S1 Site Research Articles

Phytoplankton diversity in relation to physicochemical attributes and water quality of Mandakini River, Garhwal Himalaya.

Phytoplankton are important biological indicators of water quality. This current study assessed the physicochemical parameters and phytoplankton diversity of Mandakini River, an important tributary of the River Ganga. Water and phytoplankton samples were collected from three sampling sites located at three different altitudes for a period of twelve months (July 2018-June 2019). Water samples were analyzed for fourteen important physicochemical parameters along with the identification of phytoplankton by following the standard methodology. A total of 21 species of phytoplankton under three major groups Bacillariophyceae (Cymbella aequalis, Diatoma vulgaris, Fragilaria arcus, Frustulia rhomboids, Gomphonema geminatum, Navicula confervacea, Nitzchia diversa, and Synedra ulna); Chlorophyceae (Volvox sp., Cladophora glomerata, Closterium longissima, Hydrodictyon sp., Microspora amoena, Spirogyra sp., Oedogonium sp., Ulothrix zonata, and Zygnema cylindrospermum); and Cyanophyceae (Anabaena ambigua, Chlorococcum humicola, Nodularia sp., and Oscillatoria sancta) were observed and recorded during the study period. Site S3 (Rudraprayag) had the highest species diversity. From this study, the effect of physicochemical parameters on the diversity and density of phytoplankton was observed. It also includes the overall significance of phytoplankton and physicochemical parameters to the water quality of the Mandakini River along with the key factors that were responsible for the degradation of water quality. The current study also provides baseline information to future researchers working in a similar discipline.

Analaysis of oligosaccharide binding to LysM domains of KEG15107 from Mycobacterium avium

Background: The LysM domain principally binds N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM) sugars, major constituents of molecules such as peptidoglycan. This module is widely distributed in all domains of life. This study reports an analysis of the molecular recognition of oligosaccharide by KEG15107, a protein that contains four LysM domains from Mycobacterium avium. Methods & Materials: Gene cloning and protein expression were initially performed followed by crystallization of the KEG15107 protein with and without polyNAG substrates in various solution at 19 °C. The grown crystals were sent to the Diamond Light Source, Didcot, UK for diffracted data collection. Oligosaccharide binding to LysM domains of KEG15107 was analysed using crystallography observation and mass spectrometry analysis on the KEG17107-NAG complexes. Results: Structure analysis revealed that KEG15107 formed a protease-resistant globular structure with the four LysM domains (Domains 1, 2, 3 and 4) tightly packed against each other. Structural studies show that apo KEG15107 forms a tetramer whereas, in the presence of different oligosaccharides, the protein consistently formed a dimer. This difference in quaternary structures of the protein could be seen to be due to the binding of an oligosaccharide chain to Domain 1. Whilst the structural studies suggested that the oligosaccharide chains only bound to Domain 1, mass spectrometry indicated that all four domains are capable of binding oligosaccharide. Analysis of the high-resolution structure of complexes of KEG15107 with polyNAG substrates suggest that there are five oligosaccharide binding sites (S0, S1, S2, S3 and S4) where sites S1 and S3 exclusively recognize the smaller NAG moiety with the other sites being capable of binding either NAG or the larger sugar, NAM, in an orientation where its more bulky side chain faces the solvent. Conclusion: The confirmation in studies presented here that in proteins containing multiple LysM domains, each of the domains can bind oligosaccharide chains to suggest that they might act together and relative orientation of their oligosaccharide binding sites might relate the underline separation of oligosaccharide chains in the cell wall. This could lead to a deeper understanding of the cell wall and to design inhibitors that might be used as novel antimicrobial agents.

Assessment the Seasonal Variability and Enrichment of Toxic Trace Metals Pollution in Sediments of Damietta Branch, Nile River, Egypt

