Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV–vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV–vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate

Faster subsequence recognition in compressed strings

Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to Lempel--Ziv compression. For an SLP-compressed text of length $\bar m$, and an uncompressed pattern of length $n$, C{\'e}gielski et al. gave an algorithm for local subsequence recognition running in time $O(\bar mn^2 \log n)$. We improve the running time to $O(\bar mn^{1.5})$. Our algorithm can also be used to compute the longest common subsequence between a compressed text and an uncompressed pattern in time $O(\bar mn^{1.5})$; the same problem with a compressed pattern is known to be NP-hard

Causes of Higher Climate Sensitivity in CMIP6 Models

Equilibrium climate sensitivity, the global surface temperature response to CO urn:x-wiley:grl:media:grl60047:grl60047-math-0001 doubling, has been persistently uncertain. Recent consensus places it likely within 1.5–4.5 K. Global climate models (GCMs), which attempt to represent all relevant physical processes, provide the most direct means of estimating climate sensitivity via CO urn:x-wiley:grl:media:grl60047:grl60047-math-0002 quadrupling experiments. Here we show that the closely related effective climate sensitivity has increased substantially in Coupled Model Intercomparison Project phase 6 (CMIP6), with values spanning 1.8–5.6 K across 27 GCMs and exceeding 4.5 K in 10 of them. This (statistically insignificant) increase is primarily due to stronger positive cloud feedbacks from decreasing extratropical low cloud coverage and albedo. Both of these are tied to the physical representation of clouds which in CMIP6 models lead to weaker responses of extratropical low cloud cover and water content to unforced variations in surface temperature. Establishing the plausibility of these higher sensitivity models is imperative given their implied societal ramifications

Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum

© 2014 Bachmann et al.; licensee BioMed Central Ltd. Background: Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced.Results: Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations.Conclusions: The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen

A baseline evaluation of oceanographic and sea ice conditions in the Hudson Bay Complex during 2016-2018

In this paper, we examine sea surface temperatures (SSTs) and sea ice conditions in the Hudson Bay Complex as a baseline evaluation for the BaySys 2016–2018 field program time frame. Investigated in particular are spatiotemporal patterns in SST and sea ice state and dynamics, with rankings of the latter to highlight extreme conditions relative to the examined 1981–2010 climatology. Results from this study show that SSTs in northwestern Hudson Bay from May to July, 2016–2018, are high relative to the climatology for SST (1982–2010). SSTs are also warmer in 2016 and 2017 than in 2018 relative to their climatology. Similarly, unusually low sea ice cover existed from August to December of 2016 and July to September of 2017, while unusually high sea ice cover existed in January, February, and October of 2018. The ice-free season was approximately 20 days longer in 2016 than in 2018. Unusually high ice-drift speeds occurred in April of 2016 and 2017 and in May of 2018, coinciding with strong winds in 2016 and 2018 and following strong winds in March 2017. Strong meridional circulation was observed in spring of 2016 and winter of 2017, while weak meridional circulation existed in 2018. In a case study of an extreme event, a blizzard from 7 to 9 March 2017, evaluated using Lagrangian dispersion statistics, is shown to have suppressed sea ice deformation off the coast of Churchill. These results are relevant to describing and planning for possible future pathways and scenarios under continued climate change and river regulation

How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories

Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no rigorous guarantees. Determining the amount of data needed to correctly reconstruct population histories is a major challenge. Using a variety of tools from information theory, the theory of extremal polynomials, and approximation theory, we prove new sharp information-theoretic lower bounds on the problem of reconstructing population structure -- the history of multiple subpopulations that merge, split and change sizes over time. Our lower bounds are exponential in the number of subpopulations, even when reconstructing recent histories. We demonstrate the sharpness of our lower bounds by providing algorithms for distinguishing and learning population histories with matching dependence on the number of subpopulations. Along the way and of independent interest, we essentially determine the optimal number of samples needed to learn an exponential mixture distribution information-theoretically, proving the upper bound by analyzing natural (and efficient) algorithms for this problem.Comment: 38 pages, Appeared in RECOMB 201

A baseline evaluation of atmospheric and river discharge conditions in the Hudson Bay Complex during 2016-2018

