The Influence of Lithology on Stream Metabolism in Mountain Systems

Physical disturbance in streams has important effects on the metabolic rates of gross primary production (GPP) and ecosystem respiration (ER). Underlying lithology can control sediment size, amount, and evolution in the stream, influencing substrate stability and its effect on benthic organisms. We assessed the patterns of disturbance and recovery of metabolic rates after periods of increased flow and suspended sediment flux in different lithologies. We modeled whole-stream metabolism during the winter-spring period between December and April in two streams in the Oregon Coast Range: one with basalt lithology, and one with sandstone lithology. Our results indicated that the two streams varied in their patterns of response and recovery to storms. Both streams were heterotrophic during the entirety of the study period, but changes in heterotrophy were driven by changes in ER. Post-storm GPP decreased in both streams, but the basalt basin had greater proportional decreases. Decreases were also greater later in the study period, when pre-storm rates of GPP were higher. Rates of ER increased in the basalt basin post-storm and did not change from pre- to post-storm in the sandstone basin. Recovery of GPP was more rapid in the sandstone basin than the basalt basin. The P/R ratio recovery period was similar in both streams, but recovery was faster in the sandstone basin. Overall, our results indicated that the underlying lithology of small mountain streams drives variability in heterotrophy through differing effects on ER

SN 2014ab: An Aspherical Type IIn Supernova with Low Polarization

We present photometry, spectra, and spectropolarimetry of supernova (SN) 2014ab, obtained through $\sim 200$ days after peak brightness. SN 2014ab was a luminous Type IIn SN ($M_V < -19.14$ mag) discovered after peak brightness near the nucleus of its host galaxy, VV 306c. Prediscovery upper limits constrain the time of explosion to within 200 days prior to discovery. While SN 2014ab declined by $\sim 1$ mag over the course of our observations, the observed spectrum remained remarkably unchanged. Spectra exhibit an asymmetric emission-line profile with a consistently stronger blueshifted component, suggesting the presence of dust or a lack of symmetry between the far side and near side of the SN. The Pa$\beta$ emission line shows a profile very similar to that of H$\alpha$, implying that this stronger blueshifted component is caused either through obscuration by large dust grains, occultation by optically thick material, or a lack of symmetry between the far side and near side of the interaction region. Despite these asymmetric line profiles, our spectropolarimetric data show that SN 2014ab has little detected polarization after accounting for the interstellar polarization. This suggests that we are seeing emission from a photosphere that has only small deviation from circular symmetry face-on. We are likely seeing a SN IIn with nearly circular symmetry in the plane normal to our line of sight, but with either large-grain dust or significant asymmetry in the density of circumstellar material or SN ejecta along our line of sight. We suggest that SN 2014ab and SN 2010jl (as well as other SNe IIn) may be similar events viewed from different directions.Comment: 20 pages, 19 figure

A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis

Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations just as in wild populations and, in addition to being a source of useful alleles for genetic studies, can impact efforts to identify induced mutations in sequence-based genetic screens. The Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as a model system for studying the genetic control of embryonic development and a variety of other areas of research. Its diploid genome has been extensively sequenced and efforts are underway to isolate mutants by phenotype- and genotype-based approaches. Here, we describe a study of genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism was detected in the coding and non-coding regions of developmental genes distributed widely across the genome. Laboratory strains exhibit unexpectedly high frequencies of genetic polymorphism, with alleles carrying a variety of synonymous and non-synonymous codon substitutions and nucleotide insertions/deletions. Inter-strain comparisons of polymorphism uncover a high proportion of shared alleles between Nigerian and Ivory Coast strains, in spite of their distinct geographical origins. These observations will likely influence the design of future sequence-based mutation screens, particularly those using DNA mismatch-based detection methods which can be disrupted by the presence of naturally occurring sequence variants. The existence of a significant reservoir of alleles also suggests that existing laboratory stocks may be a useful source of novel alleles for mapping and functional studies

Publisher Correction: Methylation deficiency disrupts biological rhythms from bacteria to humans

