An assessment of metal absorption competence of indigenous metal tolerant bacterial species- an in-vitro study.

Heavy metals pose a serious global threat to the environment. Hence, removing hazardous metals from soil samples has become complicated over the past few years. The current work looked into the remediation of heavy metals from aqueous solutions using a bacterial community and a unique bacterium obtained from metal-contaminated soil. In this investigation, the isolates of Bacillus anthracis A1-7, Bacillus. thuringiensis A1-3, Bacillus. cereus A1-5, and Pseudomonas aeruginosa A-33 actively demonstrated metal tolerances to various tested metals. Furthermore, an in-vitro biosorption study was performed under ideal concentration. The bacterial consortia achieved the highest biosorption effectiveness for Cu & Zn, 92.7% and 90.3%, respectively. When compared with a single bacterium, the group exhibited inferior Pb biosorption (86%). Since then, P. aeruginosa A33 has had the highest Pb biosorption. Finally, a bacterial consortium has devised an intriguing strategy for eliminating Cu and Pb from the polluted medium. P. aeruginosa A33 was found to be a mighty microbe that extracts Zn from polluted water. This metal-tolerant bacterium also exhibited specific proportions of selective commercially available antibiotics, which were analyzed using the Multiple Antibiotic Resistance (MAR) Index. In conclusion, these findings indicated that bacterial consortia composed of four bacterial isolates can remove metals from a metal-polluted medium.

Individual-based landscape genomics for conservation: An analysis pipeline.

Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

Molecular investigation of the multi-phase photochemistry of Fe(III)-citrate in aqueous solution.

Iron (Fe) is ubiquitous in nature and found as FeII or FeIII in minerals or as dissolved ions Fe2+ or Fe3+ in aqueous systems. The interactions of soluble Fe have important implications for fresh water and marine biogeochemical cycles, which have impacts on global terrestrial and atmospheric environments. Upon dissolution of FeIII into natural aquatic systems, organic carboxylic acids efficiently chelate FeIII to form [FeIII-carboxylate]2+ complexes that undergo a wide range of photochemistry-induced radical reactions. The chemical composition and photochemical transformations of these mixtures are largely unknown, making it challenging to estimate their environmental impact. To investigate the photochemical process of FeIII-carboxylates at the molecular level, we conduct a comprehensive experimental study employing UV-visible spectroscopy, liquid chromatography coupled to photodiode array and high-resolution mass spectrometry detection, and oil immersion flow microscopy. In this study, aqueous solutions of FeIII-citrate were photolyzed under 365 nm light in an experimental setup with an apparent quantum yield of (φ) ∼0.02, followed by chemical analyses of reacted mixtures withdrawn at increment time intervals of the experiment. The apparent photochemical reaction kinetics of Fe3+-citrates (aq) were expressed as two generalized consecutive reactions of with the experimental rate constants of j1 ∼ 0.12 min-1 and j2 ∼ 0.05 min-1, respectively. Molecular characterization results indicate that R and I consist of both water-soluble organic and Fe-organic species, while P compounds are a mixture of water-soluble and colloidal materials. The latter were identified as Fe-carbonaceous colloids formed at long photolysis times. The carbonaceous content of these colloids was identified as unsaturated organic species with low oxygen content and carbon with a reduced oxidation state, indicative of their plausible radical recombination mechanism under oxygen-deprived conditions typical for the extensively photolyzed mixtures. Based on the molecular characterization results, we discuss the comprehensive reaction mechanism of FeIII-citrate photochemistry and report on the formation of previously unexplored colloidal reaction products, which may contribute to atmospheric and terrestrial light-absorbing materials in aquatic environments.

Molecular Characterization of Water-Soluble Brown Carbon Chromophores in Snowpack from Northern Xinjiang, China.

This study reports molecular-level characterization of brown carbon (BrC) attributed to water-soluble organic carbon in six snowpack samples collected from northern Xinjiang, China. The molecular composition and light-absorbing properties of BrC chromophores were unraveled by application of high-performance liquid chromatography (HPLC) coupled to a photodiode array (PDA) detector and high-resolution mass spectrometry. The chromophores were classified into five major types, that is, (1) phenolic/lignin-derivedcompounds, (2) flavonoids, (3) nitroaromatics, (4) oxygenated aromatics, and (5) other chromophores. Identified chromophores account for ∼23-64% of the total light absorption measured by the PDA detector in the wavelength range of 300-370 nm. In the representative samples from urban and remote areas, oxygenated aromatics and nitroaromatics dominate the absorption in the wavelengths below and above 320 nm, respectively. The highly polluted urban sample shows the most complex HPLC-PDA chromatogram, and more other chromophores contribute to the bulk absorption. Phenolic/lignin-derived compounds are the most light-absorbing species in the soil-influenced sample. Chromophores in two remote samples exhibit ultraviolet-visible features distinct from other samples, which are attributed to flavonoids. Identification of individual chromophores and quantitative analysis of their optical properties are helpful for elucidating the roles of BrC in snow radiative balance and photochemistry.

