Multi-Omics and Genome Editing Studies on Plant Cell Walls to Improve Biomass Quality

Biomass is one of the most important sources of renewable energy and plays an important role in reducing our reliance on fossil fuels. Efficient biomass production is essential to obtain large amounts of sustainable energy with minimal environmental cost. However, the biochemical and molecular processes behind the synthesis of the main components of biomass are still not fully understood. This review provides a comprehensive summary of the most relevant studies on cell wall biosynthesis and degradation mechanisms, focusing on the lignocellulosic component, in which the conversion process to fermentable sugars is expensive, due to its recalcitrant nature. A focus is placed on multi-omics research involving genomics, transcriptomics, proteomics, metabolomics, and phenomics, since multi-omics approaches offer a unique opportunity to investigate the biological pathways underlying the genotype traits characterizing cell wall energy crops. Furthermore, our study highlights the advances in genome editing approaches and proposes the modification of the genes that are involved in the complex cell wall structure as a feasible solution to an efficient biomass production. Several key points for future research activities based on these emerging technologies are also discussed, focusing on the combination of multi-omics and gene editing approaches, which offer potential for improved biomass valorization and the development of tangible bioproducts

N-terminal probrain natriuretic peptide is a stronger predictor of cardiovascular mortality than C-reactive protein and albumin excretion rate in elderly patients with type 2 diabetes: the Casale Monferrato population-based study.

OBJECTIVE: To study whether N-terminal probrain natriuretic peptide (NT-proBNP) is a short-term independent predictor of both all-cause and cardiovascular (CV) mortality in type 2 diabetic patients and to establish whether albuminuria and C-reactive protein (CRP) affect this relationship. RESEARCH DESIGN AND METHODS: The prospective study included 1,825 type 2 diabetic patients from the population-based cohort of the Casale Monferrato study. CV risk factors, preexisting CVD, and NT-proBNP levels were evaluated at baseline. All-cause and CV mortality were assessed 5.5 years after baseline examination. Multivariate Cox proportional hazards modeling was used to estimate mortality hazard ratios (HRs). RESULTS: During the follow-up period, 390 people died (175 for CVD) out of 9,101 person-years of observations. A significantly increased mortality risk by quartiles of NT-proBNP was observed (test for trend, P < 0.001). NT-proBN P values >91 pg/mL conferred HRs of 2.05 (95% CI 1.47–2.86) for all-cause and 4.47 (2.38–8.39) for CV mortality, independently of CV risk factors, including CRP and albumin excretion rate (AER). The association was also significant for modest rises in NT-proBNP levels and in patients without microalbuminuria and CVD at baseline (upper quartiles HRs 3.82 [95% CI 1.24–13.75]) and 3.14 [1.00–9.94]). Albuminuria and NT-proBNP had an additive effect on mortality, though the association was stronger for NT-proBNP. CONCLUSIONS: NT-proBNP is a strong independent predictor of short-term CV mortality risk in elderly people with type 2 diabetes, including those without preexisting CVD. This association is evident even in people with slightly increased values, is not modified by CRP, and is additive to that provided by AER

Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles

For seagrasses, seasonal and daily variations in light and temperature represent the mains factors driving their distribution along the bathymetric cline. Changes in these environmental factors, due to climatic and anthropogenic effects, can compromise their survival. In a framework of conservation and restoration, it becomes crucial to improve our knowledge about the physiological plasticity of seagrass species along environmental gradients. Here, we aimed to identify differences in transcriptomic and proteomic profiles, involved in the acclimation along the depth gradient in the seagrass Posidonia oceanica, and to improve the available molecular resources in this species, which is an important requisite for the application of eco-genomic approaches. To do that, from plant growing in shallow (−5 m) and deep (−25 m) portions of a single meadow, (i) we generated two reciprocal Expressed Sequences Tags (EST) libraries using a Suppressive Subtractive Hybridization (SSH) approach, to obtain depth/specific transcriptional profiles, and (ii) we identified proteins differentially expressed, using the highly innovative USIS mass spectrometry methodology, coupled with 1D-SDS electrophoresis and labeling free approach. Mass spectra were searched in the open source Global Proteome Machine (GPM) engine against plant databases and with the X!Tandem algorithm against a local database. Transcriptional analysis showed both quantitative and qualitative differences between depths. EST libraries had only the 3% of transcripts in common. A total of 315 peptides belonging to 64 proteins were identified by mass spectrometry. ATP synthase subunits were among the most abundant proteins in both conditions. Both approaches identified genes and proteins in pathways related to energy metabolism, transport and genetic information processing, that appear to be the most involved in depth acclimation in P. oceanica. Their putative rules in acclimation to depth were discussed

