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.

Autocrine TGF-ß-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-ß plays an exclusive role in promoting lung fibroblast-to-myofibroblast differentiation. Moreover, the autocrine TGF-ß-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.

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.

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. Gse1 mutant (Gse1Δex3/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 Gse1Δex3/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.

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.

Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish.

Recent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genus Takifugu, in which one strong candidate sex-determining gene, Amhr2, has been identified. To trace the processes involved in transitions in the sex-determination system in this genus, we studied 12 species and found that while the Amhr2 locus likely determines sex in the majority of Takifugu species, three species have acquired sex-determining loci at different chromosomal locations. Nevertheless, the generation of genome assemblies for the three species revealed that they share a portion of the male-specific supergene that contains a candidate sex-determining gene, GsdfY, along with genes that potentially play a role in male fitness. The shared supergene spans ∼100 kb and is flanked by two duplicated regions characterized by CACTA transposable elements. These results suggest that the shared supergene has taken over the role of sex-determining locus from Amhr2 in lineages leading to the three species, and repeated translocations of the supergene underlie the turnover of sex chromosomes in these lineages. These findings highlight the underestimated role of a mobile supergene in the turnover of sex chromosomes in vertebrates.

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 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.

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.

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.

The Negative Relationship between Fouling Organisms and the Content of Eicosapentaenoic Acid and Docosahexaenoic Acid in Cultivated Pacific Oysters, Crassostrea gigas.

Bivalves serve as an important aquaculture product, as they are the source of essential fatty acids, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), in our diet. However, their cultivation in the wild can be affected by fouling organisms that, in turn, affect their EPA and DHA content. The effects of fouling organisms on the EPA and DHA contents of cultivated bivalves have not been well documented. We examined the effects of fouling organisms on the EPA and DHA contents and condition index of cultured oysters, Crassostrea gigas, in an aquaculture system. We sampled two-year-old oysters from five sites in Shizugawa Bay, Japan, in August 2014. Most of the fouling organisms were sponges, macroalgae, and Mytilus galloprovincialis. A significant negative relationship existed between the DHA content in C. gigas and the presence of sponges and macroalgae. A lower C. gigas EPA content corresponded to a higher M. galloprovincialis fouling mass and a lower C. gigas condition index. This can be explained by dietary competition between C. gigas and M. galloprovincialis for diatoms, which were the main producer of EPA in our study sites. Our findings indicate that fouling organisms likely reduce the EPA and DHA content in cultivated oysters. Therefore, our results suggest that the current efforts to remove fouling organisms from oyster clusters is an effective strategy to enhance the content of EPA and DHA in oysters.

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.

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.

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.

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.

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.