Evaluation and Comparison of 300-yd and 500-yd Shallow Water Run Tests as Predictors of Aerobic Power

The purposes of the study were to assess and compare the validity of both 300-yd and 500-yd shallow water run (SWR) tests to predict peak aerobic power (VO2peak). Subjects included 18 women and 18 men who performed a graded exercise treadmill test to predict VO2peak and then performed a 300-yd and 500-yd SWR for time. In addition to SWR times, other independent variables included age, gender, body weight, height, leg length, percent body fat, and 300-yd and 500-yd SWR heart rate and rating of perceived exertion. Correlation coefficients with measured VO2peak were r = -.84 and -.87 for the 300-yd and 500-yd SWR times, respectively. Multiple regression analyses revealed that prediction of VO2peak from 300-yd SWR time improved by including gender and body weight (R = .919; SEE = 0.360 L.min-1). Similarly, prediction of VO2peak improved from 500-yd SWR time by including gender, body weight, and leg length (R = .940; SEE = 0.316 L.min-1). Equations were also developed for use in pools of varying water depths. In conclusion, the 300-yd and 500-yd SWR tests can provide accurate and valid estimates of aerobic power

Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub

Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products

Bulk and single-molecule analysis of a bacterial DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor

DNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterised Geobacillus stearothermophilus Bad, a bacterial DNA helicase-nuclease with similarity to human DNA2. We show that Bad contains an Fe-S cluster and identify four cysteine residues that are likely to co-ordinate the cluster by analogy to DNA2. The purified enzyme specifically recognises ss-dsDNA junctions and possesses ssDNA-dependent ATPase, ssDNA binding, ssDNA endonuclease, 5' to 3' ssDNA translocase and 5' to 3' helicase activity. Single molecule analysis reveals that Bad is a processive DNA motor capable of moving along DNA for distances of >4 kb at a rate of ∼200 bp per second at room temperature. Interestingly, as reported for the homologous human and yeast DNA2 proteins, the DNA unwinding activity of Bad is cryptic and can be unmasked by inactivating the intrinsic nuclease activity. Strikingly, our experiments show that the enzyme loops DNA while translocating, which is an emerging feature of processive DNA unwinding enzymes. The bacterial Bad enzymes will provide an excellent model system for understanding the biochemical properties of DNA2-like helicase-nucleases and DNA looping motor proteins in general.Wellcome Trust [100401/Z/12/Z to M.D.]; EuropeanResearch Council [681299 to F.M.-H.]; Spanish Min-istry of Economy and Competitiveness [BFU2017-83794-PAEI/FEDER, UE to F.M.-H.]; Comunidad de MadridTec4Bio [S2018/NMT-4443 to F.M.-H.]; NanoBioCancer[Y2018/BIO-4747 to F.M.-H.]. Funding for open accesscharge: Wellcome Trust [100401/Z/12/Z].Peer reviewe

The S. pombe translation initiation factor eIF4G is sumoylated and associates with the SUMO protease Ulp2

SUMO is a small post-translational modifier, that is attached to lysine residues in target proteins. It acts by altering proteinprotein interactions, protein localisation and protein activity. SUMO chains can also act as substrates for ubiquitination, resulting in proteasome-mediated degradation of the target protein. SUMO is removed from target proteins by one of a number of specific proteases. The processes of sumoylation and desumoylation have well documented roles in DNA metabolism and in the maintenance of chromatin structure. To further analyse the role of this modification, we have purified protein complexes containing the S. pombe SUMO protease, Ulp2. These complexes contain proteins required for ribosome biogenesis, RNA stability and protein synthesis. Here we have focussed on two translation initiation factors that we identified as co-purifying with Ulp2, eIF4G and eIF3h. We demonstrate that eIF4G, but not eIF3h, is sumoylated. This modification is increased under conditions that produce cytoplasmic stress granules. Consistent with this we observe partial co-localisation of eIF4G and SUMO in stressed cells. Using HeLa cells, we demonstrate that human eIF4GI is also sumoylated; in vitro studies indicate that human eIF4GI is modified on K1368 and K1588, that are located in the C-terminal eIF4A- and Mnk-binding sites respectively

Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA

Human DNA helicase B (HELB) is a poorly characterized helicase suggested to play both positive and negative regulatory roles in DNA replication and recombination. In this work, we used bulk and single-molecule approaches to characterize the biochemical activities of HELB protein with a particular focus on its interactions with Replication Protein A (RPA) and RPA–single-stranded DNA (ssDNA) filaments. HELB is a monomeric protein that binds tightly to ssDNA with a site size of ∼20 nucleotides. It couples ATP hydrolysis to translocation along ssDNA in the 5′ to 3′ direction accompanied by the formation of DNA loops. HELB also displays classical helicase activity, but this is very weak in the absence of an assisting force. HELB binds specifically to human RPA, which enhances its ATPase and ssDNA translocase activities but inhibits DNA unwinding. Direct observation of HELB on RPA nucleoprotein filaments shows that translocating HELB concomitantly clears RPA from ssDNA. This activity, which can allow other proteins access to ssDNA intermediates despite their shielding by RPA, may underpin the diverse roles of HELB in cellular DNA transactions.[Significance] Single-stranded DNA (ssDNA) is a key intermediate in many cellular DNA transactions, including DNA replication, repair, and recombination. Nascent ssDNA is rapidly bound by the Replication Protein A (RPA) complex, forming a nucleoprotein filament that both stabilizes ssDNA and mediates downstream processing events. Paradoxically, however, the very high affinity of RPA for ssDNA may block the recruitment of further factors. In this work, we show that RPA–ssDNA nucleoprotein filaments are specifically targeted by the human HELB helicase. Recruitment of HELB by RPA–ssDNA activates HELB translocation activity, leading to processive removal of upstream RPA complexes. This RPA clearance activity may underpin the diverse roles of HELB in replication and recombination.Work in the laboratory of M.S.D. was supported by an Elizabeth Blackwell Early Career Fellowship from the University of Bristol (to O.J.W.) and Wellcome Trust Investigator Grant 100401/Z/12/Z (to M.S.D.). Work in the laboratory of E.A. was supported by NIH Grants GM130746 (to E.A.) and GM133967 (to E.A.). F.M.-H. acknowledges support from the European Research Council under European Union Horizon 2020 Research and Innovation Program Grant Agreement 681299. Work in the laboratory of F.M.-H. was also supported by Spanish Ministry of Science and Innovation Grants BFU2017-83794-P (AEI/FEDER, UE; to F.M.-H.) and PID2020-112998GB-100 (AEI/10.13039/501100011033; to F.M.-H.) and Comunidad de Madrid Grants Tec4-Bio–S2018/NMT-4443 (to F.M.-H.) and NanoBioCancer–Y2018/BIO-4747 (to F.M.-H.)

Spatio-temporal variational Gaussian processes

We introduce a scalable approach to Gaussian process inference that combines spatio-temporal filtering with natural gradient variational inference, resulting in a non-conjugate GP method for multivariate data that scales linearly with respect to time. Our natural gradient approach enables application of parallel filtering and smoothing, further reducing the temporal span complexity to be logarithmic in the number of time steps. We derive a sparse approximation that constructs a state-space model over a reduced set of spatial inducing points, and show that for separable Markov kernels the full and sparse cases exactly recover the standard variational GP, whilst exhibiting favourable computational properties. To further improve the spatial scaling we propose a mean-field assumption of independence between spatial locations which, when coupled with sparsity and parallelisation, leads to an efficient and accurate method for large spatio-temporal problems

Hydrodynamic characterization of soil compaction using integrated electrical resistivity and X‐ray computed tomography

Modern agricultural practices can cause significant stress on soil, which ultimately has degrading effects, such as compaction. There is an urgent need for fast, noninvasive methods to characterize and monitor compaction and its impact on hydraulic processes. Electrical resistivity tomography (ERT) is a well-established method used for the assessment of soil hydraulic properties due to its high temporal resolution and sensitivity to changes in moisture content and salinity, whereas X-ray computed tomography (CT) can be used for high-spatial-resolution imaging of soil structure. We used the combined strengths of both methods to study soil under three different levels of compaction. The soils were X-ray scanned and electrically monitored after the application of a saline solution to the soil surface. The scans revealed the pore network architecture and allowed us to compute its size and connectivity. The ERT models revealed inhibited percolation rates for soils with a lower bulk density, but also how resistivity changes are spatiotemporally distributed within the soil columns. Furthermore, we obtained a quantitative link between the two methods, by which voxels more densely populated with pores were associated with higher temporal variations in electrical resistivity. Building on this, we established a spatial collocation between pore structure and distribution of solution during percolation. This demonstrates the potential of the combined strengths of the two tomographic methods to obtain an enhanced characterization of soil hydrodynamic properties

Phylogenetic relationships of African microhylid frogs inferred from DNA sequences of mitochondrial 12S and 16S rRNA genes

The phylogenetic relationships of microhylid frogs are poorly understood. The first molecular phylogeny for continental African microhylids is presented, including representatives of all subfamilies, six of the eight genera, and the enigmatic hemisotid Hemisus. Mitochondrial 12S and 16S rRNA sequence data were analysed using parsimony, likelihood and Bayesian methods. Analyses of the data are consistent with the monophyly of all sampled subfamilies and genera. Hemisus does not nest within either brevicipitines or non-brevicipitines. It is possibly the sister group to brevicipitines, in which case brevicipitines might not be microhylids. Phrynomantis and Hoplophryne potentially group with non-African, non-brevicipitine microhylids, in agreement with recent morphological and molecular data. Within brevicipitines, Breviceps is recovered as the sister group to a clade of Callulina+Spelaeophryne+Probreviceps. The relationships among the genera within this latter clade are unclear, being sensitive to the method of analysis. Optimal trees suggest the Probreviceps macrodactylus subspecies complex might be paraphyletic with respect to P. uluguruensis, corroborating preliminary morphological studies indicating that P. m. rungwensis may be a distinct species. P. m. loveridgei may be paraphyletic with respect to P. m. macrodactylus, though this is not strongly supported. Some biogeographic hypotheses are examined in light of these findings

