Molecular phylogenies disprove a hypothesized C4 reversion in Eragrostis walteri (Poaceae)

Background and Aims

The main assemblage of the grass subfamily Chloridoideae is the largest known clade of C₄ plant species, with the notable exception of Eragrostis walteri Pilg., whose leaf anatomy has been described as typical of C₃ plants. Eragrostis walteri is therefore classically hypothesized to represent an exceptional example of evolutionary reversion from C₄ to C₃ photosynthesis. Here this hypothesis is tested by verifying the photosynthetic type of E. walteri and its classification.

Methods

Carbon isotope analyses were used to determine the photosynthetic pathway of several E. walteri accessions, and phylogenetic analyses of plastid rbcL and ndhF and nuclear internal transcribed spacer DNA sequences were used to establish the phylogenetic position of the species.

Results

Carbon isotope analyses confirmed that E. walteri is a C₃ plant. However, phylogenetic analyses demonstrate that this species has been misclassified, showing that E. walteri is positioned outside Chloridoideae in Arundinoideae, a subfamily comprised entirely of C₃ species.

Conclusions

The long-standing hypothesis of C₄ to C₃ reversion in E. walteri is rejected, and the classification of this species needs to be re-evaluated.     

Root signals and stomatal closure in relation to photosynthesis, chlorophyll a fluorescence and adventitious rooting of flooded tomato plants

Background and Aims

An investigation was carried out to determine whether stomatal closure in flooded tomato plants (Solanum lycopersicum) results from decreased leaf water potentials (ψ_L), decreased photosynthetic capacity and attendant increases in internal CO₂ (C_i) or from losses of root function such as cytokinin and gibberellin export.

Methods

Pot-grown plants were flooded when 1 month old. Leaf conductance was measured by diffusion porometry, the efficiency of photosystem II (PSII) was estimated by fluorimetry, and infrared gas analysis was used to determine C_i and related parameters.

Key Results

Flooding starting in the morning closed the stomata and increased ψ_L after a short-lived depression of ψ_L. The pattern of closure remained unchanged when ψ_`L depression was avoided by starting flooding at the end rather than at the start of the photoperiod. Raising external CO₂ concentrations by 100 µmol mol⁻¹ also closed stomata rapidly. Five chlorophyll fluorescence parameters [F_q′/F_m′, F_q′/F_v′, F_v′/F_m′, non-photochemical quenching (NPQ) and F_v/F_m] were affected by flooding within 12–36 h and changes were linked to decreased C_i. Closing stomata by applying abscisic acid or increasing external CO₂ substantially reproduced the effects of flooding on chlorophyll fluorescence. The presence of well-aerated adventitious roots partially inhibited stomatal closure of flooded plants. Allowing adventitious roots to form on plants flooded for >3 d promoted some stomatal re-opening. This effect of adventitious roots was not reproduced by foliar applications of benzyl adenine and gibberellic acid.

Conclusions

Stomata of flooded plants did not close in response to short-lived decreases in ψ_L or to increased C_i resulting from impaired PSII photochemistry. Instead, stomatal closure depressed C_i and this in turn largely explained subsequent changes in chlorophyll fluorescence parameters. Stomatal opening was promoted by the presence of well-aerated adventitious roots, implying that loss of function of root signalling contributes to closing of stomata during flooding. The possibility that this involves inhibition of cytokinin or gibberellin export was not well supported.Key words: Root to shoot communication, flooding stress, stomatal closure, photosynthesis, chlorophyll fluorescence, gas exchange, adventitious roots, plant hormones, abscisic acid, cytokinins, gibberellic acid     

Diversity in forms of C4 in the genus Cleome (Cleomaceae)

Background and Aims

Cleomaceae is one of 19 angiosperm families in which C₄ photosynthesis has been reported. The aim of the study was to determine the type, and diversity, of structural and functional forms of C₄ in genus Cleome.

