radiation to confirm radiosensitivity. γ-H2AX foci assays were used to determine the efficiency of DNA double-strand break (DSB) repair in cells. Quantitative PCR (Q-PCR) established the expression levels of key DNA DSB repair genes. Imaging flow cytometry using annexin V-FITC was used to compare artemis expression and apoptosis in cells. RESULTS: Clonogenic cellular hypersensitivity in the 84BR and 175BR cell lines was associated with a defect in DNA DSB repair measured by the γ-H2AX foci assay. The Q-PCR analysis and imaging flow cytometry revealed a two-fold overexpression of the artemis DNA repair gene, which was associated with an increased level of apoptosis in the cells before and after radiation exposure. Overexpression of normal artemis protein in a normal immortalised fibroblast cell line NB1-Tert resulted in increased radiosensitivity and apoptosis. CONCLUSION: We conclude that elevated expression of artemis is associated with higher levels of DNA DSB, radiosensitivity and elevated apoptosis in two radio-hypersensitive cell lines. These data reveal a potentially novel mechanism responsible for radiosensitivity and show that increased artemis expression in cells can result in either radiation resistance or enhanced sensitivity.

Weathering of post-impact hydrothermal deposits from the Haughton impact structure: implications for microbial colonization and biosignature preservation.

Meteorite impacts are among the very few processes common to all planetary bodies with solid surfaces. Among the effects of impact on water-bearing targets is the formation of post-impact hydrothermal systems and associated mineral deposits. The Haughton impact structure (Devon Island, Nunavut, Canada, 75.2 °N, 89.5 °W) hosts a variety of hydrothermal mineral deposits that preserve assemblages of primary hydrothermal minerals commonly associated with secondary oxidative/hydrous weathering products. Hydrothermal mineral deposits at Haughton include intra-breccia calcite-marcasite vugs, small intra-breccia calcite or quartz vugs, intra-breccia gypsum megacryst vugs, hydrothermal pipe structures and associated surface "gossans," banded Fe-oxyhydroxide deposits, and calcite and quartz veins and coatings in shattered target rocks. Of particular importance are sulfide-rich deposits and their associated assemblage of weathering products. Hydrothermal mineral assemblages were characterized structurally, texturally, and geochemically with X-ray diffraction, micro X-ray diffraction, optical and electron microscopy, and inductively coupled plasma atomic emission spectroscopy. Primary sulfides (marcasite and pyrite) are commonly associated with alteration minerals, including jarosite (K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6), rozenite FeSO(4)·4(H(2)O), copiapite (Fe,Mg)Fe(4)(SO(4))(6)(OH)(2)·20(H(2)O), fibroferrite Fe(SO(4))(OH)·5(H(2)O), melanterite FeSO(4)·7(H(2)O), szomolnokite FeSO(4)·H(2)O, goethite α-FeO(OH), lepidocrocite γ-FeO(OH) and ferrihydrite Fe(2)O(3)·0.5(H(2)O). These alteration assemblages are consistent with geochemical conditions that were locally very different from the predominantly circumneutral, carbonate-buffered environment at Haughton. Mineral assemblages associated with primary hydrothermal activity, and the weathering products of such deposits, provide constraints on possible microbial activity in the post-impact environment. The initial period of active hydrothermal circulation produced primary mineral assemblages, including Fe sulfides, and was succeeded by a period dominated by oxidation and low-temperature hydration of primary minerals by surface waters. Active hydrothermal circulation can enable the rapid delivery of nutrients to microbes. Nutrient availability following the cessation of hydrothermal circulation is likely more restricted; therefore, the biological importance of chemical energy from hydrothermal mineral deposits increases with time. Weathering of primary hydrothermal deposits and dissolution and reprecipitation of mobile weathering products also create many potential habitats for endolithic microbes. They also provide a mechanism that may preserve biological materials, potentially over geological timescales.

Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400.

