Alkyl Polyglucoside (APG) Amendment for Improving the Phytoremediation of Pb-PAH Contaminated Soil by the AquaticPlant Scirpus triqueter

This study assessed the potential abilities of Scirpus triqueter for phytoremediation of soils contaminated with Pb-PAHs, amended with environment-friendly surfactant alkyl polyglucoside (APG). The effects of APG on the removal of PAHs from soil and the plant uptake and translocation of Pb were tested with plant growth and soil enzymatic activities. Experiments demonstrated that APG has an ability to facilitate PAH degradation and Pb uptake in the plant body at appropriate concentrations (20–40mg L^?1). The highest PAH removal rate was observed in 30 mg L^?1 APG treatment, and the highest accumulation of Pb was detected as 40 mg L^?1 APG. Experiments documented the effects of APG on plant growth, soil enzymatic activity, bioaccumulation and translocation of Pb in Scirpus triqueter. Results indicated that the addition of appropriate APG enhanced PAH removal rate and increased plant uptake and translocation of Pb.     

Effects of Temperature,pH and Salt Concentrations on the Adsorption of Bacillus subtilis on Soil Clay Minerals Investigated by Microcalorimetry

Adsorption of microorganisms on minerals is a ubiquitous interfacial phenomenon in soil. Knowledge of the extent and mechanisms of bacterial adsorption on minerals is of great agronomic and environmental importance. This study examined adsorption of Bacillus subtilis on three common minerals in soils such as kaolinite, montmorillonite and goethite under various environmental conditions. Isothermal titration calorimetry (ITC) was used to investigate the effects of temperature (20, 30, and 40°C), pH (5.0, 7.0, and 9.0) and KNO₃ concentration (0.001, 0.01, and 0.1 mol L^?1) on the adsorption by direct measurement of enthalpies. The results revealed that the adsorption process in all the mineral systems were exothermic, with the enthalpy changes (ΔH_ads ) ranging from ?52 to ?137, ?33 to ?147, and ?53 to ?141 kJ kg^?1 (dry weight of adsorbed bacteria) for kaolinite, montmorillonite, and goethite, respectively. No obvious dependence of ΔH_ads on temperature was observed. The heat release for all the systems generally declined with pH and decrease of salt concentration, which can be explained by the variations of hydrophobicity and electrostatic force with pH or salt concentration. The largest decrease was found for goethite among the three minerals from pH 5.0 to 7.0, suggesting that electrostatic attraction may play a more important role in bacterial adsorption on this mineral. The ΔH_ads values for all the minerals became nearly the same at pH 9.0, indicating that the same force probably hydrophobicity governing the adsorption for the minerals in alkaline environment. It is assumed that acidic or saline soils and the associated environments favor the adsorption of B. subtilis on clay minerals. In addition, the negative enthalpies expressed as kJ kg^?1 (carbon) revealed an energy flow into the environment accompanied by the carbon adsorption on the minerals in soil.     

Sorption and desorption of copper by and from clay minerals

Summary The sorption of Cu by different clay minerals from dilute CuSO₄ solutions was studied as a function of pH. It was found that Cu sorption increased with increasing the equilibrium pH. The low sorption at low pH values was attributed to the competition effect of H⁺ ions and the release of octahedral Mg, Fe and Al from the 2: 1 minerals in acid solutions. The higher sorption of copper at higher pH values was related to the absence of H⁺ ions and to the increase in the pH-dependent negative charge in kaolinite and gibbsite.The desorption of copper using solutions of 1 N NaCl at different pH values indicated that kaolinite and montmorillonite released large amounts of their adsorbed Cu even at high pH values. Vermiculite, on the other hand, exhibited a strong retention of Cu against extraction with NaCl. Oven-drying had no significant effect on the desorption characteristics of the Cu-saturated clays.The Ca-Cu exchange isotherms on montmorillonite were studied at two different pH values. The isotherms indicated a preference of Ca at the lower pH (pH 3.5), with K = 0.931 and G = +41.0 cal./mole. At the higher pH (5.2) the isotherms indicated a preference of Cu with K = 1.282 and G = –141.0 cal./mole. The difference was attributed to the competition of H⁺ at low pH.     

