Ocean acidification mediates photosynthetic response to UV radiation and temperature increase in the diatom Phaeodactylum tricornutum

Increasing atmospheric CO2 concentration is responsible for progressive ocean acidification, ocean warming as well as decreased thickness of upper mixing layer (UML), thus exposing phytoplankton cells not only to lower pH and higher temperatures but also to higher levels of solar UV radiation. In order to evaluate the combined effects of ocean acidification, UV radiation and temperature, we used the diatom Phaeodactylum tricornutum as a model organism and examined its physiological performance after grown under two CO2 concentrations (390 and 1000 µatm) for more than 20 generations. Compared to the ambient CO2 level (390 µatm), growth at the elevated CO2 concentration increased non-photochemical quenching (NPQ) of cells and partially counteracted the harm to PS II (photosystem II) caused by UV-A and UV-B. Such an effect was less pronounced under increased temperature levels. The ratio of repair to UV-B induced damage decreased with increased NPQ, reflecting induction of NPQ when repair dropped behind the damage, and it was higher under the ocean acidification condition, showing that the increased pCO2 and lowered pH counteracted UV-B induced harm. As for photosynthetic carbon fixation rate which increased with increasing temperature from 15 to 25 °C, the elevated CO2 and temperature levels synergistically interacted to reduce the inhibition caused by UV-B and thus increase the carbon fixation.

The response of Antarctic sea ice algae to changes in pH and CO2

Ocean acidification substantially alters ocean carbon chemistry and hence pH but the effects on sea ice formation and the CO2 concentration in the enclosed brine channels are unknown. Microbial communities inhabiting sea ice ecosystems currently contribute 10-50% of the annual primary production of polar seas, supporting overwintering zooplankton species, especially Antarctic krill, and seeding spring phytoplankton blooms. Ocean acidification is occurring in all surface waters but the strongest effects will be experienced in polar ecosystems with significant effects on all trophic levels. Brine algae collected from McMurdo Sound (Antarctica) sea ice was incubated in situ under various carbonate chemistry conditions. The carbon chemistry was manipulated with acid, bicarbonate and bases to produce a pCO2 and pH range from 238 to 6066 µatm and 7.19 to 8.66, respectively. Elevated pCO2 positively affected the growth rate of the brine algal community, dominated by the unique ice dinoflagellate, Polarella glacialis. Growth rates were significantly reduced when pH dropped below 7.6. However, when the pH was held constant and the pCO2 increased, growth rates of the brine algae increased by more than 20% and showed no decline at pCO2 values more than five times current ambient levels. We suggest that projected increases in seawater pCO2, associated with OA, will not adversely impact brine algal communities.

Seagrass ecosystem response to long-term high CO2 in a Mediterranean volcanic vent

We examined the long-term effect of naturally acidified water on a Cymodocea nodosa meadow growing at a shallow volcanic CO2 vent in Vulcano Island (Italy). Seagrass and adjacent unvegetated habitats growing at a low pH station (pH = 7.65 ± 0.02) were compared with corresponding habitats at a control station (pH = 8.01 ± 0.01). Density and biomass showed a clear decreasing trend at the low pH station and the below- to above-ground biomass ratio was more than 10 times lower compared to the control. C content and delta 13C of leaves and epiphytes were significantly lower at the low pH station. Photosynthetic activity of C. nodosa was stimulated by low pH as seen by the significant increase in Chla content of leaves, maximum electron transport rate and compensation irradiance. Seagrass community metabolism was intense at the low pH station, with significantly higher net community production, respiration and gross primary production than the control community, whereas metabolism of the unvegetated community did not differ between stations. Productivity was promoted by the low pH, but this was not translated into biomass, probably due to nutrient limitation, grazing or poor environmental conditions. The results indicate that seagrass response in naturally acidified conditions is dependable upon species and geochemical characteristics of the site and highlight the need for a better understanding of complex interactions in these environments.

