Distribution characteristics of microplastics in storm-drain inlet sediments affected by the types of urban functional areas, economic and demographic conditions in southern Beijing.

A storm-drain inlet is an important link in the transport of microplastic pollutants in urban rainwater runoff. In three functional districts (agricultural, commercial, and residential) from Beijing South 2nd Ring Road to South 6th Ring Road, microplastics in storm-drain inlet sediments were analyzed for abundance and characteristics. The abundance of microplastics in the collected samples ranged from 1121 ± 247 items kg-1 to 7393 ± 491 items kg-1. Among the sample areas, the commercial area had the greatest abundance (11094 items kg-1), while the agricultural area had the lowest (833 items kg-1). The microplastics in the samples were mainly fragments, accounting for 50.4%. Microplastics of less than 1 mm accounted for 74.8%. The color of microplastics was diverse, with colored MPs accounting for 26% and transparent ones for 47.8%. Most of the polymers detected were PET, PS, and PP, which are the most commonly used polymers. Overall, the results provide baseline data on microplastic pollution and its associated risks, in addition to guidelines for controlling runoff pollution.

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae- A Hairpin-swapped Dimer and its Conformational Change.

VxrA and VxrB are cognate histidine kinase (HK) - response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the Type VI Secretion System, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. In this study, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual ß hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK.IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the Type Six Secretion System, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structure of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown, however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

Ratio-Adjustable Upconversion Luminescence Nanoprobe for Ultrasensitive In Vitro Diagnostics.

The development of precise medicine requires diagnostic probes to simultaneously satisfy an excellent detection limit and a wide linear analysis range because of enormous individual-discrepancy of disease biomarker concentrations, yet it remains challenging. Herein, an upconverison nanoprobe with a luminescence ratio flexibly tailored was designed for ultrasensitive monitoring exhaled nitric oxide to indicate the clinical course of asthma. Two independent emissions from the same nanoprobe can be discretionarily modulated to vary their intensity ratios for adapting different analysis requirements. Delightfully, this novel nanoprobe demonstrated a 100-fold lower detection limit compared with the traditional ratiometric fluorescence manner and a more broad linear detection range from the subpart per billion (ppb) level to hundreds of ppb. This ratio-adjustable fluorescence detection strategy holds great potential for miscellaneous disease diagnosis applications.

Acceleration of soil salinity accumulation and soil degradation due to greenhouse cultivation: a survey of farmers' practices in China.

Soil environment and water quality face large pressure due to the rapid expansion of greenhouse cultivation in China. However, studies rarely provide the linkage between farmers' practices and soil degradation in greenhouse cultivation field. In this study, a field survey and sampling of greenhouse cultivation soil were conducted in five regions of China to investigate the accumulation and variation characteristics of soil ion compositions in the field. First, the pH, ion compositions, and electrical conductivity (EC) of 132 composite soil samples were analyzed. Second, farmers' practices with regard to fertilizer, crop yield, and soil degradation processes were surveyed. Lastly, soil nutrient status was evaluated by different grades, and the principal component analysis method was used to analyze the main sources of soil ion compositions. Results of the study reveal the following: (1) Enrichment of greenhouse soil nutrient was mainly caused by excessive fertilization, which introduced the secondary salinization phenomenon for 3-5 years in plastic greenhouse and 1-3 years in multispan greenhouse. (2) Significant changes between the EC and salt ion composition of open soil and greenhouse cultivated soil were observed. The contents of nitrate nitrogen and ammonium nitrogen in the greenhouse soil were high. (3) After a certain period of cultivation in the greenhouse, salt accumulation, pH decline, and varying degrees of acidification were observed in the soil profile. The relationship between soil pH and EC values indicated that the balance of soil compositions was broken. The recommended methods for sustaining greenhouse cultivation include balanced fertilization, rotation practices, and reasonable water utilization in the field.

Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor.