This work appraises the extent of toxic trace metals and seasonal pollution degree in Damietta branch sediments of the River Nile of Egypt. The toxic trace metals Fe, Mn, Cd, Co, Cu, Ni, Pb, and Zn were analysed in sediments from six sites during the summer and winter seasons. The metal concentrations and organic matter were determined using inductively-coupled-plasma mass spectrometry and loss-on-ignition, respectively. Multivariate statistical methods were used in order to allocate the possible metals sources and their relationships in sediments. The seasonal mean sequence of toxic trace metals was: Fe > Mn > Zn > Pb > Cu > Ni > Co > Cd. The mean Cd, Pb, and Zn values exceeded the sediment quality guidelines and average shale and they represent severe potential toxicity for aquatic organisms. Cu and Co were enriched during winter. The geo-accumulation index stipulated that metal pollution degree in the sequence of: Pb > Zn > Cd > Co > Cu > Mn > Ni > Fe. The highest metal pollution index reported in winter in sites S4/S5 and during summer in sites S4–S6. Different agricultural, wastewater discharge, fisheries, and industrial activities, as well as the effect of dilution/concentration during summer/winter seasons, are the main factors that contributed to metal accumulations in Damietta branch sediments. Continuous monitoring and evaluation of toxic trace metal concentrations of the Damietta sediments and similar localities worldwide can help to protect the ecosystem from harmful metal contaminations.

Effect of Salinity on the Zooplankton Community in the Pearl River Estuary

Understanding the relationship between the zooplankton distribution and salinity may provide key information to understand ecosystem function under the condition of a global mean sea level rise caused by global climate change. However, little is known about how increasing salinity level will affect the entire zooplankton community on a large scale. Here we completed 1 year of field investigations on the Pearl River Estuary and analyzed the distribution and structure of the zooplankton community. A total of 68 zooplankton species were identified during the survey. The number and diversity (richness, evenness, Shannon index, and Simpson’s index) of the zooplankton species decreased as salinity increased from 0.10 to 21.26. Salinity negatively affected the abundances of rotifers, cladocerans, and total zooplankton, while it had little effect on copepod abundance. Some salt-tolerant species, such as Keratella tropica, Polyarthra vulgaris, and Paracalanus crassirostris, survived at high-salinity sites. A pattern was observed at all sites: the peak in copepod abundance always occurred when rotifers were abundant (sites S1 and S2) or after rotifer abundance reached a maximum level (sites S3, S4, and S5). In general, salinity was the most important environmental factor shaping zooplankton biodiversity and abundance. This study provides insight into potential biodiversity and structure of the zooplankton community in response to salinity change.

Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection.

Legionella pneumophila causes a severe pneumonia known as Legionnaires' disease. During the infection, Legionella injects more than 300 effector proteins into host cells. Among them are enzymes involved in altering the host-ubiquitination system. Here, we identified two LegionellaOTU (ovarian tumor)-like deubiquitinases (LOT-DUBs; LotB [Lpg1621/Ceg23] and LotC [Lpg2529]). The crystal structure of the LotC catalytic core (LotC14-310) was determined at 2.4 Å. Unlike the classical OTU-family, the LOT-family shows an extended helical lobe between the Cys-loop and the variable loop, which defines them as a unique class of OTU-DUBs. LotB has an additional ubiquitin-binding site (S1'), which enables the specific cleavage of Lys63-linked polyubiquitin chains. By contrast, LotC only contains the S1 site and cleaves different species of ubiquitin chains. MS analysis of LotB and LotC identified different categories of host-interacting proteins and substrates. Together, our results provide new structural insights into bacterial OTU-DUBs and indicate distinct roles in host-pathogen interactions.

Selectivity filter ion binding affinity determines inactivation in a potassium channel

Potassium channels can become nonconducting via inactivation at a gate inside the highly conserved selectivity filter (SF) region near the extracellular side of the membrane. In certain ligand-gated channels, such as BK channels and MthK, a Ca2+-activated K+ channel from Methanobacterium thermoautotrophicum, the SF has been proposed to play a role in opening and closing rather than inactivation, although the underlying conformational changes are unknown. Using X-ray crystallography, identical conductive MthK structures were obtained in wide-ranging K+ concentrations (6 to 150 mM), unlike KcsA, whose SF collapses at low permeant ion concentrations. Surprisingly, three of the SF's four binding sites remained almost fully occupied throughout this range, indicating high affinities (likely submillimolar), while only the central S2 site titrated, losing its ion at 6 mM, indicating low K+ affinity (∼50 mM). Molecular simulations showed that the MthK SF can also collapse in the absence of K+, similar to KcsA, but that even a single K+ binding at any of the SF sites, except S4, can rescue the conductive state. The uneven titration across binding sites differs from KcsA, where SF sites display a uniform decrease in occupancy with K+ concentration, in the low millimolar range, leading to SF collapse. We found that ions were disfavored in MthK's S2 site due to weaker coordination by carbonyl groups, arising from different interactions with the pore helix and water behind the SF. We conclude that these differences in interactions endow the seemingly identical SFs of KcsA and MthK with strikingly different inactivating phenotypes.