Physiological response to elevated temperature and pCO2 varies across four Pacific coral species: Understanding the unique host + symbiont response

The physiological response to individual and combined stressors of elevated temperature and pCO2 were measured over a 24-day period in four Pacific corals and their respective symbionts (Acropora millepora/Symbiodinium C21a, Pocillopora damicornis/Symbiodinium C1c-d-t, Montipora monasteriata/Symbiodinium C15, and Turbinaria reniformis/Symbiodinium trenchii). Multivariate analyses indicated that elevated temperature played a greater role in altering physiological response, with the greatest degree of change occurring within M. monasteriata and T. reniformis. Algal cellular volume, protein, and lipid content all increased for M. monasteriata. Likewise, S. trenchii volume and protein content in T. reniformis also increased with temperature. Despite decreases in maximal photochemical efficiency, few changes in biochemical composition (i.e. lipids, proteins, and carbohydrates) or cellular volume occurred at high temperature in the two thermally sensitive symbionts C21a and C1c-d-t. Intracellular carbonic anhydrase transcript abundance increased with temperature in A. millepora but not in P. damicornis, possibly reflecting differences in host mitigated carbon supply during thermal stress. Importantly, our results show that the host and symbiont response to climate change differs considerably across species and that greater physiological plasticity in response to elevated temperature may be an important strategy distinguishing thermally tolerant vs. thermally sensitive species.

Simulation of oil productivity and quality of N-S oriented olive hedgerow orchards in response to structure and interception of radiation

Simulations of oil yield and quality are presented for N–S oriented, hedgerow olive orchards of a range of structures (viz. canopy depth, canopy width, canopy slope and row spacing) using responses of yield and quality parameters to solar irradiance on canopy walls measured in a range of orchards, cv. Arbequina, in Spain. Results reveal that orchard yield of hedgerows of rectangular shape reaches a maximum when canopy depth equals alley width (row spacing−canopy width) and decreases at wider spacing, and/or with wider canopies, as the length of productive row decreases per unit area. Maximum yields for 4-m deep canopies were 2885 kg ha−1 at 1-m width and 5-m row spacing, 2400 kg ha−1 at 2-m width and 6-m spacing, and 2050 kg ha−1 at 3-m width and 7-m spacing. Illumination of canopies can be increased by applying slopes to form rhomboidal hedgerows. Substantial yield advantage can be achieved, especially for wide hedgerows, partly by closer row spacing that increases row length per unit area. By comparison, responses to latitude in the range 30–40◦ are small and do not warrant different row spacing. Oil quality parameters also respond to orchard structure. Responses are presented for oleic and palmitic acid, stability, and maturity index. Oleic acid content declines as alley spacing increases and is smaller, shallow than in wide, deep canopies. Palmitic acid content, stability, and maturity index increase with row alley spacing and are greater in narrow, shallow than in wide, deep canopies.

Polyploid formation created unique avenues for response to selection in Gossypium (cotton)

A detailed restriction fragment length polymorphism map was used to determine the chromosomal locations and subgenomic distributions of quantitative trait loci (QTLs) segregating in a cross between cultivars of allotetraploid (AADD) Gossypium hirsutum (“Upland” cotton) and Gossypium barbadense (“Sea Island,” “Pima,” or “Egyptian” cotton) that differ markedly in the quality and quantity of seed epidermal fibers. Most QTLs influencing fiber quality and yield are located on the “D” subgenome, derived from an ancestor that does not produce spinnable fibers. D subgenome QTLs may partly account for the fact that domestication and breeding of tetraploid cottons has resulted in fiber yield and quality levels superior to those achieved by parallel improvement of “A” genome diploid cottons. The merger of two genomes with different evolutionary histories in a common nucleus appears to offer unique avenues for phenotypic response to selection. This may partly compensate for reduction in quantitative variation associated with polyploid formation and be one basis for the prominence of polyploids among extant angiosperms. These findings impel molecular dissection of the roles of divergent subgenomes in quantitative inheritance in many other polyploids and further exploration of both “synthetic” polyploids and exotic diploid genotypes for agriculturally useful variation.

