Gaussian-distributed codon frequencies of genomes

Mapping Intimacies ◽

10.1101/480152 ◽

2018 ◽

Author(s):

Bohdan B. Khomtchouk ◽

Wolfgang Nonner

Keyword(s):

Codon Usage ◽

Gaussian Distribution ◽

Large Set ◽

Empirical Relations ◽

A Genome ◽

Wide Range ◽

Protein Primary Structure ◽

Prokaryotic Genomes ◽

Rank Relations

AbstractDNA encodes protein primary structure using 64 different codons to specify 20 different amino acids and a stop signal. Frequencies of codon occurrence when ordered in descending sequence provide a global characterization of a genome’s preference (bias) for using the different codons of the redundant genetic code. Whereas frequency/rank relations have been described by empirical relations, here we propose a statistical model in which two different forms of codon usage co-exist in a genome. We investigate whether such a model can account for the range of codon usages observed in a large set of genomes from different taxa. The differences in frequency/rank relations across these genomes can be expressed in a single parameter, the proportion of the two codon compartments. One compartment uses different codons with weak bias according to a Gaussian distribution of frequency, the other uses different codons with strong bias. In prokaryotic genomes both compartments appear to be present in a wide range of proportions, whereas in eukaryotic genomes the compartment with Gaussian distribution tends to dominate. Codon frequencies that are Gaussian-distributed suggest that many evolutionary conditions are involved in shaping weakly-biased codon usage, whereas strong bias in codon usage suggests dominance of few evolutionary conditions.

Characterization of a Novel Ourmia-Like Mycovirus Infecting Magnaporthe oryzae and Implications for Viral Diversity and Evolution

Viruses ◽

10.3390/v11030223 ◽

2019 ◽

Vol 11 (3) ◽

pp. 223 ◽

Cited By ~ 10

Author(s):

Chang Li ◽

Jun Zhu ◽

Bi Gao ◽

Hong Zhu ◽

Qian Zhou ◽

...

Keyword(s):

Magnaporthe Oryzae ◽

Expressed Sequence Tag ◽

Phytopathogenic Fungus ◽

Mycelium Growth ◽

Reading Frame ◽

A Genome ◽

Wide Range ◽

Host Fungus ◽

Shotgun Assembly

Here, the molecular characterization of a novel mycovirus that was isolated from a phytopathogenic fungus Magnaporthe oryzae and designed as Magnaporthe oryzae ourmia-like virus 4 (MOLV4) is reported. MOLV4 has a genome that is 2497 bp long and possesses a single open reading frame (ORF), which encodes the product RNA-dependent RNA polymerase (RdRp). Sequence similarities were found between the MOLV4 encoded RdRp and the counterparts of a few previously reported ourmia-like mycoviruses. Virus-curing and biological comparison indicate that the virus has no or mild effects on the morphology and mycelium growth rate of the host fungus. Phylogenetic analysis using the RdRp aa sequences was performed. The results show that MOLV4 is clustered with the ourmia-like mycoviruses, forming a clade closely related to ourmiaviruses but distinct from narnaviruses. In addition, database searches revealed that several MOLV4-related sequences are present in the transcriptome shotgun assembly (TSA) library, expressed sequence tag database (ESTdb), whole-genome shotgun (WGS) library, and genomic survey sequences (GSS) libraries of a few other species of eukaryote organisms. Our results show that MOLV4, together with other similar ourmia-like mycoviruses, might represent a virus clade that links the plant ourmiaviruses and fungal narnaviruses and has a wide range of hosts.

A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data

BioMed Research International ◽

10.1155/2014/765648 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11

Author(s):

Yu Bai ◽

Yuki Iwasaki ◽

Shigehiko Kanaya ◽

Yue Zhao ◽

Toshimichi Ikemura

Keyword(s):

Genomic Sequence ◽

Sequence Data ◽

Self Organizing Map ◽

Genome Signature ◽

A Genome ◽

Wide Range ◽

Oligonucleotide Composition ◽

Species Specific

With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a “genome signature,” and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).