Adhesion of the dissimilatory Fe(III)-reducing bacterium Shewanella alga BrY to crystalline Fe(III) oxides

Shewanella alga BrY adhesion to hydrous ferric oxide, goethite, and hematite was examined. Adhesion to each oxide followed the Langmuir adsorption model. No correlation between adhesion and Fe(III) oxide surface area or crystallinity was observed. Zeta potential measurements suggested that electrostatic interactions do not influence S. alga BrY adhesion to these minerals. Cell adhesion does not appear to explain the recalcitrance of crystalline Fe(III) oxides to bacterial reduction. Received: 12 May 2000 / Accepted: 19 June 2000     

Presence of Siderophores on Grape Marc Aerated Compost Tea

Please click here to view a statement of retraction concerning this article.     

Integrating Microbial Composting and Vermicomposting for Effective Utilization of By-products of Sugar Cane–Processing Industries

Please click here to view a statement of retraction concerning this article.     

Tropomyosin Isoform Expression Regulates the Transition of Adhesions To Determine Cell Speed and Direction

The balance of transition between distinct adhesion types contributes to the regulation of mesenchymal cell migration, and the characteristic association of adhesions with actin filaments led us to question the role of actin filament-associating proteins in the transition between adhesive states. Tropomyosin isoform association with actin filaments imparts distinct filament structures, and we have thus investigated the role for tropomyosins in determining the formation of distinct adhesion structures. Using combinations of overexpression, knockdown, and knockout approaches, we establish that Tm5NM1 preferentially stabilizes focal adhesions and drives the transition to fibrillar adhesions via stabilization of actin filaments. Moreover, our data suggest that the expression of Tm5NM1 is a critical determinant of paxillin phosphorylation, a signaling event that is necessary for focal adhesion disassembly. Thus, we propose that Tm5NM1 can regulate the feedback loop between focal adhesion disassembly and focal complex formation at the leading edge that is required for productive and directed cell movement.Among the different modes of migration that cells adopt, mesenchymal cell migration is dependent on integrin-based adhesion to the extracellular matrix (14), and the cellular mechanisms regulating integrin adhesion formation and turnover (adhesion dynamics) are integral to this process. The fate of integrin adhesions is intimately linked with filaments of polymerized actin (4). At the molecular level, actin filaments are highly dynamic, and this aspect of actin polymer biology provides an important control mechanism by which cells can organize filaments into structures with distinct properties. Tropomyosins are a multi-isoform family of actin-associating proteins that confer isoform-specific regulation of diverse actin filaments (3, 16, 34, 35). The interdependence of integrin adhesions and actin filaments suggests that expression of actin-associated proteins such as the tropomyosins may represent a mechanism for the regulation of adhesion dynamics that determine cell migration.In migrating cells small integrin-based focal complexes form at the periphery of lamellipodial extensions (32). These complexes are characterized by their subcellular distribution, dot-like shape, dependence on Rac activity, phosphorylated paxillin, and association with the network of short, branched actin filaments at the leading edge. The focal complexes are short lived (43) but provide strong traction forces at the leading edge (2) and most likely regulate directional migration (19). Subsets of focal complexes mature into focal adhesions, structures characterized by: Rho GTPase and Rho kinase dependence, dash-like shape, high levels of paxillin and phosphorylated paxillin, and low levels of the actin-binding molecule tensin (43, 44). The focal adhesions play an important role in anchoring bundles of polymerized actin stress fibers, providing the contractile force necessary for the translocation of the cell body during migration. There are at least three distinct classes of stress fibers observed in migrating cells (20, 27). Dorsal stress fibers are inserted into focal adhesions at the ventral surface of the cell. The distal end of the dorsal fibers can associate with a second type of actin fiber, the transverse arcs that run parallel to the leading edge and are not directly connected to focal adhesions. Ventral stress fibers have focal adhesions at either end and can be established following the contraction of two dorsal stress fibers and the associated transverse arc to form one actin bundle (20).Increased ventral stress fibers and focal adhesions are characteristic of nonmotile cells, in contrast, cell migration depends on focal adhesion turnover at the leading edge, allowing the formation of newly protruding regions of membrane and focal complex formation (28, 39). While the precise mechanism of focal adhesion turnover is incompletely understood, activation and phosphorylation of Src kinase, p130Cas, and paxillin (13, 39, 45) have all been implicated in focal adhesion turnover. A biphasic relationship between cell adhesion and cell speed suggests that conditions that alter the turnover rate of focal adhesions (either too much or too little) can reduce cell speed (18, 22).In cells with a fibroblastic phenotype, increased levels of acto-myosin contractility promote focal adhesion transition to fibrillar adhesions (also known as ECM contacts) (6, 7): elongated, thin, central arrays of dots or elongated fibrils that characteristically contain tensin but low levels of phosphorylated paxillin (29, 44, 45) and bind fibrils of fibronectin parallel to actin bundles (23, 29). These adhesions are formed by ligand-occupied fibronectin integrin receptor translocation from focal adhesions along bundles of actin filaments toward the cell center, and the process is dependent on an intact actin cytoskeleton and myosin activity (29). Receptor translocation stimulates matrix reorganization by transmitting cytoskeleton-generated tension through the integrin receptors onto the surrounding matrix (25, 29). The rate of receptor translocation is apparently independent from the rate of cell migration (29). However, the cytoskeletal tension that causes the fibrillar adhesion formation is also reported to decrease paxillin phosphorylation (45). Since phosphorylated paxillin is required for the generation of new focal complexes (45), conditions which switch the balance of adhesion in favor of fibrillar adhesion should presumably result in significantly reduced paxillin phosphorylation, leading to reduced focal adhesion turnover and correspondingly decreased cell migration.The cytoskeletal tropomyosin Tm5NM1 is a broadly distributed isoform (37) that alters cell shape (34), localizes to and promotes stress fibers that are resistant to actin depolymerizing drugs (9), enhances myosin IIA activation and recruitment to stress fibers, and inhibits cell migration (3). Therefore, we hypothesized that Tm5NM1 expression might determine cell migration by coordinating actin-dependent transition toward a predominance of focal adhesions and fibrillar adhesions. Using overexpression, knockdown, and genetic knockout models, we demonstrate that Tm5NM1 inhibits cell migration by promoting selective stabilization of focal adhesions and transition to fibrillar adhesions via the regulation of paxillin phosphorylation.     

