The Physiological and Ecological Characterisation of the First Cultivated Species of the Candidate Division OP10

Bacteria are one of the three taxonomic domains and play a major role in the biological processes on Earth, yet their taxonomy and constituent species are poorly understood. OP10 is a candidate division within the domain Bacteria that up until recently has no cultivated representative. Until the recent isolation of the cultivated OP10 strains T49 and P488 from the Taupo Volcanic Zone in New Zealand (Stott et al. 2008), little was known about this putative phylum despite the fact that its presence was detected in various environmental surveys. This study aims to (i) characterise the physiology of one of the first isolated OP10 species, strain T49; and (ii) investigate and expand upon known OP10 diversity by using targeted oligonucleotide primers. Optimal growth temperature and pH of T49 was determined by cultivation in liquid medium. T49 substrate utilisation was investigated by culturing T49 with various substrates, with a focus on its sugar utilisation profiles. T49 was also characterised for its cell morphology through transmission and scanning electron microscopy as well as phase contrast microscopy. The total fatty acid profile of T49 was characterised through gas chromatography and mass spectroscopy. OP10 diversity was investigated at several geothermal sites using OP10-specific primers designed in the course of this study. The primers target conserved regions of the 16S rRNA gene sequence specific to clades within OP10. The primers were designed in silico by obtaining publically available OP10 16S rRNA gene sequences (through the Greengenes and SILVA databases) as references and dividing the candidate division into distinct clades through phylogenetic analysis with ARB. Primers were selected for specificity and coverage of the reference sequences within each of the clades. The performance of the primers were investigated by applying the primers against environmental DNA samples where OP10 sequences were previously identified, as well as various negative controls. The results were validated by sequencing PCR products generated to identify positive OP10 hits and false positive non-OP10 hits. This study found that T49 had a rod-shape morphology with the dimensions of 0.5-0.7 m by 2.5-3.0 m, more than half (67.4%) of the total fatty acids of the bacteria consisted of stearic acid (18:0 ) and palmitic acid (16:0), and GC content of 54.6%. Furthermore, T49 was found to have a growth temperature range of less than 50 degrees C to 73 degrees C and optimum at 68 degrees C, growth pH range of 4.9 to 5.8 and optimum at pH 5.3. Substrate utilisation experiments showed that strain T49 grew optimally using mono- and di- saccharides such as arabinose, mannose, ribose, galactose, and maltose, as well as amorphous polysaccharides including starch, glycogen, and dextrin. The OP10-specific primers successfully identified the presence of OP10 in environmental samples from Waikite, Waipahihi, and Mount Ngauruhoe , confirming previous unpublished 16S rRNA gene sequence surveys. Furthermore, the OP10-specific primers also identified previously undetected genetic diversity in Tikitere and Mount Ngauruhoe, demonstrating the advantage of the primers over traditional universal primers with their high specificity for OP10 DNA sequences which enabled more sensitive surveys of OP10 in the environment. The characterisation of the first OP10 species and the development of OP10-specific primers enable further investigation into this major taxonomic group within the Bacteria domain. T49 and its related strains may play important role within their environments, which can now be investigated based on these known physiologies. The effectiveness of the OP10-specific primers experimented may be use to detect presence of OP10 species in the environment at a higher sensitivity and selectiveness than traditional primers. The results from this research have expanded our knowledge on this previously unknown phylum. By increasing our knowledge of the OP10 candidate division, we also increase our understanding of the global bacterial diversity and this may help bring about insights into biology and global climate processes as well generating practical solutions in these fields. Many of these initial observations of T49 merit further investigation. These include: The production of pigments and lipids, two distinct cytosolic structures, and interesting growth behaviours such as quorum sensing and biofilm formation. OP10-specific primers developed in this study can be improved upon through further validations with environmental DNA representing clades that were not tested during this study due to unavailability. The improved primers can be developed as a rapid diagnostic tool to detect OP10 in the environment for isolation efforts. The primers may also act as fluorescent probes to identify OP10 in microbial consortia such as biofilms while preserving the structure of the microenvironments

The First Insights into the Phylogeny, Genomics, and Ecology of the Novel Bacterial Phylum Armatimonadetes

