Logogenesis and Appraisal: A Systemic Functional Analysis of English and Japanese Language Arts Textbooks

The purpose of this thesis is to demonstrate the distinct and purposeful differences of the language of evaluation between English textbooks and Japanese textbooks. This thesis applies Appraisal system in Systemic Functional Linguistics to the language arts textbooks used in 2nd to 4th grade classrooms in Japan and in the U.S. The analysis shows that the number of Attitudinal lexical items, especially invoked Attitude, is notably higher than that in the English texts. The analysis also shows that the Japanese texts employ Judgment lexis, which is a resource to form a sense of group harmony, more than the other Attitudinal lexis. On the other hand, although the overall frequency of Attitudinal lexis is not high, the English texts employ Affect and Appreciation lexical items more frequently than Judgment lexical items. The analysis on the deployment of Attitudinal lexis in the texts illustrates that the Japanese texts favor inscribed Judgment items to tell readers the protagonists’ characteristic in the initial stage of the story, whereas the English texts deploy the protagonists’ emotional states first. This thesis argues that the language of evaluation used in the texts is responsible for instructing readers, that is elementary school students, on how to interpret interpersonal meanings as well as ideational meanings. Furthermore, the purposeful differences analyzed in this thesis reveal how knowledge is selected in the curriculum guidelines, and presented in culture-specific ways

Language Learners as Agentive Meaning-Makers: Exploring Learners\u27 Investment and Meaning-Making

The motivation for this research is the subordinated position of writing in Japanese language education. As many studies indicate, writing in Japanese language education is often perceived as a space for teachers to monitor learners’ acquisition of grammar structures and kanji (Hirose, 2015; Kumagai & Fukai, 2009; Ramzan & Thomson, 2013). Such discourse of writing conceives Japanese writers, especially elementary writers, as individuals who have little agency in making meaning. The purpose of my dissertation study is to explore alternative discourses of writing that position elementary Japanese language learners as agentive meaning-makers. For this inquiry, first, I explore literatures that inform this dissertation study. This literature review explores systemic functional linguistics, or SFL, which explicitly situates one’s meaning-making in a social context. This review also explores critical instantiations of SFL, which emerged across disciplines. Then, I design a conceptual framework that is essential for my inquiry. I revisit (critical) SFL theories of text and context, and weave them together with post-structuralist theories of identity to investigate collegiate Japanese language learners’ identity and their meaning-making. Based on this conceptual framing, I propose a new pedagogy. This pedagogy resides in literacy practices which enhance learners’ awareness of linguistic choice in a social context (Rose & Martin, 2012), while it also actively incorporates literacy practices in which individuals can invest their time and effort in negotiation with their future affiliation (Norton Peirce, 1995; Norton 2013). I utilized this pedagogy to teach a personal narrative genre in a US college level elementary Japanese course. By drawing on Fairclough’s critical discourse analysis (1989; 1992; 2003), I conducted textual analysis on each participant’s personal narrative texts and interpreted the linguistic cues in reference to their negotiations with identities and writing tasks. Overall, the four case studies of Mary, Andrea, Jean, and Lapis showcase a complex picture of investment and meaning-making. Their meaning-making is, on the one hand, to achieve the intended goal and purpose of writing, but on the other hand, is to organize and reorganize who they are and how they relate to the social world (Norton, 2013, p. 4). This suggests L2 learners’ meaning-making is enabled and/or constrained in certain ways, and equally important, contingent on learners’ agency, investment, and identity

High-susceptibility of photosynthesis to photoinhibition in the tropical plant Ficus microcarpa L. f. cv. Golden Leaves

BACKGROUND: The tropical plant Ficus microcarpa L. f. cv. Golden Leaves (GL) is a high-light sensitive tropical fig tree in which sun-leaves are yellow and shade-leaves are green. We compared the response of photosynthetic activities to strong light between GL and its wild-type (WT, Ficus microcarpa L. f.). RESULTS: Field measurements of maximum photosystem II (PSII) efficiency (F(v)/F(m)) of intact sun-leaves in GL showed that photo synthetic activity was severely photoinhibited during the daytime (F(v)/F(m) = 0.46) and subsequently recovered in the evening (F(v)/F(m) = 0.76). In contrast, WT did not show any substantial changes of F(v)/F(m) values throughout the day (between 0.82 and 0.78). Light dependency of the CO(2) assimilation rate in detached shade-leaves of GL showed a response similar to that in WT, suggesting no substantial difference in photosynthetic performance between them. Several indicators of photoinhibition, including declines in PSII reaction center protein (D1) content, F(v)/F(m) value, and O(2) evolution and CO(2) assimilation rates, all indicated that GL is much more susceptible to photoinhibition than WT. Kinetics of PAM chlorophyll a fluorescence revealed that nonphotochemical quenching (NPQ) capacity of GL was lower than that of WT. CONCLUSION: We conclude that the photosynthetic apparatus of GL is more highly susceptible to photoinhibition than that of WT

Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway

The brown alga, Nemacystus decipiens ("ito-mozuku" in Japanese), is one of the major edible seaweeds, cultivated principally in Okinawa, Japan. N. decipiens is also a significant source of fucoidan, which has various physiological activities. To facilitate brown algal studies, we decoded the ~154 Mbp draft genome of N. decipiens Onna-1 strain. The genome is estimated to contain 15,156 protein-coding genes, ~78% of which are substantiated by corresponding mRNAs. Mitochondrial genes analysis showed a close relationship between N. decipiens and Cladosiphon okamuranus. Comparisons with the C. okamuranus and Ectocarpus siliculosus genomes identified a set of N. decipiens-specific genes. Gene ontology annotation showed more than half of these are classified as molecular function, enzymatic activity, and/or biological process. Extracellular matrix analysis revealed domains shared among three brown algae. Characterization of genes that encode enzymes involved in the biosynthetic pathway for sulfated fucan showed two sets of genes fused in the genome. One is a fusion of L-fucokinase and GDP-fucose pyrophosphorylase genes, a feature shared with C. okamuranus. Another fusion is between an ST-domain-containing gene and an alpha/beta hydrolase gene. Although the function of fused genes should be examined in future, these results suggest that N. decipiens is another promising source of fucoidan

Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus

BACKGROUND: The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. Four strains, denominated S, K, O, and C, with distinctively different morphologies, have been cultivated commercially since the early 2000s. We previously reported a draft genome of the S-strain. To facilitate studies of seaweed biology for future aquaculture, we here decoded and analyzed genomes of the other three strains (K, O, and C). RESULTS: Here we improved the genome of the S-strain (ver. 2, 130 Mbp, 12,999 genes), and decoded the K-strain (135 Mbp, 12,511 genes), the O-strain (140 Mbp, 12,548 genes), and the C-strain (143 Mbp, 12,182 genes). Molecular phylogenies, using mitochondrial and nuclear genes, showed that the S-strain diverged first, followed by the K-strain, and most recently the C- and O-strains. Comparisons of genome architecture among the four strains document the frequent occurrence of inversions. In addition to gene acquisitions and losses, the S-, K-, O-, and C-strains possess 457, 344, 367, and 262 gene families unique to each strain, respectively. Comprehensive Blast searches showed that most genes have no sequence similarity to any entries in the non-redundant protein sequence database, although GO annotation suggested that they likely function in relation to molecular and biological processes and cellular components. CONCLUSIONS: Our study compares the genomes of four strains of C. okamuranus and examines their phylogenetic relationships. Due to global environmental changes, including temperature increases, acidification, and pollution, brown algal aquaculture is facing critical challenges. Genomic and phylogenetic information reported by the present research provides useful tools for isolation of novel strains

A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster

Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals

Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes

The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures

Genome‐wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration

1. It is essential to consider genetic composition for both conventional coral restoration management and for initiating new interventions to counter the significant global decline in living corals. Population genetic structure at a fine spatial scale should be carefully evaluated before implementing strategies to achieve self-sustaining ecosystems via coral restoration. 2. This study investigated the population genetic structure of two acroporid species at Kume Island, Okinawa, Japan. There were 140 colonies of Acropora digitifera collected from seven study sites, and 81 colonies of Acropora tenuis from six sites. In total, 384 single nucleotide polymorphism (SNP) loci for A. digitifera and 470 SNPs for A. tenuis were obtained using a comparatively economical technique, Multiplexed ISSR Genotyping by sequencing. 3. Observed heterozygosity was significantly lower than expected heterozygosity at all SNP sites in both acroporid species, suggesting deficient genetic diversity possibly caused by past massive coral bleaching. Even though both species are broadcast spawners, the population structure was different in the two species. No detectable structure was evident in A. digitifera, but two distinct clades were found in A. tenuis. The genetic homogeneity of A. digitifera at Kume Island suggests that this species could be used as a focal species for active restoration in terms of genetic differentiation at this island. By contrast, A. tenuis unexpectedly included two distinct clades with little or no admixture within a small study area, possibly representing two reproductively isolated cryptic species. Thus, when using A. tenuis, it would be prudent to avoid disturbing the genetic composition of wild populations until this question is answered.journal articl