Adaptation and mitigation potential of roadside trees with bio-extraction of heavy metals under vehicular emissions and their impact on physiological traits during seasonal regimes

A massive increase in air emissions resulted from the growing population and the increasing use of automobiles. This air pollution adversely affects living beings including humans, plants as well as a physical property of the surrounding environment. In this way, tree species standing along with the roadside and in their proximity act as defense guard against vehicular emission. In view of this, the present investigation was conducted to assess the adaptation and mitigation potential of roadside tree species (Pinus roxburghii, Quercus leucotrichophora, Cupressus cashmeriana, Daphniphyllum himalense and Lyonia ovalifolia) towards air pollution and their physiological response during different seasons i.e. spring, summer and autumn, under heavy metal accumulation. The higher accumulation of heavy metals was observed in P. roxburghii during summer season at S1 (near to road) and S2 (1.5 km far from S1) site over the control site S3 (5 km far from S1), while physiological traits viz. CO2 assimilation, stomatal conductance, and transpiration were recorded higher in Q. leucotrichophora during summer season at control site S3 and decreased at S2 and S1. Chlorophyll a, b, carotenoid contents and cooling impact were also higher in Q. leucotrichophora during summer season at control site S3 and decreased at S2 and S1 site. However, during the summer season at control site S3, the air pollution tolerance index (APTI) was higher for P. roxburghii and Q. leucotrichophora, and decreased at site S2 and S1. Thus we found that all tree species performed well and to be used as one of the potential tree species for roadside plantation to mitigate air pollution.

Exosite binding drives substrate affinity for the activation of coagulation factor X by the intrinsic Xase complex

Factor X activation by the intrinsic Xase complex, composed of factor IXa bound to factor VIIIa on membranes, is essential for the amplified blood coagulation response. The biological significance of this step is evident from bleeding arising from deficiencies in factors VIIIa or IXa in hemophilia. Here, we assess the mechanism(s) that enforce the distinctive specificity of intrinsic Xase for its biological substrate. Active-site function of IXa was assessed with a tripeptidyl substrate (PF-3688). The reversible S1 site binder, 4-aminobenzamidine (pAB), acted as a classical competitive inhibitor of PF-3688 cleavage by Xase. In contrast, pAB acted as a noncompetitive inhibitor of factor X activation. This disconnect between peptidyl substrate and protein substrate cleavage indicates a major role for interactions between factor X and extended sites on Xase in determining substrate affinity. Accordingly, an uncleavable factor X variant, not predicted to engage the active site of IXa within Xase, acted as a classical competitive inhibitor of factor X activation. Fluorescence studies confirmed the binding of factor X to Xase assembled with IXa with a covalently blocked active site. Our findings suggest that the recognition of factor X by the intrinsic Xase complex occurs through a multistep "dock-and-lock" pathway in which the initial interaction between factor X and intrinsic Xase occurs at exosites distant from the active site, followed by active-site docking and bond cleavage.

K2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions.

K2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K2Ps is unknown. Here, combining K2P2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K2P C-type gating. These asymmetric order-disorder transitions, enabled by the K2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K2P SF2-M4 loop and conserved "M3 glutamate network," and are suppressed by the K2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K2P channel modulator development.

Sediment records of polybrominated diphenyl ethers (PBDEs) in Yangtze River Delta of Yangtze River in China

The spatial and temporal distributions of polybrominated diphenyl ethers (PBDEs) were investigated in five sediment cores from the Yangtze River Delta of Yangtze River in China. The surficial concentrations of nine tri- through hepta-BDE congeners (Σ9BDEs) and BDE209 were highest at urban sites S3 and S2, followed by rural site S1 and estuary sites S5 and S4, respectively, based on dry sediment weight. Both BDE209 and ∑9BDE concentrations exponentially increased between 1990 and 2008. Commercial deca-BDE, penta-BDE, and octa-BDE products were likely PBDE sources in the study area. The relative abundances of BDE209 were higher in sediment cores from estuary than those from urban and rural locations, ascribing to the atmospheric transport from the adjacent densely populated northern and eastern coastal regions. This conclusion was further confirmed by the higher ratios of BDE47/BDE99 and BDE100/BDE99 in cores from the estuary than those from other locations.