Methods

Plants of Cleome species were grown from seeds, and leaves were subjected to carbon isotope analysis, light and scanning electron microscopy, western blot analysis of proteins, and in situ immunolocalization for ribulose bisphosphate carboxylase oxygenase (Rubisco) and phosphoenolpyruvate carboxylase (PEPC).

Key Results

Three species with C₄-type carbon isotope values occurring in separate lineages in the genus (Cleome angustifolia, C. gynandra and C. oxalidea) were shown to have features of C₄ photosynthesis in leaves and cotyledons. Immunolocalization studies show that PEPC is localized in mesophyll (M) cells and Rubisco is selectively localized in bundle sheath (BS) cells in leaves and cotyledons, characteristic of species with Kranz anatomy. Analyses of leaves for key photosynthetic enzymes show they have high expression of markers for the C₄ cycle (compared with the C₃–C₄ intermediate C. paradoxa and the C₃ species C. africana). All three are biochemically NAD-malic enzyme sub-type, with higher granal development in BS than in M chloroplasts, characteristic of this biochemical sub-type. Cleome gynandra and C. oxalidea have atriplicoid-type Kranz anatomy with multiple simple Kranz units around individual veins. However, C. angustifolia anatomy is represented by a double layer of concentric chlorenchyma forming a single compound Kranz unit by surrounding all the vascular bundles and water storage cells.

Conclusions

NAD-malic enzyme-type C₄ photosynthesis evolved multiple times in the family Cleomaceae, twice with atriplicoid-type anatomy in compound leaves having flat, broad leaflets in the pantropical species C. gynandra and the Australian species C. oxalidea, and once by forming a single Kranz unit in compound leaves with semi-terete leaflets in the African species C. angustifolia. The leaf morphology of C. angustifolia, which is similar to that of the sister, C₃–C₄ intermediate African species C. paradoxa, suggests adaptation of this lineage to arid environments, which is supported by biogeographical information.     

Quantification and optimization of Candida albicans DNA in blood samples using Real- Time PCR

Background:

Candida albicans (C. albicans) is a major cause of candidaemia in people with impaired immunity. Blood culture is a “gold standard” for candidaemia detection but is time-consuming and relatively insensitive. We established a real-time PCR assay for C. albicans detection in blood by LightCycler PCR and melting curve analysis.

Methods:

Five milliliter blood samples from healthy volunteers were spiked with 10⁰-10⁶ C. albicans cells to determine the detection limit of our method. DNA was extracted from whole blood using glass beads and the QIAamp DNA Blood Mini Kit (Qiagen, Hilden Germany). DNA from C. albicans isolates were amplified with primers and inserted into Escherichia coli (E. coli) DH5α.1 cells with the TA cloning vector (Invitrogen). The plasmid was used for standardization and optimization. A quantitative PCR assay with the LightCycler amplification and detection system based on fluorescence resonance energy transfer (FRET) with two different specific probes was established. To assess the precision and reproducibility of real-time PCR the intra-assay precision was determined in six consecutive assays.

Results:

No cross-reactivity of the hybridization probes with the DNA of non-C. albicans species or human genomic DNA was observed, which confirmed its 100% specificity. The minimum limit detected was one C. albicans cell or 10⁰ CFU/ml (10 fg) per PCR reaction. The real-time PCR efficiency rate for Candida was high (E = 1.95). Melting curve analysis of C. albicans showed a specific melting peak temperature of 65.76 °C.

Conclusion:

The real-time PCR assay we developed is highly specific and sufficiently sensitive to detect the fungal load for early diagnosis of invasive candidiasis. Key Words: Invasive candidiasis, Real-time PCR, Candida albicans     

Measurement of the Infection and Dissemination of Bluetongue Virus in Culicoides Biting Midges Using a Semi-Quantitative RT-PCR Assay and Isolation of Infectious Virus

Background

Culicoides biting midges (Diptera: Ceratopogonidae) are the biological vectors of globally significant arboviruses of livestock including bluetongue virus (BTV), African horse sickness virus (AHSV) and the recently emerging Schmallenberg virus (SBV). From 2006–2009 outbreaks of BTV in northern Europe inflicted major disruption and economic losses to farmers and several attempts were made to implicate Palaearctic Culicoides species as vectors. Results from these studies were difficult to interpret as they used semi-quantitative RT-PCR (sqPCR) assays as the major diagnostic tool, a technique that had not been validated for use in this role. In this study we validate the use of these assays by carrying out time-series detection of BTV RNA in two colony species of Culicoides and compare the results with the more traditional isolation of infectious BTV on cell culture.

