Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals

The diversity of neural stem cells is a hallmark of the cerebral cortex development in gyrencephalic mammals, such as Primates and Carnivora. Among them, ferrets are a good model for mechanistic studies. However, information on their neural progenitor cells (NPC), termed radial glia (RG), is limited. Here, we surveyed the temporal series of single-cell transcriptomes of progenitors regarding ferret corticogenesis and found a conserved diversity and temporal trajectory between human and ferret NPC, despite the large timescale difference. We found truncated RG (tRG) in ferret cortical development, a progenitor subtype previously described in humans. The combination of in silico and in vivo analyses identified that tRG differentiate into both ependymal and astrogenic cells. Via transcriptomic comparison, we predict that this is also the case in humans. Our findings suggest that tRG plays a role in the formation of adult ventricles, thereby providing the architectural bases for brain expansion.

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization

Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus Our analysis using a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes show a gradualism of chromosome length with remarkable length-dependent characteristics-shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in nonmammalian vertebrates. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced at high quality.

Autocrine TGF-β-positive feedback in profibrotic AT2-lineage cells plays a crucial role in non-inflammatory lung fibrogenesis

The molecular etiology of idiopathic pulmonary fibrosis (IPF) has been extensively investigated to identify new therapeutic targets. Although anti-inflammatory treatments are not effective for patients with IPF, damaged alveolar epithelial cells play a critical role in lung fibrogenesis. Here, we establish an organoid-based lung fibrosis model using mouse and human lung tissues to assess the direct communication between damaged alveolar type II (AT2)-lineage cells and lung fibroblasts by excluding immune cells. Using this in vitro model and mouse genetics, we demonstrate that bleomycin causes DNA damage and activates p53 signaling in AT2-lineage cells, leading to AT2-to-AT1 transition-like state with a senescence-associated secretory phenotype (SASP). Among SASP-related factors, TGF-β plays an exclusive role in promoting lung fibroblast-to-myofibroblast differentiation. Moreover, the autocrine TGF-β-positive feedback loop in AT2-lineage cells is a critical cellular system in non-inflammatory lung fibrogenesis. These findings provide insights into the mechanism of IPF and potential therapeutic targets.

Single-cell transcriptome atlas of Drosophila gastrula 2.0

During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing accurate spatial and lineage information are still lacking. Here, we report a single-cell transcriptome atlas of Drosophila gastrulae, divided into 77 transcriptomically distinct clusters. We find that the expression profiles of plasma-membrane-related genes, but not those of transcription-factor genes, represent each germ layer, supporting the nonequivalent contribution of each transcription-factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstruct the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.

Control of Synaptic Levels of Nicotinic Acetylcholine Receptor by the Sequestering Subunit Dα5 and Secreted Scaffold Protein Hig

The presentation of nicotinic acetylcholine receptors (nAChRs) on synaptic membranes is crucial for generating cholinergic circuits, some of which are associated with memory function and neurodegenerative disorders. Although the physiology and structure of nAChR, a cation channel comprising five subunits, have been extensively studied, little is known about how the receptor levels in interneuronal synapses are determined and which nAChR subunits participate in the regulatory process in cooperation with synaptic cleft matrices and intracellular proteins. By a genetic screen of Drosophila, we identified mutations in the nAChR subunit Dα5 gene as suppressors that restored the mutant phenotypes of hig, which encodes a secretory matrix protein localized to cholinergic synaptic clefts in the brain. Only the loss of function of Dα5 among the 10 nAChR subunits suppressed hig mutant phenotypes in both male and female flies. Dα5 behaved as a lethal factor when Hig was defective; loss of Dα5 in hig mutants rescued lethality, upregulating Dα6 synaptic levels. By contrast, levels of Dα5, Dα6, and Dα7 subunits were all reduced in hig mutants. These three subunits have distinct properties for interaction with Hig or trafficking, as confirmed by chimeric subunit experiments. Notably, the chimeric Dα5 protein, which has the extracellular sequences that display no positive interaction with Hig, exhibited abnormal distribution and lethality even in the presence of Hig. We propose that the sequestering subunit Dα5 functions by reducing synaptic levels of nAChR through internalization, and this process is blocked by Hig, which tethers Dα5 to the synaptic cleft matrix.SIGNIFICANCE STATEMENT Because the cholinergic synapse is one of the major synapses that generate various brain functions, numerous studies have sought to reveal the physiology and structure of the nicotinic acetylcholine receptor (nAChR). However, little is known about how synaptic levels of nAChR are controlled and which nAChR subunits participate in the regulatory process in cooperation with synaptic cleft matrices. By a genetic screen of Drosophila, we identified mutations in the nAChR subunit Dα5 gene as suppressors that restored the mutant phenotypes of hig, which encodes a secretory matrix protein localized to cholinergic synaptic clefts. Our data indicate that Dα5 functions in reducing synaptic levels of nAChR, and this process is blocked by Hig, which tethers Dα5 to the synaptic cleft matrix.

Gse1, a component of the CoREST complex, is required for placenta development in the mouse

Gse1 is a component of the CoREST complex that acts as an H3K4 and H3K9 demethylase and regulates gene expression. Here, we examined the expression and role of Gse1 in mouse development. Gse1 is expressed in male and female germ cells and plays both maternal and zygotic roles. Thus, maternal deletion of Gse1 results in a high incidence of prenatal death, and zygotic deletion leads to embryonic lethality from embryonic day 12.5 (E12.5) and perinatal death. Gse1 is expressed in the junctional zone and the labyrinth of the developing placenta. Cultured trophoblast stem cells lacking Gse1 showed impaired in vitro cell differentiation into spongiotrophoblasts. Gse1 mutant (Gse1^Δex3/Δex3) placenta begins to exhibit histological defects from E14.5, being deficient in MCT4⁺ syncytiotrophoblast II. The number of various cell types was largely maintained in the mutant placenta at E10.5, but several genes were upregulated in giant trophoblasts at E10.5. Placenta-specific deletion of Gse1 with Tat-Cre suggested that defects in Gse1^Δex3/Δex3 embryos are due to placental function deficiency. These results suggest that Gse1 is required for placental development in mice, and in turn, is essential for embryonic development.

Squalomix: shark and ray genome analysis consortium and its data sharing platform

The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.

Efficient use of electrons in a double-anode microbial fuel cell-biofilm electrode reactor self-powered coupled system for degradation of azo dyes

A coupled system consisting of a double-anode microbial fuel cell (MFC) unit and a biofilm electrode reactor (BER) has been applied to degrade the azo dye reactive brilliant red X-3B. In this system, the MFC effluent was used as the input of the BER. The MFC preliminarily degraded X-3B while generating electricity, and the BER obtained electrons from the MFC through the external circuit to continue degrading pollutants without the need for an external power supply. The X-3B removal efficiency was 41.93% higher in the coupled system than the control when the X-3B concentration was 3000 mg/L. The analysis of intermediate products showed that the azo bond of X-3B broke in the MFC, generating a large number of complex intermediates such as anthraquinones, which were further degraded into simple organic compounds in the BER. Meanwhile, the abundance of microbial taxa related to the degradation of refractory organics in the MFC was high, as was that of microbial taxa related to the degradation of simple organics in the BER. Furthermore, the abundance of microorganisms related to power generation in the MFC increased. These results provided an efficient strategy for improving electron utilization efficiency in the coupling system of bioelectrochemical system.