Isolation and Characterization of a Lytic Staphylococcus aureus Phage WV against Staphylococcus aureus Biofilm

Intervirology ◽

10.1159/000515282 ◽

2021 ◽

pp. 1-9

Author(s):

Yaxian Jiang ◽

Qian Xu ◽

Liming Jiang ◽

Rui Zheng

Keyword(s):

Staphylococcus Aureus ◽

Optimal Growth ◽

Clinical Settings ◽

High Concentration ◽

Biofilm Growth ◽

Isolation And Characterization ◽

Biological Surfaces ◽

A Genome ◽

Wide Range

Background: Staphylococcus aureus is a Gram-positive, pathogenic bacterium that causes a wide range of symptoms in humans and can form biofilm, which is a multicellular community of microorganisms that attaches to nonbiological and biological surfaces. Methods: Here, we aimed to isolate and characterize an S. aureus phage and examine the bactericidal activity alone and in conjunction with streptomycin treatment. Results: We isolated a virulent phage, WV, from a slaughterhouse in Jiangsu, China. This strain belonged to the family Myoviridae and presented a genome size of 141,342 bp. The optimal pH of the preservation buffer was 6–7, optimal growth temperature was 37°C, and optimal multiplicity of infection was 0.01. Phage WV can sterilize most clinical strains of S. aureus that had been isolated from clinical patients in the First People’s Hospital of the Yunnan Province. Against low-concentration S. aureus culture, streptomycin demonstrated a greater antibiofilm effect than that of phage WV. By contrast, in high-concentration S. aureus culture, phage WV demonstrated greater antibiofilm effect than that of streptomycin. The use of phage WV and streptomycin together had a substantially greater overall antibiofilm effect than that achieved using either component alone. Conclusion: This study provides strong evidence for the effectiveness of phage application for the reduction of S. aureus biofilm growth and suggests that phages can be considered as a viable alternative to antibiotics in clinical settings.

Polymer Chemistry

10.1093/oso/9780198503095.001.0001 ◽

2004 ◽

Keyword(s):

Conducting Polymers ◽

Liquid Crystalline ◽

Polymer Chemistry ◽

Chain Growth ◽

Crystalline Polymers ◽

Wide Range ◽

Cyclic Oligomers ◽

Step Growth

Polymer Chemistry: A Practical Approach in Chemistry has been designed for both chemists working in and new to the area of polymer synthesis. It contains detailed instructions for preparation of a wide-range of polymers by a wide variety of different techniques, and describes how this synthetic methodology can be applied to the development of new materials. It includes details of well-established techniques, e.g. chain-growth or step-growth processes together with more up-to-date examples using methods such as atom-transfer radical polymerization. Less well-known procedures are also included, e.g. electrochemical synthesis of conducting polymers and the preparation of liquid crystalline elastomers with highly ordered structures. Other topics covered include general polymerization methodology, controlled/"living" polymerization methods, the formation of cyclic oligomers during step-growth polymerization, the synthesis of conducting polymers based on heterocyclic compounds, dendrimers, the preparation of imprinted polymers and liquid crystalline polymers. The main bulk of the text is preceded by an introductory chapter detailing some of the techniques available to the scientist for the characterization of polymers, both in terms of their chemical composition and in terms of their properties as materials. The book is intended not only for the specialist in polymer chemistry, but also for the organic chemist with little experience who requires a practical introduction to the field.

Organelle Genetics in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms22042104 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2104

Author(s):

Pedro Robles ◽

Víctor Quesada

Keyword(s):

Rna Editing ◽

Posttranscriptional Regulation ◽

Genome Engineering ◽

Plant Mitochondria ◽

Plastid Dna ◽

Chloroplast Genomes ◽

Wide Range ◽

Organelle Genetics ◽

Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

Separate Universe calibration of the dependence of halo bias on cosmic web anisotropy

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/staa2999 ◽

2020 ◽

Vol 499 (3) ◽

pp. 4418-4431 ◽

Cited By ~ 1

Author(s):

Sujatha Ramakrishnan ◽

Aseem Paranjape

Keyword(s):