The relationship between zooplankton community and environmental factors of Ghrib Dam in Algeria.

The effect of environmental factors on zooplankton diversity, abundance, and distribution in the Ghrib Dam water body was investigated for 2years from June 2013 to May 2015. A total of 61 species of zooplankton were recorded, including 45 rotifers, 13 cladocerans, and 3 copepods. The zooplankton abundance fluctuated between 4 and 3363ind.L-1, and its Shannon-Wiener index of zooplankton diversity in Ghrib Dam varied from H' = 1.15 to 3.77 during the 2-year study period. The highest diversity index was recorded at sampling site S1 in January 2015, due to the increase of specific richness (Ni = 27, Dmg = 5.75). Canonical correspondence analysis (CCA) was used to determine the influence of environmental factors in structuring the zooplankton species for each group. The results of CCA revealed that the most significant environmental factors influencing zooplankton community were water temperature (WT), dissolved oxygen (DO), phosphorus (PO4-), and NO3- (p < 0.05, Monte Carlo permutation test). Meanwhile, the appearance of Hexarthra sp., Collotheca pelagica, and Diaphanosoma brachyurum indicated a rise in WT. The existence of Filinia longiseta, Keratella quadrata, and Cyclops strenuus correlated with a rising of DO. Brachionus urceolaris, Filinia passa, Keratella tecta, Notholca acuminata, and Polyarthra dolichoptera positively coexisted in an increased PO4-. Daphnia longispina and Oxyurella tenuicaudis were positively associated with high concentration of NO3-.

Correlation between physical and chemical parameters of water and biotic indices: The case study the White Drin River basin, Kosovo

The major impacts on aquatic ecosystems worldwide caused by land use lead to changes in their natural conditions and limitation of water use for various needs. This paper presents the results of the study of the physical and chemical parame-ters and macroinvertebrate assemblage in the White Drin River (or: the Drim River, Alb. the Drini i Bardhë River) basin, the largest in Kosovo. Macroinvertebrate sampled at 11 sites in the river resulted in 5946 collected benthic organisms, which in taxonomic terms belong to 12 orders and 51 families. Of the total number of organisms, 72.28% were Insects, 25.39% Amphipoda crustaceans and 2.33% were Annelide worms and Mollusk. The used biotic indices Biological Moni-toring Working Party (BMWP), Ephemeroptera, Plecoptera, and Trichoptera (EPT), average score per taxon (ASPT) and Stroud Water Research Center (SWRC) classify water quality in excellent category in the sampling site S1 near the source of the White Drin River, whereas in other sampling sites, as a result of pollution, water quality varies on category II–IV. The Pearson's correlation analyses shown that the physical and chemical parameters affect the water quality and the com-position of macroinvertebrates. Our results show that the parameters that adversely affect the BMWP, EPT and ASPT bio-tic indices as well as the Shannon–Wiener, Mergalef and Menhinik diversity indices are: pH, electrical conductivity (EC), total suspended solids (TSS), nitrates (NO3–) and chlorides (Cl–). We can conclude that the anthropogenic impact on White Drin basin affects the physical, chemical and biological parameters of the water therefore these parameters should be con-stantly included in Biomonitoring and Management plans for water resources in Kosovo.

Direct Evidence of Plasticity within Human Primary Motor and Somatosensory Cortices of Patients with Glioblastoma

