pinecone/core-2020-05-10-deduplication huggingface dataset:
Influence of hydraulic retention time, sludge retention time, and ozonation on the removal of free and conjugated estrogens in Japanese activated sludge treatment plants

This study describes the occurrence, fate, and removal of free estrogens (estrone (E1), 17 beta-estradiol (E2), estriol (E3), 17 alpha-ethynylestradiol (EE2)) and their glucuronide and sulfate conjugates (estrone-3-sulphate (E1-3S), 17 beta-estradiol-3-sulfate (E2-3S), estriol-3-sulfate (E3-3S), estrone-3-glucuronide (E1-3G), 17 beta-estradiol-3-glucuronide (E2-3G), and estriol-3-glucuronide (E3-3G)) in 12 sewage treatment plants in Japan. Glucuronide conjugates were only rarely detected in sewage influents and entirely eliminated within the treatment plants. E1 was found at 69 ng/L, E2 at 108 ng/L, E1-3S at 18 ng/L, and E2-3S at 78 ng/L in the sewage influents. The average removal efficiency for E1, E2, and sulfate conjugates was 88, 92, and 93%, respectively, following activated sludge treatment. The removal of E1 and E2 was improved with increasing the sludge retention time (SRT), with the highest removal typically found from 12 days SRT onward. The removal of sulfate conjugates was also related to SRT with highest removals found from eight days SRT onward. No correlation was found between the hydraulic retention time and the removal of any of the estrogens. The ozone dosage of 4-7 mg/L reduced E3 and E2-3S and E3-3S to below detection levels. Overall ozonation reduced the estrogenicity of the effluents as expressed as estradiol equivalents from 8.4 to 0.7 ng/L. The results suggest adequate river basin management of estrogens in Japan could be accomplished by a mixture of activated sludge plants with long SRT and where necessary, the addition of tertiary ozonation
Differentiating between pollutants build-up on roads and roofs: Significance of roofs as a stormwater pollutant source

Impervious surfaces in an urban catchment are the primary stormwater pollutant contributing areas. Appropriate treatment of stormwater runoff from these impervious surfaces is essential to safeguard the urban water environment. While urban roads have received significant research attention in this regard, roofs have not been well investigated. Key pollutant processes such as build-up on roads and roofs can be different due to the different surface characteristics. This entails different treatment strategies being needed for road and roofs. The research study characterized roof pollutants build-up by differentiating with road surfaces. It was noted that pollutants are more highly concentrated on particles and particularly finer particles in the case of roof surfaces, compared to road surfaces. Additionally, pollutants built-up on roof surfaces tend to be relatively more variable from one day to another in terms of pollutant loads. These results highlight the significance of roofs as a stormwater pollutant source and the important need for a specific stormwater treatment strategy rather than the application of a combined approach for treating stormwater runoff from both, roads and roofs
Degradation of Toxic Compounds at Low and Medium Temperature Conditions Using Isolated Fungus

In the present study, a fungal strain isolated from the Antarctic soil was identified as Penicillium sp. CHY-2 based on its 5.8S rRNA gene sequence analysis. Furthermore, its biodegradation ability towards 13 different toxic compounds such as 4-butylphenol (4-BP), 4-sec-butylphenol (4-s-BP), 4-tert-butylphenol (4-t-BP), 4-nonylphenol (4-NP), 4-tert-octylphenol (4-t-OP), 4-chlorophenol (4-CP), phenol, bisphenol A (BPA), benzene, toluene, xylene, naphthalene, and phenanthrene at low (4°C) and medium (15°C) temperature conditions was evaluated using high pressure liquid chromatography. Among the 13 compounds, the strain CHY-2 effectively degraded the six compounds i.e., 4-BP, 4-s-BP, 4-t-BP, 4-NP, 4-CP, and phenol at 15°C within one week, and at 4°C within 3 weeks. Also CHY-2 effectively degraded the 4-t-OP at 15°C (70%), but not at 4°C (35%). Among different carbon sources tested, glucose was found to be the most suitable and the growth of CHY-2 at 4°C was slower than at 15°C. Addition of Tween 80 increased the growth and degradation ability of CHY-2 towards 4-BP at 4 and 15°C. The metabolites produced during the degradation of 4-BP were identified by gas chromatography-mass spectrometry. Also, bacteria present in the Antarctic soil were determined by denaturing gradient gel electrophoresis and the result showed the presence of Pseudomonas and Syntrophus groups of bacteria
Proportion of sewage sludge to soil influences the survival of Salmonella Dublin, and Escherichia coli

