Nutrient-induced signal transduction through the protein kinase A pathway and its role in the control of metabolism, stress resistance, and growth in yeast

Yeast cells growing in the presence of glucose or a related rapidly-fermented sugar differ strongly in a variety of physiological properties compared to cells growing in the absence of glucose. Part of these differences appear to be caused by the protein kinase A (PKA) and related signal transduction pathways. Addition of glucose to cells previously deprived of glucose triggers cAMP accumulation, which is apparently mediated by the Gpr1-Gpa2 G-protein coupled receptor system. However, the resulting effect on PKA-controlled properties is only transient when there is no complete growth medium present. When an essential nutrient is lacking, the cells arrest in the stationary phase G0. At the same time they acquire all characteristics of cells with low PKA activity, even if there is ample glucose present. When the essential nutrient is added again, a similar PKA-dependent protein phosphorylation cascade is triggered as observed after addition of glucose to glucose-deprived cells, but which is not cAMP-mediated. Because the pathway involved requires a fermentable carbon source and a complete growth medium, at least for its sustained activation, it has been called “fermentable growth medium (FGM)-induced pathway.”     

Reproductive biology of a large, aggregation-spawning serranid, Epinephelus fuscoguttatus (Forsskål): management implications

The reproductive biology of Great Barrier Reef populations of the long-lived grouper Epinephelus fuscoguttatus (brown-marbled grouper or flowery cod) was investigated using histological analyses. Evidence provided by gonad morphology and age-based demographics suggested monandric protogynous hermaphroditism. Younger age groups contained only immature and mature females, and all males were above the size and age of 100% female maturity, consistent with secondary males derived from mature females by adult sex change. Fishing records confirmed that spawning aggregations of this species and the co-occurring Epinephelus polyphekadion (camouflage grouper) are sometimes targeted on the Great Barrier Reef. Sampling data revealed strong spawning seasonality for E. fuscoguttatus , with a relatively narrow annual spawning period (November to January). The temporal pattern of reproductive activity within the spawning period, based on occurrence of near spawning ovaries (containing hydrated oocytes), indicated spawning events may occur throughout much of the lunar cycle and only partly coincide with seasonal fishing closure periods on the Great Barrier Reef. The results indicate that protection would be enhanced by a longer seasonal closure.     

Woody plants optimise stomatal behaviour relative to hydraulic risk

Stomatal response to environmental conditions forms the backbone of all ecosystem and carbon cycle models, but is largely based on empirical relationships. Evolutionary theories of stomatal behaviour are critical for guarding against prediction errors of empirical models under future climates. Longstanding theory holds that stomata maximise fitness by acting to maintain constant marginal water use efficiency over a given time horizon, but a recent evolutionary theory proposes that stomata instead maximise carbon gain minus carbon costs/risk of hydraulic damage. Using data from 34 species that span global forest biomes, we find that the recent carbon‐maximisation optimisation theory is widely supported, revealing that the evolution of stomatal regulation has not been primarily driven by attainment of constant marginal water use efficiency. Optimal control of stomata to manage hydraulic risk is likely to have significant consequences for ecosystem fluxes during drought, which is critical given projected intensification of the global hydrological cycle.     

Geography and island geomorphology shape fish assemblage structure on isolated coral reef systems

