Impact of prescribed fire on soil microbial communities in a Southern Appalachian Forest clear-cut.

Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.

SARS-CoV-2 raw wastewater surveillance from student residences on an urban university campus.

The COVID-19 pandemic brought about an urgent need to monitor the community prevalence of infection and detect the presence of SARS-CoV-2. Testing individual people is the most reliable method to measure the spread of the virus in any given community, but it is also the most expensive and time-consuming. Wastewater-based epidemiology (WBE) has been used since the 1960s when scientists implemented monitoring to measure the effectiveness of the Polio vaccine. Since then, WBE has been used to monitor populations for various pathogens, drugs, and pollutants. In August 2020, the University of Tennessee-Knoxville implemented a SARS-CoV-2 surveillance program that began with raw wastewater surveillance of the student residence buildings on campus, the results of which were shared with another lab group on campus that oversaw the pooled saliva testing of students. Sample collection began at 8 am, and the final RT-qPCR results were obtained by midnight. The previous day's results were presented to the campus administrators and the Student Health Center at 8 am the following morning. The buildings surveyed included all campus dormitories, fraternities, and sororities, 46 buildings in all representing an on-campus community of over 8,000 students. The WBE surveillance relied upon early morning "grab" samples and 24-h composite sampling. Because we only had three Hach AS950 Portable Peristaltic Sampler units, we reserved 24-h composite sampling for the dormitories with the highest population of students. Samples were pasteurized, and heavy sediment was centrifuged and filtered out, followed by a virus concentration step before RNA extraction. Each sample was tested by RT-qPCR for the presence of SARS-CoV-2, using the CDC primers for N Capsid targets N1 and N3. The subsequent pooled saliva tests from sections of each building allowed lower costs and minimized the total number of individual verification tests that needed to be analyzed by the Student Health Center. Our WBE results matched the trend of the on-campus cases reported by the student health center. The highest concentration of genomic copies detected in one sample was 5.06 × 107 copies/L. Raw wastewater-based epidemiology is an efficient, economical, fast, and non-invasive method to monitor a large community for a single pathogen or multiple pathogen targets.

Coding-Complete Genome Sequence of a SARS-CoV-2 Variant Obtained from Raw Sewage at the University of Tennessee-Knoxville Campus.

Reported here is a coding-complete genome sequence of a SARS-CoV-2 variant obtained from raw wastewater samples at the University of Tennessee-Knoxville campus. This sequence provides insight into SARS-CoV-2 variants that circulate on large college campuses but remain mostly undetected.

Development of a microscale land use regression model for predicting NO2 concentrations at a heavy trafficked suburban area in Auckland, NZ.

Land use regression (LUR) analysis has become a key method to explain air pollutant concentrations at unmeasured sites at city or country scales, but little is known about the applicability of LUR at microscales. We present a microscale LUR model developed for a heavy trafficked section of road in Auckland, New Zealand. We also test the within-city transferability of LUR models developed at different spatial scales (local scale and city scale). Nitrogen dioxide (NO2) was measured during summer at 40 sites and a LUR model was developed based on standard criteria. The results showed that LUR models are able to capture the microscale variability with the model explaining 66% of the variability in NO2 concentrations. Predictor variables identified at this scale were street width, distance to major road, presence of awnings and number of bus stops, with the latter three also being important determinants at the local scale. This highlights the importance of street and building configurations for individual exposure at the street level. However, within-city transferability was limited with the number of bus stops being the only significant predictor variable at all spatial scales and locations tested, indicating the strong influence of diesel emissions related to bus traffic. These findings show that air quality monitoring is necessary at a high spatial density within cities in capturing small-scale variability in NO2 concentrations at the street level and assessing individual exposure to traffic related air pollutants.

Thermal stress exposure, bleaching response, and mortality in the threatened coral Acropora palmata.

Demographic data for Elkhorn coral, Acropora palmata, and in situ water temperature data from seven upper Florida Keys (USA) reefs revealed three warm thermal stress events between 2010 and 2016. During a mild bleaching event in 2011, up to 59% of colonies bleached, but no mortality resulted. In both 2014 and 2015, severe and unprecedented bleaching was observed with up to 100% of colonies bleached. A. palmata live tissue cover declined by one-third following the 2014-2015 events. Colony mortality of mildly- and non-bleached colonies did not differ but increased significantly with more severe bleaching. Increased bleaching prevalence corresponded to maximum daily average water temperatures above 31.3°C. However, the cumulative days with daily average exceeding 31.0°C provided a better predictor of bleaching response. The bleaching response of surviving colonies in 2015 was not consistent with acclimatization as most individual colonies bleached at least as badly as in 2014.