The general stress response sigma factor σE1 directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection in the zoonotic pathogen Brucella abortus Characterizing the functions of σE1-regulated genes therefore would contribute to our understanding of B. abortus physiology and infection biology. σE1 indirectly activates transcription of the IclR family regulator Bab2_0215, but the function of this regulator remains undefined. Here, we present a structural and functional characterization of Bab2_0215, which we have named B rucella adipic acid-activated regulator (BaaR). We found that BaaR adopts a classic IclR-family fold and directly represses the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase (acaD2), and it represses transcription of both genes. We identified three carboxylic acids (adipic acid, tetradecanedioic acid, and ϵ-aminocaproic acid) and a lactone (ϵ-caprolactone) that enhance transcription from the baaR and acaD2 promoters. However, neither the activating acids nor caprolactone enhanced transcription by binding directly to BaaR. Induction of baaR transcription by adipic acid required the gene bab2_0213, which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a suite of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program in B. abortus that is downstream of σE1.

Zearalenone exposure elevated the expression of tumorigenesis genes in mouse ovarian granulosa cells.

Zearalenone (ZEA) is one of mycotoxins which are from corn, sorghum and wheat. As an estrogenic compound, ZEA mainly affects animal growth and reproduction with causing abnormal reproduction capability. Previous studies have shown that ZEA poses adverse effects on follicular development, but the mechanism of genetic toxicity of ZEA is not understood. The purpose of this study was to explore the effects of ZEA exposure on granulosa cells which play vital roles during follicular development. Mouse granulosa cells were exposed to 10 µM or 30 µM ZEA for 72 h in vitro, and the differences in gene expression patterns between control and ZEA exposures were analyzed by RNA-seq. The data demonstrated that 30 µM ZEA had a significant effect on the gene expression, especially ZEA exposure increased the expression of many genes related to different kinds of cancers and cancer related pathways like Hippo signaling pathway and the related genes, such as Ccnd1, Smad3, Tead3, Yap1 and Wwtr1. Furthermore, immunohistochemistry confirmed the increase in the protein levels of YAP1, WWTR1 and CCND1 in 30 µM ZEA exposure group. Collectively, this investigation indicated that ZEA exposure promoted the expression of tumorigenesis genes in mouse granulosa cells to.

Ochratoxin A exposure decreased sperm motility via the AMPK and PTEN signaling pathways.

Ochratoxin A (OTA), a common mycotoxin found in nature, has been implicated as effecting the function of male reproductive systems. OTA exposure has been shown to decrease sperm production and quality, however, the underlying mechanisms remain unknown. In the current investigation boar sperm exposed to 10 and 100µM OTA in vitro for 24h resulted in significantly decreased motility, in the 100µM OTA treatment group when compared with the control group. The level of reactive oxygen species (ROS) was significantly increased in both of the OTA treatment groups. The increase in ROS activated phosphatase and the tensin homolog deleted on chromosome ten (PTEN) and inhibited the activation of protein kinase B (PKB, AKT), activated adenosine 5'-monophosphate (AMP), and activated protein kinase (AMPK) in the exposed sperm. Furthermore, activation of AMPK was enhanced by a decrease in ATPase. These changes culminated in a decline in boar sperm motility. PTEN/AMPK inhibitors significantly inhibited the expression of the two proteins in the OTA treatment group. In addition, there was increased expression of apoptosis markers in the OTA exposed sperm. In conclusion, these data suggest that OTA exposure affects the sperm motility via the AMPK and PTEN signaling pathways.

Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes.

Multiprotein complexes play essential roles in all cells and X-ray crystallography can provide unparalleled insight into their structure and function. Many of these complexes are believed to be sufficiently stable for structural biology studies, but the production of protein-protein complexes using recombinant technologies is still labor-intensive. We have explored several strategies for the identification and cloning of heterodimers and heterotrimers that are compatible with the high-throughput (HTP) structural biology pipeline developed for single proteins. Two approaches are presented and compared which resulted in co-expression of paired genes from a single expression vector. Native operons encoding predicted interacting proteins were selected from a repertoire of genomes, and cloned directly to expression vector. In an alternative approach, Helicobacter pylori proteins predicted to interact strongly were cloned, each associated with translational control elements, then linked into an artificial operon. Proteins were then expressed and purified by standard HTP protocols, resulting to date in the structure determination of two H. pylori complexes.