Methodology/Principal Findings

A BTV serotype 1 strain mixed with horse blood was fed to several hundred individuals of Culicoides sonorensis (Wirth & Jones) and C. nubeculosus (Mg.) using a membrane-based assay and replete individuals were then incubated at 25°C. At daily intervals 25 Culicoides of each species were removed from incubation, homogenised and BTV quantified in each individual using sqPCR (C_q values) and virus isolation on a KC-C. sonorensis embryonic cell line, followed by antigen enzyme-linked immunosorbent assay (ELISA). In addition, comparisons were also drawn between the results obtained with whole C. sonorensis and with individually dissected individuals to determine the level of BTV dissemination.

Conclusions/Significance

C_q values generated from time-series infection experiments in both C. sonorensis and C. nubeculosus confirmed previous studies that relied upon the isolation and detection of infectious BTV. Implications on the testing of field-collected Culicoides as potential virus vectors by PCR assays and the use of such assays as front-line tools for use in diagnostic laboratories in this role are discussed.     

Differences in drought sensitivities and photosynthetic limitations between co-occurring C3 and C4 (NADP-ME) Panicoid grasses

Background and Aims

The success of C₄ plants lies in their ability to attain greater efficiencies of light, water and nitrogen use under high temperature, providing an advantage in arid, hot environments. However, C₄ grasses are not necessarily less sensitive to drought than C₃ grasses and are proposed to respond with greater metabolic limitations, while the C₃ response is predominantly stomatal. The aims of this study were to compare the drought and recovery responses of co-occurring C₃ and C₄ NADP-ME grasses from the subfamily Panicoideae and to determine stomatal and metabolic contributions to the observed response.

Methods

Six species of locally co-occurring grasses, C₃ species Alloteropsis semialata subsp. eckloniana, Panicum aequinerve and Panicum ecklonii, and C₄ (NADP-ME) species Heteropogon contortus, Themeda triandra and Tristachya leucothrix, were established in pots then subjected to a controlled drought followed by re-watering. Water potentials, leaf gas exchange and the response of photosynthetic rate to internal CO₂ concentrations were determined on selected occasions during the drought and re-watering treatments and compared between species and photosynthetic types.

Key Results

Leaves of C₄ species of grasses maintained their photosynthetic advantage until water deficits became severe, but lost their water-use advantage even under conditions of mild drought. Declining C₄ photosynthesis with water deficit was mainly a consequence of metabolic limitations to CO₂ assimilation, whereas, in the C₃ species, stomatal limitations had a prevailing role in the drought-induced decrease in photosynthesis. The drought-sensitive metabolism of the C₄ plants could explain the observed slower recovery of photosynthesis on re-watering, in comparison with C₃ plants which recovered a greater proportion of photosynthesis through increased stomatal conductance.

Conclusions

Within the Panicoid grasses, C₄ (NADP-ME) species are metabolically more sensitive to drought than C₃ species and recover more slowly from drought.     