Seawater carbonate chemistry and photosynthetic response of Emiliania huxleyi (CS-369) to UV radiation and elevated temperature duirng experiments, 2011

Changes in calcification of coccolithophores may affect their photosynthetic responses to both, ultraviolet radiation (UVR, 280-400 nm) and temperature. We operated semi-continuous cultures of Emiliania huxleyi (strain CS-369) at reduced (0.1 mM, LCa) and ambient (10 mM, HCa) Ca2+ concentrations and, after 148 generations, we exposed cells to six radiation treatments (>280, >295, >305, >320, >350 and >395 nm by using Schott filters) and two temperatures (20 and 25 °C) to examine photosynthesis and calcification responses. Overall, our study demonstrated that: (1) decreased calcification resulted in a down regulation of photoprotective mechanisms (i.e., as estimated via non-photochemical quenching, NPQ), pigments contents and photosynthetic carbon fixation; (2) calcification (C) and photosynthesis (P) (as well as their ratio) have different responses related to UVR with cells grown under the high Ca2+ concentration being more resistant to UVR than those grown under the low Ca2+ level; (3) elevated temperature increased photosynthesis and calcification of E. huxleyi grown at high Ca2+concentrations whereas decreased both processes in low Ca2+ grown cells. Therefore, a decrease in calcification rates in E. huxleyi is expected to decrease photosynthesis rates, resulting in a negative feedback that further reduces calcification.

Advantage of single-trial models for response to selection in wheat breeding multi-environment trials

An investigation was conducted to evaluate the impact of experimental designs and spatial analyses (single-trial models) of the response to selection for grain yield in the northern grains region of Australia (Queensland and northern New South Wales). Two sets of multi-environment experiments were considered. One set, based on 33 trials conducted from 1994 to 1996, was used to represent the testing system of the wheat breeding program and is referred to as the multi-environment trial (MET). The second set, based on 47 trials conducted from 1986 to 1993, sampled a more diverse set of years and management regimes and was used to represent the target population of environments (TPE). There were 18 genotypes in common between the MET and TPE sets of trials. From indirect selection theory, the phenotypic correlation coefficient between the MET and TPE single-trial adjusted genotype means [r(p(MT))] was used to determine the effect of the single-trial model on the expected indirect response to selection for grain yield in the TPE based on selection in the MET. Five single-trial models were considered: randomised complete block (RCB), incomplete block (IB), spatial analysis (SS), spatial analysis with a measurement error (SSM) and a combination of spatial analysis and experimental design information to identify the preferred (PF) model. Bootstrap-resampling methodology was used to construct multiple MET data sets, ranging in size from 2 to 20 environments per MET sample. The size and environmental composition of the MET and the single-trial model influenced the r(p(MT)). On average, the PF model resulted in a higher r(p(MT)) than the IB, SS and SSM models, which were in turn superior to the RCB model for MET sizes based on fewer than ten environments. For METs based on ten or more environments, the r(p(MT)) was similar for all single-trial models.

Pattern analysis on grain yield performance of Chinese and CIMMYT spring wheat cultivars sown in China and CIMMYT

Understanding the relationships among testing environments is essential for better targeting cultivars to production environments. To identify patterns of cultivar, environment, cultivar-by-environment interactions, and opportunities for indirect selection for grain yield, a set of 25 spring wheat cultivars from China and the International Maize and Wheat Improvement Center (CIMMYT) was evaluated in nine environments in China and four management environments at CIMMYT in Cd. Obregon, Mexico, during two wheat seasons. Genetic background and original environment were the main factors influencing grain yield performance of the cultivars. Baviacora M 92, Xinchun 2 and Xinchun 6 showed relatively more stable and higher grain yields, whereas highly photoperiod sensitive cultivars Xinkehan 9, Kefeng 6 and Longmai 19 proved consistently inferior across environments, except in Harbin and Keshan, the two high latitude environments. Longmai 26, also from high latitude environments in the northeastern Heilongjiang province, was however probably not as photoperiodicly sensitive as other cultivars; from that region, and produced much higher grain yield and expressed a broader adaptation. None of the environments reported major diseases. Pattern analyses revealed that photoperiod response and planting option on beds were the two main factors underlying the observed interactions for grain yield. The production environment of planting on the flat in Mexico grouped together with Huhhot and Urumqi in both wheat seasons, indicating an indirect response to selection for grain yield in this CIMMYT managed environment could benefit the two Chinese environments. Both the environment of planting on the flat with Chinese Hejin and Yongning, and the three CIMMYT enviromnents planting on raised beds with Chinese Yongning grouped together only in one season, showing that repeatability may not be stable in this case.

