Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein

BACKGROUND: A large number of papers have been published on analysis of microarray data with particular emphasis on normalization of data, detection of differentially expressed genes, clustering of genes and regulatory network. On other hand there are only few studies on relation between expression level and composition of nucleotide/protein sequence, using expression data. There is a need to understand why particular genes/proteins express more in particular conditions. In this study, we analyze 3468 genes of Saccharomyces cerevisiae obtained from Holstege et al., (1998) to understand the relationship between expression level and amino acid composition. RESULTS: We compute the correlation between expression of a gene and amino acid composition of its protein. It was observed that some residues (like Ala, Gly, Arg and Val) have significant positive correlation (r > 0.20) and some other residues (Like Asp, Leu, Asn and Ser) have negative correlation (r < -0.15) with the expression of genes. A significant negative correlation (r = -0.18) was also found between length and gene expression. These observations indicate the relationship between percent composition and gene expression level. Thus, attempts have been made to develop a Support Vector Machine (SVM) based method for predicting the expression level of genes from its protein sequence. In this method the SVM is trained with proteins whose gene expression data is known in a given condition. Then trained SVM is used to predict the gene expression of other proteins of the same organism in the same condition. A correlation coefficient r = 0.70 was obtained between predicted and experimentally determined expression of genes, which improves from r = 0.70 to 0.72 when dipeptide composition was used instead of residue composition. The method was evaluated using 5-fold cross validation test. We also demonstrate that amino acid composition information along with gene expression data can be used for improving the function classification of proteins. CONCLUSION: There is a correlation between gene expression and amino acid composition that can be used to predict the expression level of genes up to a certain extent. A web server based on the above strategy has been developed for calculating the correlation between amino acid composition and gene expression and prediction of expression level . This server will allow users to study the evolution from expression data

Low-velocity anisotropic Dirac fermions on the side surface of topological insulators

We report anisotropic Dirac-cone surface bands on a side-surface geometry of the topological insulator Bi$_2$Se$_3$ revealed by first-principles density-functional calculations. We find that the electron velocity in the side-surface Dirac cone is anisotropically reduced from that in the (111)-surface Dirac cone, and the velocity is not in parallel with the wave vector {\bf k} except for {\bf k} in high-symmetry directions. The size of the electron spin depends on the direction of {\bf k} due to anisotropic variation of the noncollinearity of the electron state. Low-energy effective Hamiltonian is proposed for side-surface Dirac fermions, and its implications are presented including refractive transport phenomena occurring at the edges of tological insulators where different surfaces meet.Comment: 4 pages, 2 columns, 4 figure

Scutellinia (Pezizales) In Korea, With A New Species and Eight New Records

Eleven species of the genus Scutellinia (Pyronemataceae, Pezizales) are recognized in Korea by analysis of macro- and micro-morphological characteristics, substrates and geographical distributions. Eight species are recorded new to Korea, namely, S. ahmadiopsis, S. badio-berbis, S. colensoi, S. jilinensis, S. nigrohirtula, S. olivascens, S. setosa and S. patagonica. Based on the exceptional length of marginal hairs and tuberculate ascospore wall ornamentation, two Korean specimens occurring on wood are described as a new species. Infraspecific morphological variations among collections within S. scutellata and S. patagonica were found. These are tentative treat as species complexes. The highly questionable occurrence of S. setosa in Asia was confirmed. Descriptions and taxonomic notes of the recognized species of Scutellinia are provided with a taxonomic key, illustrations and photographs of these species from Korea.Organismic and Evolutionary Biolog

Motor complications in Parkinson's disease: 13-year follow-up of the CamPaIGN cohort.

BACKGROUND: Long-term population-representative data on motor fluctuations and levodopa-induced dyskinesias in Parkinson's disease is lacking. METHODS: The Cambridgeshire Parkinson's Incidence from GP to Neurologist (CamPaIGN) cohort comprises incident PD cases followed for up to 13 years (n = 141). Cumulative incidence of motor fluctuations and levodopa-induced dyskinesias and risk factors were assessed using Kaplan-Meyer and Cox regression analyses. RESULTS: Cumulative incidence of motor fluctuations and levodopa-induced dyskinesias was 54.3% and 14.5%, respectively, at 5 years and 100% and 55.7%, respectively, at 10 years. Higher baseline UPDRS-total and SNCA rs356219(A) predicted motor fluctuations, whereas higher baseline Mini-mental State Examination and GBA mutations predicted levodopa-induced dyskinesias. Early levodopa use did not predict motor complications. Both early motor fluctuations and levodopa-induced dyskinesias predicted reduced mortality in older patients (age at diagnosis >70 years). CONCLUSIONS: Our data support the hypothesis that motor complications are related to the severity of nigrostriatal pathology rather than early levodopa use and indicate that early motor complications do not necessarily confer a negative prognosis. © 2019 International Parkinson and Movement Disorder Society.This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2013-R1A1A2010499). CWG is supported by a Medical Research Council Clinician Scientist Fellowship. The CamPaIGN study was supported by the Wellcome Trust, the Medical Research Council, the Patrick Berthoud Trust, and the National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre Dementia and Neurodegeneration Theme (Grant Reference Number 146281). RAB is an NIHR Senior Investigator

Generation of Multiple Bioactive Macrolides by Hybrid Modular Polyketide Synthases in Streptomyces venezuelae