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value

For real-time monitoring of PCR amplification of DNA, quantitative PCR (qPCR) assays use various fluorescent reporters. DNA binding molecules and hybridization reporters (primers and probes) only fluoresce when bound to DNA and result in the non-cumulative increase in observed fluorescence. Hydrolysis reporters (TaqMan® probes and QZyme? primers) become fluorescent during DNA elongation and the released fluorophore remains fluorescent during further cycles; this results in a cumulative increase in observed fluorescence. Although the quantification threshold is reached at a lower number of cycles when fluorescence accumulates, in qPCR analysis no distinction is made between the two types of data sets. Mathematical modeling shows that ignoring the cumulative nature of the data leaves the estimated PCR efficiency practically unaffected but will lead to at least one cycle underestimation of the quantification cycle (C_q value), corresponding to a 2-fold overestimation of target quantity. The effect on the target–reference ratio depends on the PCR efficiency of the target and reference amplicons. The leftward shift of the C_q value is dependent on the PCR efficiency and with sufficiently large C_q values, this shift is constant. This allows the C_q to be corrected and unbiased target quantities to be obtained.     

Methanol Assimilation in Methylobacterium extorquens AM1: Demonstration of All Enzymes and Their Regulation

Background

Methylobacterium extorquens AM1 is an aerobic facultative methylotrophic α-proteobacterium that can use reduced one-carbon compounds such as methanol, but also multi-carbon substrates like acetate (C₂) or succinate (C₄) as sole carbon and energy source. The organism has gained interest as future biotechnological production platform based on methanol as feedstock.

Methodology/Principal Findings

We present a comprehensive study of all postulated enzymes for the assimilation of methanol and their regulation in response to the carbon source. Formaldehyde, which is derived from methanol oxidation, is assimilated via the serine cycle, which starts with glyoxylate and forms acetyl-CoA. Acetyl-CoA is assimilated via the proposed ethylmalonyl-CoA pathway, which thereby regenerates glyoxylate. To further the understanding of the central carbon metabolism we identified and quantified all enzymes of the pathways involved in methanol assimilation. We observed a strict differential regulation of their activity level depending on whether C₁, C₂ or C₄ compounds are used. The enzymes, which are specifically required for the utilization of the individual substrates, were several-fold up-regulated and those not required were down-regulated. The enzymes of the ethylmalonyl-CoA pathway showed specific activities, which were higher than the calculated minimal values that can account for the observed growth rate. Yet, some enzymes of the serine cycle, notably its first and last enzymes serine hydroxymethyl transferase and malate thiokinase, exhibit much lower values and probably are rate limiting during methylotrophic growth. We identified the natural C₁ carrying coenzyme as tetrahydropteroyl-tetraglutamate rather than tetrahydrofolate.

Conclusion/Significance

This study provides the first complete picture of the enzymes required for methanol assimilation, the regulation of their activity levels in response to the growth substrate, and the identification of potential growth limiting steps.     

Abbott RealTime HBV Assay Is More Sensitive in Detection of Low Viral Load and Little Impacted by Drug Resistant Mutation in Chronic Hepatitis B Patients under Nucleot(s)ide Analogues Therapy

Background

Selection of drug-resistant strains may lead to failure of HBV antiviral therapy. There is little information whether there is detection difference in drug resistant mutations between different viral load assays of HBV.

Objectives

This study is aimed to investigate whether there is drug-resistant strains related detection difference between Abbott RealTime HBV (RealTime) and CobasAmpliPrep/CobasTaqMan HBV assays 2.0 (TaqMan).

Study Design

One hundred and thirty-four CHB patients who received HBV anti-viral therapy were enrolled. HBV virological markers were tested 3 months apart regularly. Serum HBV DNA levels were determined using the TaqMan and RealTime. YMDD (rt180M and rt204V) mutation was checked in patients who experienced virologic breakthrough (VBT).

Results

The correlation of HBV DNA observed between the RealTime and TaqMan was good for all 571 samples (R² = 0.797; P<0.001). However, the correlation in the 434 samples with HBV DNA level <3 log₁₀ IU/ml was not as good as in all samples (R² = 0.457). Overall, 21.5% of samples had a detection difference of ≥1 log₁₀ IU/ml with 91.9% of these having HBV DNA level <3 log₁₀ IU/ml. Twenty-four patients experiencedVBT. Three of these patients had acquired the YMDD mutation and exhibited discordant viral load results between the two methods tested. In each case, persistent HBV DNA was detected by RealTime and undetectable with TaqMan. Of the patients who experienced a VBT and had acquired YMDD mutation, 4.7% had undetectable HBV DNA by TaqMan while all were detectable with RealTime.