The survival of enteric pathogens in sewage sludge could lead to their transferral into the soil environment and subsequent contamination of crops and water courses. This, in turn, could increase the potential spread of gastrointestinal disease. This work aimed to determine the persistence of several microorganisms, co-introduced with sewage sludge, when exposed to varying proportions of sewage sludge to soil. Three microcosm-based studies were established, inoculated with Salmonella Dublin or an environmentally-persistent strain of Escherichia coli (quantified periodically over a period of 42 days), or indigenous sewage sludge E. coli (quantified over a period of 56 days). Treatments consisted of a mixture containing: 0, 15, 25, 50, 75 and 100% soil or sludge, depending upon the experiment. Each introduced microorganism declined significantly over time, with greater quantities of soil generally instigating greater die-off particularly in the cases of environmentally-persistent E. coli and S .Dublin. However, this relationship was not proportionally related as sludge/soil mixtures showed greater declines than pure soil treatments. In contrast, indigenous sewage sludge E. coli had a more consistent decline across all treatments. This may indicate that indigenous strains are more resilient and may be indicative of natural behaviour. Moreover, the effects of soil-borne factors on pathogen attenuation were context dependent and non-linear, possibly arising from the relative spatial distribution of introduced sludge and attendant microbes in soil
WAVE2 is regulated by multiple phosphorylation events within its VCA domain.

addresses: Department of Biochemistry, Faculty of Medical and Veterinary Sciences, University of Bristol, Bristol, United Kingdom.notes: PMCID: PMC2798068OnlineOpen Article. This is a copy of an article published in Cell Motility and the Cytoskeleton. This journal is available online at: http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1949-3592The definitive version is available at www3.interscience.wiley.comThe (Wiskott-Aldrich Syndrome Protein)-family verprolin homologous protein (WAVE) family of proteins occupies a pivotal position in the cell, converting extracellular signals into the formation of branched filamentous (F) actin structures. WAVE proteins contain a verprolin central acidic (VCA) domain at their C-terminus, responsible for binding to and activating the Arp2/3 complex, which in-turn nucleates the formation of new actin filaments. Here we identify five Casein Kinase 2 (CK2) phosphorylation sites within the VCA domain of WAVE2, serines 482, 484, 488, 489, and 497. Phosphorylation of these sites is required for a high affinity interaction with the Arp2/3 complex. Phosphorylation of ser 482 and 484 specifically inhibits the activation of the Arp2/3 complex by the WAVE2 VCA domain, but has no effect on the affinity for the Arp2/3 complex when the other phosphorylation sites are occupied. We demonstrate phosphorylation of all five sites on endogenous WAVE2 and show that their mutation to non-phosphorylatable alanine residues inhibits WAVE2 function in vivo, inhibiting cell ruffling and disrupting the integrity of the leading edge of migrating cells
Bend propagation in the flagella of migrating human sperm

A pre-requisite for sexual reproduction is successful unification of the male and female gametes; in externally-fertilising echinoderms the male gamete is brought into close proximity to the female gamete through chemotaxis, the associated signalling and flagellar beat changes being elegantly characterised in several species. In the human, sperm traverse a relatively high-viscosity mucus coating the tract surfaces, there being a tantalising possible role for chemotaxis. To understand human sperm migration and guidance, studies must therefore employ similar viscous in vitro environments. High frame rate digital imaging is used for the first time to characterise the flagellar movement of migrating sperm in low and high viscosities. While qualitative features have been reported previously, we show in precise spatial and temporal detail waveform evolution along the flagellum. In low viscosity the flagellum continuously moves out of the focal plane, compromising the measurement of true curvature, nonetheless the presence of torsion can be inferred. In high viscosities curvature can be accurately determined and we show how waves propagate at approximately constant speed. Progressing waves increase in curvature approximately linearly except for a sharper increase over a distance 20-27 m from the head/midpiece junction. Curvature modulation, likely influenced by the outer dense fibres, creates the characteristic waveforms of high viscosity swimming, with remarkably effective cell progression against greatly increased resistance, even in high viscosity liquids. Assessment of motility in physiological viscosities will be essential in future basic research, studies of chemotaxis and novel diagnostics
Intrinsic structural disorder in cytoskeletal proteins.

