Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterising cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialised compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterised. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and heme, is incomplete. We discuss tools that may aid characterisation of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterisation of individual proteins

Larvae of Deep-Sea Invertebrates Harbor Low-Diversity Bacterial Communities

Microbial symbionts are a common life-history character of marine invertebrates and their developmental stages. Communities of bacteria that associate with the eggs, embryos, and larvae of coastal marine invertebrates tend to be species specific and correlate with aspects of host biology and ecology. The richness of bacteria associated with the developmental stages of coastal marine invertebrates spans four orders of magnitude, from single mutualists to thousands of unique taxa. This understanding stems predominately from the developmental stages of coastal species. If they are broadly representative of marine invertebrates, then we may expect deep-sea species to associate with bacterial communities that are similar in diversity. To test this, we used amplicon sequencing to profile the bacterial communities of invertebrate larvae from multiple taxonomic groups (annelids, molluscs, crustaceans) collected from 2500 to 3670 m in depth in near-bottom waters near hydrothermal vents in 3 different regions of the Pacific Ocean (the East Pacific Rise, the Mariana Back-Arc, and the Pescadero Basin). We find that larvae of deep-sea invertebrates associate with low-diversity bacterial communities (similar to 30 bacterial taxa) that lack specificity between taxonomic groups. The diversity of these communities is estimated to be similar to 7.9 times lower than that of coastal invertebrate larvae, but this result depends on the taxonomic group. Associating with a low-diversity community may imply that deep-sea invertebrate larvae do not have a strong reliance on a microbiome and that the hypothesized lack of symbiotic contributions would differ from expectations for larvae of coastal marine invertebrates

Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology

Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community

CKS VIII: Eccentricities of Kepler Planets and Tentative Evidence of a High Metallicity Preference for Small Eccentric Planets

Characterizing the dependence of the orbital architectures and formation environments on the eccentricity distribution of planets is vital for understanding planet formation. In this work, we perform statistical eccentricity studies of transiting exoplanets using transit durations measured via Kepler combined with precise and accurate stellar radii from the California-Kepler Survey and Gaia. Compared to previous works that characterized the eccentricity distribution from transit durations, our analysis benefits from both high precision stellar radii ($\sim$3%) and a large sample of $\sim$1000 planets. We observe that that systems with only a single observed transiting planet have a higher mean eccentricity ($\bar{e} \sim 0.21$) than systems with multiple transiting planets ($\bar{e} \sim 0.05$), in agreement with previous studies. We confirm the preference for high and low eccentricity subpopulations among the singly transiting systems. Finally, we show suggestive new evidence that high $e$ planets in the Kepler sample are preferentially found around high metallicity ([Fe/H] $>0$) stars. We conclude by discussing the implications on planetary formation theories

Active positioning of vent larvae at a mid-ocean ridge

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 92 (2013): 46-57, doi:10.1016/j.dsr2.2013.03.032.The vertical position of larvae of vent species above a mid-ocean ridge potentially has a strong effect on their dispersal. Larvae may be advected upward in the buoyant vent plume, or move as a consequence of their buoyancy or active swimming. Alternatively, they may be retained near bottom by the topography of the axial trough, or by downward swimming. At vents near 9°50’N on the axis of the East Pacific Rise, evidence for active larval positioning was detected in a comparison between field observations of larvae in the plankton in 2006 and 2007 and distributions of non-swimming larvae in a two-dimensional bio-physical model. In the field, few vent larvae were collected at the level of the neutrally buoyant plume (~75 m above bottom); their relative abundances at that height were much lower than those of simulated larvae from a near-bottom release in the model. This discrepancy was observed for many vent species, particularly gastropods, suggesting that they may actively remain near bottom by sinking or swimming downward. Near the seafloor, larval abundance decreased from the ridge axis to 1000 m off axis much more strongly in the observations than in the simulations, again pointing to behavior as a potential regulator of larval transport. We suspect that transport off axis was reduced by downward-moving behavior, which positioned larvae into locations where they were isolated from cross-ridge currents by seafloor topography, such as the walls of the axial valley – which are not resolved in the model. Cross-ridge gradients in larval abundance varied between gastropods and polychaetes, indicating that behavior may vary between taxonomic groups, and possibly between species. These results suggest that behaviorally mediated retention of vent larvae may be common, even for species that have a long planktonic larval duration and are capable of long-distance dispersal.We gratefully acknowledge the support of NSF grants OCE-0424953 and OCE-0525361, which funded the Larval Dispersal on the Deep East Pacific Rise (LADDER) project. WHOI provided additional support to LSM as an Ocean Life Fellow, to DJM as the Holger Jannasch Chair for Excellence in Oceanography, and to JRL as the Edward W. and Betty J. Scripps Senior Scientist Chair. JWL was supported by the National Oceanic and Atmospheric Administration’s (NOAA) Vents Program and by NOAA’s Pacific Marine Environmental Laboratory

Using high-frequency phosphorus monitoring for water quality management: a case study of the upper River Itchen, UK

