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Purpose Although reports suggest that the pancreatic volume decreases after gastrectomy for gastric cancer, the relationship between the pancreatic volume and secretory function after gastrectomy remains unclear. In this study, we examined the relationship between the pancreatic volume and exocrine and endocrine functions after total gastrectomy. Methods The pancreatic volumes of 18 distal gastrectomy and 15 total gastrectomy patients were retrospectively measured using computed tomography volumetry up to 5 years postoperatively. Ten low anterior resection patients were selected as controls. In addition, the pancreatic volume and exocrine function evaluated by fecal elastase and the insulin secretory function evaluated by glucagon tolerance testing were prospectively examined before and one year after surgery in nine cases of total gastrectomy. Results After low anterior resection, the pancreatic volume did not change, but after distal and total gastrectomy, the pancreatic volume decreased continuously until the fifth year. After total gastrectomy, fecal elastase decreased significantly from 865.8 μg/g to 603.2 μg/g in the first year (p = 0.0316), and the insulin secretion capacity also decreased significantly from 3.83 ng/mL to 2.26 ng/mL (p = 0.0019). Conclusions The pancreatic volume decreases continuously after gastrectomy for gastric cancer, and the pancreatic exocrine and endocrine functions decrease along with pancreatic atrophy after total gastrectomy.

Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.

Background: Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid’s parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. Results: We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC’s performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO’s output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. Conclusions: The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO., MC genomics, 22 (1), ISSN:1471-2164

Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.

Ralstonia eutropha is a facultative chemolithoautotrophic bacterium that uses the Calvin–Benson–Bassham (CBB) cycle for CO2 fixation. This study showed that R. eutropha strain H16G incorporated 13CO2, emitted by the oxidative decarboxylation of [1-13C1]-glucose, into key metabolites of the CBB cycle and finally into poly(3-hydroxybutyrate) [P(3HB)] with up to 5.6% 13C abundance. The carbon yield of P(3HB) produced from glucose by the strain H16G was 1.2 times higher than that by the CBB cycle-inactivated mutants, in agreement with the possible fixation of CO2 estimated from the balance of energy and reducing equivalents through sugar degradation integrated with the CBB cycle. The results proved that the ‘gratuitously’ functional CBB cycle in R. eutropha under aerobic heterotrophic conditions participated in the reutilization of CO2 emitted during sugar degradation, leading to an advantage expressed as increased carbon yield of the storage compound. This is a new insight into the role of the CBB cycle and may be applicable for more efficient utilization of biomass resources.

To evaluate the effect of low-molecular-weight glutenin subunit (LMW-GS) genes on dough strength, locus-specific primers of LMW-GS genes and gliadin bands tightly linked to LMW-GS genes were analyzed in common wheat. Segregation analysis of the F2 progeny from a cross between ‘Haruhikari’, a good bread-making quality cultivar, and ‘Asakaze-komugi’, a poor bread-making quality cultivar, showed that dough strength significantly correlated with one amplified LMW-GS gene located at the Glu-B3 locus from ‘Haruhikari’. There was no specific reference to the gliadin bands identified as promising markers in the cross under study. The LMW-GS gene of ‘Haruhikari’ had a seven amino-acid deletion in the repetitive domain relative to ‘Asakaze-komugi’, as well as six amino-acid substitutions, three of which would be expected to cause changes in hydrophilicity. The presence of the LMW-GS gene and other LMW-GS genes tightly linked to it may affect the dough strength of wheat.