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Tidal marshes are significant sources of colored (or chromophoric) dissolved organic carbon (CDOC) to adjacent waters and, as a result, contribute substantially to their optical complexity and ultimately affect their water quality. Despite this, our mechanistic understanding of the processes that regulate the exchange and transformation of CDOC at the tidal marsh–estuarine interface remains limited. We hypothesized that tidal marsh soils regulate this exchange and transformation subject to soil mineralogy and salinity environment. To test this hypothesis, we generated initial mass sorption isotherms of CDOC and noncolored dissolved organic carbon (NCDOC) using anaerobic batch incubations of Great Dismal Swamp DOC with four tidal wetland soils, representing a range of organic carbon content (1.77 ± 0.12 % to 36.2 ± 2.2 %) and across four salinity treatments (0, 10, 20, and 35). CDOC sorption followed Langmuir isotherms that were similar in shape to those of total DOC, but with greater maximum sorption capacity and lower binding affinity. Like isotherms of total DOC, CDOC maximum sorption capacity increased and binding affinity decreased with greater salinity. Initial natively adsorbed colored organic carbon was low and increased with soil organic content. In contrast, NCDOC desorbed under all conditions with desorption increasing linearly with initial CDOC concentration. This suggests that for our test solutions CDOC displaced NCDOC on tidal marsh soils. Parallel factor analysis of 3-D excitation emission matrices and specific ultraviolet absorbance measurements suggested that CDOC sorption was driven primarily by the exchange of highly aromatic humic-like CDOC. Taken together, these results suggest that tidal marsh soils regulate export and composition of CDOC depending on the complex interplay between soil mineralogy, water salinity, and CDOC vs. NCDOC composition.

Abstract Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. We demonstrate that Top2 activity is surprisingly uncorrelated with transcriptional activity, suggesting that superhelical stress is obscured from Top2 within chromatin in vivo. We test this idea using osmotic perturbation—a treatment that transiently destabilises chromatin in vivo—revealing that Top2 activity redistributes within sub-minute timescales into broad zones patterned by long genes, convergent gene arrays, and transposon elements—and also by acute transcriptional induction. We propose that latent superhelical stress is normally absorbed by the intrinsic topological buffering capacity of chromatin, helping to avoid spurious topoisomerase activity arising within the essential coding regions of the genome.

A model that predicts UV effects on marine primary productivity using a biological weighting function (BWF) coupled to the photosynthesis–irradiance response (BWF/P-E model) has been implemented for two strains of the picoplanktonic cyanobacteria Synechococcus, WH7803 and WH8102, which were grown at two irradiances (77 and 174 μmol m−2 s−1 photosynthetically available radiation (PAR)) and two temperatures (20 and 26 °C). The model was fit using photosynthesis measured in a polychromatic incubator with 12 long-pass filter configurations with 50% wavelength cutoffs ranging from 291 to 408 nm, giving an effective wavelength range of 280–400 nm. Examination of photosynthetic response vs. weighted exposure revealed that repair rate progressively increases at low exposure but reaches a maximum rate above a threshold exposure ("Emax"). Adding Emax as a parameter to the BWF/P-E model provided a significantly better fit to Synechococcus data than the existing "E" or "T" models. Sensitivity to UV inhibition varied with growth conditions for both strains, but this was mediated mainly by variations in Emax for WH8102 while both the BWF and Emax changed for WH7803. Higher growth temperature was associated with a considerable reduction in sensitivity, consistent with an important role of repair in regulating sensitivity to UV. Based on nominal water column conditions (noon, solstice, 23° latitude, "blue" water), the BWFEmax/P-E model estimates that UV + PAR exposure inhibits Synechococcus photosynthesis from 78 to 91% at 1 m, and integrated productivity to 150 m 17–29% relative to predicted rates in the absence of inhibition.

