Insight into the molecular recognition of human and polar bear pregnane X receptor by three organic pollutants using molecular docking and molecular dynamics simulations.

Pregnane X receptor (PXR) is a heterologous biosensor that is involved in the metabolic pathway of environmental pollutants, regulating the transcription of genes involved in biotransformation. There are significant differences in the selectivity and specificity of organic pollutants (OPs) toward polar bear PXR (pbPXR) and human PXR (hPXR), but the detailed dynamical characteristics of their interactions are unclear. Homology Modeling, molecular docking, molecular dynamics simulation, and free energy calculation were used to analyze the recognition of pbPXR and hPXR by three OPs: BPA, chlordane and toxaphene. Comparing interaction patterns along with binding free energy of pbPXR and hPXR with these three OPs revealed that although pbPXR and hPXR interact similar with these three OPs, these OPs have different effects on the internal dynamics of pbPXR and hPXR. This results in significant alterations in the interaction of key residues near Leu209, Met243, Phe288, Met323, and His407 with OPs, thereby influencing their binding energy. Non-polar interactions, especially van der Waals interactions, were found to be the dominating factors in interacting of these OPs with PXRs. The region surrounding these key residues facilitates hydrophobic contacts with PXR, which are crucial for the selective activation of PXRs in different species by these three OPs. These findings are of significant guidance in understanding the impacts of environmental endocrine disruptors on different organisms.

An idea to explore: A systematic approach for solving plasmid double-digest puzzles.

A common exercise given to students early in a molecular biology course is the creation of a restriction map of a plasmid "digested" by two restriction enzymes (RE). Meanwhile, students have learned from an early age about the properties and analyses of circles in their mathematics courses. But it is rare for students to learn using puzzle-based assignments at the intersection of molecular biology and mathematics. Therefore, we should present students with a puzzle that allows them to combine knowledge and skills from these seemingly disconnected disciplines. Here, we present a method for analyzing RE digests of circular plasmids using basic geometric principles.

Quantifying Protein Dynamics by Kymograph Analysis.

Time-lapse imaging of the subcellular localization and dynamic behavior of proteins is critical to understand their biological functions in cells. With the advent of various methodologies and computational tools, the precise tracking and quantification of protein spatiotemporal dynamics have become feasible. Kymograph analysis, in particular, has been extensively adopted for the quantitative assessment of proteins, vesicles, and organelle movements. However, conventional kymograph analysis, which is based on a single linear trajectory, may not comprehensively capture the complexity of proteins that alter their course during intracellular transport and activity. In this chapter, we introduced an advanced protocol for whole-cell kymograph analysis that allows for three-dimensional (3D) tracking of protein dynamics. This method was validated through the analysis of tip-focused endocytosis and exocytosis processes in growing tobacco pollen tubes by employing both the advanced whole-cell and classical kymograph methods. In addition, we enhanced this method by integrating pseudo-colored kymographs that enables the direct visualization of changes in protein fluorescence intensity with fluorescence recovery after photobleaching to advance our understanding of protein localization and dynamics. This comprehensive method offers a novel insight into the intricate dynamics of protein activity within the cellular context.

Polar Localization Analysis of Anionic Phospholipids and Their Binding Proteins in Arabidopsis Pollen Tubes.

Pollen tubes are typical polarized growth cells whose elongation occurs only in tip regions and is highly dependent on precise and ordered exocytosis/endocytosis in the top regions of the tubes. Although anionic phospholipids have been proven to be involved in regulating vesicle trafficking and the proper localization and functions of proteins in pollen tubes, the underlying cellular and molecular mechanisms remain poorly understood. To further understand how anionic phospholipids are involved in vesicle trafficking and in the control of protein localization and functions, assay methods to analyze the polar localization of anionic phospholipids and their binding proteins, and identifying phospholipid-protein interactions, should be developed. Here, we describe detailed protocols for analyzing anionic phospholipid polar localization and colocalization with their binding proteins in Arabidopsis pollen tubes and examining phospholipid-protein interactions in vitro.

Assessing the risk of climate maladaptation for Canadian polar bears.