We quantify the relative importance of multi‐scale drivers of reef fish assemblage structure on isolated coral reefs at the intersection of the Indian and Indo‐Pacific biogeographical provinces. Large (>30 cm), functionally‐important and commonly targeted species of fish, were surveyed on the outer reef crest/front at 38 coral reef sites spread across three oceanic coral reef systems (i.e. Christmas Island, Cocos (Keeling) Islands and the Rowley Shoals), in the tropical Indian Ocean (c. 1.126 x 106 km²). The effects of coral cover, exposure, fishing pressure, lagoon size and geographical context, on observed patterns of fish assemblage structure were modelled using Multivariate Regression Trees. Reef fish assemblages were clearly separated in space with geographical location explaining ~53 % of the observed variation. Lagoon size, within each isolated reef system was an equally effective proxy for explaining fish assemblage structure. Among local‐scale variables, ‘distance from port’, a proxy for the influence of fishing, explained 5.2% of total variation and separated the four most isolated reefs from Cocos (Keeling) Island, from reefs with closer boating access. Other factors were not significant. Major divisions in assemblage structure were driven by sister taxa that displayed little geographical overlap between reef systems and low abundances of several species on Christmas Island corresponding to small lagoon habitats. Exclusion of geographical context from the analysis resulted in local processes explaining 47.3% of the variation, highlighting the importance of controlling for spatial correlation to understand the drivers of fish assemblage structure. Our results suggest reef fish assemblage structure on remote coral reef systems in the tropical eastern Indian Ocean reflects a biogeographical legacy of isolation between Indian and Pacific fish faunas and geomorphological variation within the region, more than local fishing pressure or reef condition. Our findings re‐emphasise the importance that historical processes play in structuring contemporary biotic communities.     

In Vivo Visualizations of Drought-Induced Embolism Spread in Vitis vinifera

Long-distance water transport through plant xylem is vulnerable to hydraulic dysfunction during periods of increased tension on the xylem sap, often coinciding with drought. While the effects of local and systemic embolism on plant water transport and physiology are well documented, the spatial patterns of embolism formation and spread are not well understood. Using a recently developed nondestructive diagnostic imaging tool, high-resolution x-ray computed tomography, we documented the dynamics of drought-induced embolism in grapevine (Vitis vinifera) plants in vivo, producing the first three-dimensional, high-resolution, time-lapse observations of embolism spread. Embolisms formed first in the vessels surrounding the pith at stem water potentials of approximately –1.2 megapascals in drought experiments. As stem water potential decreased, embolisms spread radially toward the epidermis within sectored vessel groupings via intervessel connections and conductive xylem relays, and infrequently (16 of 629 total connections) through lateral connections into adjacent vessel sectors. Theoretical loss of conductivity calculated from the high-resolution x-ray computed tomography images showed good agreement with previously published nuclear magnetic resonance imaging and hydraulic conductivity experiments also using grapevine. Overall, these data support a growing body of evidence that xylem organization is critically important to the isolation of drought-induced embolism spread and confirm that air seeding through the pit membranes is the principle mechanism of embolism spread.Water is transported through the xylem under tension and in a metastable state, making it inherently vulnerable to cavitation, the rapid phase change of liquid water to vapor (Dixon and Joly, 1895; Hayward, 1971; Tyree and Sperry, 1989). The resulting gas embolisms block water transport in the affected xylem vessel. It is widely accepted that embolisms spread between adjacent conduits when the pressure differential between gas-filled and water-filled conduits reaches a critical point where water vapor is aspirated through the pit membrane from the neighboring conduit (Tyree and Sperry, 1989; Tyree and Zimmermann, 2002). The resulting spread of embolisms through the xylem effectively reduces the hydraulic conductivity of the network, impairing the capacity to replace transpired water. The consequences of embolism formation can be dramatic, and it is now considered to be one of the major physiological factors driving reductions in forest primary productivity and drought-induced mortality in woody plants (Anderegg et al., 2012; Choat et al., 2012).Embolism spread between conduits is necessarily dependent on the number and orientation of the interconduit connections, but little is known about the organization of those connections or the spatial dynamics of embolism spread in vivo (Tyree and Zimmermann, 2002; Brodersen et al., 2010). This knowledge gap is largely due to the lack of a nondestructive visualization tool with sufficient resolution to study the propagation and spread of embolism. Previous efforts to visualize embolism in vivo utilized either cryo-scanning electron microscopy (cryo-SEM) or NMR imaging. Cryo-SEM yields fine resolution of frozen plant tissue, revealing the functional status of xylem conduits (i.e. water- or air-filled) at the time of freezing (Canny, 1997; Melcher et al., 2003; Cobb et al., 2007; Mayr et al., 2007; Johnson et al., 2012). Both transverse (Hukin et al., 2005; Sun et al., 2007; Johnson et al., 2012) and longitudinal (Utsumi et al., 1999) cryo-SEM sections have been prepared, but only provide a snapshot of a single point in time and in a single, two-dimensional plane. Similarly, NMR imaging was used in several studies as a nondestructive visualization tool to study the functional status of the xylem in vivo (Holbrook et al., 2001; Clearwater and Clark, 2003). However, the resulting images are typically of insufficient resolution to determine anything other than whether xylem conduits were filled with water or air. Three-dimensional (3D) imaging with NMR is challenging and is not frequently employed (Kuroda et al., 2006). Despite the availability of NMR, studies using this technology are largely focused to the spread of embolism over long periods of time (e.g. weeks [Umebayashi et al., 2011] or months [Pérez-Donoso et al., 2007]) rather than the short-term dynamics of embolism spread over the course of a few hours.Recently, high-resolution x-ray computed tomography (HRCT), a nondestructive diagnostic imaging tool, has been successfully used to study plant tissue in vivo (Brodersen et al., 2010, 2011). Synchrotron-based HRCT is based on the same principles as medical computed tomography systems but yields data with a spatial resolution of less than 5 µm and a temporal resolution of less than 30 min. Brodersen et al. (2011) expanded on this technology to study and map the 3D organization of grapevine (Vitis vinifera) stems and found that the functional status of the xylem could be determined in vivo. Brodersen et al. (2010) visualized the dynamics of embolism repair (i.e. the metabolically active refilling of embolized xylem conduits) in live plants using HRCT, including the growth of water droplets emerging from xylem parenchyma surrounding embolized vessels that eventually led to the dissolution of trapped gas inside the vessels. While we now have a better understanding of embolism repair and the physiological consequences of embolism spread are well documented (Tyree and Zimmermann, 2002; McDowell et al., 2008; Cochard et al., 2009; Zwieniecki and Holbrook, 2009; Choat et al., 2012), the spatial dynamics and biophysics of embolism formation and spread in vivo have yet to be fully explored. Clearly, the spatial organization of xylem conduits plays a critical role in embolism repair and is likely even more influential in embolism spread, as direct connections between conduits are the most likely pathway through the network. Building on these findings and new techniques, we aimed to take advantage of HRCT imaging to provide the first high-resolution visualization of the spread of drought-induced embolism.     

