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

Adiabaticity Conditions for Volatility Smile in Black-Scholes Pricing Model

Our derivation of the distribution function for future returns is based on the risk neutral approach which gives a functional dependence for the European call (put) option price, C(K), given the strike price, K, and the distribution function of the returns. We derive this distribution function using for C(K) a Black-Scholes (BS) expression with volatility in the form of a volatility smile. We show that this approach based on a volatility smile leads to relative minima for the distribution function ("bad" probabilities) never observed in real data and, in the worst cases, negative probabilities. We show that these undesirable effects can be eliminated by requiring "adiabatic" conditions on the volatility smile

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

Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates

BACKGROUND: Clinical isolates of the gastric pathogen Helicobacter pylori display a high level of genetic macro- and microheterogeneity, featuring a panmictic, rather than clonal structure. The ability of H. pylori to survive the stomach acid is due, in part, to the arginase-urease enzyme system. Arginase (RocF) hydrolyzes L-arginine to L-ornithine and urea, and urease hydrolyzes urea to carbon dioxide and ammonium, which can neutralize acid. RESULTS: The degree of variation in arginase was explored at the DNA sequence, enzyme activity and protein expression levels. To this end, arginase activity was measured from 73 minimally-passaged clinical isolates and six laboratory-adapted strains of H. pylori. The rocF gene from 21 of the strains was cloned into genetically stable E. coli and the enzyme activities measured. Arginase activity was found to substantially vary (>100-fold) in both different H. pylori strains and in the E. coli model. Western blot analysis revealed a positive correlation between activity and amount of protein expressed in most H. pylori strains. Several H. pylori strains featured altered arginase activity upon in vitro passage. Pairwise alignments of the 21 rocF genes plus strain J99 revealed extensive microheterogeneity in the promoter region and 3' end of the rocF coding region. Amino acid S232, which was I232 in the arginase-negative clinical strain A2, was critical for arginase activity. CONCLUSION: These studies demonstrated that H. pylori arginase exhibits extensive genotypic and phenotypic variation which may be used to understand mechanisms of microheterogeneity in H. pylori

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

Subaru FOCAS Spectroscopic Observations of High-Redshift Supernovae

We present spectra of high-redshift supernovae (SNe) that were taken with the Subaru low resolution optical spectrograph, FOCAS. These SNe were found in SN surveys with Suprime-Cam on Subaru, the CFH12k camera on the Canada-France-Hawaii Telescope (CFHT), and the Advanced Camera for Surveys (ACS) on the Hubble Space Telescope (HST). These SN surveys specifically targeted z>1 Type Ia supernovae (SNe Ia). From the spectra of 39 candidates, we obtain redshifts for 32 candidates and spectroscopically identify 7 active candidates as probable SNe Ia, including one at z=1.35, which is the most distant SN Ia to be spectroscopically confirmed with a ground-based telescope. An additional 4 candidates are identified as likely SNe Ia from the spectrophotometric properties of their host galaxies. Seven candidates are not SNe Ia, either being SNe of another type or active galactic nuclei. When SNe Ia are observed within a week of maximum light, we find that we can spectroscopically identify most of them up to z=1.1. Beyond this redshift, very few candidates were spectroscopically identified as SNe Ia. The current generation of super red-sensitive, fringe-free CCDs will push this redshift limit higher.Comment: 19 pages, 26 figures. PASJ in press. see http://www.supernova.lbl.gov/2009ClusterSurvey/ for additional information pertaining to the HST Cluster SN Surve

Laser treatment monitoring with reflectance confocal microscopy

Laser treatments have become popular in Dermatology. In parallel to technologic development enabling the availability of different laser wavelengths, non-invasive skin imaging techniques, such as reflectance confocal microscopy (RCM), have been used to explore morphologic and qualitative skin characteristics. Specifically, RCM can be applied to cosmetically sensitive skin areas such as the face, without the need for skin biopsies. For these reasons, apart from its current use in skin cancer diagnosis, our systematic review reveals how RCM can be employed in the field of laser treatment monitoring, being particularly suitable for the evaluation of variations in epidermis and dermis, and pigmentary and vascular characteristics of the skin. This systematic review article aims to provide an overview on current applications of RCM laser treatment monitoring, while describing RCM features identified for different applications. Studies on human subjects treated with laser treatments, monitored with RCM, were included in the current systematic review. Five groups of treatments were identified and described: skin rejuvenation, scar tissue, pigmentary disorders, vascular disorders and other. Interestingly, RCM can assist treatments with lasers targeting all chromophores in the skin and exploiting laser induced optical breakdown. Treatment monitoring encompasses assessment at baseline and examination of changes after treatment, therefore revealing details in morphologic alterations underlying different skin conditions and mechanisms of actions of laser therapy, as well as objectify results after treatment

New Results from the Cryogenic Dark Matter Search Experiment

Using improved Ge and Si detectors, better neutron shielding, and increased counting time, the Cryogenic Dark Matter Search (CDMS) experiment has obtained stricter limits on the cross section of weakly interacting massive particles (WIMPs) elastically scattering from nuclei. Increased discrimination against electromagnetic backgrounds and reduction of neutron flux confirm WIMP-candidate events previously detected by CDMS were consistent with neutrons and give limits on spin-independent WIMP interactions which are >2X lower than previous CDMS results for high WIMP mass, and which exclude new parameter space for WIMPs with mass between 8-20 GeV/c^2.Comment: 4 pages, 4 figure

Spectroscopic Observations and Analysis of the Unusual Type Ia SN 1999ac

We present optical spectra of the peculiar Type Ia supernova (SN Ia) 1999ac. The data extend from -15 to +42 days with respect to B-band maximum and reveal an event that is unusual in several respects. Prior to B-band maximum, the spectra resemble those of SN 1999aa, a slowly declining event, but possess stronger SiII and CaII signatures (more characteristic of a spectroscopically normal SN). Spectra after B-band maximum appear more normal. The expansion velocities inferred from the Iron lines appear to be lower than average; whereas, the expansion velocity inferred from Calcium H and K are higher than average. The expansion velocities inferred from SiII are among the slowest ever observed, though SN 1999ac is not particularly dim. The analysis of the parameters v_10, R(SiII), dv(SiII)/dt, and d_m15 further underlines the unique characteristics of SN 1999ac. We find convincing evidence of CII 6580 in the day -15 spectrum with ejection velocity v > 16,000 km/s, but this signature disappears by day -9. This rapid evolution at early times highlights the importance of extremely early-time spectroscopy.Comment: 40 pages, 24 figures, accepted for publication in The Astronomical Journa