The Arctic is warming four times faster than the rest of the world, threatening the persistence of many Arctic species. It is uncertain if Arctic wildlife will have sufficient time to adapt to such rapidly warming environments. We used genetic forecasting to measure the risk of maladaptation to warming temperatures and sea ice loss in polar bears (Ursus maritimus) sampled across the Canadian Arctic. We found evidence for local adaptation to sea ice conditions and temperature. Forecasting of genome-environment mismatches for predicted climate scenarios suggested that polar bears in the Canadian high Arctic had the greatest risk of becoming maladapted to climate warming. While Canadian high Arctic bears may be the most likely to become maladapted, all polar bears face potentially negative outcomes to climate change. Given the importance of the sea ice habitat to polar bears, we expect that maladaptation to future warming is already widespread across Canada.

High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation.

The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.

Lipid Quality Changes in French Fries, Chicken Croquettes, and Chicken Nuggets Fried with High-Linoleic and High-Oleic Sunflower Oils in Domestic Deep Fryers.

The quality of fried products greatly depends on the changes occurring during frying. The purpose of this work was to study the lipid quality changes taking place in selected frozen foods after domestic deep-frying. Conventional, high-linoleic sunflower oil (HLSO) and high-oleic sunflower oil (HOSO) were used, and the frozen foods selected were French fries, croquettes, and nuggets. The foods were fried in domestic fryers under discontinuous conditions. Analyses included fatty acid composition, sterols, tocopherols, squalene, and lipid alteration levels. In all fried foods, the content of lipids increased after frying, which is consistent with previous findings. However, the lipid exchange between the food and the oil greatly depended on the food characteristics. Specifically, the levels of frying oil in the food lipids were about 90, 40, and 58% for French fries, croquettes, and nuggets, respectively. The main results obtained showed that lipid alteration levels considerably decreased and amounts of sterols and tocopherols significantly increased in French fries' lipids after frying. In both chicken products, croquettes and nuggets, the best quality improvement observed was a significant decrease in cholesterol in food lipids due to the lipid exchange. Overall, frying with HLSO and HOSO improved the quality and nutritional properties of all products tested.

Occurrence, sources and transport of triazine herbicides in the Antarctic marginal seas.

The extensively applied triazine herbicides are easily transported by ocean currents over long distances. This study analyzed ten triazine herbicides in the Antarctic marginal seas and the Southern Indian Ocean during the austral summer for the first time, addressing their largely unexplored behavior in remote marine environments. The total triazine herbicides showed great spatial heterogeneity, with a range of 20-790 pg/L and an average of 31 ± 66 pg/L. The waterborne transport of triazine herbicides in the Antarctic was affected by hydrological processes, especially the blocking and accumulation effect of the polar front. Variations in sea ice extent and temperature were also important influencing factors, resulting in elevated triazine herbicides in surface seawater of East Antarctica, but reduced levels in West Antarctica. Furthermore, the source apportionment results indicated that approximately 55 % of the herbicides originated from sugarcane cultivation, 28 % from algaecide use, and 16 % from corn and sorghum farming.

Unraveling Anomalies in Preferential Liquid Transport through the Intrinsic Pores of Cyclodextrin in Polyester Nanofilms.

The precise manipulation of the porous structure of the nanofiltration membrane is critical for unlocking enhanced separation efficiencies across various liquids and solutes. Ultrathin films of crosslinked macrocycles, specifically cyclodextrins (CDs), have drawn considerable attention in this area owing to their ability to facilitate precise molecular separation with high liquid permeance for both polar and non-polar liquids, resembling Janus membranes. However, the functional role of the intrinsic cavity of CD in liquid transport remains inadequately understood, demanding immediate attention in designing nanofiltration membranes. Here, the synthesis of polyester nanofilms derived from crosslinked ß-CD, demonstrating remarkable Na2SO4 rejection (≈92 - 99.5%), high water permeance (≈4.4 - 37.4 Lm-2h-1bar-1), extremely low hexane permeance (<1 Lm-2h-1bar-1), and extremely high ratio (α > 500) of permeances for polar and non-polar liquids, is reported. Molecular simulations support the findings, indicating that neither the polar nor the non-polar liquids flow through the ß-CD cavity in the nanofilm. Instead, liquid transport predominantly occurs through the 2.2 nm hydrophilic aggregate pores. This challenges the presumed functional role of macrocyclic cavities in liquid transport and raises questions about the existence of the Janus structure in nanofiltration membranes produced from the macrocyclic monomers.

Dietary Milk Phospholipids Increase Body Fat and Modulate Gut Permeability, Systemic Inflammation, and Lipid Metabolism in Mice.