Cytoskeleton, the internal scaffold of the cell, displays an exceptional combination of stability and dynamics. It is composed of three major filamentous  networks, microfilaments (actin filaments), intermediate filaments (neurofilaments), and microtubules. Together, they ensure the physical and structural stability of the cell, whereby also mediating its large-scale structural rearrangements, motility, stress response, division, and internal transport. All three cytoskeletal systems are built upon the same basic design: they have a central repetitive scaffold assembled from folded building elements,  surrounded and regulated by accessory regions/proteins that regulate its formation and mediate its countless interactions with its environment, serving to send regulatory signals to and from the cytoskeleton. Here, we elaborate on the idea that the opposing features of stability and dynamics are also manifest in the dichotomy of the structural status of its components, the core being highly structured and the accessory proteins/regions being highly disordered, and are responsible for most of the regulatory (post-translational) input promoting adaptive responses and providing dynamics necessary for each of the cytoskeletal  systems. This pattern entails special consequences, in which the manifold functional advantages of structural disorder, most pronounced in regulatory and signaling functions, are all exploited by nature. (c) 2013 Wiley Periodicals, Inc
Purification of Tropomyosin Br-3 and 5NM1 and Characterization of Their Interactions with Actin

Tropomyosins were first identified in neuronal systems\ud
in 1973. Although numerous isoforms were found and\ud
described since then, many aspects of their function\ud
and interactions remained unknown. Tropomyosin isoforms\ud
show different sorting pattern in neurogenesis.\ud
As one example, TM5NM1/2 is present in developing\ud
axons, but it is replaced by TMBr-3 in mature neurons,\ud
suggesting that these tropomyosin isoforms contribute\ud
differently to the establishment of the functional features\ud
of the neuronal actin networks. We developed a\ud
method for the efficient purification of TMBr-3 and\ud
TM5NM1 as recombinant proteins using bacterial\ud
expression system and investigated their interactions\ud
with actin. We found that both isoforms bind actin filaments,\ud
however, the binding of TM5NM1 was much\ud
stronger than that of TMBr-3. TMBr-3 and TM5NM1\ud
modestly affected actin assembly kinetics, in an opposite\ud
manner. Consistently with the higher affinity of\ud
TM5NM1 it inhibited actin filament disassembly more\ud
efficiently than TMBr-3. Similarly to other previously\ud
studied tropomyosins TM5NM1 inhibited the Arp2/3\ud
complex-mediated actin assembly. Notably, TMBr-3 did\ud
not influence the Arp2/3 complex-mediated polymerization.\ud
This is a unique feature of TMBr-3, since so\ud
far it is the only known tropomyosin supporting the\ud
activity of the Arp2/3 complex, indicating that TMBr-3\ud
may colocalize and work simultaneously with Arp2/3\ud
complex in neuronal cells
Abelson Phosphorylation of CLASP2 Modulates its Association With Microtubules and Actin

The Abelson (Abl) non-receptor tyrosine kinase regulates the cytoskeleton during multiple stages of neural development, from neurulation, to the articulation of axons and dendrites, to synapse formation and maintenance. We previously showed that Abl is genetically linked to the microtubule (MT) plus end tracking protein (+TIP) CLASP in Drosophila. Here we show in vertebrate cells that Abl binds to CLASP and phosphorylates it in response to serum or PDGF stimulation. In vitro, Abl phosphorylates CLASP with a Km of 1.89 µM, indicating that CLASP is a bona fide substrate. Abl-phosphorylated tyrosine residues that we detect in CLASP by mass spectrometry lie within previously mapped F-actin and MT plus end interaction domains. Using purified proteins, we find that Abl phosphorylation modulates direct binding between purified CLASP2 with both MTs and actin. Consistent with these observations, Abl-induced phosphorylation of CLASP2 modulates its localization as well as the distribution of F-actin structures in spinal cord growth cones. Our data suggest that the functional relationship between Abl and CLASP2 is conserved and provides a means to control the CLASP2 association with the cytoskeleton. © 2014 The Authors. Cytoskeleton Published by Wiley Periodicals, Inc
Drosophila comes of age as a model system for understanding the function of cytoskeletal proteins in cells, tissues, and organisms