The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection

RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.

The water temperature changes the effect of pH on copper toxicity to the green microalgae Raphidocelis subcapitata

Rising temperature enhances the algal growth, which in turn increases the water pH. Ecotoxicity studies have suggested that copper becomes more toxic to microalgae species by increasing the temperature (within 20-30 °C) and pH. In this study, the joined effect of pH and temperature on copper toxicity to the microalgae Raphidocelis subcapitata was investigated using acclimated cells. Algal growth and toxicity tests were conducted using the medium recommended by the Organisation for Economic Co-operation and Development (OECD medium) at pH 6, 7, and 8 units from 15 to 30 °C, spaced by 3 °C. The specific growth rate of R. subcapitata increased by raising the pH and temperature, attributed to the higher membrane permeability and metabolism. The ecotoxicity tests showed that temperature changes the effect of pH on copper toxicity. Copper became less toxic when rising the temperature from 15 to 18 °C and from 6 to 8 pH-unit, suggesting that high pH controls copper bioavailability and toxicity. In contrast, from 21 to 30 °C, the effect of copper was not significantly altered by temperature, but it became more toxic at high pH. Results of this study warn about the higher risk of copper in cold seasons rather than warm conditions.

Temperature affects growth, geosmin/2-methylisoborneol production, and gene expression in two cyanobacterial species

Cyanobacterial blooms accompanied by taste and odor (T&O) compounds affect the recreational function and safe use of drinking water. Geosmin and 2-methylisoborneol (2-MIB) are the most common T&O compounds. In this study, we investigated the effect of temperature on geosmin and 2-MIB production in Dolichospermum smithii and Pseudanabaena foetida var. intermedia. More specifically, transcription of one geosmin synthase gene (geoA) and two 2-MIB synthase genes (mtf and mtc) was explored. Of the three temperatures (15, 25, and 35 °C) tested, the maximum Chl-a content was determined at 25 °C in both D. smithii and P. foetida var. intermedia. The maximum total geosmin concentration (19.82 μg/L) produced by D. smithii was detected at 25 °C. The total 2-MIB concentration (82.5 μg/L) produced by P. foetida var. intermedia was the highest at 35 °C. Besides, the lowest Chl-a content and minimum geosmin/2-MIB concentration were observed at 15 °C. There was a good positive correlation between geosmin/2-MIB concentration and Chl-a content. The expression levels of the geoA, mtf, and mtc genes at 15 °C were significantly higher than those at 25 and 35 °C. The transcription of the mtf and mtc genes in P. foetida var. intermedia was higher at 35 °C than at 25 °C. The results highlight unfavorable temperature can increase the potential of geosmin/2-MIB synthesis from the gene expression level in cyanobacteria. This study could provide basic knowledge of geosmin/2-MIB production by cyanobacteria for better understanding and management of T&O problems in drinking water.

Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies

The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome‐scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi‐C, a method for genome‐wide chromosome conformation capture that was originally developed for investigating the long‐range interaction of chromatins. Performing genomic scaffolding using Hi‐C data is highly resource‐demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi‐C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi‐C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome‐scale genome assemblies using single‐copy reference orthologues.

Impact of nitrogen compound variability of sewage treated water on N2O production in riverbeds

Nitrous oxide (N₂O), a strong greenhouse and ozone depleting gas, is known to be generated in the river environment. However, the impact of sewage treated water on the production mechanism has not been clarified. In this study, N₂O production in the upper reach of a river was evaluated by field survey and activity test. The results demonstrated that the N₂O production activity of the river pebbles increased with the inflow of the sewage treated water, which was supported by field survey results, such as the dissolved N₂O concentrations and water quality. The emission factors of N₂O were determined to be 0.02-0.05% in nitrification and 0.01-0.025% in denitrification. Our study shows that combining a field survey and an activity test improves the reliability of the results and leads to the appropriate quantitative evaluation. From a perspective of controlling the N₂O emissions from the sewage treatment plant, N₂O generation inside the plant is critical. However, appropriate nitrogen removal in the treatment plant is connected to the reduction of N₂O generation in the river environment.

Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset

Cynomolgus macaque (Macaca fascicularis) and common marmoset (Callithrix jacchus) have been widely used in human biomedical research. Long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performed de novo genome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. We assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data, which were further refined based on Hi-C contact maps and alternate de novo assemblies. The assemblies achieved scaffold N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively. The high fidelity of our assembly is also ascertained by BAC-end concordance in common marmoset. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research.

Predictive water virology using regularized regression analyses for projecting virus inactivation efficiency in ozone disinfection

Wastewater reclamation and reuse have been practically applied to water-stressed regions, but waterborne pathogens remaining in insufficiently treated wastewater are of concern. Sanitation Safety Planning adopts the hazard analysis and critical control point (HACCP) approach to manage human health risks upon exposure to reclaimed wastewater. HACCP requires a predetermined reference value (critical limit: CL) at critical control points (CCPs), in which specific parameters are monitored and recorded in real time. A disinfection reactor of a wastewater treatment plant (WWTP) is regarded as a CCP, and one of the CCP parameters is the disinfection intensity (e.g., initial disinfectant concentration and contact time), which is proportional to the log reduction value (LRV) of waterborne pathogens. However, the achievable LRVs are not always stable because the disinfection intensity is affected by water quality parameters, which vary among WWTPs. In this study, we established models for projecting virus LRVs using ozone, in which water quality and operational parameters were used as explanatory variables. For the model construction, we used five machine learning algorithms and found that automatic relevance determination with interaction terms resulted in better prediction performances for norovirus and rotavirus LRVs. Poliovirus and coxsackievirus LRVs were predicted well by a Bayesian ridge with interaction terms and lasso with quadratic terms, respectively. The established models were relatively robust to predict LRV using new datasets that were out of the range of the training data used here, but it is important to collect LRV datasets further to make the models more predictable and flexible for newly obtained datasets. The modeling framework proposed here can help WWTP operators and risk assessors determine the appropriate CL to protect human health in wastewater reclamation and reuse.