Glioblastoma multiforme (GBM) is a devastating disease without cure. It is also the most common primary brain tumor in adults. Although aggressive surgical resection is standard of care, these operations are limited by tumor infiltration of critical cortical and subcortical regions. A better understanding of how the brain can recover and reorganize function in response to GBM would provide valuable clinical data. This ability, termed neuroplasticity, is not well understood in the adult human brain. A better understanding of neuroplasticity in GBM could allow for improved extent of resection, even in areas classically thought to have critical, static function. The best evidence to date has demonstrated neuroplasticity only in slower growing tumors or through indirect measures such as functional MRI or transcranial magnetic stimulation. In this novel study, we utilize a unique experimental paradigm to show direct evidence of plasticity via serial direct electrocortical stimulation (DES) within primary motor (M1) and somatosensory (S1) cortices in GBM patients. Six patients with glioblastoma multiforme in or near the primary motor or somatosensory cortex were included in this retrospective observational study. These patients had two awake craniotomies with DES to map cortical motor and sensory sites in M1 and S1. Five of six patients exhibited at least one site of neuroplasticity within M1 or S1. Out of the 51 total sites stimulated, 32 (62.7%) demonstrated plasticity. Of these sites, 14 (43.7%) were in M1 and 18 (56.3%) were in S1. These data suggest that even in patients with GBM in or near primary brain regions, significant functional reorganization is possible. This is a new finding which may lead to a better understanding of the fundamental factors promoting or inhibiting plasticity. Further exploration may aid in treatment of patients with brain tumors and other neurologic disorders.

Natural Versus Anthropic Influence on North Adriatic Coast Detected by Geochemical Analyses

This study focused on the geochemical and sedimentological characterization of recent sediments from two marine sites (S1 and E1) located in the North Adriatic Sea, between the Po River prodelta and the Rimini coast. Major and trace metal concentrations reflect the drainage area of the Po River and its tributaries, considered one of the most polluted areas in Europe. Sediment geochemistry of the two investigated sites denote distinct catchment areas. High values of Cr, Ni, Pb and Zn detected in sediments collected in the Po River prodelta (S1 site) suggest the Po River supply, while lower levels of these elements characterize sediments collected in front of the Rimini coast (E1 site), an indication of Northern Apennines provenance. Historical trends of Pb and Zn reconstructed from the sedimentary record around the E1 site document several changes that can be correlated with the industrialization subsequent to World War II, the implementation of the environmental policy in 1976 and the effects of the Comacchio dumping at the end of 1980. At the S1 site, the down core distributions of trace elements indicate a reduction of contaminants due to the introduction of the Italian Law 319/76 and the implementation of anti-pollution policies on automotive Pb (unleaded fuels) in the second half of the 1980s.

Distribution of potentially toxic elements in soils surrounding abandoned mining waste located in Taltal, Northern Chile

Taltal is a commune located in Northern Chile, where former activities in copper ores processing left large amounts of mining waste enriched with potentially toxic elements, PTE. A soil pollution assessment using geochemistry and spatial distribution maps was conducted. A total of 101 surrounding soil samples from 3 abandoned mining waste sites (S1, S2, and S3) were taken to determine their content of PTE (Cu, Mo, Sb, Hg, Pb, Ni, Co, As, Mn, Cr, Cd, and Zn) and major elements. As guideline values of PTE in soils have not been established, the soil pollution index (PI) was assessed by comparing the soil PTE concentrations with the regional geochemical baseline (GBL) values and, for the first time, health risk for residents near Taltal city was evaluated.The measured PTE concentrations (mgkg−1) were Cu 18–6740, Mo 0.2–44, Sb 0.2–90, Hg 0.005–47, Pb 2.8–1510, Ni 7.0–138, Co 1.1–77.1, As 4.2–2691, Mn 83.4–11,400, Cr 7.7–46.1, Cd 0.05–23, and Zn 14.1–1394. Spatial distributions maps showed greatly polluted zones and under special concern are the concentrations of As, Co, Cu, Mo, Ni, Pb, Sb, Hg, Cd and Zn, which exceeded the GBL, the world-soil average and the USEPA and Finnish soil guidelines. Arsenic in site S2 and Cu and Pb in site S3 are the key factor that influences the potential ecological risk. Moreover, As in sites S1 and S2, and As, Pb and Cu in site S3 may pose non-carcinogenic effects for adults and children. Total cancer risk values were above the acceptable risk limit due to As, Cr, and Cd in sites S1 and S2, and due to As, Cr, Cd and Pb in site S3. Site S3, the largest abandoned site, represents the main environmental concern because of its high volume of waste and content of PTE. Based on the results, it can be suggested that the abandoned mining waste were dispersed and are the source of soil pollution in Taltal city. It is concluded that the abandoned mining waste sites have led to substantial contamination of the surrounding soils with As, Cu, Pb, Cr and Cd, which exceed ecological and/or human health risk guideline concentrations.

Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2.

The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin‐binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non‐covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self‐processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS‐CoV‐2 infection model.