Biochemical and structural analysis of an Eis family aminoglycoside acetyltransferase from bacillus anthracis.

Proteins from the enhanced intracellular survival (Eis) family are versatile acetyltransferases that acetylate amines at multiple positions of several aminoglycosides (AGs). Their upregulation confers drug resistance. Homologues of Eis are present in diverse bacteria, including many pathogens. Eis from Mycobacterium tuberculosis (Eis_Mtb) has been well characterized. In this study, we explored the AG specificity and catalytic efficiency of the Eis family protein from Bacillus anthracis (Eis_Ban). Kinetic analysis of specificity and catalytic efficiency of acetylation of six AGs indicates that Eis_Ban displays significant differences from Eis_Mtb in both substrate binding and catalytic efficiency. The number of acetylated amines was also different for several AGs, indicating a distinct regiospecificity of Eis_Ban. Furthermore, most recently identified inhibitors of Eis_Mtb did not inhibit Eis_Ban, underscoring the differences between these two enzymes. To explain these differences, we determined an Eis_Ban crystal structure. The comparison of the crystal structures of Eis_Ban and Eis_Mtb demonstrates that critical residues lining their respective substrate binding pockets differ substantially, explaining their distinct specificities. Our results suggest that acetyltransferases of the Eis family evolved divergently to garner distinct specificities while conserving catalytic efficiency, possibly to counter distinct chemical challenges. The unique specificity features of these enzymes can be utilized as tools for developing AGs with novel modifications and help guide specific AG treatments to avoid Eis-mediated resistance.

Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability.

In the F family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal domains from the prototypic F plasmid (TraJF(11-130)) and from the Salmonella virulence plasmid pSLT (TraJpSLT(1-128)). Both structures contain similar Per-ARNT-Sim (PAS) folds, which further homodimerize through the N-terminal helix and the structurally conserved ß-sheet of the PAS fold from each protomer. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. TraJ is specific in activating its cognate tra operon promoter; however, heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that the allelic specificity of TraJ is solely mediated by the region C-terminal to the PAS domain.

Construction of MXene-mediated inorganic-organic quaternary ammonium salt-hybrid coating for fire safety and multi-mode synergistic antibacterial of cotton fabric.

With the continuous development of the society, there is a growing demand for the durability, versatility and multifunction of cott fabrics. In this work, the cotton fabric is coated with multifunctional coating via dip-coating of transition metal carbide (MXene) and then encapsulation of dimethyloctadecyl [3-trimethoxysilopropyl] ammonium chloride (QAS). In view of MXene with excellent light absorption and photothermal conversion efficiency, the controllable antibacterial performance of the cotton fabric is further improved. Benefiting from the encapsulation of QAS, CF@P@M@QAS fabric shows mechanical stability (24 h washing, 1000 cycles folding test and 100 cyclic abrasion) and hydrophobicity. Meantime, the QAS on the surface of multifunctional cotton fabric significantly increases antibacterial activity, and the antibacterial rate can reach to 100 % against Staphylococcus aureus (S. aureus) and 98 % Escherichia coli (E. coli). Besides, CF@P@M@QAS cotton fabric also integrates functions of fire safety and physical therapy. Thus, this multifunctional cotton fabric based MXene offers a novel solution for extending its application in medical electronics and physical therapy.

Self-Supplied Reactive Oxygen Species-Responsive Mitoxantrone Polyprodrug for Chemosensitization-Enhanced Chemotherapy under Moderate Hyperthermia.

