964 research outputs found
Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities
Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments
Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing
Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure
Matrix cadmium accumulation depolarizes mitochondria isolated from mouse brain
Cadmium (Cd2+) is an environmental contaminant commonly found in industrial settings with a biological half-life of 30 years. Although the accumulation and subsequent cytotoxicity of Cd2+ in nervous tissue is well documented, it is unclear exactly how Cd2+ kills cells. One potential mechanism involves inhibition of cellular energy production. In this study, we used fluorescence microscopy to monitor the effects of Cd2+ on mitochondrial membrane potential (ΔΨm) in individual mitochondria isolated from mouse brain. Mitochondria were attached to microscopy glass and loaded with rhodamine 123, a fluorescent indicator that collects in energized and respiring mitochondria, i.e., those with a robust ΔΨm. We found that Cd2+ at relatively low concentrations quickly and completely abolished ΔΨm. Cd2+ actions were concentration- dependent, and were relatively potent and efficacious when compared to calcium (Ca2+) and zinc (Zn2+). Moreover, the Ca2+ uniporter blocker ruthenium red protected against Cd2+-induced depolarization, suggesting that matrix entry of Cd2+ through this traditional Ca2+ pathway is necessary for its effect. These results demonstrate that Cd2+ substantially inhibits mitochondrial function and provide important insight regarding the mechanism of Cd2+-mediated neurotoxicity
Designing Chatbots for Crises: A Case Study Contrasting Potential and Reality
Chatbots are becoming ubiquitous technologies, and their popularity and adoption are rapidly spreading. The potential of chatbots in engaging people with digital services is fully recognised. However, the reputation of this technology with regards to usefulness and real impact remains rather questionable. Studies that evaluate how people perceive and utilise chatbots are generally lacking. During the last Kenyan elections, we deployed a chatbot on Facebook Messenger to help people submit reports of violence and misconduct experienced in the polling stations. Even though the chatbot was visited by more than 3,000 times, there was a clear mismatch between the users’ perception of the technology and its design. In this paper, we analyse the user interactions and content generated through this application and discuss the challenges and directions for designing more effective chatbots
Freezing by Monte Carlo Phase-Switch
We describe a Monte Carlo procedure which allows sampling of the disjoint
configuration spaces associated with crystalline and fluid phases, within a
single simulation. The method utilises biased sampling techniques to enhance
the probabilities of gateway states (in each phase) which are such that a
global switch (to the other phase) can be implemented. Equilibrium
freezing-point parameters can be determined directly; statistical uncertainties
prescribed transparently; and finite-size effects quantified systematically.
The method is potentially quite general; we apply it to the freezing of hard
spheres.Comment: 5 pages, 2 figure
Towards Better Integrators for Dissipative Particle Dynamics Simulations
Coarse-grained models that preserve hydrodynamics provide a natural approach
to study collective properties of soft-matter systems. Here, we demonstrate
that commonly used integration schemes in dissipative particle dynamics give
rise to pronounced artifacts in physical quantities such as the compressibility
and the diffusion coefficient. We assess the quality of these integration
schemes, including variants based on a recently suggested self-consistent
approach, and examine their relative performance. Implications of
integrator-induced effects are discussed.Comment: 4 pages, 3 figures, 2 tables, accepted for publication in Phys. Rev.
E (Rapid Communication), tentative publication issue: 01 Dec 200
Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton
Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I β subunit in the P-SSP7 genome, together with phylogenetic analysis of the α and β subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR β subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify
Iroki: automatic customization and visualization of phylogenetic trees
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki
Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences
Local transmission of chikungunya virus (CHIKV) was first
detected in the Americas in December 2013, after which it spread
rapidly throughout the Caribbean islands and American mainland,
causing a major chikungunya fever epidemic. Previous
phylogenetic analysis of CHIKV from a limited number of
countries in the Americas suggests that an Asian genotype strain
was responsible, except in Brazil where both Asian and
East/Central/South African (ECSA) lineage strains were detected.
In this study, we sequenced thirty-three complete CHIKV genomes
from viruses isolated in 2014 from fourteen Caribbean islands,
the Bahamas and two mainland countries in the Americas.
Phylogenetic analyses confirmed that they all belonged to the
Asian genotype and clustered together with other Caribbean and
mainland sequences isolated during the American outbreak,
forming an 'Asian/American' lineage defined by two amino acid
substitutions, E2 V368A and 6K L20M, and divided into two
well-supported clades. This lineage is estimated to be evolving
at a mean rate of 5 x 10-4 substitutions per site per year (95%
higher probability density, 2.9-7.9 x 10-4) and to have arisen
from an ancestor introduced to the Caribbean (most likely from
Oceania) in about March 2013, 9 months prior to the first report
of CHIKV in the Americas. Estimation of evolutionary rates for
individual gene regions and selection analyses indicate that (in
contrast to the Indian Ocean Lineage that emerged from the ECSA
genotype followed by adaptive evolution and with a significantly
higher substitution rate) the evolutionary dynamics of the
Asian/American lineage are very similar to the rest of the Asian
genotype and natural selection does not appear to have played a
major role in its emergence. However, several codon sites with
evidence of positive selection were identified within the
non-structural regions of Asian genotype sequences outside of
the Asian/American lineage
Family A DNA Polymerase Phylogeny Uncovers Diversity and Replication Gene Organization in the Virioplankton
Shotgun metagenomics, which allows for broad sampling of viral diversity, has uncovered genes that are widely distributed among virioplankton populations and show linkages to important biological features of unknown viruses. Over 25% of known dsDNA phage carry the DNA polymerase I (polA) gene, making it one of the most widely distributed phage genes. Because of its pivotal role in DNA replication, this enzyme is linked to phage lifecycle characteristics. Previous research has suggested that a single amino acid substitution might be predictive of viral lifestyle. In this study Chesapeake Bay virioplankton were sampled by shotgun metagenomic sequencing (using long and short read technologies). More polA sequences were predicted from this single viral metagenome (virome) than from 86 globally distributed virome libraries (ca. 2,100, and 1,200, respectively). The PolA peptides predicted from the Chesapeake Bay virome clustered with 69% of PolA peptides from global viromes; thus, remarkably the Chesapeake Bay virome captured the majority of known PolA peptide diversity in viruses. This deeply sequenced virome also expanded the diversity of PolA sequences, increasing the number of PolA clusters by 44%. Contigs containing polA sequences were also used to examine relationships between phylogenetic clades of PolA and other genes within unknown viral populations. Phylogenic analysis revealed five distinct groups of phages distinguished by the amino acids at their 762 (Escherichia coli IAI39 numbering) positions and replication genes. DNA polymerase I sequences from Tyr762 and Phe762 groups were most often neighbored by ring-shaped superfamily IV helicases and ribonucleotide reductases (RNRs). The Leu762 groups had non-ring shaped helicases from superfamily II and were further distinguished by an additional helicase gene from superfamily I and the lack of any identifiable RNR genes. Moreover, we found that the inclusion of ribonucleotide reductase associated with PolA helped to further differentiate phage diversity, chiefly within lytic podovirus populations. Altogether, these data show that DNA Polymerase I is a useful marker for observing the diversity and composition of the virioplankton and may be a driving factor in the divergence of phage replication components
- …