Hierarchical Bayesian modeling for predictive environmental microbiology toward a safe use of human excreta: Systematic review and meta-analysis

The pathogen concentration in human excreta needs to be managed appropriately, but a predictive approach has yet to be implemented due to a lack of kinetics models for pathogen inactivation that are available under varied environmental conditions. Our goals were to develop inactivation kinetics models of microorganisms applicable under varied environmental conditions of excreta matrices and to identify the appropriate indicators that can be monitored during disinfection processes. We conducted a systematic review targeting previous studies that presented time-course decay of a microorganism and environmental conditions of matrices. Defined as a function of measurable factors including treatment time, pH, temperature, ammonia concentration and moisture content, the kinetic model parameters were statistically estimated using hierarchical Bayesian modeling. The inactivation kinetics models were constructed for Escherichia coli, Salmonella, Enterococcus, Ascaris eggs, bacteriophage MS2, enterobacteria phage phiX174 and adenovirus. The inactivation rates of a microorganism were predicted using the established model. Ascaris eggs were identified as the most tolerant microorganisms, followed by bacteriophage MS2 and Enterococcus. Ammonia concentration, temperature and moisture content were the critical factors for the Ascaris inactivation. Our model predictions coincided with the current WHO guidelines. The developed inactivation kinetics models enable us to predict microbial concentration in excreta matrices under varied environmental conditions, which is essential for microbiological risk management in emerging resource recovery practices from human excreta.

Measuring potential effects of the developmental burden associated with the vertebrate notochord

The notochord functions primarily as a supporting tissue to maintain the anteroposterior axis of primitive chordates, a function that is replaced entirely by the vertebral column in many vertebrates. The notochord still appears during vertebrate embryogenesis and plays a crucial role in the developmental pattern formation of surrounding structures, such as the somites and neural tube, providing the basis for the vertebrate body plan. The indispensable role of the notochord has often been referred to as the developmental burden and used to explain the evolutionary conservation of notochord; however, the existence of this burden has not been successfully exemplified so far. Since the adaptive value of target tissues appears to result in the evolutionary conservation of upstream structures through the developmental burden, we performed comparative gene expression profiling of the notochord, somites, and neural tube during the mid‐embryonic stages in turtles and chicken to measure their evolutionary conservation. When compared with the somites and neural tube, overall gene expression profiles in the notochord showed significantly lower or merely comparable levels of conservation. However, genes involved in inductive signalings, such as the sonic hedgehog (Shh) cascade and the formation of functional primary cilia, showed relatively higher levels of conservation in all the three structures analyzed. Collectively, these results suggest that shh signals are critical as the inductive source and receiving structures, possibly constituting the inter‐dependencies of developmental burden.

Potential evolutionary effects toward notochord by developmental burden was evaluated by Laser Micro Dissection RNAseq (LMDseq). Notochord was less conserved than neural tube and somites; however, genes in sonic hedgehog (shh) signaling cascade was found to be evolutionarily conserved (not only in notochord but also in somites and neural tube). These results suggest that Shh signals are critical as the inductive source and receiving structures, possibly constituting the inter‐dependencies of developmental burden. Further studies that directly measure the burden required to verify the hypothesis are awaited.

Developmental hourglass and heterochronic shifts in fin and limb development

How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here, we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open-chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls.

Animals come in all shapes and sizes. This diversity arose through genetic mutations during evolution, but it is unclear exactly how these variations led to the formation of new shapes. There is increasing evidence to suggest that not all shapes are possible and that variability between animals is limited by a phenomenon known as “developmental constraint”. These limitations direct parts of the body towards a specific shape as they develop in the embryo. Therefore, understanding the mechanisms underlying these developmental constraints could help explain how different body shapes evolved.

The limbs of humans and other mammals evolved from the fins of fish, and this transition is often used to study the role developmental constraints play in evolution. This is an ideal model as there is already a detailed fossil record mapping this evolutionary event, and data pinpointing some of the genes involved in the development of limbs and fins. But this data is incomplete, and a full comparison between the genes activated in the fin and the limb during embryonic development had not been achieved. This is because most fish used for research have undergone recent genetic changes, making it hard to spot which genetic differences are linked to the evolution of the limb.

To overcome this barrier, Onimaru et al. compared genetic data from the developing limbs of mice to the developing fins of the brown-banded bamboo shark, which evolves much slower than other fish. This revealed that although many genes commonly played a role in the development of the fin and the limb in the embryo, the activity of these shared genes was not the same. For example, genes that switched on in the late stages of limb development, switched off in the late stages of fin development. But in the middle of development, those differences were relatively small and both species activated very similar sets of genes. Many of these genes were pleiotropic, which means they have important roles in other tissues and therefore mutate less often. This suggests that the mid-stage of limb development is under the strongest level of constraint.

Darwin’s theory of natural selection explains that mutations drive evolution. But the theory cannot predict what kinds of new body shapes new mutations will produce. Understanding how the activity levels of different genes affect development could help to fill this knowledge gap. This has potential medical applications, for example, understanding why some genetic changes cause more serious problems than others. This work suggests that mutations in genes that are active during the mid-stage of limb development may have the most serious impact.

Limitation of voltage reversal in the degradation of azo dye by a stacked double-anode microbial fuel cell and characterization of the microbial community structure

In this study, two double-anode microbial fuel cells (MFCs) were connected in series for degradation of the azo dye reactive brilliant red X-3B. After the series connection, the electricity generation of one of the MFCs decreased, and the other was not affected too much. Due to the special structure in the double-anode MFC reduced the imbalanced performance between the MFC units, the occurrence of voltage reversal was limited. The removal efficiencies in two MFC reactors were not consistent after the series connection, the results showed that the MFC with the reduced electricity generation had the higher removal efficiencies, it was 12.90, 11.66, and 40.05% higher than in the MFC in which the power generation capacity was not affected after the series connection, the MFC without serial connection, and the control group, respectively. Meanwhile, the microbial communities related to the degradation of refractory organic compounds increased and related to electricity generation decreased in the MFC with the reduced electricity generation, the changes of the microbial communities were consistent with its electricity generation and the removal efficiencies. The degradation products in the effluent from two MFC units showed that had the products generated from the MFC with the reduced electricity generation had simpler structures comparing the other MFC unit.

Assessment of nitrous oxide production in eutrophicated rivers with inflow of treated wastewater based on investigation and statistical analysis

Accurate estimation and control of greenhouse gas emissions have been recognized as imperative in recent years. Therefore, frequent investigations under uniform environmental conditions are required to better understand this concept. Thus, six sampling sites with characteristic concentrations of nitrogen and other water quality parameters were selected to investigate the behavior of water quality parameters throughout the year and to statistically examine the correlations among the parameters. Dissolved nitrous oxide (D-N₂O) showed the highest positive correlation coefficient with NO₂-N among nitrogen species. The results of the principal component analysis suggested that river water quality could be broadly classified based on photosynthesis and contamination from treated wastewater. Photosynthesis caused an increase in pH, with concomitant decrease in D-N₂O concentration. Using the results of multiple regression analysis, D-N₂O was accurately estimated based on nitrogen concentration, pH, and concentration of organic matter in various situations. The results of a detailed survey suggested that D-N₂O was produced in the river from nitrogen sources released from the wastewater treatment plant. The main roles of the wastewater treatment plant for D-N₂O behavior in the river were the supply of the nitrogen source that was the precursor of D-N₂O, the supply of the nutrients that induced the photosynthesis, and the direct supply of D-N₂O at a low water temperature. The models based on multiple regression analysis could efficiently predict the D-N₂O concentration produced in rivers at sites downstream of the wastewater treatment plant, except for the direct supply of D-N₂O as an effluent at low water temperature.