Contribution of potential yield, drought tolerance and escape to adaptation of 15 rice varieties in rainfed lowlands in Cambodia

In Cambodia, grain yield in rainfed lowland rice is often affected by drought during late vegetative or reproductive stage. Several experiments were conducted to quantify the contribution of potential yield, drought tolerance and drought escape mechanisms to yield under water stress conditions. In total nine pairs of well irrigated and simulated drought (by draining water) experiments were conducted. Potential yield was obtained under irrigation. Grain yields and flowering dates were recorded in 15 varieties. Drought tolerance was quantified by using drought response index (DRI), which is grain yield under drought adjusted for potential yield and flowering date of the variety. Drought escape is expressed as days to flower under drought conditions. Mean yield reduction due to drought of nine experiments was 27 % (range 12-44). The relative contribution of yield potential, flowering date and DRI to observe yield under drought were evaluated by multiple regression for each experiment. Potential yield accounted for 54% (with a range of 10-80) of the variation in actual yield under drought. This was followed by DRI and flowering date with 34 (with a range of 0-60) and 12 (with a range of 0-30) of the contribution, respectively. It is concluded that selecting for drought tolerance as well as for high yield potential would be important in developing cultivars for rainfed lowlands in Cambodia. Although flowering dates are important for drought escape, it had a small contribution probably because drought developed slowly in these experiments in Cambodia.

Design of improved membrane protein production experiments:quantitation of the host response

Eukaryotic membrane proteins cannot be produced in a reliable manner for structural analysis. Consequently, researchers still rely on trial-and-error approaches, which most often yield insufficient amounts. This means that membrane protein production is recognized by biologists as the primary bottleneck in contemporary structural genomics programs. Here, we describe a study to examine the reasons for successes and failures in recombinant membrane protein production in yeast, at the level of the host cell, by systematically quantifying cultures in high-performance bioreactors under tightlydefined growth regimes. Our data show that the most rapid growth conditions of those chosen are not the optimal production conditions. Furthermore, the growth phase at which the cells are harvested is critical: We show that it is crucial to grow cells under tightly-controlled conditions and to harvest them prior to glucose exhaustion, just before the diauxic shift. The differences in membrane protein yields that we observe under different culture conditions are not reflected in corresponding changes in mRNA levels of FPS1, but rather can be related to the differential expression of genes involved in membrane protein secretion and yeast cellular physiology. Copyright © 2005 The Protein Society.

Acoustic emission and yield in sand

An experimental investigation into the Acoustic Emission (AE) response of sand has been undertaken, and the use of AE as a method of yield point identification has been assessed. Dense, saturated samples of sand were tested in conventional triaxial apparatus. The measurements of stresses and strains were carried out according to current research practice. The AE monitoring system was integrated with the soil mechanics equipment in such a way that sample disturbance was minimised. During monotonically loaded, constant cell pressure tests the total number of events recorded was found to increase at an increasing rate in a manner which may be approximated by a power law. The AE response of the sand was found to be both stress level and stress path dependent. Undrained constant cell pressure tests showed that, unlike drained tests, the AE event rate increased at an increasing rate; this was shown to correlate with the mean effective stress variation. The stress path dependence was most noticeable in extension tests, where the number of events recorded was an order of magnitude less than that recorded in comparable compression tests. This stress path dependence was shown to be due to the differences in the work done by the external stresses. In constant cell pressure tests containing unload/reload cycles it was found that yield could be identified from a discontinuity in the event rate/time curve which occurred during reloading. Further tests involving complex stress paths showed that AE was a useful method of yield point identification. Some tests involving large stress reversals were carried out, and AE identified the inverse yield points more distinctly than conventional methods of yield point identification.