Raman on a disc: high-quality Raman spectroscopy in an open channel on a centrifugal microfluidic disc.

The implausible combination of centrifugal disc microfluidics and un-covered channels provides a simple way in which Raman spectroscopy can be implemented in industrially-relevant lab-on-a disc technology. Here we demonstrate these advantages by detecting very low concentrations of melamine in liquid milk, without pre-processing, without surface enhancement of the Raman signal and with no evidence of spectral contamination from the polymeric chip itself. A limit of detection (LOD) of 203 ppm for melamine in milk was achieved from Raman spectra of milk after drying. The centrifugal disc rotation and microchannel geometry results in rapid and reliable filling of the channels and in meniscus shape control, enabling reproducible Raman detection with quantitative precision.

Use of a dense monitoring network of low-cost instruments to observe local changes in the diurnal ozone cycles as marine air passes over a geographically isolated urban centre.

Ozone (O3) concentrations in urban areas are spatially and temporally variable, influenced by chemical production, depletion through deposition and chemical titration processes and dispersion. To date, analysis of intra-urban variability of O3 concentrations, and the influence of local controls on production and depletion rates, has been limited due to the low spatial and/or temporal resolution of measurements. We demonstrate that measurements made using a carefully managed multi-sensor network of low-cost gas-sensitive semiconductor instruments are sufficiently precise to resolve subtle but significant variations in ozone concentration across a region. Ozone was measured at 12 sites in the isolated subtropical city of Auckland, New Zealand. Overall O3 concentrations in the Auckland region were low (annual mean: 19ppb) across all seasons, with a minimum in summer. Higher O3 concentrations (max. 57ppb) were observed when wind speeds were >5ms-1 and from the W/SW, and were associated with maritime air masses. Ozone formation in the Auckland region is low, which is attributed to a combination of the low O3 background concentrations, the negligible contribution of long-range transport and the effect of NOx titration. Intra-urban variability showed that the lowest O3 concentrations were measured at the residential sites, particularly at night and during rush hours. Ozone depletion from reaction with traffic-generated NO explains the rush-hour minima but did not fully account for the low night-time values. The results suggest that night-time depletion may result from other processes such as the reaction of ozone with nitrite on surfaces such as concrete, pointing towards the need for further studies concerning the rate and mechanism of dry deposition at night in urban areas.

Rapid, sensitive, and reproducible screening of liquid milk for adulterants using a portable Raman spectrometer and a simple, optimized sample well.

We have developed a powerful general spectroscopic method for rapidly screening liquid milk for adulterants by combining reflective focusing wells simply fabricated in aluminum with a small, portable Raman spectrometer with a focusing fiber optic probe. Hemispherical aluminum sample wells were specially designed to optimize internal reflection and sampling volume by matching the focal length of the mirror to the depth of focus of the laser probe. The technique was tested on milk adulterated with 4 different nitrogen-rich compounds (melamine, urea, dicyandiamide, and ammonium sulfate) and sucrose. No sample preparation of the milk was needed, and the total analysis time was 4min. Reliable sample presentation enabled average reproducibility of 8% residual standard deviation. The limit of detection interval measured from partial least squares calibrations ranged between 140 and 520mg/L for the 4 N-rich compounds and between 7,000 and 36,000mg/L (0.7-3.6%) for sucrose. The portability of the system and the reliability and reproducibility of this technique open opportunities for general, reagentless screening of milk for adulterants at the point of collection.

Raman spectroscopy as an effective screening method for detecting adulteration of milk with small nitrogen-rich molecules and sucrose.

Adulteration of milk for commercial gain is acknowledged as a serious issue facing the dairy industry. Several analytical techniques can be used to detect adulteration but they often require time-consuming sample preparation, expensive laboratory equipment, and highly skilled personnel. Here we show that Raman spectroscopy provides a simple, selective, and sensitive method for screening milk, specifically for small nitrogen-rich compounds, such as melamine, urea, ammonium sulfate, dicyandiamide, and for sucrose. Univariate and multivariate statistical methods were used to determine limits of detection and quantification from Raman spectra of milk spiked with 50 to 1,000 mg/L of the N-rich compounds and 0.25 to 4% sucrose. Partial least squares (PLS) calibration provided limit of detection minimum thresholds <200mg/L (0.02%) for the 4 N-rich compounds and <0.8% for sucrose, without the need for surface-enhanced Raman spectroscopy. The results show high reproducibility (7% residual standard deviation) and 100% efficiency for screening of milk for these adulterants.