AbstractThe plasmid-based replacement of the multifunctional protein subunits of the pikromycin PKS in S. venezuelae by the corresponding subunits from heterologous modular PKSs resulted in recombinant strains that produce both 12- and 14-membered ring macrolactones with predicted structural alterations. In all cases, novel macrolactones were produced and further modified by the DesVII glycosyltransferase and PikC hydroxylase, leading to biologically active macrolide structures. These results demonstrate that hybrid PKSs in S. venezuelae can produce a multiplicity of new macrolactones that are modified further by the highly flexible DesVII glycosyltransferase and PikC hydroxylase tailoring enzymes. This work demonstrates the unique capacity of the S. venezuelae pikromycin pathway to expand the toolbox of combinatorial biosynthesis and to accelerate the creation of novel biologically active natural products

A highly active and redox stable novel ceramic anode with in-situ exsolution of nanocatalysts

Layered perovskite novel ceramic anode (referred to as SGNM) phases were evaluated for use in solid oxide fuel cells (SOFCs). Hydrogen temperature programmed reduction (H2-TPR) analysis of the SGNM materials revealed that significant exsolution of Ni nanoparticles occurred. Consistently, the SGNM on the LSGM electrolyte showed low electrode polarization resistance in H2 at 800 °C. Moreover, after 10 redox cycles at 750 °C, the electrode area specific resistance of the SGNM anode in H2 slightly increased during cycle, indicating excellent redox stability in both reducing and oxidizing atmospheres. An LSGM-electrolyte supported SOFC employing an SGNM-based anode yielded a high power density of ~1 W cm-2 at 800 °C, which is the best performance among the any SOFCs with Ruddlesden-Popper based ceramic anodes to date. After performance measurement, we observed that metallic Ni nanoparticles (~ 25 nm) were grown in situ and homogeneously distributed on the SGNM anode surface. These exsolved nanocatalysts are believed to significantly enhance the hydrogen oxidation activity of the SGNM material. These results demonstrate that the novel SGNM material is promising as a high catalytically active and redox-stable anode for SOFCs.. Please click Additional Files below to see the full abstract

Chemoenzymatic Synthesis of Glycosylated Macrolactam Analogues of the Macrolide Antibiotic YC‐17

YC‐17 is a 12‐membered ring macrolide antibiotic produced from Streptomyces venezuelae ATCC 15439 and is composed of the polyketide macrolactone 10‐deoxymethynolide appended with D‐desosamine. In order to develop structurally diverse macrolactam analogues of YC‐17 with improved therapeutic potential, a combined approach involving chemical synthesis and engineered cell‐based biotransformation was employed. Eight new antibacterial macrolactam analogues of YC‐17 were generated by supplying a novel chemically synthesized macrolactam aglycone to S. venezuelae mutants harboring plasmids capable of synthesizing several unnatural sugars for subsequent glycosylation. Some YC‐17 macrolactam analogues were active against erythromycin‐resistant bacterial pathogens and displayed improved metabolic stability in vitro. The enhanced therapeutic potential demonstrated by these glycosylated macrolactam analogues reveals the unique potential of chemoenzymatic synthesis in antibiotic drug discovery and development.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113147/1/adsc_201500250_sm_miscellaneous_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/113147/2/2697_ftp.pd

Sr\u3csub\u3e2\u3c/sub\u3eIr\u3csub\u3e1−\u3cem\u3ex\u3c/em\u3e\u3c/sub\u3eRh\u3csub\u3e\u3cem\u3ex\u3c/em\u3e\u3c/sub\u3eO\u3csub\u3e4\u3c/sub\u3e(x\u3c0.5): An Inhomogeneous \u3cem\u3ej\u3c/em\u3e\u3csub\u3eeff\u3c/sub\u3e=1/2 Hubbard system

In a combined experimental and theoretical study, we investigate the properties of Sr2Ir1−xRhxO4. From the branching ratios of the L-edge isotropic x-ray absorption spectra, we determine that the spin-orbit coupling is remarkably independent of x for both iridium and rhodium sites. DFT+U calculations show that the doping is close to isoelectronic and introduces impurity bands of predominantly rhodium character close to the lower Hubbard band. Overlap of these two bands leads to metallic behavior. Since the low-energy states for xjeff=1/2 character, we suggest that the electronic properties of this material can be described by an inhomogeneous Hubbard model, where the on-site energies change due to local variations in the spin-orbit interaction strength combined with additional changes in binding energy

Interrater reliability of motor severity scales for hemifacial spasm

To compare the inter-rater reliability (IRR) of five clinical rating scales for video-based assessment of hemifacial spasm (HFS) motor severity. We evaluated the video recordings of 45 HFS participants recruited through the Dystonia Coalition. In Round 1, six clinicians with expertise in HFS assessed the participants\u27 motor severity with five scales used to measure motor severity of HFS: the Jankovic rating scale (JRS), Hemifacial Spasm Grading Scale (HSGS), Samsung Medical Center (SMC) grading system for severity of HFS spasms (Lee\u27s scale), clinical grading of spasm intensity (Chen\u27s scale), and a modified version of the Abnormal Involuntary Movement Scale (Tunc\u27s scale). In Round 2, clinicians rated the same cohort with simplified scale wording after consensus training. For each round, we evaluated the IRR using the intraclass correlation coefficient [ICC (2,1) single-rater, absolute-agreement, 2-way random model]. The scales exhibited IRR that ranged from poor to moderate ; the mean ICCs were 0.41, 0.43, 0.47, 0.43, and 0.65 for the JRS, HSGS, Lee\u27s, Chen\u27s, and Tunc\u27s scales, respectively, for Round 1. In Round 2, the corresponding IRRs increased to 0.63, 0.60, 0.59, 0.53, and 0.71. In both rounds, Tunc\u27s scale exhibited the highest IRR. For clinical assessments of HFS motor severity based on video observations, we recommend using Tunc\u27s scale because of its comparative reliability and because clinicians interpret the scale easily without modifications or the need for consensus training