The H+ ATPase regulatory subunit of Methanococcus thermolithotrophicus: Amplification of an 800 bp fragment by polymerase chain reaction

AbstractAn 800 bp fragment of Methanococcus thermolithotrophicus genomic DNA was amplified by the polymerase chain reaction method using primers designed from conserved regions of the V-type H+ ATPase regulatory subunits from the archaebacterium Sulfolobus, and several eukaryotes. Although more than one product was obtained, only one of them had the expected size and was exclusively amplified in the presence of the left and right primers. The DNA and the deduced protein sequences of the putative Methanococcus H+ ATPase subunit revealed homology to the corresponding sequences in Sulfolobus and eukaryotes (about 60% identical residues) and a less evident homology to the eubacterial F1 -ATPase α-subunit (22% identical residues with E. coli)

Characterisation of spatial network-like patterns from junctions' geometry

We propose a new method for quantitative characterization of spatial network-like patterns with loops, such as surface fracture patterns, leaf vein networks and patterns of urban streets. Such patterns are not well characterized by purely topological estimators: also patterns that both look different and result from different morphogenetic processes can have similar topology. A local geometric cue -the angles formed by the different branches at junctions- can complement topological information and allow to quantify the large scale spatial coherence of the pattern. For patterns that grow over time, such as fracture lines on the surface of ceramics, the rank assigned by our method to each individual segment of the pattern approximates the order of appearance of that segment. We apply the method to various network-like patterns and we find a continuous but sharp dichotomy between two classes of spatial networks: hierarchical and homogeneous. The first class results from a sequential growth process and presents large scale organization, the latter presents local, but not global organization.Comment: version 2, 14 page

A minimal probabilistic model for soil moisture in seasonally dry climates

In seasonally dry climates, a distinct rainy season is followed by a pronounced dry season during which rainfall often makes a negligible contribution to soil moisture. Using stochastic analytical models of soil moisture to represent the effects of this seasonal change has been hindered by the need to mathematically represent the stochastic influence of wet season climate on dry season soil water dynamics. This study presents a simple process-based stochastic model for soil moisture dynamics, which explicitly models interseasonal transient dynamics while accounting for carry over soil moisture storage between the wet and dry seasons, and allows a derivation of an analytical expression for the dry season mean first passage time below a soil moisture threshold. Such crossing times pose controls on both vegetation productivity and water stress during dry summers. The new model, along with an existing model that incorporates nonzero dry season rainfall but not variability in the soil moisture condition at the start of the dry season, are tested against data from the Tonzi Ranch Ameriflux site. Both models predict first passage times well for high soil moisture thresholds, but the new model improves prediction at lower thresholds. The annual soil moisture probability distribution function (PDF) from the new model also compares well with observations

Predicting green: really radical (plant) predictive processing

In this article we account for the way plants respond to salient features of their environment under the free-energy principle for biological systems. Biological self-organization amounts to the minimization of surprise over time. We posit that any self-organizing system must embody a generative model whose predictions ensure that (expected) free energy is minimized through action. Plants respond in a fast, and yet coordinated manner, to environmental contingencies. They pro-actively sample their local environment to elicit information with an adaptive value. Our main thesis is that plant behaviour takes place by way of a process (active inference) that predicts the environmental sources of sensory stimulation. This principle, we argue, endows plants with a form of perception that underwrites purposeful, anticipatory behaviour. The aim of the article is to assess the prospects of a radical predictive processing story that would follow naturally from the free-energy principle for biological systems; an approach that may ultimately bear upon our understanding of life and cognition more broadly