Macroinvertebrate community response to eutrophication in an oligotrophic wetland: An in situ mesocosm experiment

Eutrophication from anthropogenic nutrient enrichment is a primary threat to the oligotrophic freshwater marshes of southern Florida. Macrophyte and periphyton response to increased phosphorus (P) has been well documented in both correlative and experimental studies, but the response of consumer communities remains poorly understood, especially in southern marl prairies. We conducted a P-loading experiment in in situ mesocosms in Taylor Slough, Everglades National Park, and examined the response of macroinvertebrate communities. Mesocosms at two sites were loaded weekly with P at four levels: control (0 g P/m2/yr), low (0.2 g P/m2/yr), intermediate (0.8 g P/m2/yr), and high (3.2 g P/m2/ yr). After ∼2 yrs of P-loading, macroinvertebrates were sampled using periphyton mat and benthic floc cores. Densities of macroinvertebrate taxa (no./g AFDM) were two to 16 times higher in periphyton mats than benthic floc. Periphyton biomass decreased with enrichment at one site, and periphyton was absent from many intermediate and all high P treatments at both sites. Total macroinvertebrate density in periphyton mats increased with intermediate P loads, driven primarily by chironomids and nematodes. Conversely, total macroinvertebrate density in benthic floc decreased with enrichment, driven primarily by loss of chironomids and ceratopogonids (Dasyhelea). This study suggests that macroinvertebrate density increases with enrichment until periphyton mats are lost, after which it decreases, and mat infauna fail to move into benthic substrates in response to mat loss. These results were noted at nutrient levels too low to yield anoxia, and we believe that the decrease of macroinvertebrate density resulted from a loss of habitat. This work illustrates the importance of periphyton mats as habitat for macroinvertebrates in the Everglades. This study also indicates that in this system, macroinvertebrate sampling should be designed to target periphyton mats or conducted with special attention to inclusion of substrates relative to their coverage.

Response of spring diatoms to CO2 availability in the Western North Pacific as determined by next-generation sequencing

Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO2 levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO2 levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO2 levels (180, 350, 750, and 1000 µatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO2 levels. These results suggest that CO2 fixation capacity of diatoms decreased rapidly under elevated CO2 levels. In the high CO2 treatments (750 and 1000 µatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350µatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO2 treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO2 levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO2 levels in terms of their community composition, diversity, and photosynthetic physiology.

Quantifying Eukaryotic Gene Regulation in Hormone Response and Disease.

Quantifying the function of mammalian enhancers at the genome or population scale has been longstanding challenge in the field of gene regulation. Studies of individual enhancers have provided anecdotal evidence on which many foundational assumptions in the field are based. Genome-scale studies have revealed that the number of sites bound by a given transcription factor far outnumber the genes that the factor regulates. In this dissertation we describe a new method, chromatin immune-enriched reporter assays (ChIP-reporters), and use that approach to comprehensively test the enhancer activity of genomic loci bound by the glucocorticoid receptor (GR). Integrative genomics analyses of our ChIP-reporter data revealed an unexpected mechanism of glucocorticoid (GC)-induced gene regulation. In that mechanism, only the minority of GR bound sites acts as GC-inducible enhancers. Many non-GC-inducible GR binding sites interact with GC-induced sites via chromatin looping. These interactions can increase the activity of GC-induced enhancers. Finally, we describe a method that enables the detection and characterization of the functional effects of non-coding genetic variation on enhancer activity at the population scale. Taken together, these studies yield both mechanistic and genetic evidence that provides context that informs the understanding of the effects of multiple enhancer variants on gene expression.