Controlling colloidal stability of silica nanoparticles during bioconjugation reactions with proteins and improving their longer-term stability, handling and storage.

Despite the potential of antibody-coated nanoparticles (Ab-NPs) in many biological applications, there are very few successful, commercially available examples in which the carefully engineered nanomaterial has made it beyond the laboratory bench. Herein we explore the robustness and cost of protein-nanoparticle conjugation. Using multivalent polyamidoamine (PAMAM) dendrimers and dextran as crosslinkers, it was possible to retain colloidal stability during (i) NP-linker binding and (ii) the subsequent conjugation reaction between linker-coated NPs and proteins to generate monodisperse Ab-NPs. This was attributed to the physicochemical properties of the linkers, which were inherited by the NPs and thus benefited colloidal stability. Attaching negatively charged, EDC/sulfo-NHS-activated PAMAM to the NPs contributed to overall negative charge of particles, and in turn led to high electrostatic attraction between the protein and PAMAM-coated NPs during the reaction conditions. In contrast, using an uncharged, EDC/NHS-activated PAMAM dendrimer led to NP aggregation and lower protein binding efficiency. Dextran as a cost-effective, uncharged macromolecule allowed for steric repulsions between neighbouring particles during protein binding, thus inducing NP stability in solution, and also produced monodisperse Ab-NPs. By freeze-drying Ab-NPs from a 1% BSA solution it is possible to reconstitute the solid-form colloid back to a stable state by adding solvent and simply shaking the sample vial by hand. The consequences of the different surface chemistries and freeze-drying stabilizers on the colloidal stability of the NPs were probed by dynamic light scattering. The performance of Ab-NPs was compared in a simple fluorescence linked immunoassay in whole serum. Interestingly, the signal-to-noise ratios were similar for Ab-NPs using PAMAM and dextran, despite dextran binding fewer Abs per NP. We believe this work provides researchers with the tools and strategies for reliably generating Ab-NPs that can be used for a variety of biological applications.

SUV39H1/H3K9me3 attenuates sulforaphane-induced apoptotic signaling in PC3 prostate cancer cells.

The isothiocyanate sulforaphane is a promising molecule for development as a therapeutic agent for patients with metastatic prostate cancer. Sulforaphane induces apoptosis in advanced prostate cancer cells, slows disease progression in vivo and is well tolerated at pharmacological doses. However, the underlying mechanism(s) responsible for cancer suppression remain to be fully elucidated. In this investigation we demonstrate that sulforaphane induces posttranslational modification of histone methyltransferase SUV39H1 in metastatic, androgen receptor-negative PC3 prostate cancer cells. Sulforaphane stimulates ubiquitination and acetylation of SUV39H1 within a C-terminal nuclear localization signal peptide motif and coincides with its dissociation from chromatin and a decrease in global trimethyl-histone H3 lysine 9 (H3K9me3) levels. Exogenous SUV39H1 expression leads to an increase in H3K9me3 and decreases sulforaphane-induced apoptotic signaling. SUV39H1 is thus identified as a novel mediator of sulforaphane cytotoxicity in PC3 cells. Our results also suggest SUV39H1 dynamics as a new therapeutic target in advanced prostate cancers.

HDAC8 and STAT3 repress BMF gene activity in colon cancer cells.

Histone deacetylase (HDAC) inhibitors are undergoing clinical trials as anticancer agents, but some exhibit resistance mechanisms linked to anti-apoptotic Bcl-2 functions, such as BH3-only protein silencing. HDAC inhibitors that reactivate BH3-only family members might offer an improved therapeutic approach. We show here that a novel seleno-α-keto acid triggers global histone acetylation in human colon cancer cells and activates apoptosis in a p21-independent manner. Profiling of multiple survival factors identified a critical role for the BH3-only member Bcl-2-modifying factor (Bmf). On the corresponding BMF gene promoter, loss of HDAC8 was associated with signal transducer and activator of transcription 3 (STAT3)/specificity protein 3 (Sp3) transcription factor exchange and recruitment of p300. Treatment with a p300 inhibitor or transient overexpression of exogenous HDAC8 interfered with BMF induction, whereas RNAi-mediated silencing of STAT3 activated the target gene. This is the first report to identify a direct target gene of HDAC8 repression, namely, BMF. Interestingly, the repressive role of HDAC8 could be uncoupled from HDAC1 to trigger Bmf-mediated apoptosis. These findings have implications for the development of HDAC8-selective inhibitors as therapeutic agents, beyond the reported involvement of HDAC8 in childhood malignancy.