Geochemical distribution of heavy metal elements and potential ecological risk assessment of Matsushima Bay sediments during 2012-2016

Heavy metal pollution of marine sediments has attracted a great deal of attention because of its persistence, bioaccumulation, and toxicity. To evaluate the effects of mega-tsunami, anthropogenic activities, and redox conditions on heavy metal accumulation in coastal areas, sediments from Matsushima Bay, Miyagi Prefecture, Japan, were sampled to test variations in heavy metal spatial distribution on the bay floor during 4 years following the 2011 Tohoku Earthquake tsunami. Cluster analysis and principal component analysis were performed to assess the influencing factors and potential sources of heavy metal enrichment in the sediments of the bay. Additionally, the sediment enrichment levels of heavy metals were assessed on the basis of the enrichment factor (EF). The results of multivariate statistical analyses showed that the Ti, Fe, V, Pb, and Zn contents in Matsushima Bay sediments, which were transported mainly from Sendai Bay, depended on the mud content. The value of EF < 2 for Fe, V, Pb, and Zn indicated that these elements were not enriched. The value of EF > 7 for Cu suggested that the contamination levels in western Matsushima Bay were moderate to severe in every sampling year from 2012 to 2016 by anthropogenic activities. From the values of EF > 5 for U and Mo during 2012 and 2014, the severe enrichment of both elements in these periods may be explained by contamination with 2011 tsunami deposits; the improvement in 2015-2016 suggests that there was recovery of the tsunami-affected sediment composition to its original state. The values of EF > 3 for Mn and As indicated moderate to severe contamination with these heavy metals in the bay mouth area during 2015. This was likely explained by more oxic bottom conditions in the mouth of Matsushima Bay during that year.

Effects of elevated nitrogen on the growth and geosmin productivity of Dolichospermum smithii

Geosmin is one of the most common earthy-musty odor compounds, which is mainly produced by cyanobacteria in surface water. Nitrogen (N) is an important factor affecting the growth of cyanobacteria and its secondary metabolites production due to the eutrophication. In this study, we compared the effects of elevated N on the growth and geosmin productivity of Dolichospermum smithii NIES-824 (synonym Anabaena smithii NIES-824), aiming to better understand the mechanisms involved and give an important and fundamental knowledge to solve off-flavor problem. Results show that elevated N concentration promoted more chlorophyll a (Chl-a) production, whereas the geosmin synthesis decreased, revealing a possible competitive correlation between the Chl-a concentration and geosmin production of D. smithii NIES-824. The majority of geosmin (> 90%) was retained intracellularly during the 28 days of cultivation. The qRT-PCR analysis demonstrates that the expression level of the geosmin synthase gene (geoA) was constitutive and decreased at the higher N concentration during the exponential growth phase of cyanobacterial cells. Furthermore, the decrease of geoA expression during the decline phase suggested that geoA transcription was closely related to cell activity and isoprenoid productivity.

Identification and characterization of a fibroblast growth factor gene in the planarian Dugesia japonica

Planarians belong to the phylum Platyhelminthes and can regenerate their missing body parts after injury via activation of somatic pluripotent stem cells called neoblasts. Previous studies suggested that fibroblast growth factor (FGF) signaling plays a crucial role in the regulation of head tissue differentiation during planarian regeneration. To date, however, no FGF homologues in the Platyhelminthes have been reported. Here, we used a planarian Dugesia japonica model and identified an fgf gene termed Djfgf, which encodes a putative secreted protein with a core FGF domain characteristic of the FGF8/17/18 subfamily in bilaterians. Using Xenopus embryos, we found that DjFGF has FGF activity as assayed by Xbra induction. We next examined Djfgf expression in non-regenerating intact and regenerating planarians. In intact planarians, Djfgf was expressed in the auricles in the head and the pharynx. In the early process of regeneration, Djfgf was transiently expressed in a subset of differentiated cells around wounds. Notably, Djfgf expression was highly induced in the process of head regeneration when compared to that in the tail regeneration. Furthermore, assays of head regeneration from tail fragments revealed that combinatorial actions of the anterior extracellular signal-regulated kinase (ERK) and posterior Wnt/ß-catenin signaling restricted Djfgf expression to a certain anterior body part. This is the region where neoblasts undergo active proliferation to give rise to their differentiating progeny in response to wounding. The data suggest the possibility that DjFGF may act as an anterior counterpart of posteriorly localized Wnt molecules and trigger neoblast responses involved in planarian head regeneration.

Effects of chemical interaction of nutrients and EDTA on metals toxicity to Pseudokirckneriella subcapitata

We studied the effect of the chemical interaction of nutrients and the ethylenediamine tetraacetic acid (EDTA) on metals toxicity. Growth inhibition tests of Pseudokirchneriella subcapitata by nutrient metals copper (Cu) and zinc (Zn), and the non-nutrient metal lead (Pb), were performed. The high-enriched Bold's Basal medium (BBm) and two low-enriched standard media, recommended by the Organization for Economic Cooperation and Development (OECDm) and Environmental Protection Agency-algal assay procedure medium (AAPm), were used in this study. The metals toxicity was affected by the interaction of nutrients and EDTA. Cu⁺² was more toxic in the OECDm (EC₅₀ 20.3 μg/L), while Pb⁺² (EC₅₀ 23.1 μg/L) and Zn⁺² (EC₅₀ 99.4 μg/L) in the AAPm. Non-toxic effect of these metals was observed in BBm, but the exclusion of EDTA shifted it into a toxic medium. Finally, we found that the toxicity of the studied nutrient metals is mainly influenced by EDTA, which reduced the concentration of ionized metals, while the toxicity of the non-nutrient metal is affected by EDTA and phosphates.

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

Background

Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding.

Results

To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage.

Conclusions

This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.

Novel developmental bases for the evolution of hypobranchial muscles in vertebrates

BACKGROUND

Vertebrates are characterized by possession of hypobranchial muscles (HBMs). Cyclostomes, or modern jawless vertebrates, possess a rudimentary and superficial HBM lateral to the pharynx, whereas the HBM in jawed vertebrates is internalized and anteroposteriorly specified. Precursor cells of the HBM, marked by expression of Lbx1, originate from somites and undergo extensive migration before becoming innervated by the hypoglossal nerve. How the complex form of HBM arose in evolution is relevant to the establishment of the vertebrate body plan, but despite having long been assumed to be similar to that of limb muscles, modification of developmental mechanisms of HBM remains enigmatic.

RESULTS

Here we characterize the expression of Lbx genes in lamprey and hagfish (cyclostomes) and catshark (gnathostome; jawed vertebrates). We show that the expression patterns of the single cyclostome Lbx homologue, Lbx-A, do not resemble the somitic expression of mammalian Lbx1. Disruption of Lbx-A revealed that LjLbx-A is required for the formation of both HBM and body wall muscles, likely due to the insufficient extension of precursor cells rather than to hindered muscle differentiation. Both homologues of Lbx in the catshark were expressed in the somitic muscle primordia, unlike in amniotes. During catshark embryogenesis, Lbx2 is expressed in the caudal HBM as well as in the abdominal rectus muscle, similar to lamprey Lbx-A, whereas Lbx1 marks the rostral HBM and pectoral fin muscle.