Dark Matter ◽

High Precision ◽

Gaussian Distribution ◽

Initial Perturbation ◽

Analytical Framework ◽

Web Environment ◽

Wide Range ◽

Galaxy Assembly ◽

Very High ◽

Good Agreement

ABSTRACT We use the Separate Universe technique to calibrate the dependence of linear and quadratic halo bias b1 and b2 on the local cosmic web environment of dark matter haloes. We do this by measuring the response of halo abundances at fixed mass and cosmic web tidal anisotropy α to an infinite wavelength initial perturbation. We augment our measurements with an analytical framework developed in earlier work that exploits the near-lognormal shape of the distribution of α and results in very high precision calibrations. We present convenient fitting functions for the dependence of b1 and b2 on α over a wide range of halo mass for redshifts 0 ≤ z ≤ 1. Our calibration of b2(α) is the first demonstration to date of the dependence of non-linear bias on the local web environment. Motivated by previous results that showed that α is the primary indicator of halo assembly bias for a number of halo properties beyond halo mass, we then extend our analytical framework to accommodate the dependence of b1 and b2 on any such secondary property that has, or can be monotonically transformed to have, a Gaussian distribution. We demonstrate this technique for the specific case of halo concentration, finding good agreement with previous results. Our calibrations will be useful for a variety of halo model analyses focusing on galaxy assembly bias, as well as analytical forecasts of the potential for using α as a segregating variable in multitracer analyses.

Genetic, lifestyle, and health-related characteristics of adults without celiac disease who follow a gluten-free diet: a population-based study of 124,447 participants

American Journal of Clinical Nutrition ◽

10.1093/ajcn/nqaa291 ◽

2020 ◽

Author(s):

Thomas J Littlejohns ◽

Amanda Y Chong ◽

Naomi E Allen ◽

Matthew Arnold ◽

Kathryn E Bradbury ◽

...

Keyword(s):

Celiac Disease ◽

Genome Wide Association Study ◽

Population Based ◽

Gluten Free Diet ◽

Hospital Inpatient ◽

Gluten Free ◽

A Genome ◽

Wide Range ◽

Health Related ◽

Reported Health

ABSTRACT Background The number of gluten-free diet followers without celiac disease (CD) is increasing. However, little is known about the characteristics of these individuals. Objectives We address this issue by investigating a wide range of genetic and phenotypic characteristics in association with following a gluten-free diet. Methods The cross-sectional association between lifestyle and health-related characteristics and following a gluten-free diet was investigated in 124,447 women and men aged 40–69 y from the population-based UK Biobank study. A genome-wide association study (GWAS) of following a gluten-free diet was performed. Results A total of 1776 (1.4%) participants reported following a gluten-free diet. Gluten-free diet followers were more likely to be women, nonwhite, highly educated, living in more socioeconomically deprived areas, former smokers, have lost weight in the past year, have poorer self-reported health, and have made dietary changes as a result of illness. Conversely, these individuals were less likely to consume alcohol daily, be overweight or obese, have hypertension, or use cholesterol-lowering medication. Participants with hospital inpatient diagnosed blood and immune mechanism disorders (OR: 1.62; 95% CI: 1.18, 2.21) and non-CD digestive system diseases (OR: 1.58; 95% CI: 1.42, 1.77) were more likely to follow a gluten-free diet. The GWAS demonstrated that no genetic variants were associated with being a gluten-free diet follower. Conclusions Gluten-free diet followers have a better cardiovascular risk profile than non-gluten-free diet followers but poorer self-reported health and a higher prevalence of blood and immune disorders and digestive conditions. Reasons for following a gluten-free diet warrant further investigation.

Characterization of a Novel CaCO3-Forming Alkali-Tolerant Rhodococcus erythreus S26 as a Filling Agent for Repairing Concrete Cracks

Molecules ◽

10.3390/molecules26102967 ◽

2021 ◽

Vol 26 (10) ◽

pp. 2967

Author(s):

Seunghoon Choi ◽

Sungjin Park ◽

Minjoo Park ◽

Yerin Kim ◽

Kwang Min Lee ◽

...