For the last 100 years, Drosophila melanogaster has been a powerhouse genetic system for understanding mechanisms of inheritance, development, and behavior in animals. In recent years, advances in imaging and genetic tools have led to Drosophila becoming one of the most effective systems for unlocking the subcellular functions of proteins (and particularly cytoskeletal proteins) in complex developmental settings. In this review, written for non-Drosophila experts, we will discuss critical technical advances that have enabled these cell biological insights, highlighting three examples of cytoskeletal discoveries that have arisen as a result: (1) regulation of Arp2/3 complex in myoblast fusion, (2) cooperation of the actin filament nucleators Spire and Cappuccino in establishment of oocyte polarity, and (3) coordination of supracellular myosin cables. These specific examples illustrate the unique power of Drosophila both to uncover new cytoskeletal structures and functions, and to place these discoveries in a broader in vivo context, providing insights that would have been impossible in a cell culture model or in vitro. Many of the cellular structures identified in Drosophila have clear counterparts in mammalian cells and tissues, and therefore elucidating cytoskeletal functions in Drosophila will be broadly applicable to other organisms.available in PMC 2016 June 30National Institutes of Health (U.S.) (NIH/NINDS (DP2 NS082127))Pew Scholars Program in the Biomedical SciencesNational Institutes of Health (U.S.) (NIH/NIGMS (R01-GM084947))American Cancer Society (Research Scholar Award
Aminocyclitols as Pharmacological Chaperones for Glucocerebrosidase, a Defective Enzyme in Gaucher Disease

3 pages, 4 figures.-- PMID: 17479993 [PubMed].-- Supporting information (11 pages) available at: http://www.wiley-vch.de/contents/jc_2452/2007/z700061_s.pdfPrinted version published on Jul 7, 2007.Some genetic pathologies are associated to mutations that produce minor changes in a\ud
protein structure. Further studies to improve cell tolerance, disclose the key structural motifs required for the chaperone activity, and confer selectivity against different point mutations of the defective enzyme are currently underway in our group and will be reported in due course.Partial financial support from the Ministerio de Ciencia y Tecnología\ud
(Spain) (Project MCYT CTQ2005-00175/BQU), Fondos Feder\ud
(EU), the Ministerio de Sanidad y Consumo (Spain) (Project\ud
PIO40767), and CSIC (Projects PIF 2004-80F026) is acknowledged.\ud
We are also grateful to Genzyme for a generous donation of Imiglucerase\ud
(CerezymeK).Peer reviewe
Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors

El pdf del artículo es el manuscrito de autor.-- et al.PDE7 inhibitors regulate pro-inflammatory and immune T-cell functions, and are a potentially novel class of drugs especially useful in the treatment of a wide variety of immune and inflammatory disorders. Starting from our lead family of thioxoquinazolines, we designed, synthesized, and characterized a novel series of thioxoquinazoline derivatives. Many of these compounds showed inhibitory potencies at sub-micromolar levels against the catalytic domain of PDE7A1 and at the micromolar level against PDE4D2. Cell-based studies showed that these compounds not only increased intracellular cAMP levels, but also had interesting anti-inflammatory properties within a therapeutic window. The in silico data predict that these compounds are capable of the crossing the blood-brain barrier. The X-ray crystal structure of the PDE7A1 catalytic domain in complex with compound 15 at a resolution of 2.4 Å demonstrated that hydrophobic interactions at the active site pocket are a key feature. This structure, together with molecular modeling, provides insight into the selectivity of the PDE inhibitors and a template for the discovery of new PDE7 or PDE7/PDE4 dual inhibitors.Funded by: Fundación de Investigación Médica Mutua Madrileña, Instituto de Salud Carlos III. Grant Number: FISPI06012/MPY 1281; NIH. Grant Number: GM59791 and Spanish Ministry of Education and Science.Peer Reviewe
Pharmacophore-based discovery of small-molecule inhibitors of protein-protein interactions between HIV-1 integrase and cellular cofactor LEDGF/p75