CONCLUSIONS

We conclude that the vertebrate HBM primarily emerged as a specialized somatic muscle to cover the pharynx, and the anterior internalized HBM of the gnathostomes is likely a novelty added rostral to the cyclostome-like HBM, for which duplication and functionalization of Lbx genes would have been a prerequisite.

Inactivation kinetics modeling of Escherichia coli in concentrated urine for implementing predictive environmental microbiology in sanitation safety planning

Urine concentration (condensation) leads to the inactivation of pathogens in urine owing to a hyperosmotic environment. This study proposed an inactivation kinetic model of Escherichia coli (E. coli), a surrogate of human bacterial pathogens, in concentrated synthetic urine. The model parameters were obtained under an assumption that the inactivation rate of E. coli followed a binomial distribution, which made it possible to accurately simulate the time-course decay of E. coli in synthetic urine. The inactivation rate constant values obtained in concentrated urine samples, ammonium buffer solutions and carbonate buffer solutions indicated that the osmotic pressure was a relatively predominant cause for the inactivation of E. coli. The appropriate storage time was estimated using the approach of quantitative microbial risk assessment, which indicated that the 5-fold concentrated urine could be safely collected after 1-day storage when urea was hydrolyzed, whereas 91-hour storage was required for non-concentrated urine. The occupational risk was not negligible even with 6-month storage at 20 °C when urea was not hydrolyzed, which suggested that the urine storage styles should be clarified more minutely. The present study highlights the importance of "predictive environmental microbiology," which deals with inactivation kinetic models of microorganisms under varied environmental conditions to fully implement the hazard analysis and critical control point (HACCP) approach for the safe use of human excreta in agriculture.

Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information

With advances in sequencing technology, a vast amount of genomic sequence information has become available. However, annotating biological functions particularly of non-protein-coding regions in genome sequences without experiments is still a challenging task. Recently deep learning-based methods were shown to have the ability to predict gene regulatory regions from genome sequences, promising to aid the interpretation of genomic sequence data. Here, we report an improvement of the prediction accuracy for gene regulatory regions by using the design of convolution layers that efficiently process genomic sequence information, and developed a software, DeepGMAP, to train and compare different deep learning-based models (https://github.com/koonimaru/DeepGMAP). First, we demonstrate that our convolution layers, termed forward- and reverse-sequence scan (FRSS) layers, integrate both forward and reverse strand information, and enhance the power to predict gene regulatory regions. Second, we assessed previous studies and identified problems associated with data structures that caused overfitting. Finally, we introduce visualization methods to examine what the program learned. Together, our FRSS layers improve the prediction accuracy for gene regulatory regions.

Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain

RNA viruses form a dynamic distribution of mutant swarms (termed "quasispecies") due to the accumulation of mutations in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck effect. Human-to-human transmission exemplifies a bottleneck effect, in that only part of a viral population can reach the next susceptible hosts. In the present study, two lineages of the rhesus rotavirus (RRV) strain of rotavirus A were serially passaged five times at a multiplicity of infection (MOI) of 0.1 or 0.001, and three phenotypes (infectious titer, cell binding ability, and specific growth rate) were used to evaluate the impact of a bottleneck effect on the RRV population. The specific growth rate values of lineages passaged under the stronger bottleneck (MOI of 0.001) were higher after five passages. The nucleotide diversity also increased, which indicated that the mutant swarms of the lineages under the stronger bottleneck effect were expanded through the serial passages. The random distribution of synonymous and nonsynonymous substitutions on rotavirus genome segments indicated that almost all mutations were selectively neutral. Simple simulations revealed that the presence of minor mutants could influence the specific growth rate of a population in a mutant frequency-dependent manner. These results indicate a stronger bottleneck effect can create more sequence spaces for minor sequences.IMPORTANCE In this study, we investigated a bottleneck effect on an RRV population that may drastically affect the viral population structure. RRV populations were serially passaged under two levels of a bottleneck effect, which exemplified human-to-human transmission. As a result, the genetic diversity and specific growth rate of RRV populations increased under the stronger bottleneck effect, which implied that a bottleneck created a new space in a population for minor mutants originally existing in a hidden layer, which includes minor mutations that cannot be distinguished from a sequencing error. The results of this study suggest that the genetic drift caused by a bottleneck in human-to-human transmission explains the random appearance of new genetic lineages causing viral outbreaks, which can be expected according to molecular epidemiology using next-generation sequencing in which the viral genetic diversity within a viral population is investigated.

Effect of sedimentary organic matter on species richness of deposit feeders in enclosed bay ecosystems: Insight from fatty acid nutritional indicators

How nutritional quality of dietary resources affects species richness of consumer communities is poorly understood. We used fatty acids as indicators of nutritional quality of sedimentary organic matter to evaluate the effects of highly unsaturated fatty acid (HUFA) content in sediments and fatty acid diversity in sedimentary organic matter on species richness of deposit feeders. We sampled benthic animals and sedimentary organic matter, a potential dietary source for deposit feeders, at 54 locations in two bay ecosystems. The species richness of deposit feeders ranged between 1 and 29 and had a parabolic relationship with the organic carbon content of sediments. At intermediate range of sedimentary organic carbon content, the species richness of deposit feeders was positively related to HUFA content and fatty acid diversity. These findings indicate that nutritional quality is one of the important factors determining species richness. In particular, HUFA content and fatty acid diversity are useful indicators of the nutritional quality of potential diets and good predictors of the occurrences of benthic invertebrates in marine habitats.

Characterization of electricity generation and microbial community structure over long-term operation of a microbial fuel cell

In this study, a continuous-flow microbial fuel cell (MFC) system was constructed to treat azo dye wastewater for 400 days. The electrical properties of the MFC after 400-day operation and the removal efficiencies of the MFC after long- and short-term operation were analyzed with respect to co-substrate concentrations. The power output of the MFC system decreased from 586 to 330 mV with increasing operating time, and the removal efficiencies of the MFC remained stable after long-term operation in comparison to those after short-term operation, even when the co-substrate concentration was reduced. Analysis of the degradation products showed that products generated from long-term operation of the MFC were present at low concentrations. The microbial community analysis revealed that the relative abundance of microorganisms related to the degradation of organics in the MFC increased after long-term operation, and microorganisms related to electricity generation decreased.