The study aimed at how dietary milk polar lipids affect gut permeability, systemic inflammation, and lipid metabolism during diet-induced obesity (DIO). C57BL/6J mice (n = 6x3) were fed diets with 34% fat as energy for 15 weeks: (1) modified AIN-93G diet (CO); (2) CO with milk gangliosides (GG); (3) CO with milk phospholipids (MPL). Gut permeability was assessed by FITC-dextran and sugar absorption tests. Intestinal tight junction proteins were evaluated by Western blot. Plasma cytokines were measured by immunoassay. Body composition was assessed by magnetic resonance imaging. Tissue lipid profiles were obtained by thin layer chromatography. Hepatic expression of genes associated with lipid metabolism was assessed by RT-qPCR. MPL increased the efficiency of converting food into body fat and facilitated body fat accumulation compared with CO. MPL and GG did not affect fasting glucose or HOMA-IR during DIO. MPL increased while GG decreased plasma TG compared with CO. MPL decreased phospholipids subclasses in the muscle while increased those in the liver compared with CO. GG and MPL had little effect on hepatic expression of genes associated with lipid metabolism. Compared with CO, MPL decreased polar lipids content in colon mucosa. Small intestinal permeability decreased while colon permeability increased and then recovered during the feeding period. High-fat feeding increased plasma endotoxin after DIO but did not affect plasma cytokines. MPL and GG did not affect plasma endotoxin, adipokines and inflammatory cytokines. After the establishment of obesity, MPL increased gut permeability to large molecules but decreased intestinal absorption of small molecules while GG tended to have the opposite effects. MPL and GG decreased mannitol and sucralose excretions, which peaked at d 45 in the CO group. MPL decreased occludin in jejunum mucosa compared with CO. GG and MPL did not affect zonula occludens-1 in gut mucosa. In conclusion, during DIO, milk GG decreased gut permeability, and had little effect on systemic inflammation and lipid metabolism; MPL facilitated body fat accumulation, decreased gut permeability, did not affect systemic inflammation.

Analysis of human biological samples using porous graphitic carbon columns and liquid chromatography-mass spectrometry: a review.

Liquid chromatography-mass spectrometry (LC-MS) has emerged as a powerful analytical technique for analyzing complex biological samples. Among various chromatographic stationary phases, porous graphitic carbon (PGC) columns have attracted significant attention due to their unique properties-such as the ability to separate both polar and non-polar compounds and their stability through all pH ranges and to high temperatures-besides the compatibility with LC-MS. This review discusses the applicability of PGC for SPE and separation in LC-MS-based analyses of human biological samples, highlighting the diverse applications of PGC-LC-MS in analyzing endogenous metabolites, pharmaceuticals, and biomarkers, such as glycans, proteins, oligosaccharides, sugar phosphates, and nucleotides. Additionally, the fundamental principles underlying PGC column chemistry and its advantages, challenges, and advances in method development are explored. This comprehensive review aims to provide researchers and practitioners with a valuable resource for understanding the capabilities and limitations of PGC columns in LC-MS-based analysis of human biological samples, thereby facilitating advancements in analytical methodologies and biomedical research.

Legacy and novel contaminants in surface sediments of Admiralty Bay, Antarctica Peninsula.

Despite being one of the most remote areas on the planet, the Antarctic continent is subject to anthropogenic influences. The presence of various groups of contaminants, including persistent organic pollutants (POPs) and polycyclic aromatic hydrocarbons (PAHs), has been documented in the region over the past decades. However, a significant knowledge gap remains regarding the detection of new pollutants, such as emerging contaminants (ECs), in Antarctic coastal environments. This study analyzed the occurrence and levels of selected POPs, PAHs, ECs in surface sediments from Admiralty Bay, Antarctica Peninsula. Non-target screening was employed to identify potential novel contaminants in the region. Samples (n = 17) were extracted using an accelerated solvent extraction (ASE) system and instrumental analyses were performed using gas chromatography coupled to a triple-quadrupole mass spectrometer (GC/MS-MS). Regarding regulated contaminants, concentrations of Σ5PCBs ranged from

Spiro-buckybowls: Synthesis and Selective Transformations toward Chiral and Nonlinear Optical Polycycles.