In vitro metabolism of benzo[a]pyrene and dibenzo[def,p]chrysene in rodent and human hepatic microsomes.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and often carcinogenic contaminants released into the environment during natural and anthropogenic combustion processes. Benzo[a]pyrene (B[a]P) is the prototypical carcinogenic PAH, and dibenzo[def,p]chrysene (DBC) is a less prevalent, but highly potent transplacental carcinogenic PAH. Both are metabolically activated by isoforms of the cytochrome P450 enzyme superfamily to form reactive carcinogenic and cytotoxic metabolites. Metabolism of B[a]P and DBC was studied in hepatic microsomes of male Sprague-Dawley rats, naïve and pregnant female B6129SF1/J mice, and female humans, corresponding to available pharmacokinetic data. Michaelis-Menten saturation kinetic parameters including maximum rates of metabolism (VMAX, nmol/min/mg microsomal protein), affinity constants (KM, µM), and rates of intrinsic clearance (CLINT, ml/min/kg body weight) were calculated from substrate depletion data. CLINT was also estimated from substrate depletion data using the alternative in vitro half-life method. VMAX and CLINT were higher for B[a]P than DBC, regardless of species. Clearance for both B[a]P and DBC was highest in naïve female mice and lowest in female humans. Clearance rates of B[a]P and DBC in male rat were more similar to female human than to female mice. Clearance of DBC in liver microsomes from pregnant mice was reduced compared to naïve mice, consistent with reduced active P450 protein levels and elevated tissue concentrations and residence times for DBC observed in previous in vivo pharmacokinetic studies. These findings suggest that rats are a more appropriate model organism for human PAH metabolism, and that pregnancy's effects on metabolism should be further explored.

Intrinsically conducting polymer nanowires for biosensing.

Nanomaterials are commonly exploited to increase the sensitivity of sensors. Conductive polymers are emerging as promising sensing materials as they are easy to functionalize with the appropriate sensing probes, and also act as signal transducers. By constraining the material into one dimensional nanowires, extraordinary sensitivity is achieved. This review deals with the fabrication of these electrically conductive polymer nanowire (ECPNW) sensors and their use for detecting nucleic acid sequences, proteins and pathogens.

Retained asymptomatic third molars and risk for second molar pathology.

Prophylactic extraction of unerupted asymptomatic third molars is the most common oral surgery procedure in the United States. However, limited evidence exists to justify its costs and associated morbidity. We analyzed data collected over 25 years from 416 adult men enrolled in the Veterans Affairs Dental Longitudinal Study to evaluate the association of retained asymptomatic third molars with risk of adjacent second molar pathology (caries and/or periodontitis), based on third molar status (i.e., absent, erupted, or unerupted). Unerupted molars were further categorized as either "soft tissue" or "bony" impacted. We found that the lowest prevalence and incidence of second molar pathology occurred when the adjacent third molar was absent. The presence of a third molar that was soft tissue impacted increased the risk of incident second molar pathology 4.88-fold (95% confidence interval: 2.62, 9.08). Having an erupted or "bony" impacted third molar increased the risk of incident second molar pathology by 1.74 (95% confidence interval: 1.34, 2.25) and 2.16 (95% confidence interval: 1.56, 2.99), respectively. The retention of third molars is associated with increased risk of second molar pathology in middle-aged and older adult men.

The influence of vegetation on the horizontal and vertical distribution of pollutants in a street canyon.