Currently, a large proportion of novel microbial evolutionary lineages is poorly understood due to limited coverage of representative species. These “candidate” lineages represent significant gaps in our understanding of microbial function and ecology. This study focused on Chthonomonas calidirosea, the earliest isolated species within Armatimonadetes, the most recently-recognised bacterial phylum. The overall aim of this research was to start to understand the ecology and phylogeny of Armatimonadetes, and provide a foundation for future research into the phylum, with the benefit of narrowing the current knowledge gaps on microbial diversity. This was achieved by integrating multiple data types (phylogenetics, genomics, and community profiling metagenomics). The initial stage of this research aimed to address and clarify conflicts in reported phylogeny of the phylum Armatimonadetes. This study generated a comprehensive reference phylogenetic tree of 16S rRNA genes for the phylum, so that the phylogenetic position of newly-identified phylotypes can be reliably associated across studies. Multiple robust statistical methods were used to arrive at a consensus on the partitioning of classes and neighbouring phyla. The process also helped to identify and exclude candidate phyla previously misattributed to Armatimonadetes, thus better defining the phylum for future studies. The deeply-branching phylogenetic relationship of Armatimonadetes with other bacterial phyla was resolved by the sequencing of C. calidirosea T49T genome and analysing concatenated amino acid sequences of conserved genes against homologs in other prokaryotic genomes. The phylogenomic analysis showed Chloroflexi to be the most closely related formal phylum to Armatimonadetes. This publication was the first analysis of a genome from the phylum Armatimonadetes, and provided evolutionarily- and genetically-distinct insights to the overall knowledge of microbial genetic diversity. Analysis of the genome showed a metabolism geared towards non-cellulosic carbohydrates as the carbon and energy source, which coincides with previous culture-based physiological experiments (Lee et al., 2011). Genetic mechanisms behind leucine auxotrophy and narrow pH growth range were also identified. These observations supported the theory that C. calidirosea T49T occupies the niche of a scavenger of diverse species of carbohydrates within geothermal environments, in association with cellulolytic community members. In addition, the genome exhibited an unusual disorganisation of functionally-related genes typically found in conserved operons. The relatively high abundance of sigma factors (relative to genome size) in strain T49T may play an important role in gene regulation and coordination of metabolic pathways to compensate for the scattering of operons. Overall, this research built upon the previous physiological characterisation C. calidirosea T49T (Lee et al., 2011), resulting in a more in-depth and integrated analysis of the bacterium through both phenotypic and genotypic information. Finally, to investigate the genome dynamics of the species (particularly in genome organisation and adaptation to various environments as a scavenger), and to provide ecological and evolutionary context beyond the single genome analysed, the genomes of three additional C. calidirosea isolates cultured from diverse locations across the Taupō Volcanic Zone were extracted, sequenced, and compared to T49T. The genomes exhibited higher within-species conservation than other thermophilic species such as Thermus thermophilus (Henne et al., 2004; Jiang et al., 2013; Oshima & Ariga, 1975) and Sulfolobus islandicus (Reno et al., 2009) isolated from similar geographical distance. No genomic rearrangements were identified between C. calidirosea isolates. The majority of variation was limited to single nucleotide polymorphisms, with a limited number of horizontally-transferred genes and differentially-present fast-evolving genes, such as restriction modification system. The phylogeny and carbohydrate utilisation profiles of the isolates correlated with the geographical relationship between the sample sites rather than with other factors, such as soil geochemistry or microbial communities of the sites. The correlation between geography and phylogeny, low abundance of C. calidirosea at all sample sites (ranging from 0.006 % to 0.3 %), and the high genomic conservation indicated rapid aeolian dispersal and localised extinction as the most probable causes of homogeneity between the populations. The findings contribute to a better understanding of the genome dynamics and ecology of C. calidirosea, as well as the dispersal possibilities of free-living bacteria between distinct and discrete habitats. These studies addressed the overarching aim to investigate the ecology and phylogeny of Armatimonadetes through the research outlined above. This body of work contributed greatly to our understanding of Armatimonadetes phylogeny, both by clarifying its internal taxonomy and its position relative to neighbouring clades. Furthermore, it contributed to understanding of Armatimonadetes ecology by richly describing the ecological niche, genome, and lifestyle of C. calidirosea. Not only does this work greatly increase our understanding of the newest of the 30 prokaryotic phyla (Euzéby, 2011, Retrieved in December 2014), it also provides a rich foundation for future study

Missing link in community psychiatry: When a patient with schizophrenia was expelled from her home

Treatment and disposition of homeless patients with schizophrenia represent a great challenge in clinical practice. We report a case of this special population, and discuss the development of homelessness, the difficulty in disposition, their utilization of health services, and possible applications of mandatory community treatment in this group of patients. A 51-year-old homeless female was brought to an emergency department for left femur fracture caused by an assault. She was diagnosed with schizophrenia about 20 years ago but received little help from mental health services over the decades. During hospitalization, her psychotic symptoms were only partially responsive to treatment. Her family refused to handle caretaking duties. The social welfare system was mobilized for long-term disposition. Homeless patients with schizophrenia are characterized by family disruption, poor adherence to health care, and multiple emergency visits and hospitalization. We hope this article can provide information about the current mental health policy to medical personnel. It is possible that earlier intervention and better outcome can be achieved by utilizing mandatory community treatment in the future, as well as preventing patients with schizophrenia from losing shelters

Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets

Healthcare Engineering Defined: A White Paper

Engineering has been playing an important role in serving and advancing healthcare. The term "Healthcare Engineering" has been used by professional societies, universities, scientific authors, and the healthcare industry for decades. However, the definition of "Healthcare Engineering" remains ambiguous. The purpose of this position paper is to present a definition of Healthcare Engineering as an academic discipline, an area of research, a field of specialty, and a profession. Healthcare Engineering is defined in terms of what it is, who performs it, where it is performed, and how it is performed, including its purpose, scope, topics, synergy, education/training, contributions, and prospects

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

Genetic Drivers of Heterogeneity in Type 2 Diabetes Pathophysiology

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P \u3c 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care