Traveler: Navigating Task Parallel Traces for Performance Analysis.

Understanding the behavior of software in execution is a key step in identifying and fixing performance issues. This is especially important in high performance computing contexts where even minor performance tweaks can translate into large savings in terms of computational resource use. To aid performance analysis, developers may collect an execution trace-a chronological log of program activity during execution. As traces represent the full history, developers can discover a wide array of possibly previously unknown performance issues, making them an important artifact for exploratory performance analysis. However, interactive trace visualization is difficult due to issues of data size and complexity of meaning. Traces represent nanosecond-level events across many parallel processes, meaning the collected data is often large and difficult to explore. The rise of asynchronous task parallel programming paradigms complicates the relation between events and their probable cause. To address these challenges, we conduct a continuing design study in collaboration with high performance computing researchers. We develop diverse and hierarchical ways to navigate and represent execution trace data in support of their trace analysis tasks. Through an iterative design process, we developed Traveler, an integrated visualization platform for task parallel traces. Traveler provides multiple linked interfaces to help navigate trace data from multiple contexts. We evaluate the utility of Traveler through feedback from users and a case study, finding that integrating multiple modes of navigation in our design supported performance analysis tasks and led to the discovery of previously unknown behavior in a distributed array library.

A method to experimentally clamp leaf water content to defined values to assess its effects on apoplastic pH.

BACKGROUND: Leaf hydration is controlled by feedback mechanisms, e.g. stomatal responses, adjustments of osmotic potential and hydraulic conductivity. Leaf water content thus is an input into related feedback-loops controlling the balance of water uptake and loss. Apoplastic alkalisation upon leaf dehydration is hypothesized to be involved together and in interaction with abscisic acid (ABA) in water stress related signaling on tissue level. However, important questions are still unresolved, e.g. the mechanisms leading to pH changes and the exact nature of its interaction with ABA. When studying these mechanisms and their intermediate signaling steps, an experimenter has only poor means to actually control the central experimental variable, leaf water content (LWC), because it is not only dependent on external variables (e.g. air humidity), which are under experimental control, but is also governed by the biological influences controlling transpiration and water uptake. Those are often unknown in their magnitude, unpredictable and fluctuating throughout an experiment and will prevent true repetitions of an experiment. The goal of the method presented here is to experimentally control and manipulate leaf water content (LWC) of attached intact leaves enclosed in a cuvette while simultaneously measuring physiological parameters like, in this case, apoplastic pH. RESULTS: An experimental setup was developed where LWC is measured by a sensor based on IR-transmission and its signal processed to control a pump which circulates air from the cuvette through a cold trap. Hereby a feedback-loop is formed, which by adjusting vapour pressure deficit (VPD) and consequently leaf transpiration can precisely control LWC. This technique is demonstrated here in a combination with microscopic fluorescence imaging of apoplastic pH (pHapo) as indicated by the excitation ratio of the pH sensitive dye OregonGreen. Initial results indicate that pHapo of the adaxial epidermis of Vicia faba is linearly related to reductions in LWC. CONCLUSIONS: Using this setup, constant LWC levels, step changes or ramps can be experimentally applied while simultaneously measuring physiological responses. The example experiments demonstrate that bringing LWC under experimental control in this way allows better controlled and more repeatable experiments to probe quantitative relationships between LWC and signaling and regulatory processes.

Alkali salt stress causes fast leaf apoplastic alkalinization together with shifts in ion and metabolite composition and transcription of key genes during the early adaptive response of Vicia faba L.

The mechanisms by which plants respond to alkali salt stress are still obscure, and the relevance of alkaline pH under combined alkali salt stress. Early stress responses can indicate mechanisms leading to damage and plant resistance. The apoplast contains essential determinants for plant growth, specifically early apoplastic pH fluctuations are induced by many stressors and hypothesized to be involved in stress signalling. Hence, this study aims to identify fast responses specific to alkaline pH and alkali salt stress by exposing the root of hydroponically grown Vicia faba L. plants to 150 min of either 50 mM NaHCO3 (pH 9) treatment or alkaline pH 9 alone. Apoplastic pH was monitored in real-time by ratiometric fluorescence microscopy simultaneously with SWIR transmission-based measurements of leaf water content (LWC). Moreover, we examined the effect of these stresses on apoplastic, symplastic and xylem ion and metabolite composition together with transcriptions of certain stress-responsive genes. Physiological and transcriptional changes were observed in response to NaHCO3 but not to alkaline pH alone. NaHCO3 elicited a transient reduction in LWC, followed by a transient alkalinization of the apoplast and stomatal closure. Simultaneously, organic acids and sugars accumulated. Fast upregulation of stress-responsive genes showed the significance of gene regulation for early plant adaptation to alkali salt stress.

One-time abscisic acid priming induces long-term salinity resistance in Vicia faba: Changes in key transcripts, metabolites, and ionic relations.

Abscisic acid (ABA) priming is known to enhance plant growth and survival under salinity. However, the mechanisms mediating this long-term acclimatization to salt stress are still obscure. Specifically, the long-term transcriptional changes and their effects on ion relations were never investigated. This motivated us to study the long-term (8 days) effect of one-time 24 h root priming treatment with 10 µM ABA on transcription levels of relevant regulated key genes, osmotically relevant metabolites, and ionic concentrations in Vicia faba grown under 50 mM NaCl salinity. The novelty of this study is that we could demonstrate long-term effects of a one-time ABA application. ABA-priming was found to prevent the salt-induced decline in root and shoot dry matter, improved photosynthesis, and inhibited terminal wilting of plants. It substantially increased the mRNA level of AAPK and 14-3-3 ABA inducible kinases and ion transporters (PM H+ -ATPase, VFK1, KUP7, SOS1, and CLC1). These ABA-induced transcriptional changes went along with altered tissue ion patterns. Primed plants accumulated less Na+ and Cl- but more K+ , Ca2+ , Zn2+ , Fe2+ , Mn2+ , NO3 - , and SO4 2- . Priming changed the composition pattern of organic osmolytes under salinity, with glucose and fructose being dominant in unprimed, whereas sucrose was dominant in the primed plants. We conclude that one-time ABA priming mitigates salt stress in Vicia faba by persistently changing transcription patterns of key genes, stabilizing the ionic and osmotic balance, and improving photosynthesis and growth.