A Calibration of NICMOS Camera 2 for Low Count-Rates

NICMOS 2 observations are crucial for constraining distances to most of the existing sample of z > 1 SNe Ia. Unlike the conventional calibration programs, these observations involve long exposure times and low count rates. Reciprocity failure is known to exist in HgCdTe devices and a correction for this effect has already been implemented for high and medium count-rates. However observations at faint count-rates rely on extrapolations. Here instead, we provide a new zeropoint calibration directly applicable to faint sources. This is obtained via inter-calibration of NIC2 F110W/F160W with WFC3 in the low count-rate regime using z ~ 1 elliptical galaxies as tertiary calibrators. These objects have relatively simple near-IR SEDs, uniform colors, and their extended nature gives superior signal-to-noise at the same count rate than would stars. The use of extended objects also allows greater tolerances on PSF profiles. We find ST magnitude zeropoints (after the installation of the NICMOS cooling system, NCS) of 25.296 +- 0.022 for F110W and 25.803 +- 0.023 for F160W, both in agreement with the calibration extrapolated from count-rates 1,000 times larger (25.262 and 25.799). Before the installation of the NCS, we find 24.843 +- 0.025 for F110W and 25.498 +- 0.021 for F160W, also in agreement with the high-count-rate calibration (24.815 and 25.470). We also check the standard bandpasses of WFC3 and NICMOS 2 using a range of stars and galaxies at different colors and find mild tension for WFC3, limiting the accuracy of the zeropoints. To avoid human bias, our cross-calibration was "blinded" in that the fitted zeropoint differences were hidden until the analysis was finalized.Comment: Accepted for Publication in the Astronomical Journal. New version contains added referenc

A New Determination of the High Redshift Type Ia Supernova Rates with the Hubble Space Telescope Advanced Camera for Surveys

We present a new measurement of the volumetric rate of Type Ia supernova up to a redshift of 1.7, using the Hubble Space Telescope (HST) GOODS data combined with an additional HST dataset covering the North GOODS field collected in 2004. We employ a novel technique that does not require spectroscopic data for identifying Type Ia supernovae (although spectroscopic measurements of redshifts are used for over half the sample); instead we employ a Bayesian approach using only photometric data to calculate the probability that an object is a Type Ia supernova. This Bayesian technique can easily be modified to incorporate improved priors on supernova properties, and it is well-suited for future high-statistics supernovae searches in which spectroscopic follow up of all candidates will be impractical. Here, the method is validated on both ground- and space-based supernova data having some spectroscopic follow up. We combine our volumetric rate measurements with low redshift supernova data, and fit to a number of possible models for the evolution of the Type Ia supernova rate as a function of redshift. The data do not distinguish between a flat rate at redshift > 0.5 and a previously proposed model, in which the Type Ia rate peaks at redshift >1 due to a significant delay from star-formation to the supernova explosion. Except for the highest redshifts, where the signal to noise ratio is generally too low to apply this technique, this approach yields smaller or comparable uncertainties than previous work.Comment: Accepted for publication in Ap

The Hubble Space Telescope Cluster Supernova Survey: VI. The Volumetric Type Ia Supernova Rate

We present a measurement of the volumetric Type Ia supernova (SN Ia) rate out to z ~ 1.6 from the Hubble Space Telescope Cluster Supernova Survey. In observations spanning 189 orbits with the Advanced Camera for Surveys we discovered 29 SNe, of which approximately 20 are SNe Ia. Twelve of these SNe Ia are located in the foregrounds and backgrounds of the clusters targeted in the survey. Using these new data, we derive the volumetric SN Ia rate in four broad redshift bins, finding results consistent with previous measurements at z > 1 and strengthening the case for a SN Ia rate that is equal to or greater than ~0.6 x 10^-4/yr/Mpc^3 at z ~ 1 and flattening out at higher redshift. We provide SN candidates and efficiency calculations in a form that makes it easy to rebin and combine these results with other measurements for increased statistics. Finally, we compare the assumptions about host-galaxy dust extinction used in different high-redshift rate measurements, finding that different assumptions may induce significant systematic differences between measurements.Comment: 11 pages, 7 figures. Submitted to the Astrophysical Journal. Revised version following referee comments. See the HST Cluster SN Survey website at http://supernova.lbl.gov/2009ClusterSurvey for control time simulations in a machine-readable table and a complete listing of transient candidates from the surve

Spectra of High-Redshift Type Ia Supernovae and a Comparison with their Low-Redshift Counterparts