Increased concentrations of phosphorus (P) in riverine systems lead to eutrophication and can contribute to other environmental effects. Chalk rivers are known to be particularly sensitive to elevated P levels. We used high-frequency (daily) automatic water sampling at five distinct locations in the upper River Itchen (Hampshire, UK) between May 2016 and June 2017 to identify the main P species (including filterable reactive phosphorus, total filterable phosphorus, total phosphorus and total particulate phosphorus) present and how these varied temporally. Our filterable reactive phosphorus (considered the biologically available fraction) data were compared with the available Environment Agency total reactive phosphorus (TRP) values over the same sampling period. Over the trial, the profiles of the P fractions were complex; the major fraction was total particulate phosphorus with the mean percentage value ranging between 69 and 82% of the total P present. Sources were likely to be attributable to wash off from agricultural activities. At all sites, the FRP and Environment Agency TRP mean concentrations over the study were comparable. However, there were a number of extended time periods (1 to 2 weeks) where the mean FRP concentration (e.g. 0.62 mg L−1) exceeded the existing regulatory values (giving a poor ecological status) for this type of river. Often, these exceedances were missed by the limited regulatory monitoring procedures undertaken by the Environment Agency. There is evidence that these spikes of elevated concentrations of P may have a biological impact on benthic invertebrate (e.g. blue-winged olive mayfly) communities that exist in these ecologically sensitive chalk streams. Further research is required to assess the ecological impact of P and how this might have implications for the development of future environmental regulations

Effectiveness of Community versus Hospital Eye Service follow-up for patients with neovascular age-related macular degeneration with quiescent disease (ECHoES): a virtual non-inferiority trial

Objectives: To compare the ability of ophthalmologists versus optometrists to correctly classify retinal lesions due to neovascular age-related macular degeneration (nAMD). Design: Randomised balanced incomplete block trial. Optometrists in the community and ophthalmologists in the Hospital Eye Service classified lesions from vignettes comprising clinical information, colour fundus photographs and optical coherence tomographic images. Participants' classifications were validated against experts' classifications (reference standard). Setting: Internet-based application. Participants: Ophthalmologists with experience in the age-related macular degeneration service; fully qualified optometrists not participating in nAMD shared care. Interventions: The trial emulated a conventional trial comparing optometrists' and ophthalmologists' decision-making, but vignettes, not patients, were assessed. Therefore, there were no interventions and the trial was virtual. Participants received training before assessing vignettes. Main outcome measures: Primary outcome- correct classification of the activity status of a lesion based on a vignette, compared with a reference standard. Secondary outcomes-potentially sight-threatening errors, judgements about specific lesion components and participants' confidence in their decisions. Results: In total, 155 participants registered for the trial; 96 (48 in each group) completed all assessments and formed the analysis population. Optometrists and ophthalmologists achieved 1702/2016 (84.4%) and 1722/2016 (85.4%) correct classifications, respectively (OR 0.91, 95% CI 0.66 to 1.25; p=0.543). Optometrists' decision-making was non-inferior to ophthalmologists' with respect to the prespecified limit of 10% absolute difference (0.298 on the odds scale). Optometrists and ophthalmologists made similar numbers of sight-threatening errors (57/994 (5.7%) vs 62/994 (6.2%), OR 0.93, 95% CI 0.55 to 1.57; p=0.789). Ophthalmologists assessed lesion components as present less often than optometrists and were more confident about their classifications than optometrists. Conclusions: Optometrists' ability to make nAMD retreatment decisions from vignettes is not inferior to ophthalmologists' ability. Shared care with optometrists monitoring quiescent nAMD lesions has the potential to reduce workload in hospitals

Packed Red Blood Cell Transfusion Associates with Acute Kidney Injury After Transcatheter Aortic Valve Replacement

Background: Acute kidney injury after cardiac surgery significantly associates with morbidity and mortality. Despite not requiring cardiopulmonary bypass, transcatheter aortic valve replacement patients have an incidence of post-procedural acute kidney injury similar to patients who undergo open surgical aortic valve replacement. Packed red blood cell transfusion has been associated with morbidity and mortality after cardiac surgery. We hypothesized that packed red blood cell transfusion independently associates with acute kidney injury after transcatheter aortic valve replacement, after accounting for other risk factors. Methods: This is a single-center retrospective cohort study of 116 patients undergoing transcatheter aortic valve replacement. Post-transcatheter aortic valve replacement acute kidney injury was defined by Kidney Disease: Improving Global Outcomes serum creatinine-based criteria. Univariate comparisons between patients with and without post-transcatheter aortic valve replacement acute kidney injury were made for clinical characteristics. Multivariable logistic regression was used to assess independent association of packed red blood cell transfusion with post-transcatheter aortic valve replacement acute kidney injury (adjusting for pre-procedural renal function and other important clinical parameters). Results: Acute kidney injury occurred in 20 (17.2%) subjects. Total number of packed red blood cells transfused independently associated with post-procedure acute kidney injury (OR = 1.67 per unit, 95% CI 1.13–2.47, P = 0.01) after adjusting for pre-procedure estimated glomerular filtration rate (OR = 0.97 per ml/min/1.73m2, 95% CI 0.94–1.00, P = 0.05), nadir hemoglobin (OR = 0.88 per g/dL increase, CI 0.61–1.27, P = 0.50), and post-procedure maximum number of concurrent inotropes and vasopressors (OR = 2.09 per inotrope or vasopressor, 95% CI 1.19–3.67, P = 0.01). Conclusion: Packed red blood cell transfusion, along with post-procedure use of inotropes and vasopressors, independently associate with acute kidney injury after transcatheter aortic valve replacement. Further studies are needed to elucidate the pathobiology underlying these associations