Background: The absence of menstruation is common in women who use drugs. This can give a belief that conception is unlikely. When stabilised on Opioid Substitution Treatment (OST), fertility often returns, initially without realisation as ovulation precedes menstruation. This leaves women vulnerable to unplanned pregnancies. Community pharmacists (CPs) are frequently in contact with this patient group through the Supervised Consumption of OST service. This provides a timely opportunity to provide reproductive health (RH) advice. The aim of this study was to investigate pharmacists' views on providing a RH service to women receiving OST. Methods: Twenty semi-structured interviews based on the Capability-Opportunity-Motivation to Behaviour (COM-B) model and the Theoretical Domains Framework (TDF) were conducted between 2016 and 2017. Data analysis involved deductive coding using the TDF domains. The TDF domains were mapped onto the elements of the COM-B and used in the second step to create the framework and chart the data. The third step involved re-reading and clustering the codes, and inductive themes were generated to explain the data in depth. Results: Nine of the 14 TDF domains, mapped into five elements of the COM-B, were identified. Five inductive themes were generated: 1) The pharmacists' experience and knowledge of reproductive health (RH) needs of women receiving OST, 2) The pharmacists' approach to providing advice, 3) The pharmacists' perception of the relationship with women receiving OST, 4) Social influences, and 5) Environmental factors. Community pharmacists feared causing offense to women receiving OST and described requiring cues as to when the service was needed. Pharmacists' highlighted a power imbalance in the relationship with women receiving OST. This could influence how receptive this patient group would be to pharmacy RH interventions. Conclusions: CPs' concerns of providing RH service could hinder a proactive service provision. Supporting good rapport and providing a structured consultation would increase the accessibility of such a service.

Topoisomerase 2 (Top2) is known to resolve DNA topological stress through double strand breaks (DSBs), yet Top2 inhibition has been reported to result in a significant amount of single-strand breaks (SSBs). Here the authors develop CC-seq—a method that allows direct mapping of both Top2-linked SSBs and DSBs—and reveal a significant impact of primary DNA sequence on Top2 directed cleavage.

During meiotic prophase chromosomes organise into a series of chromatin loops, but the mechanisms of assembly remain unclear. Here the authors use Saccharomyces cerevisiae to elucidate how this elaborate three-dimensional chromosome organisation is linked to genomic sequence, and demonstrate an essential role for cohesin during this process.

An amendment to this paper has been published and can be accessed via the original article.

It has previously been established that DNA end resection in yeast and in humans is under CDK control. Here the authors explain how phosphorylation regulates the capacity of Sae2 — the yeast orthologue of human CtIP — to promote DNA end resection.

Spray drying of milk powder is an energy intensive process and there remains a significant opportunity to reduce energy consumption by applying process integration principles. The ability to optimally integrate the drying process with the other processing steps has the potential to improve the overall efficiency of the entire process, especially when exhaust heat recovery is considered. However, achieving the minimum energy targets established using pinch analysis results in heat exchanger networks that, while theoretically feasible, are impracticable, unrealistic, contain large number of units, and ultimately uneconomic. Integration schemes that are acceptable from an operational point of view are examined in this paper. The use of evaporated water is an important factor to achieve both energy and water reductions. The economics of additional heat recovery seem favourable and exhaust heat recovery is economically justifiable on its own merits, although milk powder deposition should be minimised by selecting an appropriate target temperature for the exhaust air. This will restrict the amount of heat recovery but minimise operational risk from heat exchanger fouling. The thermodynamic constraints caused by the operating temperatures of the dryer and the poor economics exclude the use of heat pumps for exhaust heat recovery in the short to medium term.

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Abstract DNA replication and transcription generate DNA supercoiling, which can cause topological stress and intertwining of daughter chromatin fibers, posing challenges to the completion of DNA replication and chromosome segregation. Type II topoisomerases (Top2s) are enzymes that relieve DNA supercoiling and decatenate braided sister chromatids. How Top2 complexes deal with the topological challenges in different chromatin contexts, and whether all chromosomal contexts are subjected equally to torsional stress and require Top2 activity is unknown. Here we show that catalytic inhibition of the Top2 complex in interphase has a profound effect on the stability of heterochromatin and repetitive DNA elements. Mechanistically, we find that catalytically inactive Top2 is trapped around heterochromatin leading to DNA breaks and unresolved catenates, which necessitate the recruitment of the structure specific endonuclease, Ercc1-XPF, in an SLX4- and SUMO-dependent manner. Our data are consistent with a model in which Top2 complex resolves not only catenates between sister chromatids but also inter-chromosomal catenates between clustered repetitive elements.

