Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress.

Calcium (Ca) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca deficiency in orphan crops such as Tef [(Eragrostis tef) (Zucc.) Trotter], which accumulate high levels of Ca in the grains, remained unknown.

Analysis of miRNAs responsive to long-term calcium deficiency in tef ( (Zucc.) Trotter).

MicroRNAs (miRNAs) play an important role in growth, development, stress resilience, and epigenetic modifications of plants. However, the effect of calcium (Ca) deficiency on miRNA expression in the orphan crop tef ( remains unknown. In this study, we analyzed expression of miRNAs in roots and shoots of tef in response to Ca treatment.

Complete mitochondrial genome of Ortmann, 1894 (Crustacea: Decapoda: Grapsoidea) specimen collected in South Korea.

In this study, the complete 16,184 bp mitochondrial genome of was determined from a specimen collected in South Korea. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and a non-coding A + T rich region. The base composition of the heavy strand in the mitochondrial genome was 34.

A chloroplast genome of (Nakai) Nakai, an endemic species in Korea.

(Nakai) Nakai is an endemic species in Korea. We present the second complete chloroplast genome sequence of showing that the chloroplast genome is 156,376 bp in length containing four subregions: a large single-copy (LSC) region of 87,097 bp, a small single-copy (SSC) region of 17,859 bp, and a pair of inverted repeat regions (IRs) of 25,710 bp. The genome contains 131 genes including 88 protein-coding genes, 35 s, and eight rRNAs.

Silicon Enhances Biomass and Grain Yield in an Ancient Crop Tef [].

Silicon (Si) is one of the beneficial plant mineral nutrients which is known to improve biotic and abiotic stress resilience and productivity in several crops. However, its beneficial role in underutilized or "orphan" crop such as tef [] has never been studied before. In this study, we investigated the effect of Si application on tef plant performance.

Lipid Composition of Latex and Rubber Particles in and .

Natural rubber is usually synthesized in the rubber particles present in the latex of rubber-producing plants such as the Pará rubber tree () and rubber dandelion (). Since the detailed lipid compositions of fresh latex and rubber particles of the plants are poorly known, the present study reports detailed compound lipid composition, focusing on phospholipids and galactolipids in the latex and rubber particles of the plants. In the fresh latex and rubber particles of both plants, phospholipids were much more dominant (85-99%) compared to galactolipids.

Prediction of Dhurrin Metabolism by Transcriptome and Metabolome Analyses in .

Sorghum ( (L.)) Moench is an important food for humans and feed for livestock. Sorghum contains dhurrin which can be degraded into toxic hydrogen cyanide.

Heterologous activation of the Hevea PEP16 promoter in the rubber-producing laticiferous tissues of Taraxacum kok-saghyz.

Hevea brasiliensis, the most abundant rubber crop, is used widely for the commercial production of natural rubber. To reduce the risk of a shortage in the supply of natural rubber that may arise from a single major rubber crop, rubber dandelion (Taraxacum kok-saghyz) has been developed as an alternative rubber-producing crop by using a transgenic approach. However, it is necessary to identify a suitable promoter for the transfer of rubber biosynthesis-related genes to the species.

Illustrations in the Journal of Craniofacial Surgery.

The aim of this study is to analyze the medical illustrations that appeared in the Journal of Craniofacial Surgery (JCFS) during the last 3 years (2016-2018).All illustrations in 2676 articles from 24 issues were analyzed.In total, 363 articles (13.

Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology.

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. (L.

A Transcriptome Approach Toward Understanding Fruit Softening in Persimmon.

Persimmon ( Thunb.), which is a climacteric fruit, softens in 3-5 weeks after harvest. However, little is known regarding the transcriptional changes that underlie persimmon ripening.

On the study of microbial transcriptomes using second- and third-generation sequencing technologies.

Second-generation sequencing technologies transformed the study of microbial transcriptomes. They helped reveal the transcription start sites and antisense transcripts of microbial species, improving the microbial genome annotation. Quantification of genome-wide gene expression levels allowed for functional studies of microbial research.

Functional Characterization of Phalaenopsis aphrodite Flowering Genes PaFT1 and PaFD.

We show that the key flowering regulators encoded by Phalaenopsis aphrodite FLOWERING LOCUS T1 (PaFT1) and PaFD share high sequence homologies to these from long-day flowering Arabidopsis and short-day flowering rice. Interestingly, PaFT1 is specifically up-regulated during flowering inductive cooling treatment but is not subjected to control by photoperiod in P. aphrodite.