Currently, the secondary development and modification of clinical drugs has become one of the research priorities. Researchers have developed a variety of TME-responsive nanomedicine carriers to solve certain clinical problems. Unfortunately, endogenous stimuli such as reactive oxygen species (ROS), as an important prerequisite for effective therapeutic efficacy, are not enough to achieve the expected drug release process, therefore, it is difficult to achieve a continuous and efficient treatment process. Herein, a self-supply ROS-responsive cascade polyprodrug (PMTO) is designed. The encapsulation of the chemotherapy drug mitoxantrone (MTO) in a polymer backbone could effectively reduce systemic toxicity when transported in vivo. After PMTO is degraded by endogenous ROS of the TME, another part of the polyprodrug backbone becomes cinnamaldehyde (CA), which can further enhance intracellular ROS, thereby achieving a sustained drug release process. Meanwhile, due to the disruption of the intracellular redox environment, the efficacy of chemotherapy drugs is enhanced. Finally, the anticancer treatment efficacy is further enhanced due to the mild hyperthermia effect of PMTO. In conclusion, the designed PMTO demonstrates remarkable antitumor efficacy, effectively addressing the limitations associated with MTO.

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.

Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes.

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first unique step of the GMP branch of the purine nucleotide biosynthetic pathway. This enzyme is found in organisms of all three kingdoms. IMPDH inhibitors have broad clinical applications in cancer treatment, as antiviral drugs and as immunosuppressants, and have also displayed antibiotic activity. We have determined three crystal structures of Bacillus anthracis IMPDH, in a phosphate ion-bound (termed "apo") form and in complex with its substrate, inosine 5'-monophosphate (IMP), and product, xanthosine 5'-monophosphate (XMP). This is the first example of a bacterial IMPDH in more than one state from the same organism. Furthermore, for the first time for a prokaryotic enzyme, the entire active site flap, containing the conserved Arg-Tyr dyad, is clearly visible in the structure of the apoenzyme. Kinetic parameters for the enzymatic reaction were also determined, and the inhibitory effect of XMP and mycophenolic acid (MPA) has been studied. In addition, the inhibitory potential of two known Cryptosporidium parvum IMPDH inhibitors was examined for the B. anthracis enzyme and compared with those of three bacterial IMPDHs from Campylobacter jejuni, Clostridium perfringens, and Vibrio cholerae. The structures contribute to the characterization of the active site and design of inhibitors that specifically target B. anthracis and other microbial IMPDH enzymes.

High-throughput protein purification and quality assessment for crystallization.

The ultimate goal of structural biology is to understand the structural basis of proteins in cellular processes. In structural biology, the most critical issue is the availability of high-quality samples. "Structural biology-grade" proteins must be generated in the quantity and quality suitable for structure determination using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The purification procedures must reproducibly yield homogeneous proteins or their derivatives containing marker atom(s) in milligram quantities. The choice of protein purification and handling procedures plays a critical role in obtaining high-quality protein samples. With structural genomics emphasizing a genome-based approach in understanding protein structure and function, a number of unique structures covering most of the protein folding space have been determined and new technologies with high efficiency have been developed. At the Midwest Center for Structural Genomics (MCSG), we have developed semi-automated protocols for high-throughput parallel protein expression and purification. A protein, expressed as a fusion with a cleavable affinity tag, is purified in two consecutive immobilized metal affinity chromatography (IMAC) steps: (i) the first step is an IMAC coupled with buffer-exchange, or size exclusion chromatography (IMAC-I), followed by the cleavage of the affinity tag using the highly specific Tobacco Etch Virus (TEV) protease; the second step is IMAC and buffer exchange (IMAC-II) to remove the cleaved tag and tagged TEV protease. These protocols have been implemented on multidimensional chromatography workstations and, as we have shown, many proteins can be successfully produced in large-scale. All methods and protocols used for purification, some developed by MCSG, others adopted and integrated into the MCSG purification pipeline and more recently the Center for Structural Genomics of Infectious Diseases (CSGID) purification pipeline, are discussed in this chapter.

The Diagnostic Value of Serum Ferritin for Telogen Effluvium: A Cross-Sectional Comparative Study.