Abstract Childhood represents a period of significant growth and maturation for the brain, and is also associated with a heightened risk for mild traumatic brain injuries (mTBI). There is also concern that repeated-mTBI (r-mTBI) may have a long-term impact on developmental trajectories. Using an awake closed head injury (ACHI) model, that uses rapid head acceleration to induce a mTBI, we investigated the acute effects of repeated-mTBI (r-mTBI) on neurological function and cellular proliferation in juvenile male and female Long-Evans rats. We found that r-mTBI did not lead to cumulative neurological deficits with the model. R-mTBI animals exhibited an increase in BrdU + (bromodeoxyuridine positive) cells in the dentate gyrus (DG), and that this increase was more robust in male animals. This increase was not sustained, and cell proliferation returning to normal by PID3. A greater increase in BrdU + cells was observed in the dorsal DG in both male and female r-mTBI animals at PID1. Using Ki-67 expression as an endogenous marker of cellular proliferation, a robust proliferative response following r-mTBI was observed in male animals at PID1 that persisted until PID3, and was not constrained to the DG alone. Triple labeling experiments (Iba1+, GFAP+, Brdu+) revealed that a high proportion of these proliferating cells were microglia/macrophages, indicating there was a heightened inflammatory response. Overall, these findings suggest that rapid head acceleration with the ACHI model produces an mTBI, but that the acute neurological deficits do not increase in severity with repeated administration. R-mTBI transiently increases cellular proliferation in the hippocampus, particularly in male animals, and the pattern of cell proliferation suggests that this represents a neuroinflammatory response that is focused around the mid-brain rather than peripheral cortical regions. These results add to growing literature indicating sex differences in proliferative and inflammatory responses between females and males. Targeting proliferation as a therapeutic avenue may help reduce the short term impact of r-mTBI, but there may be sex-specific considerations.

Wound infection is a major clinical challenge that can significantly delay the healing process, can create pain, and requires prolonged hospital stays. Pre-clinical research to evaluate new drugs normally involves animals. However, ethical concerns, cost, and the challenges associated with interspecies variation remain major obstacles. Tissue engineering enables the development of in vitro human skin models for drug testing. However, existing engineered skin models are representative of healthy human skin and its normal functions. This paper presents a functional infected epidermis model that consists of a multilayer epidermis structure formed at an air-liquid interface on a hydrogel matrix and a three-dimensionally (3D) printed vascular-like network. The function of the engineered epidermis is evaluated by the expression of the terminal differentiation marker, filaggrin, and the barrier function of the epidermis model using the electrical resistance and permeability across the epidermal layer. The results showed that the multilayer structure enhances the electrical resistance by 40% and decreased the drug permeation by 16.9% in the epidermis model compared to the monolayer cell culture on gelatin. We infect the model with Escherichia coli to study the inflammatory response of keratinocytes by measuring the expression level of pro-inflammatory cytokines (interleukin 1 beta and tumor necrosis factor alpha). After 24 h of exposure to Escherichia coli, the level of IL-1β and TNF-α in control samples were 125 ± 78 and 920 ± 187 pg/mL respectively, while in infected samples, they were 1429 ± 101 and 2155.5 ± 279 pg/mL respectively. However, in ciprofloxacin-treated samples the levels of IL-1β and TNF-α without significant difference with respect to the control reached to 246 ± 87 and 1141.5 ± 97 pg/mL respectively. The robust fabrication procedure and functionality of this model suggest that the model has great potential for modeling wound infections and drug testing.