Multiple Xenosteroid Pollutants Biomarker Changes in Xultured Nile Tilapia Using Wastewater Effluents as Their Primary Water Source.

Simple SummaryEstrogenic endocrine disruptive chemicals (E-EDCs) are important types of pollutants in fish farms worldwide and a globally concerned problem. In this study, Nile tilapia fish farms receiving wastewater effluents in Egypt were selected as highly, moderately polluted fish farms; besides, a putative control site was deemed low in contamination. Levels of E-EDCs (natural and synthetic steroids, and industrial phenolic compound/bisphenol A (BPA)) was recorded in farm water, and fish tissues at all sites under consideration, mainly, lower levels of testosterone, progesterone, zeranol, and 17β-estradiol were detected compared to the higher level of BPA. Moreover, the effects of these pollutants on fish biometric, reproductive genes, and hormonal biomarkers was evaluated along with the observed associated histopathological alterations. Our findings revealed the detection of some steroidal compounds with a higher level of the BPA. All analyzed biomarkers were reduced to a great extent in the highly polluted sites compared to others, and the histopathological alterations observed were supportive of other measurements. These observations warrant strict monitoring of aquatic pollution sources and the development of strategic plans to control aquaculture pollution.This study was undertaken to screen levels of xenosteroids (estrogenic endocrine disrupting chemicals/E-EDCs) in Nile tilapia (Oreochromis niloticus) fish farms subjected to water fill from the drain at three sites S1 (highly polluted), S2 (moderately polluted), and a putative reference site (RS). Biometric, hormonal, gene expression, and histopathological analysis were investigated. Testosterone, progesterone, and zeranol residues were detected at (0.12–3.44 µg/L) in water samples of different sites. Bisphenol-A (BPA) exhibited a very high concentration (6.5 µg/mL) in water samples from S1. Testosterone, 17β-estradiol residues were detected in fish tissues from all sites at (0.16–3.8 µg/Kg) and (1.05–5.01 µg/Kg), respectively. BPA residues were detected at a very high concentration in the liver and muscle of fish collected from S1 at higher levels of 25.9 and 48.07 µg/Kg, respectively. The detected E-EDCs, at different sites, particularly BPA, reduced the somatic and testicular growth among sites and oversampling time points. Meanwhile, hepatosomatic index (HSI) was significantly increased in S1 compared to S2. All analyzed genes estrogen receptor-type I (er-I, er-ɑ) and II (er-II, er-ß1), polypeptide 1a (cyp19a1), SRY-box containing gene 9 (sox9), and vitellogenin (vtg) and gonadotropin hormones (luteinizing hormone (LH), follicle-stimulating hormone (FSH)), testosterone, 17β-estradiol, and anti-Mullerian hormone (AMH) were significantly expressed at S1 compared to other sites. Histopathology was more evident in S1 than other sites. These findings warrant immediate strategies development to control aquatic pollution and maintain fish welfare and aquaculture sustainability.

Ecological risk assessment of heavy metal-contaminated soil using the triad approach

Heavy metal soil-pollution is of concern due to its adverse effects on the ecosystem and human health. However, conventional ecological risk assessments considering only chemical concentration have limitations because of an increased uncertainty in assessing soil-risk. Therefore, this study applied the Triad approach, using a tier system, for assessing site-specific ecological risk in heavy metal-contaminated soil. In addition, risk-level was determined to analyze the necessity of remediation in a contaminated site. Soil samples from six different sites, including heavy metal-contaminated regions (S1–S5) and a control site (C, unpolluted with heavy metals) were collected. Soil properties were assessed based on a tier system to evaluate the ecological risk of each site. The first step tier-1, involved calculating the soil pollution index (SPI) and the second, tier-2, involved assessing site-specific ecological risk based on three lines of evidence (LoEs), viz., chemistry (ChemLoE), ecotoxicology (EcotoxLoE), and ecology (EcoLoE). The total and bioavailable fractions of heavy metals in soil and bio-accumulated heavy metals in earthworms (Eisenia fetida) were measured for ChemLoE. A bioassay involving mortality and weight reduction rates of earthworms, and a root-elongation test of lettuce (Lactuca sativa sp.) was conducted for EcotoxLoE. Soil biological properties, soil basal respiration, and soil enzyme activities, were evaluated for EcoLoE. Final integrated risk (IR) was obtained by combining the risk-values of each LoE, determined using IR values and deviation of each LoE. Although three out of the five sampling sites had SPI > 1 in tier-1, all five sampling sites were subjected to tier-2 to evaluate site-specific ecological risk. In tier-2, ChemLoE (0.53–0.99) was higher than EcotoxLoE (0.05–0.43) and EcoLoE (0.00–0.29), indicating that chemical aspects impacted risk evaluation more than the toxicological and ecological aspects. The final IR ranged between 0.24 and 0.85; risk-level was classified as low (S2, S3, S5), moderate (S1), and high (S4) according to the IR value. Based on the risk-level, site S4 could require remediation for agricultural land-use. The IR of each sampled site varied depending on the impact of heavy metals. Based tier-1 and tier-2 results, a thorough site-specific evaluation is required to understand the adverse effects of heavy metals on soil ecosystems, and the triad approach could be useful for managing heavy metals in soil.