Conclusions

RealTime assay is more sensitive and is little impacted by the development of drug resistant mutation.     

Implicating Culicoides Biting Midges as Vectors of Schmallenberg Virus Using Semi-Quantitative RT-PCR

Background

The recent unprecedented emergence of arboviruses transmitted by Culicoides biting midges in northern Europe has necessitated the development of techniques to differentiate competent vector species. At present these techniques are entirely reliant upon interpretation of semi-quantitative RT-PCR (sqPCR) data in the form of C_q values used to infer the presence of viral RNA in samples.

Methodology/Principal Findings

This study investigates the advantages and limitations of sqPCR in this role by comparing infection and dissemination rates of Schmallenberg virus (SBV) in two colony lines of Culicoides. Through the use of these behaviorally malleable lines we provide tools for demarcating arbovirus infection and dissemination rates in Culicoides which to date have prevented clear implication of primary vector species in northern Europe. The study demonstrates biological transmission of SBV in an arthropod vector, supporting the conclusions from field-caught Culicoides and provides a general framework for future assessment of vector competence of Culicoides for arboviruses using sqPCR.

Conclusions/Significance

When adopting novel diagnostic technologies, correctly implicating vectors of arboviral pathogens requires a coherent laboratory framework to fully understand the implications of results produced in the field. This study illustrates these difficulties and provides a full examination of sqPCR in this role for the Culicoides-arbovirus system.     

Photosynthetic acclimation is important for post-submergence recovery of photosynthesis and growth in two riparian species

Background and Aims

Concomitant increases in O₂ and irradiance upon de-submergence can cause photoinhibition and photo-oxidative damage to the photosynthetic apparatus of plants. As energy and carbohydrate supply from photosynthesis is needed for growth, it was hypothesized that post-submergence growth recovery may require efficient photosynthetic acclimation to increased O₂ and irradiance to minimize photo-oxidative damage. The hypothesis was tested in two flood-tolerant species: a C₃ herb, Alternanthera philoxeroides; and a C₄ grass, Hemarthria altissima. The impact of low O₂ and low light, typical conditions in turbid floodwater, on post-submergence recovery was assessed by different flooding treatments combined with shading.

Methods

Experiments were conducted during 30 d of flooding (waterlogging or submergence) with or without shading and subsequent recovery of 20 d under growth conditions. Changes in dry mass, number of branches/tillers, and length of the longest internodes and main stems were recorded to characterize growth responses. Photosynthetic parameters (photosystem II efficiency and non-photochemical quenching) were determined in mature leaves based on chlorophyll a fluorescence measurements.

Key Results

In both species growth and photosynthesis recovered after the end of the submergence treatment, with recovery of photosynthesis (starting shortly after de-submergence) preceding recovery of growth (pronounced on days 40–50). The effective quantum yield of photosystem II and non-photochemical quenching were diminished during submergence but rapidly increased upon de-submergence. Similar changes were found in all shaded plants, with or without flooding. Submerged plants did not suffer from photoinhibition throughout the recovery period although their growth recovery was retarded.

Conclusions

After sudden de-submergence the C₃ plant A. philoxeroides and the C₄ plant H. altissima were both able to maintain the functionality of the photosynthetic apparatus through rapid acclimation to changing O₂ and light conditions. The ability for photosynthetic acclimation may be essential for adaptation to wetland habitats in which water levels fluctuate.Key words: Aerenchyma, Alternanthera philoxeroides, flooding, growth, Hemarthria altissima, low light, photosynthesis, shade, submergence, waterlogging, wetland plant     

Socioeconomic Inequalities in Non-Communicable Diseases Prevalence in India: Disparities between Self-Reported Diagnoses and Standardized Measures

Background

Whether non-communicable diseases (NCDs) are diseases of poverty or affluence in low-and-middle income countries has been vigorously debated. Most analyses of NCDs have used self-reported data, which is biased by differential access to healthcare services between groups of different socioeconomic status (SES). We sought to compare self-reported diagnoses versus standardised measures of NCD prevalence across SES groups in India.