An Efficient Alternative Route To 3,6-Disubstituted-Furo[2,3-d]Pyrimidin-2-One Analogues

Copper(I)-catalyzed 5-endo-dig cyclizations of 5-(alkyn-1-yl)uracil derivatives had given poor yields of substituted furo[2 Robins, M. J. and Barr, P. J. 1983. Nucleic acid related compounds. 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides. J. Org. Chem, 48: 1854–1862. [CSA][CROSSREF][Crossref], [Web of Science ®] , [Google Scholar], 3 De Clercq, E., Descamps, J., Balzarini, J., Giziewicz, J., Barr, P. J. and Robins, M. J. 1983. Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides. J. Med. Chem, 26: 661–666. [PUBMED][INFOTRIEVE][CSA][CROSSREF][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]pyrimidin-2-ones unless the uracil ring was substituted at N1 with alkyl or glycosyl groups. This limited flexibility for the synthesis of analogues with varied substituents at N3 and/or C6 of the furo[2 Robins, M. J. and Barr, P. J. 1983. Nucleic acid related compounds. 39. Efficient conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and nucleosides. J. Org. Chem, 48: 1854–1862. [CSA][CROSSREF][Crossref], [Web of Science ®] , [Google Scholar], 3 De Clercq, E., Descamps, J., Balzarini, J., Giziewicz, J., Barr, P. J. and Robins, M. J. 1983. Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides. J. Med. Chem, 26: 661–666. [PUBMED][INFOTRIEVE][CSA][CROSSREF][Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]pyrimidin-2-one core has been overcome with 5-(3-hydroxyalkyn-1-yl)uracil compounds with no substituent at N1. Manipulation of the side-chain hydroxyl group gives access to additional furo[2,3-d]pyrimidin-2-one analogues.     