Integration of spirocycles with buckybowls is a promising strategy to construct three-dimensional (3D) curved π-systems and to endow distinctive physicochemical features arising from buckybowls. Herein, a series of carbon-bridged spiro-type heterosumanenes (spiro-HSEs) were synthesized by combining 9,9'-spirobifluorene and dichalcogenasumanenes (DCSs). It is found that spiro-conjugation plays an important role in the geometric and electronic structures of spiro-HSEs. The bowl depth of DCSs moiety becomes larger in the spiro-HSEs. Owing to the Jahn-Teller (J-T) effect, two DCSs segments of spiro-HSEs have different bowl depths accompanied with the unequal distribution of charge in radical cation state. Taking advantage of the typical reactions of DCSs, selective transformations of spiro-HSEs have been adopted in accordance to the nature of chalcogen atoms (S, Se, Te) to bestow the value-added functionalities. The emissive property is enhanced by converting the thiophene rings of S-doped spiro-HSE into thiophene S,S-dioxides. A chiroptical polycycle could be produced by ring-opening of the edge benzene of Se-doped spiro-HSE. The covalent adduct of Te-doped spiro-HSE with Br2 forms non-centrosymmetric halogen-bonded networks, resulting in the high performance second-order nonlinear optics (NLO).

Temperature-Dependent Rotational Dynamics of Non-Polar Solute in Non-Polar Solvents: Influence of Boundary Conditions.

Rotational dynamics of 3-(benzo[d]thiazol-2-yl)-7-(diethylamino)-2H-chromen-2-one (3BT7D2H-one) non-polar solute in non-polar solvents has been studied by varying temperature to find out how hydrodynamic friction is influenced by solute-size ratio. It has been observed that the rotational dynamics of 3BT7D2H-one follow the Stoke's-Einstein-Debye (SED) model in an n-hexane solvent and it follows the Gierer and Wirtz (GW) model in an n-decane solvent. The probable reason is due to the solute-solvent size ratio which influences boundary conditions parameters and consequently on rotational dynamics of solute.

Selection of Negative Charged Acidic Polar Additives to Regulate Electric Double Layer for Stable Zinc Ion Battery.

Zinc-ion batteries are promising for large-scale electrochemical energy storage systems, which still suffer from interfacial issues, e.g., hydrogen evolution side reaction (HER), self-corrosion, and uncontrollable dendritic Zn electrodeposition. Although the regulation of electric double layer (EDL) has been verified for interfacial issues, the principle to select the additive as the regulator is still misted. Here, several typical amino acids with different characteristics were examined to reveal the interfacial behaviors in regulated EDL on the Zn anode. Negative charged acidic polarity (NCAP) has been unveiled as the guideline for selecting additive to reconstruct EDL with an inner zincophilic H2O-poor layer and to replace H2O molecules of hydrated Zn2+ with NCAP glutamate. Taking the synergistic effects of EDL regulation, the uncontrollable interface is significantly stabilized from the suppressed HER and anti-self-corrosion with uniform electrodeposition. Consequently, by adding NCAP glutamate, a high average Coulombic efficiency of 99.83% of Zn metal is achieved in Zn|Cu asymmetrical cell for over 2000 cycles, and NH4V4O10|Zn full cell exhibits a high-capacity retention of 82.1% after 3000 cycles at 2 A g-1. Recapitulating, the NCAP principle posted here can quicken the design of trailblazing electrolyte additives for aqueous Zn-based electrochemical energy storage systems.

Comparative omics directed gene discovery and rewiring for normal temperature-adaptive red pigment synthesis by polar psychrotrophic fungus Geomyces sp. WNF-15A.

The Antarctic fungus Geomyces sp. WNF-15A can produce high-quality red pigments (AGRP) with good prospects for the use in food and cosmetic area. However, efficient AGRP synthesis relies on low-temperature and thus limits its industrial development. Here genome sequencing and comparative analysis were performed on the wild-type versus to four mutants derived from natural mutagenesis and transposon insertion mutation. Eleven mutated genes were identified from 2309 SNPs and 256 Indels. A CRISPR-Cas9 gene-editing system was established for functional analysis of these genes. Deficiency of scaffold1.t692 and scaffold2.t704 with unknown functions highly improved AGRP synthesis at all tested temperatures. Of note, the two mutants produced comparable levels of AGRP at 20 °C to the wild-type at 14 °C. They also broke the normal-temperature limitation and effectively synthesized AGRP at 25 °C. Comparative metabolomic analysis revealed that deficiency of scaffold1.t692 improved AGRP synthesis by regulation of global metabolic pathways especially downregulation of the competitive pathways. Knockout of key genes responsible for the differential metabolites confirmed the metabolomic results. This study shows new clues for cold-adaptive regulatory mechanism of polar fungi. It also provides references for exploitation and utilization of psychrotrophic fungal resources.