Methods

We calculated age-adjusted prevalence rates of common NCDs from the Study on Global Ageing and Adult Health, a nationally representative cross-sectional survey. We compared self-reported diagnoses to standardized measures of disease for five NCDs. We calculated wealth-related and education-related disparities in NCD prevalence by calculating concentration index (C), which ranges from −1 to +1 (concentration of disease among lower and higher SES groups, respectively).

Findings

NCD prevalence was higher (range 5.2 to 19.1%) for standardised measures than self-reported diagnoses (range 3.1 to 9.4%). Several NCDs were particularly concentrated among higher SES groups according to self-reported diagnoses (C_srd) but were concentrated either among lower SES groups or showed no strong socioeconomic gradient using standardized measures (C_sm): age-standardised wealth-related C: angina C_srd 0.02 vs. C_sm −0.17; asthma and lung diseases C_srd −0.05 vs. C_sm −0.04 (age-standardised education-related C_srd 0.04 vs. C_sm −0.05); vision problems C_srd 0.07 vs. C_sm −0.05; depression C_srd 0.07 vs. C_sm −0.13. Indicating similar trends of standardized measures detecting more cases among low SES, concentration of hypertension declined among higher SES (C_srd 0.19 vs. C_sm 0.03).

Conclusions

The socio-economic patterning of NCD prevalence differs markedly when assessed by standardized criteria versus self-reported diagnoses. NCDs in India are not necessarily diseases of affluence but also of poverty, indicating likely under-diagnosis and under-reporting of diseases among the poor. Standardized measures should be used, wherever feasible, to estimate the true prevalence of NCDs.     

Shifts in leaf vein density through accelerated vein formation in C4 Flaveria (Asteraceae)

Background and Aims

Leaf venation in many C₄ species is characterized by high vein density, essential in facilitating rapid intercellular diffusion of C₄ photosynthetic metabolites between different tissues (mesophyll, bundle sheath). Greater vein density has been hypothesized to be an early step in C₄ photosynthesis evolution. Development of C₄ vein patterning is thought to occur from either accelerated or prolonged procambium formation, relative to ground tissue development.

Methods

Cleared and sectioned tissues of phylogenetically basal C₃ Flaveria robusta and more derived C₄ Flaveria bidentis were compared for vein pattern in mature leaves and vein pattern formation in developing leaves.

Key Results

In mature leaves, major vein density did not differ between C₃ and C₄ Flaveria species, whereas minor veins were denser in C₄ species than in C₃ species. The developmental study showed that both major and minor vein patterning in leaves of C₃ and C₄ species were initiated at comparable stages (based on leaf length). An additional vein order in the C₄ species was observed during initiation of the higher order minor veins compared with the C₃ species. In the two species, expansion of bundle sheath and mesophyll cells occurred after vein pattern was complete and xylem differentiation was continuous in minor veins. In addition, mesophyll cells ceased dividing sooner and enlarged less in C₄ species than in C₃ species.

Conclusions

Leaf vein pattern characteristic to C₄ Flaveria was achieved primarily through accelerated and earlier offset of higher order vein formation, rather than other modifications in the timing of vein pattern formation, as compared with C₃ species. Earlier cessation of mesophyll cell division and reduced expansion also contributed to greater vein density in the C₄ species. The relatively late expansion of bundle sheath and mesophyll cells shows that vein patterning precedes ground tissue development in C₄ species.Key words: Bundle sheath, C₄ photosynthesis evolution, Flaveria, heterochrony, leaf development, mesophyll, vein density, vein pattern formation     

Carry-over of differential salt tolerance in plants grown from dimorphic seeds of Suaeda splendens

Background and Aims

Halophytic species often show seed dimorphism, where seed morphs produced by a single individual may differ in germination characteristics. Particular morphs are adapted to different windows of opportunity for germination in the seasonally fluctuating and heterogeneous salt-marsh environment. The possibility that plants derived from the two morphs may also differ physiologically has not been investigated previously.

