Deciphering microbial community dynamics along the fermentation course of soy sauce under different temperatures using metagenomic analysis.

Fermented soy sauce consists of microorganisms that exert beneficial effects. However, the microbial community dynamics during the fermentation course is poorly characterized. Soy sauce production is classified into the stages of mash fermentation with koji (S0), brine addition (S1), microbial transformation (S2), flavor creation (S3), and fermentation completion (S4). In this study, microbial succession was investigated across stages at different temperatures using metagenomics analyses. During mash fermentation, Aspergillus dominated the fungal microbiota in all stages, while the bacterial composition was dominated by Bacillus at room temperature and by a diverse composition of enriched lactic acid bacteria (LAB) at a controlled temperature. Compared with a stable fungal composition, bacterial dynamics were mostly attributable to fluctuations of LAB, which break down carbohydrates into lactic acid. After adding brine, increased levels of Enterococcus and decreased levels of Lactococcus from S1 to S4 may reflect differences in salinity tolerance. Staphylococcus, as a fermentation starter at S0, stayed predominant throughout fermentation and hydrolyzed soybean proteins. Meanwhile, Rhizopus and Penicillium may improve the flavor. The acidification of soy sauce was likely attributable to production of organic acids by Bacillus and LAB under room temperature and controlled temperature conditions, respectively. Metagenomic analysis revealed that microbial succession was associated with the fermentation efficiency and flavor enhancement. Controlled temperature nurture more LAB than uncontrolled temperatures and may ensure the production of lactic acid for the development of soy sauce flavor.

Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses.

The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.

Complete chloroplast genome and phylogenetic analysis of Bupleurum kaoi Liu, Chao, and Chuang, 1977: an endemic species in Taiwan.

Bupleurum kaoi Liu, Chao, and Chuang is an endemic and endangered herb in Taiwan. In this study, the complete circular chloroplast genome of B. kaoi was reconstructed and annotated using Illumina sequencing. The genome size of B. kaoi is 155,938 bp, including a pair of inverted repeat regions (IRs: 26308 bp), separated by a large single-copy (LSC) region of 85,784 bp and a small single-copy (SSC) region of 17,538 bp. The GC content of the chloroplast genome is 37.6%. There are 113 different genes in the chloroplast genome of B. kaoi, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that Bupleurum species is the monophyletic group, and B. kaoi belongs to subgenus Bupleurum and is closely related to B. scorzonerifolium.

Manual Removal versus Spontaneous Delivery of the Placenta at Cesarean Section: A Meta-Analysis of Randomized Controlled Trials.

PURPOSE: Several randomized clinical trials (RCTs) investigated the effects of the manual placental removal on hemorrhage or other hemorrhage-related complications compared with the spontaneous placental removal during cesarean section (CS), while the results remained controversial and were inconsistent. The purpose of this meta-analysis was to quantify the pooled effects of the methods of placental removal on hemorrhage during CS. PATIENTS AND METHODS: A systematic literature search was conducted using PubMed, EMBASE, Web of Science, and Google Scholar. Heterogeneity was tested by I 2 statistics and Q-statistic. The random-effects model or fixed-effects model were used to calculate the pooled effect for the included studies according to heterogeneity. And the term of standardized mean difference (SMD) with 95% confidence intervals (CI) was pooled and estimated the effects across all studies. RESULTS: A total of nine RCTs were included in this meta-analysis. Compared with spontaneous group, manual placental removal increased the amount of hemorrhage (SMD = 0.53, 95% CI [0.12, 0.94]; Z = 2.54, P = 0.011) and increased the risk of endometritis (OR = 1.84, 95% CI [1.31, 2.58]; Z = 3.52, P < 0.0001). In contrast, there was no significant difference concerning the operating time (SMD = -0.30, 95% CI [-0.85, 0.24]; Z = 1.09, P = 0.276), the length of hospital stays (SMD = 0.11, 95% CI [-0.08, 0.30]; Z = 1.11, P = 0.265), and blood transfusion requirement (OR = 1.36, 95% CI [0.91, 2.04]; Z = 1.52, P = 0.129), respectively. CONCLUSION: Comparing with spontaneous placental removal, manual placental removal appeared to be less positive effect during CS. Because of the limitations of this meta-analysis, more high-quality RCTs are needed to confirm our findings.

