NADP-malate dehydrogenase gene evolution in Andropogoneae (Poaceae): gene duplication followed by sub-functionalization

• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C(4) plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C(3); Erhartoideae) and maize (C(4); Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C(4); Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C(4) isoform has evolved over a broader range of panicoid grasses. • Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach. • Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II. • Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C(4) isoform as previously suggested. Nevertheless, some C(4) species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C(4) photosynthesis but are not required in every case

NADP-Malate Dehydrogenase Gene Evolution in Andropogoneae (Poaceae): Gene Duplication Followed by Sub-functionalization

• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C4 plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C3; Erhartoideae) and maize (C4; Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C4; Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C4 isoform has evolved over a broader range of panicoid grasses. • Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach. • Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II. • Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C4 isoform as previously suggested. Nevertheless, some C4 species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C4 photosynthesis but are not required in every cas

Noxious weed monitoring at the U.S. Air Force Academy: year 6 results

Prepared for: U.S. Air Force Academy, Dept. of Natural Resources.April 2011.Includes bibliographical references

The geochemistry of gem opals as evidence of their origin

International audienceSeventy-seven gem opals from ten countries were analyzed by inductively coupled plasma-mass spectrometry (ICP-MS) through a dilution process, in order to establish the nature of the impurities. The results are correlated to the mode of formation and physical properties and are instrumental in establishing the geographical origin of a gem opal. The geochemistry of an opal is shown to be dependant mostly on the host rock, at least for examples from Mexico and Brazil, even if modified by weathering processes. In order of decreasing concentration, the main impurities present are Al, Ca, Fe, K, Na, and Mg (more than 500 ppm). Other noticeable elements in lesser amounts are Ba, followed by Zr, Sr, Rb, U, and Pb. For the first time, geochemistry helps to discriminate some varieties of opals. The Ba content, as well as the chondritenormalized REE pattern, are the keys to separating sedimentary opals (BaN110 ppm, Eu and Ce anomalies) from volcanic opals (Bab110 ppm, no Eu or Ce anomaly). The Ca content, and to a lesser extent that of Mg, Al, K and Nb, helps to distinguish gem opals from different volcanic environments. The limited range of concentrations for all elements in precious (play-of-color) compared to common opals, indicates that this variety must have very specific, or more restricted, conditions of formation. We tentatively interpreted the presence of impurities in terms of crystallochemistry, even if opal is a poorly crystallized or amorphous material. The main replacement is the substitution of Si4+ by Al3+ and Fe3+. The induced charge imbalance is compensated chiefly by Ca2+, Mg2+, Mn2+, Ba2+, K+, and Na+. In terms of origin of color, greater concentrations of iron induce darker colors (from yellow to "chocolate brown"). This element inhibits luminescence for concentrations above 1000 ppm, whereas already a low content in U (=1 ppm) induces a green luminescence

Noxious weed monitoring at the U.S. Air Force Academy: year 5 results

Prepared for: U.S. Air Force Academy, Dept. of Natural Resources.March, 2010.Includes bibliographical references

A promising method for efficient analysis of secondary metabolites in plant extracts by a matrix-free Desorption/Ionization on self-Assembled Monolayer Surfaces (DIAMS) technique

Plants are one of the major sources for the biologically active organic compounds and play a key role in medicinal chemistry for the treatment of various diseases [1]. DIAMS method is able to determine the secondary metabolites of complex vegetal extracts. The high throughput analyses of vegetal extracts are relatively difficult to perform in MALDI mass spectrometry, since the preparation of the sample involves the co-crystallization of the matrix with the analyte. Moreover irradiation of the matrix ion produces many low-m/z vs high-intensity ions preventing the detection of low molecular weight molecules such as secondary metabolites. We have developed a matrix-free alternative to MALDI analyses by the means of an original desorption/ionization on self-assembled monolayers surfaces (DIAMS) technique [2]. Monolayers were formed by using novel thiophene and coumarin-triazole analogues that absorbs the laser beam at 337nm. We herein disclose our findings with respect to the DIAMS method which is well suitable for the detection and quantification of the low molecular weight compounds that are present in plant extracts. Some of the isoquinoline alkaloids from the root extracts of Thalictrum flavum have been detected by the DIAMS method. Indeed, this technique would be promising suitable for the qualitative and quantitative analysis of polar and non-polar organic components that are widely distributed in the plants, without any preliminary chromatographic resolution [3]

DC Energy Data Measurement and Analysis for Productivity and Waste Energy Assessment

The study and analysis of energy efficiency in Data Centers (DCs), through a set of globally accepted metrics, is an ongoing challenge. In particular, the area of productivity metrics is not completely explored, and there is no existing proposed metrics, which provides a direct measurement of the useful work in a DC. This paper proposes a methodology that addresses the problem of measurement, calculating, and evaluating the energy productivity assessment in Data Center (DC), which encompasses both the portion of energy employed for computing and energy wasted during computational work. It involves the estimation of productive energy consumption by a DC cluster based on the following: statistical data collection and interpretation, software for energy data analysis, and mathematical formulation. This current work is based on available data extracted through experiments conducted on the cluster “CRESCO4” from ENEA Data Center facilities. The dataset covers the power and job schedule characteristics running on the cluster for one year. This paper shows how to advance beyond state of the art for productivity metrics (e.g. useful work). It will also help enhance server performance and power management since the appropriate statistical data analysis provides a profile on server energy consumption behavior. Additionally, we make recommendations on how the productivity assessment could driver a new power efficiency management strategy, which is specifically targeted at DC manager and/or operators, and end-users of the facilities

Thermal Awareness to Enhance Data Center Energy Efficiency

Data centers aim at provisioning on-demand processing, storage and networking capabilities in a reliable and scalable way. In this context, proper maintenance of IT equipment within DC premises is crucial as it ensures prolonged lifetime of servers and uninterrupted availability of resources. DC management teams’ sustainable operation effort comprises various approaches to directly and indirectly reduce DC energy consumption. Thermal management aims to reduce excess energy consumption by air cooling and compute systems. This paper focuses on the analysis of the exact temperatures in a real DC cluster rather than considering device setpoints or guidelines. An extensive statistical analysis of available thermal data collected by server-level sensors, global and local thermal metrics evaluation is conducted. It enables isolating possible risks engendered by potential negative covert cooling-related factors. The ultimate outcome of this research is to bring about improvement of DC thermal management for sustainable operations