Building High-Density Polar Hybrid Perovskites via Intercalation of Cs+ and Aromatic Diamine for Passive X-ray Detection.

2D organic-inorganic hybrid perovskites (OIHPs) have shown great promise in direct X-ray detection. The development of high-performance passive X-ray detectors in 2D OIHPs calls for an increase in material density while maintaining structural polarity, which is becoming quite challenging. Here, a high-density, polar 2D alternating-cation-intercalated (ACI) perovskite, (4-AP)Cs2Pb2I8 (B, 4-AP = 4-amidinopyridinium), capable of addressing this problem is successfully constructed by introducing heavy Cs+ into the interlayer space of an aromatic Dion-Jacobson (DJ) perovskite (4-AP)PbI4 (A). Through such a DJ-to-ACI design, the newly developed 2D OIHP B not only significantly increases its density to 4.23 g cm-3 (even higher than that of 3D MAPbI3) but also crystallizes in a polar space group (Ama2), which further leads to enhanced X-ray attenuation and an obvious polar photovoltage (1.1 V) under X-ray irradiation. As a result, X-ray detectors fabricated by high-quality single crystals of B exhibit excellent and stable detection performance under self-powered mode with a high sensitivity of 107 µC Gy-1 cm-2 and a low detection limit of 289 nGy s-1. This work provides implications for the future exploration and regulation of novel ACI OIHPs for high-performance photoelectronic devices.

Enhancing soil health, microbial count, and hydrophilic methomyl and hydrophobic lambda-cyhalothrin remediation with biochar and nano-biochar.

Pesticide contamination and soil degradation present significant challenges in agricultural ecosystems, driving extensive exploration of biochar (BC) and nano-biochar (NBC) as potential solutions. This study examines their effects on soil properties, microbial communities, and the fate of two key pesticides: the hydrophilic methomyl (MET) and the hydrophobic lambda-cyhalothrin (LCT), at different concentrations (1%, 3%, and 5% w w-1) in agricultural soil. Through a carefully designed seven-week black bean pot experiment, the results indicated that the addition of BC/NBC significantly influenced soil dynamics. Soil pH and moisture content (MC) notably increased, accompanied by a general rise in soil organic carbon (SOC) content. However, in BC5/NBC5 treatments, SOC declined after the 2nd or 3rd week. Microbial populations, including total plate count (TPC), phosphate-solubilizing bacteria (PSB), and nitrogen-fixing bacteria (NFB), showed dynamic responses to BC/NBC applications. BC1/NBC1 and BC3/NBC3 applications led to a significant increase in microbial populations, whereas BC5/NBC5 treatments experienced a decline after the initial surge. Furthermore, the removal efficiency of both MET and LCT increased with higher BC/NBC concentrations, with NBC demonstrating greater efficacy than BC. Degradation kinetics, modeled by a first-order equation, revealed that MET degraded faster than LCT. These findings underscore the profound impact of BC/NBC on pesticide dynamics and microbial communities, highlighting their potential to transform sustainable agricultural practices.

The role of lysophosphatidic acid acyltransferase 1 in reproductive growth of Arabidopsis thaliana.

Lysophosphatidic acid acyltransferase1 (LPAT1) catalyzes the second step of de novo glycerolipid biosynthesis in chloroplasts. However, the embryonic-lethal phenotype of the knockout mutant suggested an unknown role for LPAT1 in non-photosynthetic reproductive organs. Reciprocal genetic crossing of the lpat1-1 heterozygous line suggested a female gametophytic defect of the lpat1-1 knockout mutant. By suppressing LPAT1 specifically during seed development, we showed that LPAT1 suppression affected silique growth and seed production. Glycerolipid analysis of the LPAT1 knockdown lines revealed a pronounced decrease of phosphatidylcholine (PC) content in mature siliques along with an altered polyunsaturation level of the polar glycerolipids. In seeds, the acyl composition of triacylglycerol (TAG) was altered albeit not the content. These results indicate that plastidic LPAT1 plays an important role in reproductive growth and extraplastidic glycerolipid metabolism involving PC and TAG.

Genomic architecture and population structure of Boreogadus saida from Canadian waters.

The polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4-16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.