We present spectra for 14 high-redshift (0.17 < z < 0.83) supernovae, which were discovered by the Supernova Cosmology Project as part of a campaign to measure cosmological parameters. The spectra are used to determine the redshift and classify the supernova type, essential information if the supernovae are to be used for cosmological studies. Redshifts were derived either from the spectrum of the host galaxy or from the spectrum of the supernova itself. We present evidence that these supernovae are of Type Ia by matching to spectra of nearby supernovae. We find that the dates of the spectra relative to maximum light determined from this fitting process are consistent with the dates determined from the photometric light curves, and moreover the spectral time-sequence for SNe Type Ia at low and high redshift is indistinguishable. We also show that the expansion velocities measured from blueshifted CaHK are consistent with those measured for low-redshift Type Ia supernovae. From these first-level quantitative comparisons we find no evidence for evolution in SNIa properties between these low- and high-redshift samples. Thus even though our samples may not be complete, we conclude that there is a population of SNe Ia at high redshift whose spectral properties match those at low redshift.Comment: Accepted for publication in AJ. Also available at http://supernova.lbl.gov

Rest-Frame R-band Lightcurve of a z~1.3 Supernova Obtained with Keck Laser Adaptive Optics

We present Keck diffraction limited H-band photometry of a z~1.3 Type Ia supernova (SN) candidate, first identified in a Hubble Space Telescope (HST) search for SNe in massive high redshift galaxy clusters. The adaptive optics (AO) data were obtained with the Laser Guide Star facility during four observing runs from September to November 2005. In the analysis of data from the observing run nearest to maximum SN brightness, the SN was found to have a magnitude H=23.9 +/- 0.14 (Vega). We present the H-band (approximately rest-frame R) light curve and provide a detailed analysis of the AO photometric uncertainties. By constraining the aperture correction with a nearby (4" separation) star we achieve 0.14 magnitude photometric precision, despite the spatially varying AO PSF.Comment: 11 pages, 8 figures, Accepted for Publication in AJ Updated the citations, fixed typo

The modulation of leaf metabolism plays a role in salt tolerance of Cymodocea nodosa exposed to hypersaline stress in mesocosms

Applying proteomics, we tested the physiological responses of the euryhaline seagrass Cymodocea nodosa to deliberate manipulation of salinity in a mesocosm system. Plants were subjected to a chronic hypersaline condition (43 psu) to compare protein expression and plant photochemistry responses after 15 and 30 days of exposure with those of plants cultured under normal/ambient saline conditions (37 psu). Results showed a general decline in the expression level of leaf proteins in hypersaline stressed plants, with more intense reductions after long-lasting exposure. Specifically, the carbon-fixing enzyme RuBisCo displayed a lower accumulation level in stressed plants relative to controls. In contrast, the key enzymes involved in the regulation of glycolysis, cytosolic glyceraldehyde-3-phosphate dehydrogenase, enolase 2 and triose-phosphate isomerase, showed significantly higher accumulation levels. These responses suggested a shift in carbon metabolism in stressed plants. Hypersaline stress also induced a significant alteration of the photosynthetic physiology of C. nodosa by means of a downregulation in structural proteins and enzymes of both PSII and PSI. However we found an over-expression of the cytochrome b559 alpha subunit of the PSII initial complex, which is a receptor for the PSII core proteins involved in biogenesis or repair processes and therefore potentially involved in the absence of effects at the photochemical level of stressed plants. As expected hypersalinity also affects vacuolar metabolism by increasing the leaf cell turgor pressure and enhancing the up-take of Na+ by overaccumulating the tonoplast specific intrinsic protein pyrophosphate-energized inorganic pyrophosphatase (H(+)-PPase) coupled to the Na+/H+-antiporter. The modulation of carbon metabolism and the enhancement of vacuole capacity in Na+ sequestration and osmolarity changes are discussed in relation to salt tolerance of C. nodosa.Postprin

Coibacins A D, Antileishmanial Marine Cyanobacterial Polyketides with Intriguing Biosynthetic Origins

Four unsaturated polyketide lactone derivatives, coibacins A-D, were isolated from a Panamanian marine cyanobacterium, cf. Oscillatoria sp. The two different types of termini observed in these co-occurring metabolites, either a methyl cyclopropyl ring as seen in curacin A or a methyl vinyl chloride similar to that observed in the jamaicamides, suggest an intriguing flexibility in the “beta branch” forming biosynthetic process. The coibacins possess selective antileishmanial activity as well as potent anti-inflammatory activity.Four unsaturated polyketide lactone derivatives, coibacins A-D, were isolated from a Panamanian marine cyanobacterium, cf. Oscillatoria sp. The two different types of termini observed in these co-occurring metabolites, either a methyl cyclopropyl ring as seen in curacin A or a methyl vinyl chloride similar to that observed in the jamaicamides, suggest an intriguing flexibility in the “beta branch” forming biosynthetic process. The coibacins possess selective antileishmanial activity as well as potent anti-inflammatory activity