Bt毒素在三种矿物表面的吸附与解吸

研究了Bt库斯塔克亚种(kurstaki）毒素（65 kDa）在高岭土、针铁矿和氧化硅表面的吸附和解吸特性.结果表明：在磷酸盐缓冲体系（pH 8）中,3种矿物的等温吸附曲线均符合Langmuir方程（R²>0.9661）,它们对Bt毒素的吸附顺序为：针铁矿﹥高岭土﹥二氧化硅.矿物对Bt毒素的吸附1 h就基本达到了吸附平衡.在pH 6～8范围内,针铁矿、高岭土和二氧化硅对Bt毒素的吸附量随pH值的升高而降低.10 ℃～50 ℃范围内,针铁矿和氧化硅对Bt毒素吸附量随温度升高有所下降（8.39％和47.06％）,高岭土对Bt毒素吸附则略有升高（5.91％）.红外光谱分析显示,Bt毒素被矿物吸附后结构仅有微小变化.被矿物吸附的Bt毒素不易被去离子水解吸,水洗3次总解吸率为28.48%～42.04%.     

A possible strategy against head and neck cancer: in silico investigation of three-in-one inhibitors

Overexpression of epidermal growth factor receptor (EGFR), Her2, and uroporphyrinogen decarboxylase (UROD) occurs in a variety of malignant tumor tissues. UROD has potential to modulate tumor response of radiotherapy for head and neck cancer, and EGFR and Her2 are common drug targets for the treatment of head and neck cancer. This study attempts to find a possible lead compound backbone from TCM Database@Taiwan (http://tcm.cmu.edu.tw/) for EGFR, Her2, and UROD proteins against head and neck cancer using computational techniques. Possible traditional Chinese medicine (TCM) lead compounds had potential binding affinities with EGFR, Her2, and UROD proteins. The candidates formed stable interactions with residues Arg803, Thr854 in EGFR, residues Thr862, Asp863 in Her2 protein, and residues Arg37, Arg41 in UROD protein, which are key residues in the binding or catalytic domain of EGFR, Her2, and UROD proteins. Thus, the TCM candidates indicated a possible molecule backbone for evolving potential inhibitors for three drug target proteins against head and neck cancer.

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:35     

Investigation of silent information regulator 1 (Sirt1) agonists from Traditional Chinese Medicine

Silent information regulator 1 (Sirt1), a class III nicotinamide adenine dinucleotide dependent histone deacetylases, is important in cardioprotection, neuroprotection, metabolic disease, calorie restriction, and diseases associated with aging. Traditional Chinese Medicine (TCM) compounds from TCM Database@Taiwan (http://tcm.cmu.edu.tw/) were employed for screening potent Sirt1 agonists, and molecular dynamics (MD) simulation was implemented to simulate ligand optimum docking poses and protein structure under dynamic conditions. TCM compounds such as (S)-tryptophan-betaxanthin, 5-O-feruloylquinic acid, and RosA exhibited good binding affinity across different computational methods, and their drug-like potential were validated by MD simulation. Docking poses indicate that the carboxylic group of the three candidates generated H-bonds with residues in the protein chain from Ser441 to Lys444 and formed H-bond, π–cation interactions, or hydrophobic contacts with Phe297 and key active residue, His363. During MD, stable π–cation interactions with residues Phe273 or Arg274 were formed by (S)-tryptophan-betaxanthin and RosA. All candidates were anchored to His363 by stable π- or H-bonds. Hence, we propose (S)-tryptophan-betaxanthin, 5-O-feruloylquinic acid, and RosA as potential lead compounds that can be further tested in drug development process for diseases associated with aging

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:28     

The Virtues of Theory: How Some Academics Succeeded – Big Time – in Reaching Non-Academic Audiences

ABSTRACT

This is a short essay stimulated by Why Anthropologists Don’t Reach the Public: A Rumination on Books of Thomas Hylland Eriksen, by Gordon Mathews (DOI: https://doi.org/10.1080/00664677.2018.1502074).     