Technology platform development for targeted plasma metabolites in human heart failure

Background

Heart failure is a multifactorial disease associated with staggeringly high morbidity and motility. Recently, alterations of multiple metabolites have been implicated in heart failure; however, the lack of an effective technology platform to assess these metabolites has limited our understanding on how they contribute to this disease phenotype. We have successfully developed a new workflow combining specific sample preparation with tandem mass spectrometry that enables us to extract most of the targeted metabolites. 19 metabolites were chosen ascribing to their biological relevance to heart failure, including extracellular matrix remodeling, inflammation, insulin resistance, renal dysfunction, and cardioprotection against ischemic injury.

Results

In this report, we systematically engineered, optimized and refined a protocol applicable to human plasma samples; this study contributes to the methodology development with respect to deproteinization, incubation, reconstitution, and detection with mass spectrometry. The deproteinization step was optimized with 20% methanol/ethanol at a plasma:solvent ratio of 1:3. Subsequently, an incubation step was implemented which remarkably enhanced the metabolite signals and the number of metabolite peaks detected by mass spectrometry in both positive and negative modes. With respect to the step of reconstitution, 0.1% formic acid was designated as the reconstitution solvent vs. 6.5 mM ammonium bicarbonate, based on the comparable number of metabolite peaks detected in both solvents, and yet the signal detected in the former was higher. By adapting this finalized protocol, we were able to retrieve 13 out of 19 targeted metabolites from human plasma.

Conclusions

We have successfully devised a simple albeit effective workflow for the targeted plasma metabolites relevant to human heart failure. This will be employed in tandem with high throughput liquid chromatography mass spectrometry platform to validate and characterize these potential metabolic biomarkers for diagnostic and therapeutic development of heart failure patients.     