Repeated concussion is becoming increasingly recognized as a serious public health concern around the world. Moreover, there is a greater awareness amongst health professionals of the potential for repeated pediatric concussions to detrimentally alter the structure and function of the developing brain. To better study this issue, we developed an awake closed head injury (ACHI) model that enabled repeated concussions to be performed reliably and reproducibly in juvenile rats. A neurological assessment protocol (NAP) score was generated immediately after each ACHI to help quantify the cumulative effects of repeated injury on level of consciousness, and basic motor and reflexive capacity. Here we show that we can produce a repeated ACHI (4 impacts in two days) in both male and female juvenile rats without significant mortality or pain. We show that both single and repeated injuries produce acute neurological deficits resembling clinical concussion symptoms that can be quantified using the NAP score. Behavioural analyses indicate repeated ACHI acutely impaired spatial memory in the Barnes maze, and an interesting sex effect was revealed as memory impairment correlated moderately with poorer NAP score performance in a subset of females. These cognitive impairments occurred in the absence of motor impairments on the Rotarod, or emotional changes in the open field and elevated plus mazes. Cresyl violet histology and structural magnetic resonance imaging (MRI) indicated that repeated ACHI did not produce significant structural damage. MRI also confirmed there was no volumetric loss in the cortex, hippocampus, or corpus callosum of animals at 1 or 7 days post-ACHI. Together these data indicate that the ACHI model can provide a reliable, high throughput means to study the effects of concussions in juvenile rats.

We have characterized the photosynthetic response to ultraviolet radiation (UV) of natural phytoplankton assemblages in Antarctic (Southern Ocean) waters. Biological weighting functions (BWFs) and exposure response curves for inhibition of photosynthesis by UV were measured during spring-time ozone depletion (October-November). Two different models were developed to relate photosynthesis to UV exposure. A model that is a function of the duration of exposure (BWF H) applied to assemblages in the well-mixed open waters of the Weddell-Scotia Confluence (WSC, 60° S, 50° W), since responses were a function of cumulative exposure and recovery rates were slow. These assemblages had a variable but generally high sensitivity to UV. A steady-state model (BWF E) applied in the shallow waters near the Antarctic Peninsula (Palmer Station, 64° S, 64° W), where inhibition was a function of irradiance (reciprocity failed), and recovery was rapid. Using information on the time-dependence of photosynthesis in assemblages with active repair, inferences were drawn on the relative contribution of damage and recovery processes to the UV weights. BWFs for Palmer phytoplankton sampled during periods of pack-ice cover had both higher damage and higher repair than BWFs for WSC assemblages. BWFs for Palmer phytoplankton sampled during open water periods had about the same damage weights as Weddell-Scotia assemblages but had a higher repair rate. Solar exposures of more than 10 min were predicted to have generally less effect on Palmer phytoplankton than the WSC phytoplanktonSe caracterizó la respuesta fotosintética a radiación ultravioleta (RUV) en poblaciones naturales de fitoplancton del Océano Antártico. Se midieron las funciones espectrales de peso biológico (BWFs) y curvas de inhibición de fotosíntesis en respuesta a la exposición de RUV durante la temporada de mayor disminución de la capa de ozono (octubre-noviembre). Se desarrollaron dos modelos distintos que relacionan fotosíntesis con exposición a RUV. Un modelo considera la curva de respuesta al tiempo de exposición (BWF H) debido a que se observo que las respuestas dependían de la exposición acumulativa y que la velocidad de recuperación fotosintéticas era lenta. Este modelo se aplica a poblaciones de fitoplancton residentes en mar abierto y en las aguas turbulentas de la Confluencia Weddell-Scotia (WSC, 60° S, 50° O). Estas poblaciones tienen una sensibilidad a la RUV variable y generalmente alta. El segundo modelo analiza el estado de equilibrio (BWF E) y se aplica a las comunidades residentes en aguas poco profundas cerca de la Península Antártica (Estación Palmer, 64° S, 64° O), donde la inhibición dependió de la irradiación (reciprocidad falló), y donde la recuperación fue rápida. Usando la información derivada de la dependencia al tiempo de fotosíntesis en poblaciones con recuperación rápida, se pudo inferir la contribución relativa de procesos de daño y recuperación al peso espectral de la RUV. El método se aplicó a datos preliminares obtenidos en la Estación Palmer. Las BWFs de poblaciones recolectadas en Palmer cuando la capa de hielo que cubre las aguas es compacta asignaron más peso al daño y a una alta recuperación que las BWFs determinadas para poblaciones de WSC. Las BWFs de muestras de fitoplancton de Palmer durante el periodo de aguas abiertas tienen el mismo peso al daño que en aquellas de poblaciones de WSC aun cuando tienen una velocidad de recuperación más alta. Se predice que la exposición solar por más de 10 min en general tiene menos efecto sobre el fitoplancton de Palmer que sobre el fitoplancton de WSC