Methods

Experiments were designed to investigate the germination characteristics of black and brown seed morphs of Suaeda splendens, an annual, C₄ shrub of non-tidal, saline steppes. The resulting seedlings were transferred to hydroponic culture to investigate their growth and photosynthetic (PSII photochemistry and gas exchange) responses to salinity.

Key Results

Black seeds germinated at low salinity but were particularly sensitive to increasing salt concentrations, and strongly inhibited by light. Brown seeds were unaffected by light, able to germinate at higher salinities and generally germinated more rapidly. Ungerminated black seeds maintained viability for longer than brown ones, particularly at high salinity. Seedlings derived from both seed morphs grew well at high salinity (400 mol m⁻³ NaCl). However, seedlings derived from brown seeds performed poorly at low salinity, as reflected in relative growth rate, numbers of branches produced, F_v/F_m and net rate of CO₂ assimilation.

Conclusions

The seeds most likely to germinate at high salinity in the Mediterranean summer (brown ones) retain a requirement for higher salinity as seedlings that might be of adaptive value. On the other hand, black seeds, which are likely to delay germination until lower salinity prevails, produce seedlings that are less sensitive to salinity. It is not clear why performance at low salinity, later in the life cycle, might have been sacrificed by the brown seeds, to achieve higher fitness at the germination stage under high salinity. Analyses of adaptive syndromes associated with seed dimorphism may need to take account of differences over the entire life cycle, rather than just at the germination stage.Key words: Chlorophyll fluorescence, germination, growth rate, halophyte, photosynthesis, photosystem II, salt tolerance, seed dimorphism, seed viability, Suaeda splendens     

Rubisco Evolution in C4 Eudicots: An Analysis of Amaranthaceae Sensu Lato

Background

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots.

Methodology/Principal Findings

We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution.

Conclusions/Significance

Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.     

Competitive reporter monitored amplification (CMA)--quantification of molecular targets by real time monitoring of competitive reporter hybridization

Background

State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests.

Methodology and Principal Findings

The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique.

Conclusions and Significance

The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a single assay and to perform the assay on simple and robust instrumentation is a prerequisite for the development of novel molecular point of care tests.     

Stomatal and pavement cell density linked to leaf internal CO2 concentration

Background and Aims

Stomatal density (SD) generally decreases with rising atmospheric CO₂ concentration, C_a. However, SD is also affected by light, air humidity and drought, all under systemic signalling from older leaves. This makes our understanding of how C_a controls SD incomplete. This study tested the hypotheses that SD is affected by the internal CO₂ concentration of the leaf, C_i, rather than C_a, and that cotyledons, as the first plant assimilation organs, lack the systemic signal.

Methods

Sunflower (Helianthus annuus), beech (Fagus sylvatica), arabidopsis (Arabidopsis thaliana) and garden cress (Lepidium sativum) were grown under contrasting environmental conditions that affected C_i while C_a was kept constant. The SD, pavement cell density (PCD) and stomatal index (SI) responses to C_i in cotyledons and the first leaves of garden cress were compared. ¹³C abundance (δ¹³C) in leaf dry matter was used to estimate the effective C_i during leaf development. The SD was estimated from leaf imprints.

Key Results

SD correlated negatively with C_i in leaves of all four species and under three different treatments (irradiance, abscisic acid and osmotic stress). PCD in arabidopsis and garden cress responded similarly, so that SI was largely unaffected. However, SD and PCD of cotyledons were insensitive to C_i, indicating an essential role for systemic signalling.

Conclusions

It is proposed that C_i or a C_i-linked factor plays an important role in modulating SD and PCD during epidermis development and leaf expansion. The absence of a C_i–SD relationship in the cotyledons of garden cress indicates the key role of lower-insertion CO₂ assimilation organs in signal perception and its long-distance transport.