Molecular Analysis of Secondary Brown Carbon Produced from the Photooxidation of Naphthalene.

We investigate the chemical composition of organic light-absorbing components, also known as brown carbon (BrC) chromophores, formed in a proxy of anthropogenic secondary organic aerosol generated from the photooxidation of naphthalene (naph-SOA) in the absence and presence of NOx. High-performance liquid chromatography equipped with a photodiode array detector and electrospray ionization high-resolution mass spectrometer is employed to characterize naph-SOA and its BrC components. We provide molecular-level insights into the chemical composition and optical properties of individual naph-SOA components and investigate their BrC relevance. This work reveals the formation of strongly absorbing nitro-aromatic chromophores under high-NOx conditions and describes their degradation during atmospheric aging. NOx addition enhanced the light absorption of naph-SOA while reducing wavelength-dependence, as seen by the mass absorption coefficient (MAC) and absorption Ångström exponent (AAE). Optical parameters of naph-SOA generated under low- and high-NOx conditions showed a range of values from MACOM 405nm ∼ 0.12 m2 g-1 and AAE300-450nm ∼ 8.87 (low-NOx) to MACOM 405nm ∼ 0.19 m2 g-1 and AAE300-450nm ∼ 7.59 (high-NOx), consistent with "very weak" and "weak" BrC optical classes, respectively. The weak-BrC class is commonly attributed to biomass smoldering emissions, which appear to have optical properties comparable with the naph-SOA. Molecular chromophores contributing to naphthalene BrC absorption were identified with substantial nitro-aromatics, indicating that these species may be used as source-specific markers of BrC related to the anthropogenic emissions.

A machine learning approach to integrating genetic and ecological data in tsetse flies (Glossina pallidipes) for spatially explicit vector control planning.

Vector control is an effective strategy for reducing vector-borne disease transmission, but requires knowledge of vector habitat use and dispersal patterns. Our goal was to improve this knowledge for the tsetse species Glossina pallidipes, a vector of human and animal African trypanosomiasis, which are diseases that pose serious health and socioeconomic burdens across sub-Saharan Africa. We used random forest regression to (i) build and integrate models of G. pallidipes habitat suitability and genetic connectivity across Kenya and northern Tanzania and (ii) provide novel vector control recommendations. Inputs for the models included field survey records from 349 trap locations, genetic data from 11 microsatellite loci from 659 flies and 29 sampling sites, and remotely sensed environmental data. The suitability and connectivity models explained approximately 80% and 67% of the variance in the occurrence and genetic data and exhibited high accuracy based on cross-validation. The bivariate map showed that suitability and connectivity vary independently across the landscape and was used to inform our vector control recommendations. Post hoc analyses show spatial variation in the correlations between the most important environmental predictors from our models and each response variable (e.g., suitability and connectivity) as well as heterogeneity in expected future climatic change of these predictors. The bivariate map suggests that vector control is most likely to be successful in the Lake Victoria Basin and supports the previous recommendation that G. pallidipes from most of eastern Kenya should be managed as a single unit. We further recommend that future monitoring efforts should focus on tracking potential changes in vector presence and dispersal around the Serengeti and the Lake Victoria Basin based on projected local climatic shifts. The strong performance of the spatial models suggests potential for our integrative methodology to be used to understand future impacts of climate change in this and other vector systems.

Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations.

Understanding the drivers of spatial patterns of genomic diversity has emerged as a major goal of evolutionary genetics. The flexibility of forward-time simulation makes it especially valuable for these efforts, allowing for the simulation of arbitrarily complex scenarios in a way that mimics how real populations evolve. Here, we present Geonomics, a Python package for performing complex, spatially explicit, landscape genomic simulations with full spatial pedigrees that dramatically reduces user workload yet remains customizable and extensible because it is embedded within a popular, general-purpose language. We show that Geonomics results are consistent with expectations for a variety of validation tests based on classic models in population genetics and then demonstrate its utility and flexibility with a trio of more complex simulation scenarios that feature polygenic selection, selection on multiple traits, simulation on complex landscapes, and nonstationary environmental change. We then discuss runtime, which is primarily sensitive to landscape raster size, memory usage, which is primarily sensitive to maximum population size and recombination rate, and other caveats related to the model's methods for approximating recombination and movement. Taken together, our tests and demonstrations show that Geonomics provides an efficient and robust platform for population genomic simulations that capture complex spatial and evolutionary dynamics.

Fundus evaluation in COVID-19 positives with non-severe disease.

