Origin of eukaryotes: What can be learned from the first successfully isolated Asgard archaeon

The origin of cellular complexity characterizing eukaryotic cells remains a central unresolved issue in the study of diversification of cellular life on Earth. The isolation by Imachi et al.1 of a member of the Asgard archaea2 – a contemporary relative of organisms thought to have given rise to eukaryotic cells about 2 billion years ago – now promises new insight. The complete genome sequence of the isolated Lokiarchaeum strain confirms that the eukaryotic signature proteins (ESPs) previously identified in the Lokiarchaeota3 and other Asgard archaea2 are indeed encoded by these archaeal genomes and do not represent contamination from eukaryotes. These ESPs encode homologs of eukaryotic actins, small GTPases and the ESCRT complex proteins and are required for the functioning of complex eukaryotic cells. The new, slowly growing, anaerobic laboratory strain allows a first direct look at these organisms and provides key insights into the morphology and metabolism of an Asgard archaeal organism. The work has provided valuable information for other laboratories that aim to isolate and characterize related organisms from other environments

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

The Phylogenetic Diversity of Metagenomes

Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context

The Unusual Luminosity Function of the Globular Cluster M10

We present the I-band luminosity function of the differentially reddened globular cluster M10. We combine photometric analysis derived from wide-field (23' x 23') images that include the outer regions of the cluster and high-resolution images of the cluster core. After making corrections for incompleteness and field star contamination, we find that the relative numbers of stars on the lower giant branch and near the main-sequence turnoff are in good agreement with theoretical predictions. However, we detect significant (> 6 \sigma) excesses of red giant branch stars above and below the red giant branch bump using a new statistic (a population ratio) for testing relative evolutionary timescales of main-sequence and red giant stars. The statistic is insensitive to assumed cluster chemical composition, age, and main-sequence mass function. The excess number of red giants cannot be explained by reasonable systematic errors in our assumed cluster chemical composition, age, or main-sequence mass function. Moreover, M10 shows excesses when compared to the cluster M12, which has nearly identical metallicity, age, and color-magnitude diagram morphology. We discuss possible reasons for this anomaly, finding that the most likely cause is a mass function slope that shows significant variations as a function of mass.Comment: 31 pages, 12 figures, accepted for Ap

Firm finances, weather derivatives and geography

This paper considers some intellectual, practical and political dimensions of collaboration between human and physical geographers exploring how firms are using relatively new financial products – weather derivatives – to displace any costs of weather-related uncertainty and risk. The paper defines weather derivatives and indicates how they differ from weather insurance products before considering the geo-political, cultural and economic context for their creation. The paper concludes by reflecting on the challenges of research collaboration across the human–physical geography divide and suggests that while such initiatives may be undermined by a range of institutional and intellectual factors, conversations between physical and human geographers remain and are likely to become increasingly pertinent. The creation of a market in weather derivatives raises a host of urgent political and regulatory questions and the confluence of natural and social knowledges, co-existing within and through the geography academy, provides a constructive and creative basis from which to engage with this new market and wider discourses of uneven economic development and climate change

Assessment of transparent and reproducible research practices in the psychiatry literature

Objective: Reproducibility is a cornerstone of scientific advancement; however, many published works may lack the core components needed for study reproducibility. In this study, we evaluate the state of transparency and reproducibility in the field of Psychiatry using specific indicators as proxies for these practices.Methods: An increasing number of publications have investigated indicators of reproducibility, including research by Harwicke et al., from which we based the methodology for our observational, cross-sectional study. From a random five-year sample of 300 publications in PubMed-indexed psychiatry journals, two researchers extracted data in a duplicate, blinded fashion using a piloted Google Form. The publications were examined for indicators of reproducibility and transparency, which included availability of: materials, data, protocol, analysis script, open-access, conflict of interest, funding, and online pre-registration.Results: This study ultimately evaluated 296 randomly-selected publications with a 3.20 median impact factor. Only 107 were available online. Most primary authors originated from the United States, United Kingdom, and Netherlands. The top three publication types were cohort studies, surveys, and clinical trials. Regarding indicators of reproducibility, 17 publications gave access to necessary materials, four provided in-depth protocol, and one contained raw data required to reproduce the outcomes. One publication offered its analysis script upon request; four provided a protocol availability statement. Only 107 publications were publicly available: 13 were registered in online repositories and four, ten, and eight publications included their hypothesis, methods, and analysis, respectively. Conflict of interest was addressed by 177 and reported by 31 publications. Of 185 publications with a funding statement, 153 were funded and 32 were unfunded.Conclusions: Currently, Psychiatry research has significant potential to improve adherence to reproducibility and transparency practices. Thus, this study presents a reference point for the state of reproducibility and transparency in Psychiatry literature. Future assessments are recommended to evaluate and encourage progress