During meiosis, formation and repair of programmed DNA double-strand breaks (DSBs) create genetic exchange between homologous chromosomes—a process that is critical for reductional meiotic chromosome segregation and the production of genetically diverse sexually reproducing populations. Meiotic DSB formation is a complex process, requiring numerous proteins, of which Spo11 is the evolutionarily conserved catalytic subunit. Precisely how Spo11 and its accessory proteins function or are regulated is unclear. Here, we use Saccharomyces cerevisiae to reveal that meiotic DSB formation is modulated by the Mec1(ATR) branch of the DNA damage signalling cascade, promoting DSB formation when Spo11-mediated catalysis is compromised. Activation of the positive feedback pathway correlates with the formation of single-stranded DNA (ssDNA) recombination intermediates and activation of the downstream kinase, Mek1. We show that the requirement for checkpoint activation can be rescued by prolonging meiotic prophase by deleting the NDT80 transcription factor, and that even transient prophase arrest caused by Ndt80 depletion is sufficient to restore meiotic spore viability in checkpoint mutants. Our observations are unexpected given recent reports that the complementary kinase pathway Tel1(ATM) acts to inhibit DSB formation. We propose that such antagonistic regulation of DSB formation by Mec1 and Tel1 creates a regulatory mechanism, where the absolute frequency of DSBs is maintained at a level optimal for genetic exchange and efficient chromosome segregation.

During meiosis, self-inflicted DNA double-strand breaks (DSBs) are created by the protein Spo11 and repaired by homologous recombination leading to gene conversions and crossovers. Crossover formation is vital for the segregation of homologous chromosomes during the first meiotic division and requires the RecA orthologue, Dmc1. We analyzed repair during meiosis of site-specific DSBs created by another nuclease, VMA1-derived endonuclease (VDE), in cells lacking Dmc1 strand-exchange protein. Turnover and resection of the VDE-DSBs was assessed in two different reporter cassettes that can repair using flanking direct repeat sequences, thereby obviating the need for a Dmc1-dependent DNA strand invasion step. Access of the single-strand binding complex replication protein A, which is normally used in all modes of DSB repair, was checked in chromatin immunoprecipitation experiments, using antibody against Rfa1. Repair of the VDE-DSBs was severely inhibited in dmc1Delta cells, a defect that was associated with a reduction in the long tract resection required to initiate single-strand annealing between the flanking repeat sequences. Mutants that either reduce Spo11-DSB formation or abolish resection at Spo11-DSBs rescued the repair block. We also found that a replication protein A component, Rfa1, does not accumulate to expected levels at unrepaired single-stranded DNA (ssDNA) in dmc1Delta cells. The requirement of Dmc1 for VDE-DSB repair using flanking repeats appears to be caused by the accumulation of large quantities of ssDNA that accumulate at Spo11-DSBs when Dmc1 is absent. We propose that these resected DSBs sequester both resection machinery and ssDNA binding proteins, which in wild-type cells would normally be recycled as Spo11-DSBs repair. The implication is that repair proteins are in limited supply, and this could reflect an underlying mechanism for regulating DSB repair in wild-type cells, providing protection from potentially harmful effects of overabundant repair proteins.

Research at the UC Hopland Research and Extension Center (HREC) has improved our understanding of how to reduce sheep depredation while minimizing the impact on coyotes. Analysis of a 14-year data set of HREC coyote-control efforts found that sheep depredation losses were not correlated with the number of coyotes removed in any of three time scales analyzed (yearly, seasonally and monthly) during corresponding intervals for the next 2 years. Field research using radiotelemetry to track coyotes supported and explained this finding. For example, in 1995, dominant “alphas” from four territories were associated with 89% of 74 coyote-killed lambs; “betas” and transients were not associated with any of these kills. Relatively few coyotes were killing sheep, and these animals were difficult to capture by conventional methods at the time of year when depredation was highest. However, selective removal of only the problem alpha coyotes effectively reduced losses at HREC.