Keyword(s):

Building Materials ◽

Culture Fluid ◽

Natural Phenomenon ◽

Environment Friendly ◽

Wide Range ◽

Filling Agent ◽

Calcium Source ◽

Alkali Tolerance ◽

High Alkali

Biomineralization, a well-known natural phenomenon associated with various microbial species, is being studied to protect and strengthen building materials such as concrete. We characterized Rhodococcus erythreus S26, a novel urease-producing bacterium exhibiting CaCO3-forming activity, and investigated its ability in repairing concrete cracks for the development of environment-friendly sealants. Strain S26 grown in solid medium formed spherical and polygonal CaCO3 crystals. The S26 cells grown in a urea-containing liquid medium caused culture fluid alkalinization and increased CaCO3 levels, indicating that ureolysis was responsible for CaCO3 formation. Urease activity and CaCO3 formation increased with incubation time, reaching a maximum of 2054 U/min/mL and 3.83 g/L, respectively, at day four. The maximum CaCO3 formation was achieved when calcium lactate was used as the calcium source, followed by calcium gluconate. Although cell growth was observed after the induction period at pH 10.5, strain S26 could grow at a wide range of pH 4–10.5, showing its high alkali tolerance. FESEM showed rhombohedral crystals of 20–60 µm in size. EDX analysis indicated the presence of calcium, carbon, and oxygen in the crystals. XRD confirmed these crystals as CaCO3 containing calcite and vaterite. Furthermore, R. erythreus S26 successfully repaired the artificially induced large cracks of 0.4–0.6 mm width.

Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier

Microorganisms ◽

10.3390/microorganisms9050890 ◽

2021 ◽

Vol 9 (5) ◽

pp. 890

Author(s):

Pietro Tedesco ◽

Fortunato Palma Esposito ◽

Antonio Masino ◽

Giovanni Andrea Vitale ◽

Emiliana Tortorella ◽

...

Keyword(s):

Phenotypic Analysis ◽

Biological Assays ◽

C Elegans ◽

Isolation And Characterization ◽

Wide Range ◽

Protein Encoding ◽

Nematocidal Activity ◽

Extremophilic Microorganisms ◽

Unique Source

Extremophilic microorganisms represent a unique source of novel natural products. Among them, cold adapted bacteria and particularly alpine microorganisms are still underexplored. Here, we describe the isolation and characterization of a novel Gram-positive, aerobic rod-shaped alpine bacterium (KRL4), isolated from sediments from the Karuola glacier in Tibet, China. Complete phenotypic analysis was performed revealing the great adaptability of the strain to a wide range of temperatures (5–40 °C), pHs (5.5–8.5), and salinities (0–15% w/v NaCl). Genome sequencing identified KRL4 as a member of the placeholder genus Exiguobacterium_A and annotation revealed that only half of the protein-encoding genes (1522 of 3079) could be assigned a putative function. An analysis of the secondary metabolite clusters revealed the presence of two uncharacterized phytoene synthase containing pathways and a novel siderophore pathway. Biological assays confirmed that the strain produces molecules with antioxidant and siderophore activities. Furthermore, intracellular extracts showed nematocidal activity towards C. elegans, suggesting that strain KRL4 is a source of anthelmintic compounds.

Towards Reduced CNNs for De-Noising Phase Images Corrupted with Speckle Noise

Photonics ◽

10.3390/photonics8070255 ◽

2021 ◽

Vol 8 (7) ◽

pp. 255

Author(s):

Marie Tahon ◽

Silvio Montresor ◽

Pascal Picart

Keyword(s):

Phase Error ◽

Speckle Noise ◽

Experimental Conditions ◽

Benchmark Data ◽

Wide Range ◽

Phase Images ◽

Different Depths ◽

Phase Data ◽

Do So

Digital holography is a very efficient technique for 3D imaging and the characterization of changes at the surfaces of objects. However, during the process of holographic interferometry, the reconstructed phase images suffer from speckle noise. In this paper, de-noising is addressed with phase images corrupted with speckle noise. To do so, DnCNN residual networks with different depths were built and trained with various holographic noisy phase data. The possibility of using a network pre-trained on natural images with Gaussian noise is also investigated. All models are evaluated in terms of phase error with HOLODEEP benchmark data and with three unseen images corresponding to different experimental conditions. The best results are obtained using a network with only four convolutional blocks and trained with a wide range of noisy phase patterns.