Adsorption of DNA by Bacteria and Their Composites with Minerals

Previous studies revealed the thermodynamic properties of DNA adsorption on pure minerals or biomasses; however, there has been little attempt to develop such studies on bacteria–mineral composites. Equilibrium adsorption experiments, attenuated total reflectance Fourier transform infrared spectroscopy, and isothermal titration calorimetry were employed to investigate the adsorption of DNA by Bacillus subtilis, Pseudomonas putida, and their composites with minerals. Similar capacity and affinity were observed for DNA adsorption on two bacterial cells. However, different patterns were found in the adsorption of DNA by bacteria–mineral composites. The Gram-positive bacterium B. subtilis enhanced the adsorption of DNA on its mineral composites compared with their individual components, while the composites of Gram-negative bacterial cells with kaolinite and goethite bound lower amounts of DNA than the predicted values. The thermodynamic parameters and the Fourier transform infrared spectra showed that van der Waals force and hydrogen bonding are responsible for the DNA adsorption on B. subtilis–minerals and P. putida–kaolinite. By contrast, the entropy increases of excluded water rearrangement and dehydration effect play key roles in the interaction between DNA and P. putida–montmorillonite/goethite composites.     

Soil Colloids and Minerals Modulate Metabolic Activity of Pseudomonas putida Measured Using Microcalorimetry

Substantial interactions of microbes with soil particles present fundamental influences on microbial activities relevant to a series of biogeochemical processes. However, how soil surface-active particles modulate microbial metabolism has received scant attention. The extent to which composition of soil colloids alter the metabolism is not well addressed. This work examined the impacts of soil colloids and minerals on the metabolic activity of Pseudomonas putida using microcalorimetry and carbon utilization. The results showed that montmorillonite remarkably improved metabolic activity of P. putida, whereas kaolinite, goethite and soil colloids significantly inhibited the activity. Humus may weaken the inhibition of soil colloids on bacterial metabolism via interfacial interaction rather than nutrient supplements. Soils bearing higher amount of kaolinite and iron oxide may have greater depression on bacterial activity. The thermodynamic method provides different and complementary information to that from other techniques in characterizing microbial activities. The quantity and affinity for the adhesion of bacteria onto soil components together with the detoxification of metabolites were assigned to the modifications of bacterial activities.     

Type I Phosphatidylinositol Phosphate Kinase Beta Regulates Focal Adhesion Disassembly by Promoting β1 Integrin Endocytosis