Cytochrome P450 monooxygenase of Acanthamoeba castellanii participates in resistance to polyhexamethylene biguanide treatment.

Acanthamoeba spp. are free-living parasites that can cause severe infections such as granulomatous amoebic encephalitis (GAE) and amoebic keratitis (AK). Polyhexamethylene biguanide (PHMB) is a topical application for AK treatment. However, PHMB is not entirely effective against all Acanthamoeba strains or isolates. The mechanisms by which Acanthamoeba protects itself against extreme drug conditions without encystation are still unknown. According to a previous study, cytochrome P450 monooxygenase (CYP450MO) plays an important role in the oxidative biotransformation of numerous drugs related to metabolism. In this study, a CYP450MO fragment was inserted into the pGAPDH-EGFP vector and transfected into Acanthamoeba castellanii. We found that CYP450MO-overexpressing Acanthamoeba had higher survival rates than those of the control cells after PHMB treatment. Moreover, we also found that encystation-related genes such as cellulose synthase I (CSI), encystation-mediating serine proteinase (EMSP), and autophagy-related protein 8 (ATG8) expression levels were not significantly different between Acanthamoeba transfected by pGAPDH-EGFP or pGAPDH-EGFP-CYP450MO. We suggest that Acanthamoeba transfected by pGAPDH-EGFP-CYP450MO may not induce encystation-related genes to resist PHMB treatment. In conclusion, these findings indicate that CYP450MO may be an additional target when PHMB is used for treatment of amoebic keratitis.

TITLE: La monooxygénase du cytochrome P450 d'Acanthamoeba castellanii participe à la résistance au traitement par le polyhexaméthylène biguanide. ABSTRACT: Les Acanthamoeba spp. sont des parasites libres qui peuvent provoquer des infections graves telles que l'encéphalite amibienne granulomateuse (EAG) et la kératite amibienne (KA). Le polyhexaméthylène biguanide (PHMB) est une application topique pour le traitement de la KA. Cependant, le PHMB n'est pas entièrement efficace contre toutes les souches ou isolats d'Acanthamoeba. Les mécanismes par lesquels Acanthamoeba se protège contre des conditions médicamenteuses extrêmes sans enkystation sont encore inconnus. Selon une étude précédente, la monooxygénase du cytochrome P450 (CYP450MO) joue un rôle important dans la biotransformation oxydative de nombreux médicaments liés au métabolisme. Dans cette étude, un fragment CYP450MO a été inséré dans le vecteur pGAPDH-EGFP et transfecté dans Acanthamoeba castellanii. Nous avons constaté que les Acanthamoeba surexprimant le CYP450MO avaient des taux de survie plus élevés que ceux des cellules témoins après un traitement au PHMB. De plus, nous avons également constaté que les gènes liés aux enkystations tels que la cellulose synthase I (CSI), la sérine protéinase médiatrice de l'enkystation (EMSP) et les niveaux d'expression de la protéine 8 liée à l'autophagie (ATG8) n'étaient pas significativement différents entre les Acanthamoeba transfectés par pGAPDH-EGFP ou par pGAPDH-EGFP-CYP450MO. Nous suggérons que les Acanthamoeba transfectés par pGAPDH-EGFP-CYP450MO ne peuvent pas induire les gènes liés à l'enkystation pour résister au traitement PHMB. En conclusion, ces résultats peuvent indiquer que la monooxygénase du cytochrome P450 peut être une cible potentielle pour le traitement par PHMB de la kératite amibienne.

Cloning and promoter analysis of palladin 90-kDa, 140-kDa, and 200-kDa isoforms involved in skeletal muscle cell maturation.

OBJECTIVE: Palladin is a ubiquitous phosphoprotein expressed in vertebrate cells that works as a scaffolding protein. Several isoforms deriving from alternative splicing are originated from the palladin gene and involved in mesenchymal and muscle cells formation, maturation, migration, and contraction. Recent studies have linked palladin to the invasive spread of cancer and myogenesis. However, since its discovery, the promoter region of the palladin gene has never been studied. The objective of this study was to predict, identify, and measure the activity of the promoter regions of palladin gene. RESULTS: By using promoter prediction programs, we successfully identified the transcription start sites for the Palld isoforms and revealed the presence of a variety of transcriptional regulatory elements including TATA box, GATA, MyoD, myogenin, MEF, Nkx2-5, and Tcf3 upstream promoter regions. The transcriptome profiling approach confirmed the active role of predicted transcription factors in the mouse genome. This study complements the missing piece in the characterization of palladin gene and certainly contributes to understanding the complexity and enrollment of palladin regulatory factors in gene transcription.

Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens.

Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and brain-transcriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing, and biting/striking occurred only during intervals between mouth-locking. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pair showed a strong gene expression correlation, whereas those in D20 fighting pairs showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in a grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in brain-transcriptomic synchronization (PIBS) suggested that this synchronization provides a physiological basis for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 group found genes enriched for ion transport, synaptic function, and learning and memory. Brain-transcriptomic synchronization could be a general phenomenon and may provide a new cornerstone with which to investigate coordinating and sustaining social interactions between two interacting partners of vertebrates.

Characterisation of the ß-lactam resistance enzyme in Acanthamoeba castellanii.

ß-Lactams are well known as the best antibiotics for inhibiting the cross-linking between adjacent polysaccharide chains and peptides in the peptidoglycan layer of bacterial cell walls, causing bacterial cell lysis. There are no reports on the action of and resistance mechanisms to ß-lactams in protozoa. Acanthamoeba castellanii is a free-living protozoan pathogen capable of causing blinding keratitis and fatal granulomatous encephalitis. When Acanthamoeba is exposed to harsh conditions, it differentiates into the cyst stage to avoid environmental stresses, such as drug treatment. In this study, it was shown that the mature encystation rate of A. castellanii is decreased by treatment with cefotaxime (CTX) and clavulanic acid (CLA); however, the drugs do not kill the amoeba. We hypothesise that ß-lactam antibiotics may disturb synthesis of the double cell wall during the encystation process of Acanthamoeba. Interestingly, CTX is considered a powerful ß-lactam, whereas CLA is considered a weak ß-lactam but an efficient ß-lactamase inhibitor. It was demonstrated that Acanthamoeba expresses ß-lactamases to prevent inhibition of the encystation process by ß-lactams. To reveal the functions of Acanthamoeba ß-lactamases, a recombinant Acanthamoeba ß-lactamase was produced in Escherichia coli that conferred resistance to ß-lactams such as CTX, cefuroxime, penicillin and meropenem. Consequently, we suggest that Acanthamoeba produces enzymes similar to ß-lactamases to avoid interference from the environment. Here we provide a new point of view on an important gene responsible for drug resistance and advocate for the development of more efficient treatment against Acanthamoeba infection.

Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.

Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.

Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes.

BACKGROUND: Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan. RESULTS: In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers. CONCLUSIONS: The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria.

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm.

As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.

Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae).

Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.

Common Stress Transcriptome Analysis Reveals Functional and Genomic Architecture Differences Between Early and Delayed Response Genes.

To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.

Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan.

Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.

BACKGROUND: Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. RESULTS: Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. CONCLUSION: Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Amyloid core formed of full-length recombinant mouse prion protein involves sequence 127-143 but not sequence 107-126.

The principal event underlying the development of prion disease is the conversion of soluble cellular prion protein (PrP(C)) into its disease-causing isoform, PrP(Sc). This conversion is associated with a marked change in secondary structure from predominantly α-helical to a high ß-sheet content, ultimately leading to the formation of aggregates consisting of ordered fibrillar assemblies referred to as amyloid. In vitro, recombinant prion proteins and short prion peptides from various species have been shown to form amyloid under various conditions and it has been proposed that, theoretically, any protein and peptide could form amyloid under appropriate conditions. To identify the peptide segment involved in the amyloid core formed from recombinant full-length mouse prion protein mPrP(23-230), we carried out seed-induced amyloid formation from recombinant prion protein in the presence of seeds generated from the short prion peptides mPrP(107-143), mPrP(107-126), and mPrP(127-143). Our results showed that the amyloid fibrils formed from mPrP(107-143) and mPrP(127-143), but not those formed from mPrP(107-126), were able to seed the amyloidogenesis of mPrP(23-230), showing that the segment residing in sequence 127-143 was used to form the amyloid core in the fibrillization of mPrP(23-230).

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).

Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.

Footprints of natural and artificial selection for photoperiod pathway genes in Oryza.

Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.