长春市儿童医院1998～2001年婴幼儿杯状病毒腹泻流行病学研究

人类杯状病毒(human calicivirus,HuCV)是引起儿童和成人非菌性胃肠炎的主要病原之一.为了掌握HuCV在我国的流行情况,1998年7月至2001年6月,从长春市儿童医院2343例5岁以下腹泻患儿中共收集粪便标本1264份,其中1056份来自2135例住院患儿.对轮状病毒检测为阴性的588份标本,经多价酶免疫试验(EIA)和两组引物反转录-聚合酶链反应(RT-PCR)检测HuCV,202份为阳性,其中住院患儿标本178份,HuCV检出率为16.9%.HuCV腹泻以2岁以下儿童为主(占96%),流行高峰季节为11月至次年3月.选择17株HuCV进行分子鉴定,15株属GⅡ-4群,1株属GⅡ-3群,另1株属GⅠ-2群,表明GⅡ-4群HuCV是我国流行的优势株.根据HuCV住院患儿的监测资料初步估计,HuCV腹泻住院率约为0.5‰～2.4‰.讨论了长春地区HuCV的流行趋势和疾病负担.以上结果为我国HuCV腹泻的预防和控制提供了科学依据.     

Hydraulic variability of tropical forests is largely independent of water availability

Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin (HSM), making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site-level hydraulic diversity of leaf turgor loss point, resistance to embolism (P₅₀), and HSMs is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P₅₀ values (< −2 MPa) are common across the wet and dry tropics. This high site-level hydraulic diversity, largely decoupled from water stress, could influence which species are favoured and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.     

The influence of predation and conspecific adults on the abundance of juvenile Evechinus chloroticus (Echinoidea:Echinometridae)

Summary Reefs dominated by red algae, associated with high echinoid densities, are consistent features of the shallow subtidal around northeastern New Zealand. Factors determining the abundance of juvenile Evechinus chloroticus were investigated in such a habitat. Using a factorial design, a field experiment was used to assess the influence of predators and adult E. chloroticus on juvenile abundance. The use of 2 m² exclusion cages enhanced juvenile E. chloroticus abundance over a 16 month period, an effect independent of conspecific adults. We attributed this effect to the exclusion of benthic-feeding, predatory fish. Several species forage over the study area at high densities and are known from gut content analysis to prey on juvenile E. chloroticus in the field. Invertebrate predators are at very low densities in the area. The possibility of caging and site artefacts confounding this interpretation is discussed.Adult E. chloroticus did not directly affect conspecific juvenile densities during the experimental period. However their removal produced a significant change in community structure toward one dominated by macroscopic brown algae. Echinoid removal led to rapid recruitment of laminarian and fucoid algae, predominantly Ecklonia radiata and Sargassum sinclairii. In addition, densities of herbivorous gastropods, particularly the limpet Cellana stellifera decreased in the echinoid exclusion area, as did the feeding rates of predatory fish. The consequences of E. chloroticus removal may be dependent upon the size of the area from which they are excluded.Despite the high densities of predatory fish, a low though consistent number of juvenile E. chloroticus escape predation. We suggest that these represent sufficient input into the adult grazing population to maintain the habitat. This interpretation argues against a key role for predators in structuring shallow water reef communities in northeastern New Zealand.     

Dangerous demographics: the lack of juvenile humphead parrotfishes Bolbometopon muricatum on the Great Barrier Reef

The humphead parrotfish, Bolbometopon muricatum, the largest of all parrotfish species, is heavily fished throughout most of its range. In remote and heavily protected locations, such as the Great Barrier Reef (GBR), it is a major component of parrotfish biomass and plays a critical role in ecosystem processes. However, extensive surveys of GBR populations have revealed a striking lack of juveniles. Of 633 individuals censused, just four were juveniles. This represents 0.6% juveniles and contrasts markedly with the 20.2–40.2% juveniles recorded in eight other medium to large parrotfish species. These low values in Bolbometopon are corroborated by over 5,000 h of independent observations and extensive museum collections. Whilst there is no evidence to suggest that this is an extraordinary new condition for GBR Bolbometopon, it may nevertheless expose them to special risks in a changing and unpredictable world. Despite excellent management on the GBR, Bolbometopon populations may be more vulnerable than previously thought.