PURPOSE: The aim of this work was to study and document retinal changes in coronavirus disease-2019 (COVID-19) positive patients with nonsevere disease using a nonmydriatic handheld fundus camera. METHODS: A cross-sectional observational study was conducted on patients affected by COVID-19 who were admitted at our center. Our study included patients with no, mild, and moderate symptoms (nonsevere cases). Intensive care unit (ICU)-admitted patients were excluded considering the difficulty in procuring the fundus image by the handheld camera due to patients positioning. Patients with systemic conditions (diabetes, hypertension, and severe anemia) known to cause retinopathy were also excluded. Bedside anterior segment examination, fundus examination using indirect ophthalmoscopy and fundus imaging of each patient using a nonmydriatic handheld fundus camera was done by a trained ophthalmologist posted for COVID duty. RESULTS: In a cohort of 138 patients, 94 (68.1%) were men and 44 (31.9%) were women. A total of 276 eyes were evaluated. The mean age of the patients was 38.51 ± 14.4 years. Anterior segment evaluation showed no abnormality in any of the eyes. On fundus screening using nonmydriatic handheld camera, a single streak of superficial retinal hemorrhage was noted at the posterior pole of the fundus in the left eye of one patient (0.72%), which was away from fovea. Laboratory tests revealed low hemoglobin (between 10 and 10.9 g/dL falling under mild Anemia) in 12 patients, elevated total leucocyte count in 6 patients, raised LDH in majority of patients (323 ± 101 Units/L) and elevated CRP (14.6 ± 30.99 mg/L). Rest of the lab parameters were within the normal range. CONCLUSION: In our study, COVID patients with mild-to-moderate symptoms did not show any inflammatory/infective or vaso-occlusive lesions in the retina attributable to COVID-19 infection, except one patient who had a single streak hemorrhage in the macula away from fovea, probably incidental.

Photosensitized Reactions of a Phenolic Carbonyl from Wood Combustion in the Aqueous Phase-Chemical Evolution and Light Absorption Properties of AqSOA.

Guaiacyl acetone (GA) is a phenolic carbonyl emitted in significant quantities by wood combustion that undergoes rapid aqueous-phase oxidation to produce aqueous secondary organic aerosol (aqSOA). We investigate the photosensitized oxidation of GA by an organic triplet excited state (3C*) and the formation and aging of the resulting aqSOA in wood smoke-influenced fog/cloud water. The chemical transformations of the aqSOA were characterized in situ using a high-resolution time-of-flight aerosol mass spectrometer. Additionally, aqSOA samples collected over different time periods were analyzed using high-performance liquid chromatography coupled with a photodiode array detector and a high-resolution Orbitrap mass spectrometer (HPLC-PDA-HRMS) to provide details on the molecular composition and optical properties of brown carbon (BrC) chromophores. Our results show efficient formation of aqSOA from GA, with an average mass yield around 80%. The composition and BrC properties of the aqSOA changed significantly over the course of reaction. Three generations of aqSOA products were identified via positive matrix factorization analysis of the aerosol mass spectrometry data. Oligomerization and functionalization dominated the production of the first-generation aqSOA, whereas fragmentation and ring-opening reactions controlled the formation of more oxidized second- and third-generation products. Significant formation of BrC was observed in the early stages of the photoreaction, while organic acids were produced throughout the experiment. High-molecular weight molecules (m/z > 180) with high aromaticity were identified via HPLC-PDA-HRMS and were found to account for a majority of the UV-vis absorption of the aqSOA.

Response of the Aerodyne Aerosol Mass Spectrometer to Inorganic Sulfates and Organosulfur Compounds: Applications in Field and Laboratory Measurements.

Organosulfur compounds are important components of secondary organic aerosols (SOA). While the Aerodyne high-resolution time-of-flight aerosol mass spectrometer (AMS) has been extensively used in aerosol studies, the response of the AMS to organosulfur compounds is not well-understood. Here, we investigated the fragmentation patterns of organosulfurs and inorganic sulfates in the AMS, developed a method to deconvolve total sulfate into components of inorganic and organic origins, and applied this method in both laboratory and field measurements. Apportionment results from laboratory isoprene photooxidation experiment showed that with inorganic sulfate seed, sulfate functionality of organic origins can contribute ∼7% of SOA mass at peak growth. Results from measurements in the Southeastern U.S. showed that 4% of measured sulfate is from organosulfur compounds. Methanesulfonic acid was estimated for measurements in the coastal and remote marine boundary layer. We explored the application of this method to unit mass-resolution data, where it performed less well due to interferences. Our apportionment results demonstrate that organosulfur compounds could be a non-negligible source of sulfate fragments in AMS laboratory and field data sets. A reevaluation of previous AMS measurements over the full range of atmospheric conditions using this method could provide a global estimate/constraint on the contribution of organosulfur compounds.