Cell migration requires the regulated disassembly of focal adhesions, but the underlying mechanisms remain poorly defined. We have previously shown that focal adhesion disassembly requires the dynamin 2- and clathrin-dependent endocytosis of ligand-activated β1 integrins. Here, we identify type I phosphatidylinositol phosphate kinase beta (PIPKIβ), an enzyme that generates phosphatidylinositol-4,5-bisphosphate (PI4,5P₂), as a key regulator of this process. We found that knockdown of PIPKIβ by RNA interference blocks the internalization of active β1 integrins and impairs focal adhesion turnover and cell migration. These defects are caused by the failure to target the endocytic machinery, including clathrin adaptors and dynamin 2, to focal adhesion sites. As a consequence, depletion of PIPKIβ blocks clathrin assembly at adhesion plaques and prevents complex formation between dynamin 2 and focal adhesion kinase (FAK), a critical step in focal adhesion turnover. Together, our findings identify PIPKIβ as a novel regulator of focal adhesion disassembly and suggest that PIPKIβ spatially regulates integrin endocytosis at adhesion sites to control cell migration.Cell migration is a highly dynamic process that depends on the ability of a cell to adhere to and deadhere from the extracellular matrix in a coordinated manner. Adhesion is mediated through focal adhesion sites, which assemble in response to activation and clustering of integrin receptors and comprise signaling and scaffolding proteins, such as focal adhesion kinase (FAK), talin, vinculin, paxillin, and zyxin (9, 55). These complexes anchor the extracellular matrix to the actin cytoskeleton and also serve as signaling platforms (9, 55). The formation of adhesive complexes is essential for the stabilization of membrane protrusions and to provide the tensile forces for migration (9, 55). However, rapid cell movement requires that focal adhesions not only be continuously formed, but also disassembled (9, 56). The coordinated control of cell adhesion, and release thereof, is therefore a critical regulatory function for migrating cells. However, while much has been learned about the mechanisms underlying focal adhesion assembly, comparatively little is known about how the turnover of adhesion sites is regulated, despite the importance of this process for cell migration.Recently, the protease calpain, FAK, and phosphatases and kinases that control the activity of FAK, as well as microtubules and the large GTPase dynamin 2, have been identified as regulators of focal adhesion disassembly (9, 10, 21, 22). In particular, a pathway has been defined in which microtubule targeting of focal adhesions leads to their disassembly (21). A critical step in this process is the formation of a protein complex between FAK and dynamin 2, a key regulator of endocytosis (21). Dynamin 2, together with components of the clathrin machinery, then mediates the turnover of focal adhesions by promoting the internalization of β1 integrins (14, 41). Notably, dynamin 2 and clathrin adaptors become enriched at focal adhesion sites prior to their disassembly (14, 21). Therefore, mechanisms that control the recruitment of the endocytic machinery to focal adhesion sites must exist. However, how this process is regulated during focal adhesion turnover remains unknown.Phosphatidylinositol-4,5-bisphosphate (PI4,5P₂) has recently emerged as an important regulator of focal adhesion dynamics (38, 47, 51, 57). In addition to serving as the precursor to other second messengers, PI4,5P₂ directly binds and modulates many focal adhesion components, including talin, vinculin, and α-actinin, that regulate adhesion assembly and their linkage to the actin cytoskeleton (38, 47, 51, 57). Adhesion to the extracellular matrix stimulates the synthesis of PI4,5P₂, and the general paradigm has been that the resulting local increase in PI4,5P₂ levels promotes focal adhesion assembly (23, 38, 40). Intriguingly, emerging evidence suggests that PI4,5P₂ also promotes the disassembly of focal adhesions (13, 46). This finding implies that PI4,5P₂ levels at adhesion sites must be tightly regulated, both spatially and temporally, to elicit its specific, yet inverse, effects on focal adhesion dynamics.The generation of PI4,5P₂ at specific subcellular sites is modulated in part by the selective targeting and activation of specific type I phosphatidylinositol phosphate kinases (PIPKI), which synthesize PI4,5P₂ (38). Three related PIPKI isoforms, designated PIPKIα, PIPKIβ, and PIPKIγ, and multiple splice variants are present in mammalian cells (27, 28, 39, 49). Recent studies have shown that the increase of PI4,5P₂ synthesis leading to focal adhesion assembly is mediated through the specific recruitment of PIPKIγ661, a splice variant of PIPKIγ, to focal adhesions (18, 37). However, whether PIPKIγ661 or another member of the PIPKI family is responsible for synthesizing the PI4,5P₂ pool regulating focal adhesion disassembly is currently unknown, and the molecular mechanisms whereby PI4,5P₂ regulates this process are not well defined.Coincidently, PI4,5P₂ is also an important organizer of clathrin assembly at the plasma membrane (17). In this study, we therefore set out to determine whether PI4,5P₂ promotes focal adhesion disassembly through its effects on endocytosis and to identify the PIPKI isoform involved in generating this pool of PI4,5P₂. We show that knockdown of one specific PIPKI isoform, PIPKIβ, blocks adhesion turnover leading to the inhibition of cell migration. We further show that PIPKIβ is necessary for the uptake of activated β1 integrins and provide evidence that PI4,5P₂ produced by PIPKIβ orchestrates the recruitment of components of the endocytic machinery to adhesion sites. Together, these studies define the role of PI4,5P₂ in the regulation of focal adhesion disassembly and identify PIPKIβ as the enzyme synthesizing this pool of PI4,5P₂.     