Bacterially produced Pt-GFP as ratiometric dual-excitation sensor for in planta mapping of leaf apoplastic pH in intact Avena sativa and Vicia faba.

BACKGROUND: Ratiometric analysis with H(+)-sensitive fluorescent sensors is a suitable approach for monitoring apoplastic pH dynamics. For the acidic range, the acidotropic dual-excitation dye Oregon Green 488 is an excellent pH sensor. Long lasting (hours) recordings of apoplastic pH in the near neutral range, however, are more problematic because suitable pH indicators that combine a good pH responsiveness at a near neutral pH with a high photostability are lacking. The fluorescent pH reporter protein from Ptilosarcus gurneyi (Pt-GFP) comprises both properties. But, as a genetically encoded indicator and expressed by the plant itself, it can be used almost exclusively in readily transformed plants. In this study we present a novel approach and use purified recombinant indicators for measuring ion concentrations in the apoplast of crop plants such as Vicia faba L. and Avena sativa L. RESULTS: Pt-GFP was purified using a bacterial expression system and subsequently loaded through stomata into the leaf apoplast of intact plants. Imaging verified the apoplastic localization of Pt-GFP and excluded its presence in the symplast. The pH-dependent emission signal stood out clearly from the background. PtGFP is highly photostable, allowing ratiometric measurements over hours. By using this approach, a chloride-induced alkalinizations of the apoplast was demonstrated for the first in oat. CONCLUSIONS: Pt-GFP appears to be an excellent sensor for the quantification of leaf apoplastic pH in the neutral range. The presented approach encourages to also use other genetically encoded biosensors for spatiotemporal mapping of apoplastic ion dynamics.

The relation between stomatal aperture and gas exchange under consideration of pore geometry and diffusional resistance in the mesophyll.

The quantitative relation between stomatal aperture and gas exchange through the stomatal pore can be described by physical models derived from Fick's first law of diffusion. Such models, usually based on a simplified pore geometry, are used to calculate leaf conductance from stomatal pore dimensions or vice versa. In this study a combination of gas-exchange measurements and simultaneous microscopical observations of stomatal apertures was used to empirically determine this relationship. The results show a substantial deviation between measured stomatal conductance and that calculated from the simplified models. The main difference is a much steeper increase of conductance with aperture at small apertures. When the calculation was based on a realistic pore geometry derived from confocal laser scanning microscopy, a good fit to the experimentally found relationship could be obtained if additionally a significant contribution of a mesophyll diffusional resistance was taken into account.

Localization of mechanisms involved in hydropassive and hydroactive stomatal responses of Sambucus nigra to dry air.

The response of stomata to a reduction of air humidity is composed of a hydropassive opening followed by active closure. Whereas the mechanisms behind the hydropassive opening are largely understood, the location and physiological basis of the sensing mechanisms leading to active closure are not yet known. This study attempts to evaluate the importance of a single pore's transpiration on its own response and that of adjacent pores. Selected stomata on attached intact leaves of Sambucus nigra were sealed with mineral oil and the response to a reduction of humidity was continuously observed in situ. Blocking a pore's transpiration had no appreciable effect on hydropassive opening and subsequent stomatal closure. If the adjacent stomata were additionally sealed, the closing response was reduced, but not the hydropassive opening. On the other hand, sealing the entire leaf surface, except a small area including the observed stomata, also reduced stomatal closure. These results indicate that strictly local processes triggered by a pore's own transpiration are not required to induce stomatal closure. To describe the effect of one pore's transpiration on the hydropassive and hydroactive responses of neighboring stomata, a simple spatial model was constructed. It suggests that 90% of the closing effect covers an area of approximately 0.5 mm2, whereas the effect on hydropassive opening affects an area of approximately 1 mm2. This divergence may suggest mechanisms other than or in addition to those involving changes of local leaf water potential.

Rapid hydropassive opening and subsequent active stomatal closure follow heat-induced electrical signals in Mimosa pudica.

In Mimosa pudica L., heat stimulation triggers leaflet folding in local, neighbouring and distant leaves. Stomatal movements were observed microscopically during this folding reaction and electrical potentials, chlorophyll fluorescence, and leaf CO(2)/H(2)O-gas exchange were measured simultaneously. Upon heat stimulation of a neighbouring pinna, epidermal cells depolarized and the stomata began a rapid and pronounced transient opening response, leading to an approximately 2-fold increase of stomatal aperture within 60 s. At the same time, net CO(2) exchange showed a pronounced transient decrease, which was followed by a similar drop in photochemical quantum yield at photosystem (PS) II. Subsequently, CO(2)-gas exchange and photochemical quantum yield recovered and stomata closed partly or completely. The transient and fast stomatal opening response is interpreted as a hydropassive stomatal movement caused by a sudden loss of epidermal turgor. Thus, epidermal cells appear to respond in a similar manner to heat-induced signals as the pulvinar extensor cells. The subsequent closing of the stomata confirms earlier reports that stomatal movements can be induced by electrical signals. The substantial delay (several minutes) of guard cell turgor loss compared with the immediate response of the extensor and epidermal cells suggests a different, less direct mechanism for transmission of the propagating signal to the guard cells.