Combined effects of elevated carbon dioxide and temperature on phytoplankton-zooplankton link: A multi-influence of climate change on freshwater planktonic communities

It is essential to understand the combined effects of elevated CO₂ and temperature on phytoplankton-zooplankton link when attempting to predict climate change responses of freshwater ecosystems. Phytoplankton species differ in stoichiometric and fatty acids composition, and this may result in phytoplankton-mediated effect on zooplankton at elevated CO₂ and temperature. Beyond the isolated analysis of CO₂ or temperature effect, few studies have assessed zooplankton growth under the phytoplankton-mediated effects of elevated CO₂ and temperature. In this study, three algal species (green alga, diatom, cyanobacteria) were fed on zooplankton Daphnia magna, under the conditions of CO₂ concentrations of ambient (390 ppm) and elevated (1000 ppm) levels and temperatures at 20, 25 and 30 °C. Elevated CO₂ increased the algal biomass, while it reduced the phosphorus (P) and ω3 polyunsaturated fatty acids (ω3 PUFAs) to carbon (C) ratios. Elevated temperature decreased the P/C ratios in all algal cultures and ω3 PUFAs/C ratios in the diatom and the cyanobacteria cultures. Phytoplankton-mediated effect of elevated CO₂ reduced the growth of zooplankton fed on the green and the mixed three algae culture. The stimulation of zooplankton fed on the diatom and the cyanobacteria by elevated temperature can be offset by decreasing food P and ω3 PUFAs contents. The combined effects of elevated CO₂ and temperature on the growth of daphnids were mainly mediated by ω3 PUFAs/C ratios in the phytoplankton. Rising temperature as a combined direct and indirectly phytoplankton-mediated effect on zooplankton may be able to ameliorate the negative effects of elevated CO₂. The results indicated that the combined effects of increased CO₂ and temperature increased the fatty acid content of the green alga but not the other algae. This study highlighted that climate change with simultaneously increasing temperature and CO₂ may entangle the carbon transfer in freshwater planktonic communities.

Approach deliberation for source identification of sedimentary organic matters via comparing freshwater lakes with multi-ecotypes

Despite of the importance of understanding the sediment quality for lacustrine management, the source evaluation of sedimentary organic matter (SOM) in freshwater lakes is still insufficient. In this study, two shallow eutrophic lakes of Lake Taihu, China and Lake Izunuma, Japan were systematically investigated. Results of fatty acid profiles demonstrated that a wide range of organic matters, varying ecotypically, was inputted into the sediments of both lakes. Interestingly, there was a strong contribution from terrestrial plants to the sediments across ecotypes, with an approximate input from bacteria, and a relatively minor input from microalgae mainly included cyanobacteria, green algae, diatom and dinoflagellates. In addition, isotopic mixing model depicted a complementary picture that a significant, but spatially variable, amount of organic matter was derived from emergent and floating-leaf plants of Phragmites, Nelumbo, Nymphoides and Trapa L in Lake Izunuma. A general indicator selection procedure for the source assignments of SOM in freshwater ecosystems was therefore proposed: fatty acids could be a valid biomarker when the potential sources are unknown or unavailable; stable isotopes could be an effective supplement approach when assessing the special or defined organic sources.

Contribution of dissolved N2O in total N2O emission from sewage treatment plant

The characteristics of nitrous oxide, N₂O, from a sewage treatment plant, which conducts nitrogen removal, and the river that receives its effluent water, were investigated by intensive daily surveys in summer and winter. N₂O production in the sewage treatment plant was promoted in winter when nitrite accumulated in the reaction tank. The dissolved N₂O concentration in the effluent water was also high in winter, which caused the dissolved N₂O concentration to increase in the river downstream. In contrast, the N₂O production inside the plant and the dissolved N₂O emission through the effluent water, the dissolved N₂O discharge, was controlled in summer when the nitrogen removal was more complete and there was no-nitrite accumulation. The dissolved N₂O in the effluent water was rapidly lost after leaving the plant by as much as 26% in summer and 59% in winter. Additionally, the amount of the dissolved N₂O discharge in winter was almost equal to that of the indirect N₂O emission. When the nitrogen removal proceeded successfully, the amount of dissolved N₂O discharge was small. In contrast, when the nitrogen removal was insufficient, the dissolved N₂O discharge became an important N₂O source.

Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei

Chondrichthyans (cartilaginous fishes) exhibit highly variable reproductive styles, categorized as viviparity and oviparity. Among these, species with oviparity provide an enormous potential of molecular experimentation with stable sample supply which does not demand the sacrifices of live mothers. Cartilaginous fishes are divided into two subclasses, chimaeras (Holocephali) and elasmobranchs (Elasmobranchii), and the latter consists of two monophyletic groups, Batoidea (rays, skates and torpedoes) and Selachimorpha (sharks). Here we report transcriptome assemblies of the ocellate spot skate Okamejei kenojei, produced by strand-specific RNA-seq of its embryonic tissues. We obtained a total of 325 million illumina short reads from libraries prepared using four different tissue domains and assembled them all together. Our assembly result confirmed the species authenticity and high continuity of contig sequences. Also, assessment of its coverage of pre-selected one-to-one orthologs supported high diversity of transcripts in the assemblies. Our products are expected to provide a basis of comparative molecular studies encompassing other chondrichthyan species with emerging genomic and transcriptomic sequence information.

Azo dye degradation pathway and bacterial community structure in biofilm electrode reactors

In this study, the degradation pathway of the azo dye X-3B was explored in biofilm electrode reactors (BERs). The X-3B and chemical oxygen demand (COD) removal efficiencies were evaluated under different voltages, salinities, and temperatures. The removal efficiencies increased with increasing voltage. Additionally, the BER achieved maximum X-3B removal efficiencies of 66.26% and 75.27% at a NaCl concentration of 0.33 g L^-1 and temperature of 32 °C, respectively; it achieved a COD removal efficiency of 75.64% at a NaCl concentration of 0.330 g L^-1. Fourier transform infrared spectrometry and gas chromatography-mass spectrometry analysis indicated that the X-3B biodegradation process first involved the interruption of the conjugated double-bond, resulting in aniline, benzodiazepine substance, triazine, and naphthalene ring formation. These compounds were further degraded into lower-molecular-weight products. From this, the degradation pathway of the azo dye X-3B was proposed in BERs. The relative abundances of the microbial community at the phylum and genus levels were affected by temperature, the presence of electrons, and an anaerobic environment in the BERs. To achieve better removal efficiencies, further studies on the functions of the microorganisms are needed.

gVolante for standardizing completeness assessment of genome and transcriptome assemblies

Motivation

Along with the increasing accessibility to comprehensive sequence information, such as whole genomes and transcriptomes, the demand for assessing their quality has been multiplied. To this end, metrics based on sequence lengths, such as N50, have become a standard, but they only evaluate one aspect of assembly quality. Conversely, analyzing the coverage of pre-selected reference protein-coding genes provides essential content-based quality assessment, but the currently available pipelines for this purpose, CEGMA and BUSCO, do not have a user-friendly interface to serve as a uniform environment for assembly completeness assessment.

Results

Here, we introduce a brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section. Completeness assessments performed on gVolante report scores based on not just the coverage of reference genes but also on sequence lengths (e.g. N50 scaffold length), allowing quality control in multiple aspects. Using gVolante, one can compare the quality of original assemblies between their multiple versions (obtained through program choice and parameter tweaking, for example) and evaluate them in comparison to the scores of public resources found in the database section.

