Genomic organization of the gene that encodes the precursor to EGF-related peptides, exogastrula-inducing peptides, of the sea urchin Anthocidaris crassispina

Exogastrula-inducing peptides (EGIPs) were identified in embryos of the sea urchin Anthocidaris crassispina as polypeptides with structural similarity to epidermal growth factor (EGF) that severely affect gastrulation of sea urchin embryos to induce exogastrulation. Here we have obtained genomic clones for the EGIP precursor gene (EGIP) and determined its genomic organization. The EGIP gene spans the length of 9 kb in the genome and is composed of seven exons and six introns. Each of the four EGF motifs in the precursor protein is encoded by a single exon, and all the exon boundaries are in phase 1, suggesting that EGIP have been generated during evolution by duplication of an exon encoding a single ancient EGIP sequence. The 5'-flanking sequence of EGIP from -4372 to +194 revealed the presence of multiple repeat sequences including direct and inverted repeats as well as two clusters of GGGG/CCCC elements. The function of the upstream flanking region of EGIP was examined by introducing the gene constructs into embryos in which different regions from the flanking DNA were placed upstream to the GFP reporter gene. Systematic deletion of the upstream DNA revealed the presence of potent enhancer activity between -372 and -210.     

Chronic Obstructive Pulmonary Disease-Related Non-Small-Cell Lung Cancer Exhibits a Low Prevalence of EGFR and ALK Driver Mutations

Lung cancer and chronic obstructive pulmonary disease (COPD) are two major lung diseases. Epidermal growth factor receptor (EGFR) mutations, v‐Ki‐ras2 Kirsten rat sarcoma (KRAS) mutations and anaplastic lymphoma kinase (ALK) gene rearrangements represent driver mutations that are frequently assessed on initial evaluation of non-small-cell lung cancer (NSCLC). The present study focused on the expression of driver mutations in NSCLC patients presenting with COPD and further evaluated the association between NSCLC and COPD. Data from 501 consecutive patients with histologically proven recurrent or metastatic NSCLC were analyzed retrospectively. The patients underwent spirometry and genotyping of EGFR, ALK, and KRAS in tissue samples. Patient characteristics and expression of driver mutations were compared between the COPD and non-COPD groups.Among 350 patients with spirometric results, 106 (30.3%) were diagnosed with COPD, 108 (30.9%) had EGFR mutations, 31 (8.9%) had KRAS mutations, and 34 (9.7%) showed ALK rearrangements. COPD was independently associated with lower prevalences of EGFR mutations (95% confidence interval [CI], 0.254–0.931, p = 0.029) and ALK rearrangements (95% CI, 0.065–0.600, p = 0.004). The proportions of EGFR mutations and ALK rearrangements decreased as the severity of airflow obstruction increased (p = 0.001). In never smokers, the prevalence of EGFR mutations was significantly lower in the COPD group than in the non-COPD group (12.7% vs. 49.0%, p = 0.002). COPD-related NSCLC patients exhibited low prevalences of EGFR mutations and ALK rearrangements compared with the non-COPD group. Further studies are required regarding the molecular mechanisms underlying lung cancer associated with COPD.     

Correlation Between Atomic Structure and Electrochemical Performance of Anodes Made from Electrospun Carbon Nanofiber Films

A systematic study is made of the effect of the nitrogen species on the performance of Li‐ion storage and the capacities of carbon‐based anodes in Li‐ion batteries (LIBs). Electrospun carbon nanofiber (CNF) films are fabricated for use as binder‐free electrodes using a polyacrylonitrile precursor. When the CNF films are subjected to carbonization, transformation occurs from an amorphous to a graphitic structure with associated reduction of nitrogen‐containing functional groups. The structural change strongly affects where the Li ions are stored in the CNF electrodes. It is revealed that Li ions can be stored not only between the graphene layers, but also at the defect sites created by nitrogen functionalization. The latter is mainly responsible for the widely reported improved electrochemical performance of LIBs due to N‐doping of carbon materials. An optimized carbonization temperature of 550 °C is identified, which gives rise to a sufficiently high nitrogen content and thus a high capacity of the electrode.     

Genome-Wide DNA Polymorphisms in Seven Rice Cultivars of Temperate and Tropical Japonica Groups

Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html).     

Genetic variations in the pre-feeding and pre-oviposition periods among four pure lines in the brown planthopper, <Emphasis Type="Italic">Nilaparvata lugens</Emphasis> (Hemiptera: Auchenorrhyncha:Delphacidae)

In the brown planthopper, Nilaparvata lugens Stål, traits related to ovarian development were compared among four pure lines predominantly expressing the designated characteristics: blackish short-winged (BS), yellowish brown short-winged (YS), blackish long-winged (BL), and yellowish brown long-winged (YL). The pre-oviposition period was longer in the following order: BS < YS < BL = YL line. The pre-feeding period, namely, the time of non-feeding after adult emergence, which was estimated from dry weight loss during starvation, was also longer in the same order: BS < YS < BL = YL. Vitellogenin, the precursor of yolk protein, first appeared in the hemolymph about 1½ days later after the initiation of feeding in respective lines. One-day’s starvation did not have any effect on the timing of vitellogenin’s appearance in the long-winged lines (BL, YL), but delayed it by 1 day in the short-winged lines (BS, YS). Further, we showed that the synthesis of vitellogenin mRNA was induced in the adults even before feeding by being topically applied with juvenile hormone III (JH III). These results suggest that feeding first triggers the increase of JH III titer, which activates vitellogenin synthesis, and enhances ovarian development. Thus, genetic differences in the pre-feeding periods cause the differences in the timings of physiological events relating to ovarian development among the four lines.     

Using marine macroalgae for carbon sequestration: a critical appraisal

There has been a good deal of interest in the potential of marine vegetation as a sink for anthropogenic C emissions (“Blue Carbon”). Marine primary producers contribute at least 50% of the world’s carbon fixation and may account for as much as 71% of all carbon storage. In this paper, we analyse the current rate of harvesting of both commercially grown and wild-grown macroalgae, as well as their capacity for photosynthetically driven CO₂ assimilation and growth. We suggest that CO₂ acquisition by marine macroalgae can represent a considerable sink for anthropogenic CO₂ emissions and that harvesting and appropriate use of macroalgal primary production could play a significant role in C sequestration and amelioration of greenhouse gas emissions.