Diurnal decline in the photosynthetic capacity of uppermost leaves in an eggplant canopy grown in a horticultural greenhouse.

Parameters representing leaf photosynthetic capacity, namely, the maximal carboxylation rate ( ), maximal electron transport rate ( ), and triose phosphate-utilization rate ( ), can vary depending on various factors. The present study investigated diurnal variations in , , and of uppermost leaves of soil-grown, well-watered eggplant in a greenhouse based on the simultaneous measurements of leaf gas exchange and chlorophyll fluorescence. The values of net photosynthetic rates and electron transport rates plotted against intercellular CO concentrations were noticeably higher in the morning than in the afternoon.

Comprehensive Metabolomic Comparison of Five Cereal Vinegars Using Non-Targeted and Chemical Isotope Labeling LC-MS Analysis.

Vinegar is used as an acidic condiment and preservative worldwide. In Asia, various black vinegars are made from different combinations of grains, such as Sichuan bran vinegar (SBV), Shanxi aged vinegar (SAV), Zhenjiang aromatic vinegar (ZAV), and Fujian Monascus vinegar (FMV) in China and Ehime black vinegar in Japan (JBV). Understanding the chemical compositions of different vinegars can provide information about nutritional values and the quality of the taste.

Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918.

Massive corals of the genus Porites, common, keystone reef builders in the Indo-Pacific Ocean, are distinguished by their relative stress tolerance and longevity. In order to identify genetic bases of these attributes, we sequenced the complete genome of a massive coral, Porites australiensis. We developed a genome assembly and gene models of comparable quality to those of other coral genomes.

Gut microbial composition of elderly women born in the Japanese longevity village Ogimi.

Ogimi is one of Japan's longevity villages and is located in Okinawa Prefecture. In this study, we focused on the elderly women living in the village, classified them into two groups based on whether or not they lived in Ogimi during the first 3 years of their lives, and compared the gut microbiota between the two groups. There were no differences in alpha and beta diversity; however, we found that the elderly women who lived in Ogimi during the first 3 years of their lives had a higher rate of colonization in their guts.

Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral-Algae Symbioses.

Reef-building corals and photosynthetic, endosymbiotic algae of the family Symbiodiniaceae establish mutualistic relationships that are fundamental to coral biology, enabling coral reefs to support a vast diversity of marine species. Although numerous types of Symbiodiniaceae occur in coral reef environments, Acropora corals select specific types in early life stages. In order to study molecular mechanisms of coral-algal symbioses occurring in nature, we performed whole-genome transcriptomic analyses of Acropora tenuis larvae inoculated with Symbiodinium microadriaticum strains isolated from an Acropora recruit.

A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis.

Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching).

Study of the More Suitable Drugs and Dosage Forms for Administration to Newborn Infants via Feeding Tube Using the Collection Rate as an Indicator.

The dosages of drugs in newborn infants are small. Small dose necessitate consideration of the loss of drug when administered via feeding tube. In this study, we conducted a tube administration test for seven kinds of antiepileptic drugs and two kinds of potassium supplements using a neonatal feeding tube and investigated the drug loss using the collection rate.

Correlation-Based Deconvolution (CorrDec) To Generate High-Quality MS2 Spectra from Data-Independent Acquisition in Multisample Studies.

Data-independent acquisition mass spectrometry (DIA-MS) is essential for information-rich spectral annotations in untargeted metabolomics. However, the acquired MS2 spectra are highly complex, posing significant annotation challenges. We have developed a correlation-based deconvolution (CorrDec) method that uses ion abundance correlations in multisample studies using DIA-MS as an update of our MS-DIAL software.

A lipidome atlas in MS-DIAL 4.

We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate.

Rearrangement analysis of multiple bacterial genomes.

Background: Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction.

Genetic diversity and DNA barcoding of the black fly (Diptera: Simuliidae) vectors of parasites causing human onchocerciasis in Guatemala.

Genetic variation based on mitochondrial cytochrome c oxidase I (COI) and II (COII) sequences was investigated for three black fly nominal species, Simulium metallicum Bellardi complex, S. callidum Dyar and Shannon, and S. ochraceum Walker complex, which are vectors of human onchocerciasis from Guatemala.

Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics.

Accurate metabolite identification remains one of the primary challenges in a metabolomics study. A reliable chemical spectral library increases the confidence in annotation, and the availability of raw and annotated data in public databases facilitates the transfer of Liquid chromatography coupled to mass spectrometry (LC-MS) methods across laboratories. Here, we illustrate how the combination of MS2 spectra, accurate mass, and retention time can improve the confidence of annotation and provide techniques to create a reliable library for all ion fragmentation (AIF) data with a focus on the characterization of the retention time.

The structure and properties of natural sheep casing and artificial films prepared from natural collagen with various crosslinking treatments.

The structure and properties of natural sheep casing and collagen films with various crosslinking treatments have been investigated in detail to develop satisfied artificial casings prepared from collagen. The sheep casing consists of large number of thick collagen fibers oriented at ±45° from longitudinal direction with high-density interwoven network structure. The structural feature of sheep casing gave the special mouthfeel of 'cracking bite' of sausages.

Lactobacillus paragasseri sp. nov., a sister taxon of Lactobacillus gasseri, based on whole-genome sequence analyses.

Three strains, JCM 5343, JCM 5344 and JCM 1130, currently identified as Lactobacillus gasseri, were investigated using a polyphasic taxonomic approach. Although these strains shared high 16S rRNA gene sequence similarities with L. gasseri ATCC 33323 (99.

Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes.

Background: The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown.

Revealing the genomic differences between two subgroups in .

Being an autochthonous species in humans, is widely used as a probiotic for fermented products. We thoroughly compared the gene contents of 75 genomes and identified two intraspecific groups by the average nucleotide identity (ANI) threshold of 94%. Group I, with 48 strains, possessed 53 group-specific genes including the gassericin T cluster (9 genes) and -acyl homoserine lactone lactonase.

Visualization of consensus genome structure without using a reference genome.

Background: Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated.

Genome Sequence of Lactobacillus paracasei Strain LC-Ikematsu, Isolated from a Pineapple in Okinawa, Japan.

The draft genome sequence of Lactobacillus paracasei strain LC-Ikematsu, isolated from a pineapple in Okinawa, was determined. The total length of the 87 contigs was 3.08 Mb with a G+C content of 46.

[Population demography in Rhinella arenarum (Anura: Bufonidae) and Physalaemus biligonigerus (Anura: Leiuperidae) in agroecosystems in the province of Córdoba, Argentina].

The advancing agricultural frontier has led to an important loss of natural habitats, with significant consequences for biodiversity. The demography for two species of anurans, Physalaemus biligonigerus and Rhinella arenarum, both associated with agricultural systems in the central region of the C6rdoba Province, were analyzed and compared in this study. Four sites were sampled: three agroecosystems with different alteration degrees (C1, C2 and SM1) and a fourth site not cultivated (SM2).