Early mortality from colorectal cancer in England: a retrospective observational study of the factors associated with death in the first year after diagnosis

Background: The United Kingdom performs poorly in international comparisons of colorectal cancer survival with much of the deficit owing to high numbers of deaths close to the time of diagnosis. This retrospective cohort study investigates the patient, tumour and treatment characteristics of those who die in the first year after diagnosis of their disease. Methods: Patients diagnosed with colon (n=65,733) or rectal (n=26,123) cancer in England between 2006 and 2008 were identified in the National Cancer Data Repository. Multivariable logistic regression was used to investigate the odds of death within 1 month, 1-3 months and 3-12 months after diagnosis. Results: In all, 11.5% of colon and 5.4% of rectal cancer patients died within a month of diagnosis: this proportion decreased significantly over the study period. For both cancer sites, older age, stage at diagnosis, deprivation and emergency presentation were associated with early death. Individuals who died shortly after diagnosis were also more likely to have missing data about important prognostic factors such as disease stage and treatment. Conclusion: Using routinely collected data, at no inconvenience to patients, we have identified some important areas relating to early deaths from colorectal cancer, which merit further research

Ecología y diagnóstico de Enallodiplosis discordis (Diptera:Cecidomyiidae): Un nuevo defoliador feroz con repercusiones directas en la pérdida del bosque seco de Prosopis y los medios de vida en Perú

The coastal desert of Peru and Chile is home to Prosopis (Leguminosae: Mimosoideae) tree species that are exceptionally well-adapted to the hyperarid conditions and keystone in dry-forest ecosystems. From 2001 to 2018, Prosopis in Peru have suffered widespread defoliation and die-back, with consequent deforestation and collapse in pod production. This paper reports a new insect plague species of Prosopis forest in Peru: Enallodiplosis discordis Gagné 1994 (Diptera: Cecidomyiidae) as a fiercely defoliating agent contributing to widespread Prosopis mortality. An analysis of E. discordis larval taxonomy, life cycle and plague infestation, following El Niño Southern Oscillation (ENSO) 1998/99 is provided. Using distinct lines of evidence, its spread, distribution, and ecology are examined. Over two decades of fieldwork, Prosopis forest die-back and loss was observed devastating rural livelihoods and ecosystem services across lowland regions of southern (Ica), central and northern coastal Peru (Lambayeque, La Libertad, Piura). The collapse in production of Prosopis pods (algarroba, huaranga) and honey was recorded. Supplementary notes provide observations of: (i) plague development, changing land-use and climate, (ii) biological and physical control of E. discordis, (iii) the moth Melipotis aff. indomita (Lepidoptera: Noctuidae) as a concurrent defoliator of Prosopis.Las regiones desérticas costeras del Pacífico de Perú y Chile albergan especies de Prosopis (Leguminosae: Mimosoideae), árboles bien adaptados a las condiciones del desierto y con funciones clave en los ecosistemas de bosques secos. Entre el 2001 y 2017, Prosopis en Perú ha sufrido una extensiva defoliación y muerte regresiva, con la consecuente deforestación y disminución de la producción de vainas de algarrobo. Aquí, se reporta una nueva especie de insecto plaga del bosque de Prosopis en Perú: Enallodiplosis discordis Gagné 1994 (Diptera: Cecidomyiidae), una feroz especie defoliadora que contribuye a la mortalidad generalizada de Prosopis. Se proporciona un análisis de la taxonomía larvaria de E. discordis, ciclo de vida y la infestación ocurrida después de El Niño Oscilación del Sur (ENSO) 1998/99. Su dispersión, distribución y ecología es examinada utilizando distintas líneas de evidencia. Durante casi dos décadas de trabajo de campo, se observó la muerte regresiva del bosque de Prosopis devastando los medios de vida rurales y los servicios de los ecosistemas en las regiones de las tierras bajas del sur (Ica), el centro y el norte de la costa peruana (Lambayeque, La Libertad, Piura). El colapso en la producción de vainas de Prosopis (algarroba, huaranga) y miel también fue registrada. Las notas complementarias proporcionan observaciones sobre: (i) el desarrollo de la plaga y el cambio de uso de la tierra y el clima, (ii) el control biológico y físico de E. discordis, (iii) la polilla Melipotis aff. indomita (Lepidoptera: Noctuidae) como defoliador concurrente de Prosopis