Genomewide and Enzymatic Analysis Reveals Efficient d-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides.

Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. The red basidiomycete yeast Rhodosporidium toruloides is a promising and robust host for lipid- and terpene-derived chemicals. Previous studies demonstrated assimilation of a range of substrates, from C5/C6 sugars to aromatic molecules similar to lignin monomers. In the current study, we analyzed the potential of R. toruloides to assimilate d-galacturonic acid, a major sugar in many pectin-rich agricultural waste streams, including sugar beet pulp and citrus peels. d-Galacturonic acid is not a preferred substrate for many fungi, but its metabolism was found to be on par with those of d-glucose and d-xylose in R. toruloides A genomewide analysis by combined transcriptome sequencing (RNA-seq) and RB-TDNA-seq revealed those genes with high relevance for fitness on d-galacturonic acid. While R. toruloides was found to utilize the nonphosphorylative catabolic pathway known from ascomycetes, the maximal velocities of several enzymes exceeded those previously reported. In addition, an efficient downstream glycerol catabolism and a novel transcription factor were found to be important for d-galacturonic acid utilization. These results set the basis for use of R. toruloides as a potential host for pectin-rich waste conversions and demonstrate its suitability as a model for metabolic studies with basidiomycetes.IMPORTANCE The switch from the traditional fossil-based industry to a green and sustainable bioeconomy demands the complete utilization of renewable feedstocks. Many currently used bioconversion hosts are unable to utilize major components of plant biomass, warranting the identification of microorganisms with broader catabolic capacity and characterization of their unique biochemical pathways. d-Galacturonic acid is a plant component of bioconversion interest and is the major backbone sugar of pectin, a plant cell wall polysaccharide abundant in soft and young plant tissues. The red basidiomycete and oleaginous yeast Rhodosporidium toruloides has been previously shown to utilize a range of sugars and aromatic molecules. Using state-of-the-art functional genomic methods and physiological and biochemical assays, we elucidated the molecular basis underlying the efficient metabolism of d-galacturonic acid. This study identified an efficient pathway for uronic acid conversion to guide future engineering efforts and represents the first detailed metabolic analysis of pectin metabolism in a basidiomycete fungus

Effects of Dietary Distillers Dried Grains with Solubles and Soybean Meal on Extruded Pellet Characteristics and Growth Responses of Juvenile Yellow Perch

A 126-d feeding trial was performed to investigate graded combinations of distillers dried grains with solubles (DDGS) and soybean meal (SBM) in diets formulated for yellow perch Perca flavescens. Six experimental diets contained DDGS and SBM at 0 and 31.5% (dry matter basis), respectively (0/31.5 diet), 10 and 26% (10/26), 20 and 20.5% (20/20.5), 30 and 15% (30/15), 40 and 9.5% (40/9.5), and 50 and 4% (50/4) to obtain similar levels of crude protein (mean ± SE = 30.1 ± 0.2%), crude lipid (16.7 ± 0.7%), and digestible energy (13.5 ± 0.2 kJ/g). Fourteen fish (initial individual weight = 19.1 ± 0.5 g) were randomly selected and stocked into each of twenty-four 110-L tanks (4 replicate tanks/diet). Common biological and mechanical filter systems were used to recirculate the water and maintain similar water quality. Fish that received the 40/9.5 diet exhibited the highest apparent absolute weight gain and percent weight gain, while fish that were fed the 10/26, 20/20.5, 30/15, and 40/9.5 diets exhibited similar absolute weight gain. Fish that were given the 20/20.5, 30/15, and 40/9.5 diets also exhibited similar percent weight gain. Fulton’s condition factor and apparent protein digestibility were significantly lower and higher, respectively, for fish that received the 50/4 diet than for all other treatment groups. Crude protein and crude lipid levels in muscle samples did not significantly differ among treatment groups. Results indicated that yellow perch can utilize DDGS plus SBM at a combined inclusion level of up to 49.5% without negative effects on growth. The mechanical strength and color of the extruded pellets were related to the level of DDGS plus SBM in the feed blends. Hepatosomatic indices were correlated with pellet color, while protein digestibility decreased with increasing pellet strength