The phenylacetyl-CoA (Paa) catabolic pathway and genome-wide gene expression responses to phenylacetate catabolism were studied in the polychlorinated biphenyl (PCB)-degrading strain Burkholderia xenovorans LB400. Microarray and RT-qPCR analyses identified three non-contiguous chromosomal clusters of genes that are predicted to encode a complete Paa pathway that were induced up to 40-fold during growth of LB400 on phenylacetate: paaGHIJKR, paaANEBDF, and paaC. Comparison of the available genome sequences revealed that this organization is unique to Burkholderiaceae. Parallel proteomic studies identified 7 of the 14 predicted Paa proteins, most of which were detected only in phenylacetate-grown cells, but not in benzoate- or succinate-grown cells. Finally, the transcriptomic and proteomic analyses revealed the induction of at least 7 predicted catabolic pathways of aromatic compounds and some aromatic plant products (phenols, mandelate, biphenyl, C(1) compounds, mevalonate, opine, and isoquinoline), as well as an oxidative stress response and a large group of transporters. Most of these genes were not induced during growth on benzoate or biphenyl, suggesting that phenylacetate or a metabolite may act as a signal that triggers multiple physiological processes. Identifying the components of the Paa pathway is important since the pathway appears to contribute to virulence of Burkholderia pathogens.

Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock.

Shewanellae are microbial models for environmental stress response; however, the sequential expression of mechanisms in response to stress is poorly understood. Here we experimentally determine the response mechanisms of Shewanella amazonensis SB2B during sodium chloride stress using a novel liquid chromatography and accurate mass-time tag mass spectrometry time-course proteomics approach. The response of SB2B involves an orchestrated sequence of events comprising increased signal transduction associated with motility and restricted growth. Following a metabolic shift to branched chain amino acid degradation, motility and cellular replication proteins return to pre-perturbed levels. Although sodium chloride stress is associated with a change in the membrane fatty acid composition in other organisms, this is not the case for SB2B as fatty acid degradation pathways are not expressed and no change in the fatty acid profile is observed. These findings suggest that shifts in membrane composition may be an indirect physiological response to high NaCl stress.

Functional biogeography as evidence of gene transfer in hypersaline microbial communities.

BACKGROUND: Horizontal gene transfer (HGT) plays a major role in speciation and evolution of bacteria and archaea by controlling gene distribution within an environment. However, information that links HGT to a natural community using relevant population-genetics parameters and spatial considerations is scarce. The Great Salt Lake (Utah, USA) provides an excellent model for studying HGT in the context of biogeography because it is a contiguous system with dispersal limitations due to a strong selective salinity gradient. We hypothesize that in spite of the barrier to phylogenetic dispersal, functional characteristics--in the form of HGT--expand beyond phylogenetic limitations due to selective pressure. METHODOLOGY AND RESULTS: To assay the functional genes and microorganisms throughout the GSL, we used a 16S rRNA oligonucleotide microarray (Phylochip) and a functional gene array (GeoChip) to measure biogeographic patterns of nine microbial communities. We found a significant difference in biogeography based on microarray analyses when comparing Sørensen similarity values for presence/absence of function and phylogeny (Student's t-test; p = 0.005). CONCLUSION AND SIGNIFICANCE: Biogeographic patterns exhibit behavior associated with horizontal gene transfer in that informational genes (16S rRNA) have a lower similarity than functional genes, and functional similarity is positively correlated with lake-wide selective pressure. Specifically, high concentrations of chromium throughout GSL correspond to an average similarity of chromium resistance genes that is 22% higher than taxonomic similarity. This suggests active HGT may be measured at the population level in microbial communities and these biogeographic patterns may serve as a model to study bacteria adaptation and speciation.

Increased plasma PYY levels following supplementation with the functional fiber PolyGlycopleX in healthy adults.

BACKGROUND/OBJECTIVES: A variety of dietary fibers have been shown to alter satiety hormone gene expression and secretion. The objective of this study was to examine plasma satiety hormone concentrations in healthy subjects consuming either PolyGlycopleX (PGX) or control (skim milk powder) for 21 days. SUBJECTS/METHODS: A randomized, double-blind, placebo-controlled clinical study was conducted in 54 healthy male and female adults. Participants consumed 5 g per day of PGX or control for 1 week followed by 2 additional weeks of 10 g per day of assigned product (n=27 per group). Primary outcomes measured at three visits (V1, V2 and V3) were plasma active glucagon-like peptide-1 (GLP-1) total ghrelin, peptide YY (PYY) and insulin. RESULTS: There was a significant effect of visit for fasting PYY with control participants experiencing decreased PYY levels over time while PGX prevented this decline. When stratified by body mass index (BMI), PGX increased fasting PYY levels from week 1 to week 3 compared with control in participants with BMI <23 kg/m(2). There was a significant effect of visit for fasting ghrelin with levels decreasing in both PGX and control groups over time. No differences were detected in fasting GLP-1 levels. Although there was a 14% reduction in fasting insulin between V1 and V3 with PGX this was not significantly different from control. CONCLUSIONS: PGX is a highly viscous, functional fiber that modifies satiety hormone secretion in healthy adults. Its' potential to act similarly in overweight adults warrants investigation.

Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400.

The principal means for microbial degradation of polychlorinated biphenyls (PCBs) is through the biphenyl pathway. Although molecular aspects of the regulation of the biphenyl pathway have been studied, information on environmental facets such as the effect of alternative carbon sources on (polychlorinated) biphenyl degradation is limited. Here we explore the effect of environmental conditions (e.g., carbon source and growth phase) on the variation in PCB degradation profiles of Burkholderia xenovorans LB400. Genome-wide expression patterns reveal 25 genes commonly up-regulated during PCB degradation and growth on biphenyl to be upregulated in the transition to stationary phase (relative to growth on succinate) including two putative detoxification pathways. Quantitative reverse transcription PCR (Q-RT-PCR) analysis of the upper biphenyl pathway (bphA, bphD, and bphR1), and detoxification genes in response to environmental conditions suggest associated regulation of the biphenyl pathway and chloroacetaldehyde dehydrogenase. The response of genes in the upper biphenyl pathway to carbon source competition and growth phase reveals inhibition of the biphenyl pathway by PCBs. Although PCBs are not degraded during growth on succinate with PCBs, expression data indicate that the biphenyl pathway is induced, suggesting that post-transcriptional regulation or active transport of biphenyl maybe limiting PCB degradation. Identification of the involvement of peripheral pathways in degradation of PCBs is crucial to understanding PCB degradation in an environmental context as bacteria capable of biodegradation experience a range of carbon sources and growth phases.

Relating perturbation magnitude to temporal gene expression in biological systems.

BACKGROUND: Most transcriptional activity is a result of environmental variability. This cause (environment) and effect (gene expression) relationship is essential to survival in any changing environment. The specific relationship between environmental perturbation and gene expression - and stability of the response - has yet to be measured in detail. We describe a method to quantitatively relate perturbation magnitude to response at the level of gene expression. We test our method using Saccharomyces cerevisiae as a model organism and osmotic stress as an environmental stress. RESULTS: Patterns of gene expression were measured in response to increasing sodium chloride concentrations (0, 0.5, 0.7, 1.0, and 1.2 M) for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied. CONCLUSION: This study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.

Biodiversity in microbial communities: system scale patterns and mechanisms.

The relationship between anthropogenic impact and the maintenance of biodiversity is a fundamental question in ecology. The emphasis on the organizational level of biodiversity responsible for ecosystem processes is shifting from a species-centred focus to include genotypic diversity. The relationship between biodiversity measures at these two scales remains largely unknown. By stratifying anthropogenic effects between scales of biodiversity of bacterial communities, we show a statistically significant difference in diversity based on taxonomic scale. Communities with intermediate species richness show high genotypic diversity while speciose and species-poor communities do not. We propose that in species-poor communities, generally comprising stable yet harsh conditions, physiological tolerance and competitive trade-offs limit both the number of species that occur and the loss of genotypes due to decreases in already constrained fitness. In species-rich communities, natural environmental conditions result in well-defined community structure and resource partitioning. Disturbance of these communities disrupts niche space, resulting in lower genotypic diversity despite the maintenance of species diversity. Our work provides a model to inform future research about relationships between species and genotypic biodiversity based on determining the biodiversity consequences of changing environmental context.

A decentralized and onsite wastewater management course: bringing together global concerns and practical pedagogy.

This paper reports on the design, implementation, and results of a course focused on decentralized and onsite wastewater treatment in global contexts. Problem-based learning was the primary pedagogical method, with which students tackled real-world problems and designed systems to meet the needs of diverse populations. Both learning and course evaluations demonstrated that the course was successful in fulfilling learning objectives, increasing student design skills, and raising awareness of global applications. Based on this experience a list of recommendations was created for co-developing and team-teaching multidisciplinary design courses. These recommendations include ideas for aligning student and teacher goals, overcoming barriers to effective group-work, and imbedding continuous course assessments.