Pathways for the Photoreduction of Fumarate on ZnS

Semiconductor mineral particles can act as photocatalysts for organic redox reactions that occur enzymatically in modern biological metabolic pathways. Semiconductor mineral-mediated photocatalysis may have contributed to the prebiotic synthesis of organic acids on the early Earth, but assessing the plausibility of this hypothesis is impeded by the lack of knowledge about the mechanisms for light-driven organic redox reactions on mineral surfaces. We selected one step in the reverse tricarboxylic acid (rTCA) cycle, the reduction of fumarate to succinate, that has been shown to be photocatalyzed by zinc sulfide (ZnS). Using static and time-resolved optical emission and absorption spectroscopy, we studied the adsorption of fumarate and the rates and pathways for charge transfer. We find that ZnS transfers photoexcited electrons to bound and dissolved fumarate on a wide range of time scales but not to succinate, supporting the concept that ZnS mediated photoreduction of fumarate could have operated in oceans of the early Earth. Optical transient absorption (TA) spectroscopy identified a signature tentatively attributed to the fumarate radical anion that is stable for at least 8 ns, providing evidence that fumarate photoreduction under solar illumination levels occurs by successive photoelectron transfer. The model for electronic excitation, relaxation, and interfacial charge-transfer processes in ZnS provided here will inform all future studies of the photochemical reactions of this mineral

Global genomic analysis of microbial biotransformation of arsenic highlights the importance of arsenic methylation in environmental and human microbiomes

Arsenic is a ubiquitous toxic element, the global cycle of which is highly affected by microbial redox reactions and assimilation into organoarsenic compounds through sequential methylation reactions. While microbial biotransformation of arsenic has been studied for decades, the past years have seen the discovery of multiple new genes related to arsenic metabolism. Still, most studies focus on a small set of key genes or a small set of cultured microorganisms. Here, we leveraged the recently greatly expanded availability of microbial genomes of diverse organisms from lineages lacking cultivated representatives, including those reconstructed from metagenomes, to investigate genetic repertoires of taxonomic and environmental controls on arsenic metabolic capacities. Based on the collection of arsenic-related genes, we identified thirteen distinct metabolic guilds, four of which combine the aio and ars operons. We found that the best studied phyla have very different combinations of capacities than less well-studied phyla, including phyla lacking isolated representatives. We identified a distinct arsenic gene signature in the microbiomes of humans exposed or likely exposed to drinking water contaminated by arsenic and that arsenic methylation is important in soil and in human microbiomes. Thus, the microbiomes of humans exposed to arsenic have the potential to exacerbate arsenic toxicity. Finally, we show that machine learning can predict bacterial arsenic metabolism capacities based on their taxonomy and the environment from which they were sampled

Mooring systems for marine energy converters

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this record.This paper discusses several new technologies for mooring floating marine energy converter (MEC) devices, such as wave energy generators, tidal current turbines and floating wind turbines. The principal mooring component is a special nylon fiber rope which provides cyclic tension fatigue endurance much superior to that of conventional nylon ropes. The nylon fiber is treated with a new proprietary coating which has excellent wet yarn abrasion properties. The parallel-subrope type rope construction further reduces internal abrasion. Extensive laboratory testing was carried out on this new nylon rope design. Cyclic tension fatigue tests were conducted at mean loads and load amplitudes typical of actual service conditions and at higher mean loads and amplitudes. These tests demonstrate that the special nylon rope has essentially the same, desirable stretch characteristics as conventional nylon rope and has much better endurance performance. The mooring connection to the floating MEC device consists of a high-modulus fiber rope pendant which passes through a low-friction bell-mouth nylon fairlead on the MEC device. This eliminates the use of heavy, unreliable chain in this critical connection. A unique bag anchor system would be used on sand, clay, rock and other sea beds in which conventional drag embedment anchors and driven piles are impractical. The bag anchor consists of a large abrasion resistant carcass with lifting straps and top closure. The bag is transported to site in a collapsed form and is filled with local sand or aggregate to provide ballast weight. Several or many such bags are enclosed within a fiber rope net for deployment and are grouped together for connection to the mooring line. The paper will be of particular interest to designers of moorings for MEC systems in shallow water and severe wave environments. It will also be of interest for other mooring applications.This work would not have been possible without the funding and support of the Scottish Government, the Carbon Trust and Innovate UK.   The project was funded under the Marine Renewables Commercialization Fund (MRCF) and Marine Energy Supporting Array Technologies (MESAT).   Other partners who contributed to this project include Lloyd’s Register, DNV‐GL, TenCate, Orion Energy Centre, Nylacast, and offshore wind developer IDEOL.    Input and encouragement was provided by tidal power developer partner Bluewater, and wave energy developers AWS Ocean Energy and Pelamis.

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.

CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Moreover, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Bacteriophages (phages) are obligate parasites that use host bacterial translation machinery to produce viral proteins. However, some phages have alternative genetic codes with reassigned stop codons that are predicted to be incompatible with bacterial translation systems. We analysed 9,422 phage genomes and found that stop-codon recoding has evolved in diverse clades of phages that infect bacteria present in both human and animal gut microbiota. Recoded stop codons are particularly over-represented in phage structural and lysis genes. We propose that recoded stop codons might function to prevent premature production of late-stage proteins. Stop-codon recoding has evolved several times in closely related lineages, which suggests that adaptive recoding can occur over very short evolutionary timescales

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

Background: The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonates via conventional broad-spectrum antibiotic treatment. We hypothesize the built environment (BE), specifically room surfaces frequently touched by humans, is a predominant source of colonizing microbes in the gut of premature VLBW infants. Here, we present the first matched fecal-BE time series analysis of two preterm VLBW neonates housed in a neonatal intensive care unit (NICU) over the first month of life.Results: Fresh fecal samples were collected every 3 days and metagenomes sequenced on an Illumina HiSeq2000 device. For each fecal sample, approximately 33 swabs were collected from each NICU room from 6 specified areas: sink, feeding and intubation tubing, hands of healthcare providers and parents, general surfaces, and nurse station electronics (keyboard, mouse, and cell phone). Swabs were processed using a recently developed 'expectation maximization iterative reconstruction of genes from the environment' (EMIRGE) amplicon pipeline in which full-length 16S rRNA amplicons were sheared and sequenced using an Illumina platform, and short reads reassembled into full-length genes. Over 24,000 full-length 16S rRNA sequences were produced, generating an average of approximately 12,000 operational taxonomic units (OTUs) (clustered at 97% nucleotide identity) per room-infant pair. Dominant gut taxa, including Staphylococcus epidermidis, Klebsiella pneumoniae, Bacteroides fragilis, and Escherichia coli, were widely distributed throughout the room environment with many gut colonizers detected in more than half of samples. Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment.Conclusions: We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut

Colonial choanoflagellate isolated from Mono Lake harbors a microbiome

Choanoflagellates offer key insights into bacterial influences on the origin and early evolution of animals. Here we report the isolation and characterization of a new colonial choanoflagellate species, Barroeca monosierra, that, unlike previously characterized species, harbors a stable microbiome. B. monosierra was isolated from Mono Lake, California and forms large spherical colonies that are more than an order of magnitude larger than those formed by the closely related Salpingoeca rosetta. By designing fluorescence in situ hybridization probes from metagenomic sequences, we found that B. monosierra colonies are colonized by members of the halotolerant and closely related Saccharospirillaceae and Oceanospirillaceae, as well as purple sulfur bacteria (Ectothiorhodospiraceae) and non-sulfur Rhodobacteraceae. This relatively simple microbiome in a close relative of animals presents a new experimental model for investigating the evolution of stable interactions among eukaryotes and bacteria

Closely related Lak megaphages replicate in the microbiomes of diverse animals

Lak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-western diet, baboons and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic PCR and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation

Dual Infection and Superinfection Inhibition of Epithelial Skin Cells by Two Alphaherpesviruses Co-Occur in the Natural Host

Hosts can be infected with multiple herpesviruses, known as superinfection; however, superinfection of cells is rare due to the phenomenon known as superinfection inhibition. It is believed that dual infection of cells occurs in nature, based on studies examining genetic exchange between homologous alphaherpesviruses in the host, but to date, this has not been directly shown in a natural model. In this report, gallid herpesvirus 2 (GaHV-2), better known as Marek’s disease virus (MDV), was used in its natural host, the chicken, to determine whether two homologous alphaherpesviruses can infect the same cells in vivo. MDV shares close similarities with the human alphaherpesvirus, varicella zoster virus (VZV), with respect to replication in the skin and exit from the host. Recombinant MDVs were generated that express either the enhanced GFP (eGFP) or monomeric RFP (mRFP) fused to the UL47 (VP13/14) herpesvirus tegument protein. These viruses exhibited no alteration in pathogenic potential and expressed abundant UL47-eGFP or -mRFP in feather follicle epithelial cells in vivo. Using laser scanning confocal microscopy, it was evident that these two similar, but distinguishable, viruses were able to replicate within the same cells of their natural host. Evidence of superinfection inhibition was also observed. These results have important implications for two reasons. First, these results show that during natural infection, both dual infection of cells and superinfection inhibition can co-occur at the cellular level. Secondly, vaccination against MDV with homologous alphaherpesvirus like attenuated GaHV-2, or non-oncogenic GaHV-3 or meleagrid herpesvirus (MeHV-1) has driven the virus to greater virulence and these results implicate the potential for genetic exchange between homologous avian alphaherpesviruses that could drive increased virulence. Because the live attenuated varicella vaccine is currently being administered to children, who in turn could be superinfected by wild-type VZV, this could potentiate recombination events of VZV as well

Special phase transformation and crystal growth pathways observed in nanoparticles†

Phase transformation and crystal growth in nanoparticles may happen via mechanisms distinct from those in bulk materials. We combine experimental studies of as-synthesized and hydrothermally coarsened titania (TiO(2)) and zinc sulfide (ZnS) with thermodynamic analysis, kinetic modeling and molecular dynamics (MD) simulations. The samples were characterized by transmission electron microscopy, X-ray diffraction, synchrotron X-ray absorption and scattering, and UV-vis spectroscopy. At low temperatures, phase transformation in titania nanoparticles occurs predominantly via interface nucleation at particle–particle contacts. Coarsening and crystal growth of titania nanoparticles can be described using the Smoluchowski equation. Oriented attachment-based crystal growth was common in both hydrothermal solutions and under dry conditions. MD simulations predict large structural perturbations within very fine particles, and are consistent with experimental results showing that ligand binding and change in aggregation state can cause phase transformation without particle coarsening. Such phenomena affect surface reactivity, thus may have important roles in geochemical cycling