Barut-Girardello coherent states for u(p,q) and sp(N,R) and their macroscopic superpositions

The Barut-Girardello coherent states (BG CS) representation is extended to the noncompact algebras u(p,q) and sp(N,R) in (reducible) quadratic boson realizations. The sp(N,R) BG CS take the form of multimode ordinary Schr\"odinger cat states. Macroscopic superpositions of 2^{n-1} sp(N,R) CS (2^n canonical CS, n=1,2,...) are pointed out which are overcomplete in the N-mode Hilbert space and the relation between the canonical CS and the u(p,q) BG-type CS representations is established. The sets of u(p,q) and sp(N,R) BG CS and their discrete superpositions contain many states studied in quantum optics (even and odd N-mode CS, pair CS) and provide an approach to quadrature squeezing, alternative to that of intelligent states. New subsets of weakly and strongly nonclassical states are pointed out and their statistical properties (first- and second-order squeezing, photon number distributions) are discussed. For specific values of the angle parameters and small amplitude of the canonical CS components these states approaches multimode Fock states with one, two or three bosons/photons. It is shown that eigenstates of a squared non-Hermitian operator A^2 (generalized cat states) can exhibit squeezing of the quadratures of A.Comment: 29 pages, LaTex, 5 figures. Improvements in text, corrections in some formulas. To appear in J. Phys. A, v. 3

On the evolution of superposition of squeezed displaced number states with the multiphoton Jaynes-Cummings model

In this paper we discuss the quantum properties for superposition of squeezed displaced number states against multiphoton Jaynes-Cummings model (JCM). In particular, we investigate atomic inversion, photon-number distribution, purity, quadrature squeezing, Mandel $Q$ parameter and Wigner function. We show that the quadrature squeezing for three-photon absorption case can exhibit revivals and collapses typical to those occurring in the atomic inversion for one-photon absorption case. Also we prove that for odd number absorption parameter there is a connection between the evolution of the atomic inversion and the evolution of the Wigner function at the origin in phase space. Furthermore, we show that the nonclassical states whose the Wigner functions values at the origins are negative will be always nonclassical when they are evolving through the JCM with even absorption parameter. Also we demonstrate that various types of cat states can be generated via this system.Comment: 27 pages, 10 figure

Superhard Phases of Simple Substances and Binary Compounds of the B-C-N-O System: from Diamond to the Latest Results (a Review)

The basic known and hypothetic one- and two-element phases of the B-C-N-O system (both superhard phases having diamond and boron structures and precursors to synthesize them) are described. The attention has been given to the structure, basic mechanical properties, and methods to identify and characterize the materials. For some phases that have been recently described in the literature the synthesis conditions at high pressures and temperatures are indicated.Comment: Review on superhard B-C-N-O phase

The birth of a human-specific neural gene by incomplete duplication and gene fusion

Background: Gene innovation by duplication is a fundamental evolutionary process but is difficult to study in humans due to the large size, high sequence identity, and mosaic nature of segmental duplication blocks. The human-specific gene hydrocephalus-inducing 2, HYDIN2, was generated by a 364 kbp duplication of 79 internal exons of the large ciliary gene HYDIN from chromosome 16q22.2 to chromosome 1q21.1. Because the HYDIN2 locus lacks the ancestral promoter and seven terminal exons of the progenitor gene, we sought to characterize transcription at this locus by coupling reverse transcription polymerase chain reaction and long-read sequencing. Results: 5' RACE indicates a transcription start site for HYDIN2 outside of the duplication and we observe fusion transcripts spanning both the 5' and 3' breakpoints. We observe extensive splicing diversity leading to the formation of altered open reading frames (ORFs) that appear to be under relaxed selection. We show that HYDIN2 adopted a new promoter that drives an altered pattern of expression, with highest levels in neural tissues. We estimate that the HYDIN duplication occurred ~3.2 million years ago and find that it is nearly fixed (99.9%) for diploid copy number in contemporary humans. Examination of 73 chromosome 1q21 rearrangement patients reveals that HYDIN2 is deleted or duplicated in most cases. Conclusions: Together, these data support a model of rapid gene innovation by fusion of incomplete segmental duplications, altered tissue expression, and potential subfunctionalization or neofunctionalization of HYDIN2 early in the evolution of the Homo lineage