In this article, we examine atmospheric and river discharge conditions within the Hudson Bay Complex for the BaySys 2016–2018 field program time frame. Investigated in particular is a subset of European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis - Interim (ERA-Interim) atmospheric forcing variables, namely 2-m surface temperature, 10-m surface winds, precipitation, and sea-level pressure, in addition to river discharge. Results from this assessment show that 2016 was characterized by unusually warm conditions (terrestrial and marine) throughout the annual cycle; 2017 by strong cyclone activity in March and high precipitation in January, October, and November; and 2018 by cold and windy conditions throughout the annual cycle. Evaluation of terrestrial conditions showed higher than normal land surface temperatures (the Hudson Bay physical watershed) for all of the 2016–2018 period (excluding a colder than normal spell August–November 2018), particularly in January (2016 and 2017), higher than normal precipitation in October (2016 and 2017), and higher than normal terrestrial discharge to the Hudson Bay Complex in March (2016 and 2017), with drier than average June through October (2016–2018)

Electromyographic Analysis of the Shoulder Girdle Musculature during External Rotation Exercises

Background: Implementation of overhead activity, a key component of many professional sports, requires an effective and balanced activation of shoulder girdle muscles particularly during forceful external rotation motions. Purpose: The study aimed to identify activation strategies of 16 shoulder girdle muscles/muscle segments during common shoulder external rotational exercises. Study Design: Cross-Sectional Study Method: EMG was recorded in 30 healthy subjects from 16 shoulder girdle muscles/muscle segments (surface electrode: anterior, middle and posterior deltoid, upper, middle and lower trapezius, serratus anterior, teres major, upper and lower latissimus dorsi, upper and lower pectoralis major; fine wire electrodes: supraspinatus, infraspinatus, subscapularis and rhomboid major) using a telemetric EMG system. Five external rotation (ER) exercises (standing ER at 0o and 90o of abduction, and with under-arm towel roll, prone ER at 90o of abduction, side-lying ER with under-arm towel) were studied. Exercise EMG amplitudes were normalised to EMGmax (EMG at maximal ER force in a standard position). Univariate analysis of variance (ANOVA) and post-hoc analysis applied on EMG activity of each muscle to assess the main effect of exercise condition. Results: Muscular activity differed significantly among the ER exercises (P<0.05 – P<0.001). The highest activation for anterior and middle deltoid, supraspinatus, upper trapezius, and serratus anterior occurred during standing ER at 90o of abduction; for posterior deltoid, middle trapezius, and rhomboid during side-lying ER at 0° of abduction; for lower trapezius, upper and lower latissimus dorsi, subscapularis, and teres major during prone ER at 90o of abduction, and for clavicular and sternal part of pectoralis major during standing ER with Under-Arm Towel. Conclusion: Key glenohumeral and scapular muscles can be optimally activated during the specific ER exercises particularly in positions that stimulate athletic overhead motions. Clinical Relevance: These results enable sport medicine professionals to target specific muscles during shoulder rehabilitation protocols while minimising the effect of others, providing a foundation for optimal evidence-based exercise prescription. They also provide information for tailored muscle training and injury prevention in overhead sports

Simulated impacts of relative climate change and river discharge regulation on sea ice and oceanographic conditions in the Hudson Bay Complex

In this analysis, we examine relative contributions from climate change and river discharge regulation to changes in marine conditions in the Hudson Bay Complex using a subset of five atmospheric forcing scenarios from the Coupled Model Intercomparison Project Phase 5 (CMIP5), river discharge data from the Hydrological Predictions for the Environment (HYPE) model, both naturalized (without anthropogenic intervention) and regulated (anthropogenically controlled through diversions, dams, reservoirs), and output from the Nucleus for European Modeling of the Ocean Ice-Ocean model for the 1981–2070 time frame. Investigated in particular are spatiotemporal changes in sea surface temperature, sea ice concentration and thickness, and zonal and meridional sea ice drift in response to (i) climate change through comparison of historical (1981–2010) and future (2021–2050 and 2041–2070) simulations, (ii) regulation through comparison of historical (1981–2010) naturalized and regulated simulations, and (iii) climate change and regulation combined through comparison of future (2021–2050 and 2041–2070) naturalized and regulated simulations. Also investigated is use of the diagnostic known as e-folding time spatial distribution to monitor changes in persistence in these variables in response to changing climate and regulation impacts in the Hudson Bay Complex. Results from this analysis highlight bay-wide and regional reductions in sea ice concentration and thickness in southwest and northeast Hudson Bay in response to a changing climate, and east-west asymmetry in sea ice drift response in support of past studies. Regulation is also shown to amplify or suppress the climate change signal. Specifically, regulation amplifies sea surface temperatures from April to August, suppresses sea ice loss by approximately 30% in March, contributes to enhanced sea ice drift speed by approximately 30%, and reduces meridional circulation by approximately 20% in January due to enhanced zonal drift. Results further suggest that the offshore impacts of regulation are amplified in a changing climate