From Springer Nature via Jisc Publications RouterHistory: registration 2020-05-27, pub-electronic 2020-06-04, online 2020-06-04, collection 2020-12Publication status: PublishedAn amendment to this paper has been published and can be accessed via a link at the top of the paper

Lick Observatory Supernova Search Follow-Up Program: Photometry Data Release of 93 Type Ia Supernovae

We present BVRI and unfiltered light curves of 93 Type Ia supernovae (SNe Ia) from the Lick Observatory Supernova Search (LOSS) follow-up program conducted between 2005 and 2018. Our sample consists of 78 spectroscopically normal SNe Ia, with the remainder divided between distinct subclasses (three SN 1991bg-like, three SN 1991T-like, four SNe Iax, two peculiar, and three super-Chandrasekhar events), and has a median redshift of 0.0192. The SNe in our sample have a median coverage of 16 photometric epochs at a cadence of 5.4 days, and the median first observed epoch is ~4.6 days before maximum B-band light. We describe how the SNe in our sample are discovered, observed, and processed, and we compare the results from our newly developed automated photometry pipeline to those from the previous processing pipeline used by LOSS. After investigating potential biases, we derive a final systematic uncertainty of 0.03 mag in BVRI for our dataset. We perform an analysis of our light curves with particular focus on using template fitting to measure the parameters that are useful in standardising SNe Ia as distance indicators. All of the data are available to the community, and we encourage future studies to incorporate our light curves in their analyses.Comment: 29 pages, 13 figures, accepted for publication in MNRA

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Crosstalk between the plant circadian clock and immunity

Molecular circadian clocks are found across taxa to anticipate predictable daily changes in the external environment. In plants, the circadian clock is important to coordinate agriculturally significant processes that are vital to plant health, such as growth and metabolism, in response to rhythmic environmental cues and stressors. The plant circadian clock comprises of a circuitry of transcriptional translational feedback loops which coordinate the diel expression of approximately a third of the genome, including many genes involved in immunity. As such, the plant clock is important for governing the outcome of plant-pathogen interactions by priming the immune system towards the time of day when pathogen attack is most likely, resulting in temporal differences in susceptibility to pathogens over the course of the day. Plants are armed with a highly sophisticated and complex immune system that consists of a tiered cellular defence signalling network: pattern-triggered immunity (PTI) is rapidly initiated upon detection of pathogen-associated molecular patterns at the cell surface, which prompts the activation of a long-lasting layer throughout the rest of the plant, called systemic acquired resistance (SAR). Evidence of the role of the plant biological clock in orchestrating PTI and SAR signalling has grown in recent years, such as clock regulation of defence gene expression, the activity of key immunity proteins and the abundance of immune hormones. Further to this, there is the fascinating phenomenon that immune players, as well as plant pathogens themselves, can crosstalk to reciprocally control the activity circadian clock. The mechanisms underpinning clock-gated immune responses, however, are poorly understood, hampering the agricultural exploitation of this system to boost plant immunity. This thesis presents the findings produced from two independent projects. In the first project, a standardised resistance screening assay was developed to determine the extent of resistance to commercially important fungicides in the devastating fungal pathogen, Botrytis cinerea in the United Kingdom. The work in the second project explores the effect that bacteria-derived PTI elicitors, (flg22 and elf18) and the key SAR hormone (salicylic acid), have on the oscillating transcriptional activity of core clock genes. Conversely, the importance of the plant clock in gating plant defence is revealed in this study, as key immunity genes are differentially regulated between subjective dawn and dusk, and that the gating of these genes is deregulated in the arrhythmic line, CCA1ox. Taken together, the findings in this study show that the reciprocal interaction between the circadian clock and different layers of the immune response shapes the outcome of plant-pathogen interactions

Stream metabolism and suspended sediment concentration data from two streams in the Oregon Coast Range

This dataset includes the datasets of suspended sediment concentration and environmental variables used to model stream metabolism, and the modeled stream metabolism results for two streams. For more information, see Cargill, SK (2019). The Influence of Lithology on Stream Metabolism in Mountain Systems. MS Thesis, Oregon State University