Mesophyll photosynthesis and guard cell metabolism impacts on stomatal behaviour

Stomata control gaseous fluxes between the internal leaf air spaces and the external atmosphere. Guard cells determine stomatal aperture and must operate to ensure an appropriate balance between CO2 uptake for photosynthesis (A) and water loss, and ultimately plant water use efficiency (WUE). A strong correlation between A and stomatal conductance (gs) is well documented and often observed, but the underlying mechanisms, possible signals and metabolites that promote this relationship are currently unknown. In this review we evaluate the current literature on mesophyll-driven signals that may coordinate stomatal behaviour with mesophyll carbon assimilation. We explore a possible role of various metabolites including sucrose and malate (from several potential sources; including guard cell photosynthesis) and new evidence that improvements in WUE have been made by manipulating sucrose metabolism within the guard cells. Finally we discuss the new tools and techniques available for potentially manipulating cell-specific metabolism, including guard and mesophyll cells, in order to elucidate mesophyll-derived signals that coordinate mesophyll CO2 demands with stomatal behaviour, in order to provide a mechanistic understanding of these processes as this may identify potential targets for manipulations in order to improve plant WUE and crop yield. © 2014 New Phytologist Trust

The potential for deep groundwater use by Acacia papyrocarpa (Western myall) in a water-limited environment

Knowledge regarding the use of groundwater by plants has implications for successful mine rehabilitation and revegetation programs in water-limited environments. In this study, we combined several approaches to investigate water sources used by Acacia papyrocarpa (Western myall) in the far west of South Australia, including stable isotopes, water potential, groundwater and soil chemistry, and root mapping techniques. Plant δ 18 O signatures and water potentials were compared against a range of possible sources: rainwater, surface soil water (≤1 m depth), and deep groundwater ( > 20 m depth). Our aim was to determine whether groundwater contributed to the mix of waters used by A. papyrocarpa. Overall, we found that trees did not source surface soil water (≤1 m), and probably sourced deep soil water (i.e. > 1 m) rather than deep groundwater. Groundwater, however, could not be dismissed as a potential source, as root mapping showed tree roots were capable of reaching groundwater at depths > 20 m, and isotope results indicated a potential contribution by groundwater to tree water use. However, low osmotic potentials and/or high acidity levels were shown to pose likely barriers to groundwater uptake, at least at the time of sampling. We conclude that because groundwater salinity and acidity are spatially variable in this region, plants with extensive root systems may be able to utilize zones of groundwater with lower salinity and pH levels. Overall, this study contributes to our limited understanding of groundwater use by trees occurring in water-limited environments where groundwater is extremely deep ( > 20 m depth)

Information flow during gene activation by signaling molecules: ethylene transduction in Arabidopsis cells as a study system

<p>Abstract</p> <p>Background</p> <p>We study root cells from the model plant <it>Arabidopsis thaliana </it>and the communication channel conformed by the ethylene signal transduction pathway. A basic equation taken from our previous work relates the probability of expression of the gene <it>ERF</it>1 to the concentration of ethylene.</p> <p>Results</p> <p>The above equation is used to compute the Shannon entropy (<it>H</it>) or degree of uncertainty that the genetic machinery has during the decoding of the message encoded by the ethylene specific receptors embedded in the endoplasmic reticulum membrane and transmitted into the nucleus by the ethylene signaling pathway. We show that the amount of information associated with the expression of the master gene <it>ERF</it>1 (Ethylene Response Factor 1) can be computed. Then we examine the system response to sinusoidal input signals with varying frequencies to determine if the cell can distinguish between different regimes of information flow from the environment. Our results demonstrate that the amount of information managed by the root cell can be correlated with the frequency of the input signal.</p> <p>Conclusion</p> <p>The ethylene signaling pathway cuts off very low and very high frequencies, allowing a window of frequency response in which the nucleus reads the incoming message as a sinusoidal input. Out of this window the nucleus reads the input message as an approximately non-varying one. From this frequency response analysis we estimate: a) the gain of the system during the synthesis of the protein ERF1 (~-5.6 dB); b) the rate of information transfer (0.003 bits) during the transport of each new ERF1 molecule into the nucleus and c) the time of synthesis of each new ERF1 molecule (~21.3 s). Finally, we demonstrate that in the case of the system of a single master gene (<it>ERF</it>1) and a single slave gene (<it>HLS</it>1), the total Shannon entropy is completely determined by the uncertainty associated with the expression of the master gene. A second proposition shows that the Shannon entropy associated with the expression of the <it>HLS</it>1 gene determines the information content of the system that is related to the interaction of the antagonistic genes <it>ARF</it>1, 2 and <it>HLS</it>1.</p