Hailey-Hailey Disease With Coexistent Herpes Virus Infection: Insights Into the Diagnostic Conundrum of Herpetic/Pseudoherpetic Features in Cutaneous Acantholytic Disorders.

The specific histopathologic diagnosis of a primary acantholytic disorder takes into account the distribution and extent of acantholysis, presence or absence of dyskeratosis, nature of the dermal inflammatory cell infiltrate, and immunofluorescence findings. Herpes virus infection is a common cause of secondary acantholysis where distinctive viral cytopathic changes aid in making it a clear-cut diagnosis in majority of cases. We present a case of coexistence of Hailey-Hailey disease and herpes simplex virus infection to compare and contrast their histopathologic features. This is imperative because acantholytic cells from primary acantholytic disorders may occasionally show cytological features traditionally associated with herpes virus infection (pseudoherpetic changes). The objective of this article is to create a greater awareness of pseudoherpetic changes and also to explore the clinical significance of coexistence of a primary acantholytic disorder and herpes virus infection, as in this case.

Water Uptake and Hygroscopic Growth of Organosulfate Aerosol.

Organosulfates (OS) are important components of secondary organic aerosol (SOA) that have been identified in numerous field studies. This class of compounds within SOA can potentially affect aerosol physicochemical properties such as hygroscopicity because of their polar and hydrophilic nature as well as their low volatility. Currently, there is a dearth of information on how aerosol particles that contain OS interact with water vapor in the atmosphere. Herein we report a laboratory investigation on the hygroscopic properties of a structurally diverse set of OS salts at varying relative humidity (RH) using a Hygroscopicity-Tandem Differential Mobility Analyzer (H-TDMA). The OS studied include the potassium salts of glycolic acid sulfate, hydroxyacetone sulfate, 4-hydroxy-2,3-epoxybutane sulfate, and 2-butenediol sulfate and the sodium salts of benzyl sulfate, methyl sulfate, ethyl sulfate, and propyl sulfate. In addition, mixtures of OS and sodium chloride were also studied. The results showed gradual deliquescence of these aerosol particles characterized by continuous uptake and evaporation of water in both hydration and dehydration processes for the OS, while the mixture showed prompt deliquescence and effloresce transitions, albeit at a lower relative humidity relative to pure sodium chloride. Hygroscopic growth of these OS at 85% RH were also fit to parameterized functional forms. This new information provided here has important implications about the atmospheric lifetime, light scattering properties, and the role of OS in cloud formation. Moreover, results of these studies can ultimately serve as a basis for the development and evaluation of thermodynamic models for these compounds in order to consider their impact on the atmosphere.

A solitary fibrous tumor of the kidney.

A solitary fibrous tumor (SFT) is an uncommon spindle cell neoplasm that usually occurs in the pleura, but may occur in extrapleural sites. Its occurrence in the kidney is rare. We report a SFT, clinically thought to be a renal cell carcinoma arising in the kidney of a 68-year-old female. The tumor was well-circumscribed and composed of a mixture of spindle cells and dense collagenous bands. Immunohistochemical studies revealed reactivity for CD34, CD99, and Bcl-2 protein, with no staining for keratin or muscle markers, confirming the diagnosis. The immunohistochemical study was the key to diagnosis. Several younger members of her family had colorectal and lung cancers suggesting the possibility of a familial or genetic susceptibility.

Diagnosis directs treatment in fungal infections of the skin.

Dermatophyte fungi are confined to the keratin layer of the epidermis and include three genera: Microsporum, Epidermophyton and Trichophyton. These infections can be transmitted by human contact (anthropophilic), from the soil (geophilic) and by animal (zoophilic) spread. Dermatophyte infections usually present as an erythematous, scaly eruption, which may or may not be itchy. Asymmetry is an important clinical clue to fungal infection, as is annular morphology. Examination under ultraviolet (Wood's light) can be helpful. The gold standard for diagnosing cutaneous fungal infections is microscopy and culture of scale, hair or nail, and a definite diagnosis is desirable before commencing treatment, especially with oral therapy. Any dermatophyte species affecting the body can affect the hands. The most common organism is T. rubrum. Tinea corporis infection affects the trunk mainly in children and adolescents, and all genera of dermatophyte can cause it. Tinea cruris infection involves the groin region and is more common in men than women. T. rubrum is the most common causative dermatophyte. The clinical features of tinea capitis include patchy hair loss with varying degrees of scale, erythema and pustules. Infected hairs tend to break at the base, leaving stubble. Occasionally, there is invasion of the visible epidermis, resulting in a boggy, painful swelling with associated alopecia and regional lymphadenopathy known as a kerion.