Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.

The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species' diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.

Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression.

A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease.

BACKGROUND: Sequencing of the genome of Propionibacterium acnes produced a catalogue of genes many of which enable this organism to colonise skin and survive exposure to the elements. Despite this platform, there was little understanding of the gene regulation that gives rise to an organism that has a major impact on human health and wellbeing and causes infections beyond the skin. To address this situation, we have undertaken a genome-wide study of gene regulation using a combination of improved differential and global RNA-sequencing and an analytical approach that takes into account the inherent noise within the data. RESULTS: We have produced nucleotide-resolution transcriptome maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for 'pervasive' transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events, which includes unusual tRNA processing. The identification of such features will inform models of complex gene regulation, as illustrated here for ribonucleotide reductases and a potential quorum-sensing, two-component system. CONCLUSIONS: The approach described here, which is transferable to any bacterial species, has produced a step increase in whole-cell knowledge of gene regulation in P. acnes. Continued expansion of our maps to include transcription associated with different growth conditions and genetic backgrounds will provide a new platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease.

Combination of High-Throughput Screening and Assembly to Discover Efficient Metal-Organic Frameworks on Kr/Xe Adsorption Separation.

Recycling Kr and Xe from used nuclear fuel (UNF) is conducive to regenerating economy and protecting the environment, and it is urgent to screen or design high-performance cutting-edge metal-organic framework (MOF) materials for Kr/Xe adsorption separation. After grand canonical Monte Carlo (GCMC) simulations of Kr/Xe adsorption separation on 11,000 frameworks in CoRE MOFs (2019), the important structure-adsorption property relationship (SAPR) was induced; that is, the porosity (φ) at 0.30-0.40, LCD/PLD at 1.00-1.49, density (ρ) range between 1.20 and 2.30 g/cm3, and PLD at 2.40-3.38 Å can be utilized to screen for high-performance G-MOFs and hMOFs. In addition, the key "genes" (metal nodes and linkers) of MOFs determining the Kr/Xe adsorption separation were data-mined by a machine learning technique, which were assembled into novel MOFs. After comprehensive consideration of thermal stability and the adsorbent performance score (APS), eight promising MOFs on Kr/Xe separation with the APS more than 1290.89 were screened out and assembled, which are better than most of the reported frameworks. Note that the adsorption isotherms of these MOFs on Kr and Xe belong to type I curve with the thermodynamic equilibrium mechanism on Kr/Xe based on the confinement effect. Furthermore, according to the electronic structure calculations of the independent gradient model based on Hirshfeld partition (IGMH) and energy decomposition analysis, it is found that the interactions between guests and frameworks are vdW forces with dominant induction energy (Eind). In addition, the electrostatic potential gradients of frameworks are generally linearly negative correlated with Kr uptakes. Therefore, both the geometrical and electronic structures dominate the adsorption separation performance on Kr/Xe. Interestingly, these eight MOFs are also suitable for the separation of CH4/H2 with considerable selectivities and CH4 uptakes of up to 2566.67 and 3.04 mmol/g, respectively. Herein, the accurately constructed SAPR and material genomics strategy should be helpful for the experimental discovery of novel MOFs on Kr/Xe separation experimentally.

The mystery of Ph3PS revealed in magic-size Ag-S cluster nucleation.

The synthesis of atomically precise semiconductors Ag-S clusters is a subject of intense research interest, yet the formation mechanism of such nanoclusters remains obscure due to their uncontrolled fast nucleation process in solution. Herein, we have investigated the reaction mechanism responsible for {Ag32S3} nucleation using UV, ESI-MS, NMR and SCXRD analyses. Triphenylphosphorus sulfide (PPh3S) was surprisingly found to slow down the kinetic process of the cluster nucleation. Furthermore, a key precursor [Ag2(Ph3PS)4]2+ was captured, which was attacked by Agn(CCBut)m and traces of water to generate {Ag32S3}. This mechanism provides valuable new insights into the synthesis of inorganic magic-size clusters.

The rectal mucosal but not fecal microbiota detects subclinical ulcerative colitis.

Ulcerative colitis (UC), a subtype of inflammatory bowel disease, is characterized by repetitive remission and relapse. Gut microbiome is critically involved in pathogenesis of UC. The shifts in microbiome profile during disease remission remain under-investigated. Recent studies revealed that UC pathogenesis is likely to originate in the mucosal barrier. Therefore, we investigated the effectiveness of mucosal tissue microbiomes to differentiate patients with subclinical UC from healthy individuals. The microbiomes of cecal and rectal biopsies and feces were characterized from 13 healthy individuals and 45 patients with subclinical UC. Total genomic DNA was extracted from the samples, and their microbial communities determined using next-generation sequencing. We found that changes in relative abundance of subclinical UC were marked by a decrease in Proteobacteria and an increase in Bacteroidetes phyla in microbiome derived from rectal tissues but not cecal tissue nor feces. Only in the microbiome of rectal tissue had significantly higher community richness and evenness in subclinical UC patients than controls. Twenty-seven operational taxonomic units were enriched in subclinical UC cohort with majority of the taxa from the Firmicutes phylum. Inference of putative microbial functional pathways from rectal biopsy microbiome suggested a differential increase in interleukin-17 signaling and T-helper cell differentiation pathways. Rectal biopsy tissue was suggested to be more suitable than fecal samples for microbiome assays to distinguish patients with subclinical UC from healthy adults. Assessment of the rectal biopsy microbiome may offer clinical insight into UC disease progression and predict relapse of the diseases.

Structure and Diversity of Soil Bacterial Communities in Offshore Islands.