Availability and implementation

gVoalte is freely available at https://gvolante.riken.jp/.

Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters

We have examined the role of Fam60a, a gene highly expressed in embryonic stem cells, in mouse development. Fam60a interacts with components of the Sin3a-Hdac transcriptional corepressor complex, and most Fam60a^-/- embryos manifest hypoplasia of visceral organs and die in utero. Fam60a is recruited to the promoter regions of a subset of genes, with the expression of these genes being either up- or down-regulated in Fam60a^-/- embryos. The DNA methylation level of the Fam60a target gene Adhfe1 is maintained at embryonic day (E) 7.5 but markedly reduced at E9.5 in Fam60a^-/- embryos, suggesting that DNA demethylation is enhanced in the mutant. Examination of genome-wide DNA methylation identified several differentially methylated regions, which were preferentially hypomethylated, in Fam60a^-/- embryos. Our data suggest that Fam60a is required for proper embryogenesis, at least in part as a result of its regulation of DNA methylation at specific gene promoters.

Role of MEKK1 in the anterior-posterior patterning during planarian regeneration

Planarians have established a unique body pattern along the anterior-posterior (AP) axis, which consists of at least four distinct body regions arranged in an anterior to posterior sequence: head, prepharyngeal, pharyngeal (containing a pharynx), and tail regions, and possess high regenerative ability. How they reconstruct the regional continuity in a head-to-tail sequence after amputation still remains unknown. We use as a model planarian Dugesia japonica head regeneration from tail fragments, which involves dynamic rearrangement of the body regionality of preexisting tail tissues along the AP axis, and show here that RNA interference of the gene D. japonica mek kinase 1 (Djmekk1) caused a significant anterior shift in the position of pharynx regeneration at the expense of the prepharyngeal region, while keeping the head region relatively constant in size, and accordingly led to development of a relatively longer tail region. Our data suggest that DjMEKK1 regulates anterior extracellular signal-regulated kinase (ERK) and posterior β-catenin signaling pathways in a positive and negative manner, respectively, to establish a proper balance resulting in the regeneration of planarian's scale-invariant trunk-to-tail patterns across individuals. Furthermore, we demonstrated that DjMEKK1 negatively modulates planarian β-catenin activity via its serine/threonine kinase domain, but not its PHD/RING finger domain, by testing secondary axis formation in Xenopus embryos. The data suggest that Djmekk1 plays an instructive role in the coordination between the establishment of the prepharyngeal region and posteriorizing of pharynx formation by balancing the two opposing morphogenetic signals along the AP axis during planarian regeneration.

The comparison of greenhouse gas emissions in sewage treatment plants with different treatment processes

Greenhouse gas emissions from different sewage treatment plants: oxidation ditch process, double-circulated anoxic-oxic process and anoxic-oxic process were evaluated based on the survey. The methane and nitrous oxide characteristics were discussed based on the gaseous and dissolved gas profiles. As a result, it was found that methane was produced in the sewer pipes and the primary sedimentation tank. Additionally, a ventilation system would promote the gasification of dissolved methane in the first treatment units. Nitrous oxide was produced and emitted in oxic tanks with nitrite accumulation inside the sewage treatment plant. A certain amount of nitrous oxide was also discharged as dissolved gas through the effluent water. If the amount of dissolved nitrous oxide discharge is not included, 7-14% of total nitrous oxide emission would be overlooked. Based on the greenhouse gas calculation, electrical consumption and the N₂O emission from incineration process were major sources in all the plants. For greenhouse gas reduction, oxidation ditch process has an advantage over the other advanced systems due to lower energy consumption, sludge production, and nitrogen removal without gas stripping.

Plasma membrane expression of ZNF185 is a prognostic factor in pancreatic ductal carcinoma

Pancreatic ductal carcinoma (PDC) is one of the major causes of cancer-associated mortality globally due to its high potential for distant metastasis. To understand hematogenous metastasis, the molecular expression profiles of weak metastatic PDC cell subline BxPC-3 and highly liver-metastatic cell subline LM-BxPC-3 were compared, and zinc finger protein 185 (ZNF185) was identified as a molecule that is upregulated in LM-BxPC-3 cells. The aim of the present study was to evaluate the clinicopathological significance of ZNF185 in PDC. Using immunohistochemistry, ZNF185 expression was investigated in 182 patients with PDC, in association with numerous clinicopathological variables. The expression profile of ZNF185 was also characterized using xenograft models. In contrast to parent BxPC-3 cells in subcutaneous transplanted tumor foci, which only expressed ZNF185 on their plasma membrane (m)ZNF185, LM-BxPC-3 cells in liver-metastatic foci that were formed subsequent to transplantation all expressed cytoplasmic (c)ZNF185. Additionally, 51% of the cells at the periphery of the tumor foci expressed mZNF185. Expression of cZNF185, and of mZNF185 and cZNF185 combined was identified in 93 and 39% of clinical patients with PDC, respectively. Patients with mZNF185-negative and -positive PDC exhibited a median survival time of 30.2 months and 21.3 months, respectively. Multivariate analysis indicated that the expression of mZNF185 is closely associated with a shorter overall survival time. Increased marked venous invasion was more prevalent in patients who were mZNF185-positive, as compared with patients who were mZNF185-negative. These data suggest that the expression of mZNF185 is an independent and unfavorable prognosticator in patients with PDC. The results suggested that the amount and subcellular location of ZNF185 are correlated with the position of the cancer cells expressing it within the nests. Additionally, the subcellular location of ZNF185 may be important to its biological function.

Response of microalgae to elevated CO2 and temperature: impact of climate change on freshwater ecosystems

To estimate the combined effects of elevated CO2 and temperature on microalgae, three typical and worldwide freshwater species, the green alga Scenedesmus acuminatus, the diatom Cyclotella meneghiniana, and the cyanobacterium Microcystis aeruginosa, as well as mixes of these three species were continuously cultured in controlled environment chambers with CO2 at 390 and 1000 ppm and temperatures of 20, 25, and 30 °C. CO2 and temperature significantly affected the production of microalgae. The cell productivity increased under elevated CO2 and temperature. Although the green alga dominated in the mixed culture within all CO2 and temperature conditions, rising temperature and CO2 intensified the competition of the cyanobacterium with other microalgae. CO2 affected the extracellular polymeric substances (EPS) characteristics of the green alga and the cyanobacterium. Elevated CO2 induced the generation of humic substances in the EPS fractions of the green alga, the cyanobacterium, and the mixed culture. The extracellular carbohydrates of the diatom and the extracellular proteins of the cyanobacterium increased with elevated CO2 and temperature, while the extracellular carbohydrates and proteins of the green alga and the mixes increased under elevated CO2 and temperature. There were synergistic effects of CO2 and temperature on the productivity and the EPS of microalgae. Climate change related CO2 and temperature increases will promote autochthonous organic carbon production in aquatic ecosystems and facilitate the proliferation of cyanobacteria, which potentially changes the carbon cycling and undermines the functioning of ecosystems.