The cellular protein lens epithelium-derived growth factor, or transcriptional coactivator p75 (LEDGF/p75), plays a crucial role in HIV integration. The protein-protein interactions (PPIs) between HIV-1 integrase (IN) and its cellular cofactor LEDGF/p75 may therefore serve as targets for the development of new anti-HIV drugs. In this work, a structure-based pharmacophore model for potential small-molecule inhibitors of HIV-1 IN-LEDGF/p75 interaction was developed using the LigandScout software. The 3D model obtained was used for virtual screening of our in-house chemical database, CHIME, leading to the identification of compound CHIBA-3002 as an interesting hit for further optimization. The rational design, synthesis and biological evaluation of four derivatives were then carried out. Our studies resulted in the discovery of a new and more potent small molecule (7, CHIBA-3003) that is able to interfere with the HIV-1 IN-LEDGF/p75 interaction at micromolar concentration, representing one of the first compounds to show activity against these specific PPIs. Docking simulations were subsequently performed in order to investigate the possible binding mode of our new lead compound to HIV-1 IN. This study is a valid starting point for the identification of anti-HIV agents with a different mechanism of action from currently available antiviral drugs.status: publishe
Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring

Plasmepsins (PMs) are essential proteases of the plasmodia parasites and are therefore promising targets for developing drugs against malaria. We have discovered six inhibitors of PM II by high-throughput fragment-based docking of a diversity set of approximately 40,000 molecules, and consensus scoring with force field energy functions. Using the common scaffold of the three most active inhibitors (IC(50)=2-5 microM), another seven inhibitors were identified by substructure search. Furthermore, these 13 inhibitors belong to at least three different classes of compounds. The in silico approach was very effective since a total of 13 active compounds were discovered by testing only 59 molecules in an enzymatic assay. This hit rate is about one to two orders of magnitude higher than those reported for medium- and high-throughput screening techniques in vitro. Interestingly, one of the inhibitors identified by docking was halofantrine, an antimalarial drug of unknown mechanism. Explicit water molecular dynamics simulations were used to discriminate between two putative binding modes of halofantrine in PM II
Silver nanoparticles mediate differential responses in keratinocytes and fibroblasts during skin wound healing

With advances in nanotechnology, pure silver has been recently engineered into nanometer-sized particles (diameter < 100 nm) for use in the treatment of wounds. In conjunction with other studies, we previously demonstrated that the topical application of silver nanoparticles (AgNPs) can promote wound healing through the modulation of cytokines. Nonetheless, the question as to whether AgNPs can affect various skin cell types - keratinocytes and fibroblasts - during the wound-healing process still remains. Therefore, the aim of this study was to focus on the cellular response and events of dermal contraction and epidermal re-epithelialization during wound healing under the influence of AgNPs; for this we used a full-thickness excisional wound model in mice. The wounds were treated with either AgNPs or control with silver sulfadiazine, and the proliferation and biological events of keratinocytes and fibroblasts during healing were studied. Our results confirm that AgNPs can increase the rate of wound closure. On one hand, this was achieved through the promotion of proliferation and migration of keratinocytes. On the other hand, AgNPs can drive the differentiation of fibroblasts into myofibroblasts, thereby promoting wound contraction. These findings further extend our current knowledge of AgNPs in biological and cellular events and also have significant implications for the treatment of wounds in the clinical setting. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.postprin
Polycyclic N-benzamido imides with potent activity against vaccinia virus

The synthesis and antiviral activity of a series of novel polycyclic analogues of the orthopoxvirus egress inhibitor tecovirimat (ST-246) is presented. Several of these compounds display sub-micromolar activity against vaccinia virus, and were more potent than cidofovir (CDV). The more active compounds were about 10-fold more active than CDV, with minimum cytotoxic concentrations above 100 μM. Chemical manipulations of the two carbon-carbon double bonds present in the compounds were carried out to further explore the structure-activity relationships of these new polycyclic imides. Hydrogenation of the two carbon-carbon double bonds decreases antiviral activity, whereas either cyclopropanation or epoxidation of the double bonds fully eliminates the antiviral activity.status: publishe