The effects of biogeographical separation and parent material differences in soil bacterial structure and diversity in offshore islands remain poorly understood. In the current study, we used next-generation sequencing to characterize the differences in soil bacterial communities in five offshore subtropical granite islands (Matsu Islets, MI) of mainland China and two offshore tropical andesite islands (Orchid [OI] and Green Islands [GI]) of Taiwan. The soils of OI and GI were more acidic and had higher organic carbon and total nitrogen content than MI soils. The bacterial communities were dominated by Acidobacteria and Proteobacteria but had different relative abundance because soils were derived from different parent material and because of geographic distance. Non-metric multi-dimensional scaling revealed that the communities formed different clusters among different parent material and geographically distributed soils. The alpha-diversity in bacterial communities was higher in tropical than subtropical soils. Mantel test and redundancy analysis indicated that bacterial diversity and compositions of OI and GI soils, respectively, were positively correlated with soil pH, organic carbon, total nitrogen, microbial biomass carbon and nitrogen. These results suggest that variations in soil properties of offshore islands could result from differences in soil parent material. Distinct soils derived from different parent material and geographic distance could in turn alter the bacterial communities.

Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome.

BACKGROUND & AIMS: Gut dysbiosis plays a role in hepatic encephalopathy (HE), while its relationship at the acute episode of overt HE (AHE), the disease progression and clinical outcomes remains unclear. We aimed to identify AHE-specific microbiome and its association to patients' outcomes. METHODS: We profiled fecal microbiome changes for a cohort of 62 patients with cirrhosis and AHE i) before treatment, ii) 2-3 days after medication and iii) 2-3 months after recovery, and three control cohorts i) healthy individuals, patients with ii) compensated or iii) decompensated cirrhosis. RESULTS: Comparison of the microbiome shift from compensated, decompensated cirrhosis, AHE to recovery revealed the AHE-specific gut-dysbiosis. The gut microbiome diversity was decreased during AHE, further reduced after medication, and only partially reversed during the recovery. The relative abundance of Bacteroidetes phylum in the microbiome decreased, whereas that of Firmicute, Proteobacteria and Actinobacteria increased in patients during AHE compared with those with compensated cirrhosis. A total of 70 operational taxonomic units (OTUs) were significantly different between AHE and decompensated cirrhosis abundances. Of them, the abundance of Veillonella parvula increased the most during AHE via a metagenomics recovery of the genomes. Moreover, the relative abundances of three (Alistipes, Bacteroides, Phascolarctobacterium) and five OTUs (Clostridium-XI, Bacteroides, Bacteroides, Lactobacillus, Clostridium-sedis) at AHE were respectively associated with HE recurrence and overall survival during the subsequent one-year follow-up. CONCLUSIONS: AHE-specific gut OTUs were identified that may be involved in HE development and able to predict clinical outcomes, providing new strategies for the prevention and treatment of HE recurrence in patients with cirrhosis.

An Improved Binary Vector and Escherichia coli Strain for Agrobacterium tumefaciens-Mediated Plant Transformation.

The plasmid vector pGreenII is widely used to produce plant transformants via a process that involves propagation in Escherichia coli However, we show here that pGreenII-based constructs can be unstable in E. coli as a consequence of them hampering cell division and promoting cell death. In addition, we describe a new version of pGreenII that does not cause these effects, thereby removing the selective pressure for mutation, and a new strain of E. coli that better tolerates existing pGreenII-based constructs without reducing plasmid yield. The adoption of the new derivative of pGreenII and the E. coli strain, which we have named pViridis and MW906, respectively, should help to ensure the integrity of genes destined for study in plants while they are propagated and manipulated in E. coli The mechanism by which pGreenII perturbs E. coli growth appears to be dysregulation within the ColE1 origin of replication.

[Linear discriminate analysis on annual and seasonal characteristics of major cations' profiles of rainwater at Zhoushan rain-sampling spot].

Rainwater samples were collected at rain-sampling Spot of Zhoushan in 2002-2003. Major cation concentrations (H+, NH4+, K+, Na+, Ca2+, Mg2+) of rainwater sample were determined. The concentration variation range and character were depicted by robust statistic analysis. Linear discriminate analysis (LDA) was used to acquire a further knowledge on the annual and seasonal characteristics of research major cations. Distribution character of samples from sample spot was clearly depicted in the new CA1-CA2 ordinates generated by linear discriminate analysis, and the reasons that caused the outliers in samples were discussed.

[Characteristic analysis on the anions and pH profiles of rainwater of Zhoushan Archipelago].

Rainwater samples were collected at Zhoushan Archipelago in 2002 - 2003, 4 main anion concentrations (F-, Cl-, NO3-, SO4(2-)) and pH value of rainwater sample were determined. The concentration variation range and character were depicted. Principal component analysis (PCA) and factor analysis (FA) were used to acquire a further knowledge on the characteristics of anions and pH value. Distribution character of samples was clearly depicted in the new PC1-PC2 ordinate generated by orthogonal projection and the reasons that caused the outliers in samples were discussed. In order to get the latent variables which most distinguishably effect the sample distribution, data profiles were investigated by factor analysis: two latent variables were responsible for the sample distribution within sufficient analysis accuracy, SO4(2-) -NO3- factor (FA1), called as "anthropogenic factor", and Cl- (FA2), called as "marine factor", which corresponding to PC1 and PC2 in orthogonal projection respectively. Results from factor analysis were more practical than from orthogonal projection, that is, the reasons attributed the outlier sample distribution at Zhoushan Archipelago were ascribed into two latent variables: anthropogenic factor (SO4(2-) -NO3-) and marine factor (Cl-).