Space constraints in cities mean that there are only limited opportunities for increasing tree density within existing urban fabric and it is unclear whether the net effect of increased vegetation in street canyons is beneficial or detrimental to urban air quality at local scales. This paper presents data from a field study undertaken in Auckland, New Zealand designed to determine the local impact of a deciduous tree canopy on the distribution of the oxides of nitrogen within a street canyon. The results showed that the presence of leaves on the trees had a marked impact on the transport of pollutants and led to a net accumulation of pollutants in the canyon below the tree tops. The incidence and magnitude of temporally localised spikes in pollutant concentration were reduced within the tree canopy itself. A significant difference in pollutant concentrations with height was not observed when leaves were absent. Analysis of the trends in concentration associated with different wind directions showed a smaller difference between windward and leeward sides when leaves were on the trees. A small relative increase in concentrations on the leeward side was observed during leaf-on relative to leaf-off conditions as predicted by previous modelling studies. However the expected reduction in concentrations on the windward side was not observed. The results suggest that the presence of leaves on the trees reduces the upwards transport of fresh vehicle emissions, increases the storage of pollutants within the canopy space and reduces the penetration of clean air downwards from aloft. Differences observed between NO and NO(2) concentrations could not be accounted for by dispersion processes alone, suggesting that there may also be some changes in the chemistry of the atmosphere associated with the presence of leaves on the trees.

Identification of estrogen-responsive vitelline envelope protein fragments from rainbow trout (Oncorhynchus mykiss) plasma using mass spectrometry.

Plasma peptides previously associated with exposure of juvenile male rainbow trout (Oncorhynchus mykiss) to the hormone 17ß-estradiol (E2) were identified using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). Specifically, plasma peptides of interest were fractionated and subsequently identified via spectra obtained by MALDI QqTOF MS/MS and LC-MALDI TOFTOF MS/MS analysis, de novo sequencing and database matching. The two peptide masses were identified as significant matches for fragments of the C-terminal propeptides from rainbow trout vitelline envelope protein (VEP)α and VEPγ isoforms. Our findings document the presence of the C-terminal propeptides from rainbow trout VEPα and VEPγ proteins in the bloodstream of juvenile male rainbow trout exposed to E2 via MALDI-TOF-MS detection. We provide three possible explanations for the presence of C-terminal propeptides in the bloodstream, as well as compare previously obtained hepatic transcriptomic results with the plasma proteomic results obtained in the present study.

Deposition of chemically reactive and repellent sites on biosensor chips for reduced non-specific binding.

The performances of new polymeric materials with excellent optical properties and good machinability have led the biomedical diagnostics industry to develop cheap disposable biosensor platforms appropriate for point of care applications. Zeonor, a type of cycloolefin polymer (COP), is one such polymer that presents an excellent platform for biosensor chips. These polymer substrates have to be modified to have suitable physico-chemical properties for immobilizing proteins. In this work, we have demonstrated the amine functionalization of COP substrates, by plasma enhanced chemical vapour deposition (PECVD), through codeposition of ethylene diamine and 3-aminopropyltriethoxysilane precursors, for building chemistries on the plastic chip. The elemental composition, adhesion, ageing and reactivity of the plasma polymerized film were examined. The Si-O functionality present in amino silane contributed for a good interfacial adhesion of the coating to COP substrates and also acted as a network building layer for plasma polymerization. Wet chemical modification was then carried out on the amine functionalized chips to create chemically reactive isothiocyanate sites and protein repellent fluorinated sites on the same chip. The density of the reactive and repellent sites was altered by choosing appropriate mixtures of homofunctional phenyldiisothiocyanate (PDITC), pentafluoroisothiocyanate (5FITC) and phenylisothiocyanate (PITC) compounds. By tailoring the density of reactive binding sites and protein repellent sites, the non-specific binding of ssDNA has been decreased to a significant extent.

Reactive amine surfaces for biosensor applications, prepared by plasma-enhanced chemical vapour modification of polyolefin materials.

Here we have demonstrated a solventless plasma-based process that integrates low-cost, high throughput, high reproducibility and ecofriendly process for the functionalization of the next-generation point-of-care device platforms. Amine functionalities were deposited by plasma-enhanced chemical vapour deposition (PECVD) using a new precursor. The influence of the plasma RF power and the deposition time on surfacial properties, as well as their effect on the reactivity and content of amino groups was investigated. The key process determinants were to have a sufficient power in the plasma to activate and partially fragment the monomer but not too much as to lose the reactive amine functionality, and sufficient deposition time to develop a reactive layer but not to consume or erode the amine reactivity. An immunoassay performed using human immunoglobulin (IgG) as a model analyte showed an improvement of the detection limit by two orders of magnitude beyond that obtained using devices activated by liquid-phase reaction.