Chemoproteomics reveals Toll-like receptor fatty acylation

Partial funding for Open Access provided by The Ohio State University Open Access Fund.Background: Palmitoylation is a 16-carbon lipid post-translational modification that increases protein hydrophobicity. This form of protein fatty acylation is emerging as a critical regulatory modification for multiple aspects of cellular interactions and signaling. Despite recent advances in the development of chemical tools for the rapid identification and visualization of palmitoylated proteins, the palmitoyl proteome has not been fully defined. Here we sought to identify and compare the palmitoylated proteins in murine fibroblasts and dendritic cells. Results: A total of 563 putative palmitoylation substrates were identified, more than 200 of which have not been previously suggested to be palmitoylated in past proteomic studies. Here we validate the palmitoylation of several new proteins including Toll-like receptors (TLRs) 2, 5 and 10, CD80, CD86, and NEDD4. Palmitoylation of TLR2, which was uniquely identified in dendritic cells, was mapped to a transmembrane domain-proximal cysteine. Inhibition of TLR2 S-palmitoylation pharmacologically or by cysteine mutagenesis led to decreased cell surface expression and a decreased inflammatory response to microbial ligands. Conclusions: This work identifies many fatty acylated proteins involved in fundamental cellular processes as well as cell type-specific functions, highlighting the value of examining the palmitoyl proteomes of multiple cell types. Spalmitoylation of TLR2 is a previously unknown immunoregulatory mechanism that represents an entirely novel avenue for modulation of TLR2 inflammatory activity.This work was supported by funding from the NIH/NIAID (grant R00AI095348 to J.S.Y.), the NIH/NIGMS (R01GM087544 to HCH), and the Ohio State University Public Health Preparedness for Infectious Diseases (PHPID) program. NMC is supported by the Ohio State University Systems and Integrative Biology Training Program (NIH/NIGMS grant T32GM068412). BWZ is a fellow of the National Science Foundation Graduate Research Fellowship Program (DGE-0937362)

Proportion and characteristics of secondary progressive multiple sclerosis in five European registries using objective classifiers

Background: To assign a course of secondary progressive multiple sclerosis (MS) (SPMS) may be difficult and the proportion of persons with SPMS varies between reports. An objective method for disease course classification may give a better estimation of the relative proportions of relapsing-remitting MS (RRMS) and SPMS and may identify situations where SPMS is under reported.Materials and methods: Data were obtained for 61,900 MS patients from MS registries in the Czech Republic, Denmark, Germany, Sweden, and the United Kingdom (UK), including date of birth, sex, SP conversion year, visits with an Expanded Disability Status Scale (EDSS) score, MS onset and diagnosis date, relapses, and disease-modifying treatment (DMT) use. We included RRMS or SPMS patients with at least one visit between January 2017 and December 2019 if ≥ 18 years of age. We applied three objective methods: A set of SPMS clinical trial inclusion criteria ("EXPAND criteria") modified for a real-world evidence setting, a modified version of the MSBase algorithm, and a decision tree-based algorithm recently published.Results: The clinically assigned proportion of SPMS varied from 8.7% (Czechia) to 34.3% (UK). Objective classifiers estimated the proportion of SPMS from 15.1% (Germany by the EXPAND criteria) to 58.0% (UK by the decision tree method). Due to different requirements of number of EDSS scores, classifiers varied in the proportion they were able to classify; from 18% (UK by the MSBase algorithm) to 100% (the decision tree algorithm for all registries). Objectively classified SPMS patients were older, converted to SPMS later, had higher EDSS at index date and higher EDSS at conversion. More objectively classified SPMS were on DMTs compared to the clinically assigned.Conclusion: SPMS appears to be systematically underdiagnosed in MS registries. Reclassified patients were more commonly on DMTs.</p