Draft Genome Sequence of a Taxonomically Unique Neisseria Strain Isolated from a Greater White-Fronted Goose (Anser albifrons) Egg on the North Slope of Alaska.

We report here the draft genome sequence of a unique Neisseria strain that was isolated from a greater white-fronted goose (Anser albifrons) egg. The sequencing was performed with an Illumina MiSeq system, and the sequence consists of 275 contigs. The total genome is 2,397,978 bp long and has a G+C content of 46.

Preferential Amplification of Pathogenic Sequences.

The application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called "Preferential Amplification of Pathogenic Sequences (PATHseq)" that can be used to greatly enrich pathogenic sequences.

A unique open reading frame within the comX gene of Streptococcus mutans regulates genetic competence and oxidative stress tolerance.

Streptococcus mutans displays complex regulation of genetic competence, with ComX controlling late competence gene transcription. The rcrRPQ operon has been shown to link oxidative stress tolerance, (p)ppGpp metabolism and competence in S. mutans.

Draft Genome Sequence of an Atypical Strain of Streptococcus pneumoniae Isolated from a Respiratory Infection.

Next-generation sequencing was used to investigate an unknown clinical respiratory infection. This new strain of Streptococcus pneumoniae, ASVL_JC_0001, was isolated from a clinical specimen from a patient with bronchitis and pulmonary inflammation. The draft genome sequence, obtained with an Illumina MiSeq sequencing system, consists of 83 large contigs, a total of 2,092,532 bp long, and has a GC content of 40.

Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3.

Trithorax group proteins are chromatin-remodeling factors that activate target gene expression by antagonistically functioning against the Polycomb group. In Arabidopsis (Arabidopsis thaliana), Arabidopsis Trithorax protein1 (ATX1) regulates flowering time and floral organ identity. Here, we observed that suppression of Oryza sativa Trithorax1 (OsTrx1), an ortholog of ATX1, delayed flowering time in rice (Oryza sativa).

Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment.

Background: Streptococcus agalactiae is a major cause of bovine mastitis, which is the dominant health disorder affecting milk production within the dairy industry and is responsible for substantial financial losses to the industry worldwide. However, there is considerable evidence for host adaptation (ecotypes) within S. agalactiae, with both bovine and human sourced isolates showing a high degree of distinctiveness, suggesting differing ability to cause mastitis.

Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans.

A bacterial transcriptome of the primary etiological agent of human dental caries, Streptococcus mutans, is described here using deep RNA sequencing. Differential expression profiles of the transcriptome in the context of carbohydrate source, and of the presence or absence of the catabolite control protein CcpA, revealed good agreement with previously-published DNA microarrays. In addition, RNA-seq considerably expanded the repertoire of DNA sequences that showed statistically-significant changes in expression as a function of the presence of CcpA and growth carbohydrate.

Replacing and additive horizontal gene transfer in Streptococcus.

The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes in one lineage to be replaced by homologs from another lineage ("replacing HGT") and events that result in the addition of substantial new genomic material ("additive HGT"). Here in, we make use of the distinct phylogenetic signatures of replacing and additive HGTs in a genome-wide study of the important human pathogen Streptococcus pyogenes (SPY) and its close relatives S. dysgalactiae subspecies equisimilis (SDE) and S.

Joint inference of population assignment and demographic history.

A new approach to assigning individuals to populations using genetic data is described. Most existing methods work by maximizing Hardy-Weinberg and linkage equilibrium within populations, neither of which will apply for many demographic histories. By including a demographic model, within a likelihood framework based on coalescent theory, we can jointly study demographic history and population assignment.

OsMADS50 and OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice.

In much of the tropics and subtropics, rice (Oryza sativa L.) is grown under long days (LDs). Therefore, LD must play a major role in inducing flowering signal in rice.

Aripiprazole in the treatment of early-onset schizophrenia spectrum disorder: A case series in Korean children and adolescents.

Objective: The aim of this case series was to assess the effectiveness and tol-erability of aripiprazole in Korean children and adolescents with early-onset schizophrenia spectrum (EOSS) disorder.

Methods: The medical records of aripiprazole-treated patients with EOSS were retrospectively reviewed. Changes in illness severity were measured using the Clinical Global Impression-Severity of Illness (CGI-S) and Clinical Global Impression-Improvement (CGI-I) scales.