Assessing groundwater recharge and transpiration in a humid northern region dominated by snowmelt using vadose-zone depth profiles

Profiles of the stable isotope ratios of pore water within the vadose zone provide fingerprints of the history of water percolation into a soil. These profiles, combined with profiles of the volumetric water content, can determine the timing and amount of water that has percolated during specific periods. This study aims to: (1) understand water percolation at two sites in Quebec (Canada) that experience thick snow coverage during the winter season; (2) calculate groundwater recharge rates using the peak-shift method; and (3) estimate the transpiration rate based on the water balance budget. A 7-m-deep borehole was drilled at two sites: one site is sparsely covered by vegetation (S1), while the second underlies a pine forest (S2). For all subsamples, δ18O and δ2H from the soil pore water were analyzed, volumetric water content of the cores was measured, and grain-size analyses to estimate the hydraulic properties were performed. For both boreholes, the winter–spring and summer–autumn periods were determined. Given the limited evapotranspiration occurring during the winter–spring period, recharge rates were high at both sites (71 and 75%), while the summer–autumn period had lower recharge rates of 63% (S1) and 41% (S2). A transpiration rate of 0.7 mm/day was estimated for the pine trees covering site S2. This study provides new field observations for estimating recharge based on water stable isotope profiles in a humid northern region dominated by snowmelt. Moreover, it confirms the accuracy of the peak-shift method for assessing groundwater recharge and estimating transpiration.

Understanding the Contribution of Individual Amino Acid Residues in the Binding of Psychoactive Substances to Monoamine Transporters.

The development of point-of-care detection methodologies for biologically relevant analytes that can facilitate rapid and appropriate treatment is at the forefront of current research efforts and interests. Among the various approaches, those exploiting host–guest chemistries where the optoelectronic signals of the chemical sensor can be modulated upon interaction with the target analyte are of particular interest. In aiding their rational development, judicious selection of peripheral functional groups anchored to core motifs with desired properties is critical. Herein, we report an in-depth investigation of the binding of three psychoactive substances, MDAI, mexedrone, and phenibut, to receptors of the monoamine transporters for dopamine, norepinephrine, and serotonin, particularly focusing on the role of individual amino acid residues. We first evaluated the conformational flexibility of the ligands by comparing their experimentally determined crystal structure geometries to those optimized by means of quantum as well as molecular mechanics, observing significant changes in the case of phenibut. Molecular docking studies were employed to identify preferential binding sites by means of calculated docking scores. In all cases, irrespective of the monoamine transporter, psychoactive substances exhibited preferred interaction with the S1 or central site of the proteins, in line with previous studies. However, we observed that experimental trends for their relative potency on the three transporters were only reproduced in the case of mexedrone. Subsequently, to further understand these findings and to pave the way for the rational development of superior chemical sensors for these substances, we computed the individual contributions of each nearest neighbor amino acid residue to the binding to the target analytes. Interestingly, these results are now in agreement with those experimental potency trends. In addition, these observations were in all cases associated with key intermolecular interactions with neighboring residues, such as tyrosine and aspartic acid, in the binding of the ligands to the monoamine transporter for dopamine. As a result, we believe this work will be of interest to those engaged in the rational development of chemical sensors for small molecule analytes as well as to those interested in the use of computational approaches to further understand protein–ligand interactions.