PURPOSE: This study aimed to explore the relationship between serum ferritin levels and telogen effluvium. PATIENTS AND METHODS: A total of 193 telogen effluvium patients and 104 female androgenetic alopecia patients were included. We collected the test result of serum ferritin levels, compared with the results of 183 healthy subjects. Receiver Operator Characteristic curves were generated to assess the potential diagnostic value of serum ferritin in telogen effluvium patients. RESULTS: The serum ferritin in telogen effluvium patients were significantly lower than that in the healthy control group (P = 0.000) or female androgenetic alopecia patients (P =0.000). Patients with lower serum ferritin levels got high odds to have telogen effluvium. The areas under the Receiver Operator Characteristic curve of serum ferritin levels were 0.735 and 0.645 for distinguishing telogen effluvium patients from healthy control subjects or female androgenetic alopecia patients. CONCLUSION: Serum ferritin could be a potential biomarker for clinical diagnosis of telogen effluvium.

Innovative use of concentrated growth factors combined with corticosteroids to treat discoid lupus erythematosus alopecia: A case report.

Alopecia for patients with discoid lupus erythematosus can sometimes be a refractory condition, where mixed infiltrates of T lymphocytes and histiocytes leads to destruction of hair follicles, which might cause permanent scarring. Early diagnosis and timely treatment can achieve hair regeneration and prevent further disease progression. Concentrated growth factor, a novel autologous plasma extract, contains various growth factors that could promote tissue regeneration. In this article, we report a case of cell growth factor combined with corticosteroids for the treatment of discoid lupus erythematosus alopecia. This case study concludes with satisfactory clinical effect.

Biochemical and structural studies of two tetrameric nucleoside 2'-deoxyribosyltransferases from psychrophilic and mesophilic bacteria: Insights into cold-adaptation.

Nucleoside 2'-deoxyribosyltransferases (NDTs) catalyze the cleavage of glycosidic bonds of 2'-deoxynucleosides and the following transfer of the 2'-deoxyribose moiety to acceptor nucleobases. Here, we report the crystal structures and biochemical properties of the first tetrameric NDTs: the type I NDT from the mesophilic bacterium Enterococcus faecalis V583 (EfPDT) and the type II NDT from the bacterium Desulfotalea psychrophila (DpNDT), the first psychrophilic NDT. This novel structural and biochemical data permitted an exhaustive comparative analysis aimed to shed light into the basis of the high global stability of the psychrophilic DpNDT, which has a higher melting temperature than EfPDT (58.5 °C versus 54.4 °C) or other mesophilic NDTs. DpNDT possesses a combination of unusual structural motifs not present neither in EfPDT nor any other NDT that most probably contribute to its global stability, in particular, a large aliphatic isoleucine-leucine-valine (ILV) bundle accompanied by a vicinal disulfide bridge and also an intersubunit disulfide bridge, the first described for an NDT. The functional and structural features of DpNDT do not fit the standard features of psychrophilic enzymes, which lead us to consider the implication of (sub)cellular levels together with the protein level in the adaptation of enzymatic activity to low temperatures.

Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains.

The recently discovered antibiotic teixobactin is produced by uncultured soil bacteria. The antibiotic inhibits cell wall synthesis of Gram-positive bacteria by binding to precursors of cell wall building blocks, and therefore it is thought to be less vulnerable to development of resistance. Teixobactin is synthesized by two nonribosomal peptide synthetases (NRPSs), encoded by txo1 and txo2 genes. Like other NRPSs, the Txo1 and Txo2 synthetases are large, multifunctional, and comprised of several modules. Each module is responsible for catalysis of a distinct step of teixobactin synthesis and contains specific functional units, commonly including a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP) domain. Here we report the structures of the C-A bidomains of the two L-Ser condensing modules, from Txo1 and Txo2, respectively. In the structure of the C domain of the L-Ser subunit of Txo1, a large conformational change is observed, featuring an outward swing of its N-terminal α-helix. This repositioning, if functionally validated, provides the necessary conformational change for the condensation reaction in C domain, and likely represents a regulatory mechanism. In an Acore subdomain, a well-coordinated Mg2+ cation is observed, which is required in the adenylation reaction. The Mg2+-binding site is defined by a largely conserved amino acid sequence motif and is coordinated by the α-phosphate group of AMP (or ATP) when present, providing some structural evidence for the role of the metal cation in the catalysis of A domain.