Molecular markers for X-ray-insensitive differentiated cells in the Inner and outer regions of the mesenchymal space in planarian Dugesia japonica

Planarian's strong regenerative ability is dependent on stem cells (called neoblasts) that are X-ray-sensitive and proliferative stem cells. In addition to neoblasts, another type of X-ray-sensitive cells was newly identified by recent research. Thus, planarian's X-ray-sensitive cells can be divided into at least two populations, Type 1 and Type 2, the latter corresponding to planarian's classically defined "neoblasts". Here, we show that Type 1 cells were distributed in the outer region (OR) immediately underneath the muscle layer at all axial levels from head to tail, while the Type 2 cells were distributed in a more internal region (IR) of the mesenchymal space at the axial levels from neck to tail. To elucidate the biological significance of these two regions, we searched for genes expressed in differentiated cells that were locate close to these X-ray-sensitive cell populations in the mesenchymal space, and identified six genes mainly expressed in the OR or IR, named OR1, OR2, OR3, IR1, IR2 and IR3. The predicted amino acid sequences of these genes suggested that differentiated cells expressing OR1, OR3, IR1, or IR2 provide Type 1 and Type 2 cells with specific extracellular matrix (ECM) environments.

Abstract 1543: Clinical significance of ZNF185 intracellular localization in pancreatic ductal carcinoma

Pancreatic cancer is one of the most aggressive human tumors because of the challenges associated with detecting it at an early stage and its high potential for dissemination and distant metastasis. Therefore, clarifying the biological mechanisms underlying distant metastasis from pancreatic cancer and accelerating the development of new treatment strategies are needed. We previously isolated ZNF185, a metastasis-related protein, using a global quantitative proteome analysis. ZNF185 contains two zinc-finger motifs in the C-terminus that fit the consensus pattern of the LIM domains inducing tumor formation and cytoskeleton organization. In the present study, we investigated the expression of ZNF185 in human pancreatic cancer in vivo and in clinical cases, and also evaluated its prognostic significance. Immunohistochemical staining of resected specimens and a xenograft model of liver metastasis was used to examine the relationship between distant metastasis in and the prognosis of pancreatic cancer and the expression of ZNF185. Cells expressing ZNF185 in the plasma membrane were detected in 71 (39.0%) out of 182 patients with resected pancreatic cancer. Patients not expressing ZNF185 in the plasma membrane had a median survival of 30.2 months, whereas those expressing ZNF185 in the plasma membrane had a median survival of 21.3 months. A multivariate analysis indicated that the expression of ZNF185 in the plasma membrane was an independent poor prognostic factor (p = 0.016). A multivariate analysis indicated that patients with cells expressing ZNF185 in the plasma membrane were more likely to develop hematogenous metastasis (p = 0.081). NOD/Shi-scid/IL-2Rγnull(NOG) mice were used to compare the expression of ZNF185 in the subcutaneous tumors of the parent cell line BxPC-3 and liver metastatic tumors of the highly liver-metastatic subline LM-BxPC-3 established in our laboratory. Cells expressing ZNF185 in the plasma membrane were more prevalent in metastatic disease in the liver than in subcutaneous tumors, and these cells were often located at the tumor margins rather than in the center of the tumor. In conclusion, ZNF185 is a protein related to hematogenous metastasis, the expression of which in the plasma membrane was identified as an independent prognostic factor for pancreatic cancer.

Citation Format: Daisuke Furukawa, Tsuyoshi Chijiwa, Masahiro Matsuyama, Masaya Mukai, Ei-ichi Matsuo, Osamu Nishimura, Kenji Kawai, Hiroshi Suemizu, Toshio Nakagohri, Seiei Yasuda, Kazuaki Shimada, Nobuyoshi Hiroka, Masato Nakamura. Clinical significance of ZNF185 intracellular localization in pancreatic ductal carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1543.

Simple blood-feeding method for live imaging of gut tube remodeling in regenerating planarians

Live cell imaging is a powerful technique to study cellular dynamics in vivo during animal development and regeneration. However, few live imaging methods have been reported for studying planarian regeneration. Here, we developed a simple method for steady visualization of gut tube remodeling during regeneration of a living freshwater planarian, Dugesia japonica. When planarians were fed blood several times, gut branches were well-visualized in living intact animals under normal bright-field illumination. Interestingly, tail fragments derived from these colored planarians enabled successive observation of the processes of the formation of a single anterior gut branch in the prepharyngeal region from the preexisting two posterior gut branches in the same living animals during head regeneration. Furthermore, we combined this method and RNA interference (RNAi) and thereby showed that a D. japonica raf-related gene (DjrafA) and mek-related gene (DjmekA) we identified both play a major role in the activation of extracellular signal-regulated kinase (ERK) signaling during planarian regeneration, as indicated by their RNAi-induced defects on gut tube remodeling in a time-saving initial screening using blood-feeding without immunohistochemical detection of the gut. Thus, this blood-feeding method is useful for live imaging of gut tube remodeling, and provides an advance for the field of regeneration study in planarians.

The seasonal variation of emission of greenhouse gases from a full-scale sewage treatment plant

The seasonal variety of greenhouse gas (GHGs) emissions and the main emission source in a sewage treatment plant were investigated. The emission coefficient to treated wastewater was 291gCO2m(-3). The main source of GHGs was CO2 from the consumption of electricity, nitrous oxide from the sludge incineration process, and methane from the water treatment process. They accounted for 43.4%, 41.7% and 8.3% of the total amount of GHGs emissions, respectively. The amount of methane was plotted as a function of water temperature ranging between 13.3 and 27.3°C. An aeration tank was the main source of methane emission from all the units. Almost all the methane was emitted from the aeration tank, which accounted for 86.4% of the total gaseous methane emission. However, 18.4% of the methane was produced in sewage lines, 15.4% in the primary sedimentation tank, and 60.0% in the aeration tank.

Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica

We established a laboratory clonal strain of freshwater planarian (Dugesia japonica) that was derived from a single individual and that continued to undergo autotomous asexual reproduction for more than 20 years, and we performed large-scale genome sequencing and transcriptome analysis on it. Despite the fact that a completely clonal strain of the planarian was used, an unusually large number of mutations were detected. To enable quantitative genetic analysis of such a unique organism, we developed a new model called the Reference Gene Model, and used it to conduct large-scale transcriptome analysis. The results revealed large numbers of mutations not only outside but also inside gene-coding regions. Non-synonymous SNPs were detected in 74% of the genes for which valid ORFs were predicted. Interestingly, the high-mutation genes, such as metabolism- and defense-related genes, were correlated with genes that were previously identified as diverse genes among different planarian species. Although a large number of amino acid substitutions were apparently accumulated during asexual reproduction over this long period of time, the planarian maintained normal body-shape, behaviors, and physiological functions. The results of the present study reveal a unique aspect of asexual reproduction.