Early Miocene rodents of Gökler (Kazan Basin,Central Anatolia,Turkey)

Abstract

The rich and relatively diverse fossil mammalian assemblage from Gökler is of special importance for understanding of faunal evolution in Central Anatolia. Large mammals were not recovered, but insectivores and rodents are abundant. The assemblage of rodents is studied in detail and comprises mainly diversified cricetids. Dormice are abundant, but are represented by only one species. Squirrels are represented only by few specimens and also beaver remains were identified. Spanocricetodon sinuosus is referred to a new genus Latocricetodon nov. gen that is tentatively assigned to the Pseudocricetodontinae. Newly named species are Cricetodon goklerensis sp. nov., Democricetodon haltmari sp. nov., Eumyarion lukasi sp. nov. and Glirudinus matusi sp. nov. The rodent assemblage is assigned to local zone C which is correlated to the European biounit MN2 (early Miocene). Our biochronological assessment is supported by radiometric dating from two volcanic ash layers.

Latocricetodon

LSID http://zoobank.org/urn:lsid:zoobank.org:act:3414DB1E-0C5E-4154-BE5E-02A9ED183B1A

Cricetodon goklerensis

LSID http://zoobank.org/urn:lsid:zoobank.org:act:1B658872-6C10-4355-B87C-3E6277AF4EDA

Democricetodon haltmari

LSID http://zoobank.org/urn:lsid:zoobank.org:act:9B13F956-7F8C-406A-9970-1F5E999E54C6

Eumyarion lukasi

LSID http://zoobank.org/urn:lsid:zoobank.org:act:34DED87E-855F-4969-AB84-10BED5C572BF

Glirudinus matusi

LSID http://zoobank.org/urn:lsid:zoobank.org:act:798ECB9A-E3B5-4C38-B5B3-FEB17AF734FE     

Molecular Architecture and Function of Matrix Adhesions

Cell adhesions mediate important bidirectional interactions between cells and the extracellular matrix. They provide an interactive interface between the extracellular chemical and physical environment and the cellular scaffolding and signaling machinery. This dynamic, reciprocal regulation of intracellular processes and the matrix is mediated by membrane receptors such as the integrins, as well as many other components that comprise the adhesome. Adhesome constituents assemble themselves into different types of cell adhesion structures that vary in molecular complexity and change over time. These cell adhesions play crucial roles in cell migration, proliferation, and determination of cell fate.With the emergence of metazoan life approximately 600 million years ago, new biological mechanisms arose during the evolution of multicellular organisms with a defined body plan. These mechanisms of cell adhesion are a fundamental feature of all metazoans, from sponges to humans; they enable cells to attach to each other or to an extracellular matrix (ECM), cementing them together and organizing them into a coherent whole. The formation of adhesions and the regulation of their dynamics are crucial for embryogenesis, immune cell function, and wound repair, but they also contribute to disease, including cancer invasion and metastasis, or immune disorders (Hay 1991; Hynes 2002; Berrier and Yamada 2007; Alberts et al. 2008; Mory et al. 2008; Dubash et al. 2009; Manevich-Mendelson et al. 2009; Svensson et al. 2009; Wolfenson et al. 2009a). Adhesive interactions can occur with remarkable temporal and spatial precision. As illustrated in Figure 1, they not only link cells together into functional tissues and organs, but they also convey to the adhering cells accurate positional information concerning their cellular and extracellular environment. This information can, in turn, affect all facets of the cell’s life—its proliferation, differentiation, and fate. In addition to responding to the matrix, cell adhesions can actively remodel and restructure the ECM, driving a reciprocal, bidirectional interaction between the cell and its surrounding matrix. These two fundamental aspects of cell–ECM adhesion—physical/structural roles and environmental sensing/signaling, as well as the dynamic molecular interrelationships between them—will be the primary subjects of this article.Open in a separate windowFigure 1.Schematic illustration highlighting the dynamic cross talk between cells and the extracellular matrix (ECM). Cells secrete and remodel the ECM, and the ECM contributes to the assembly of individual cells into tissues, affecting this process at both receptor and cytoskeletal levels. Adhesion-mediated signaling, based on the cells’ capacity to sense the chemical and physical properties of the matrix, affects both global cell physiology and local molecular scaffolding of the adhesion sites. The molecular interactions within the adhesion site stimulate, in turn, the signaling process, by clustering together the structural and signaling components of the adhesome.We will also describe the functional molecular architecture of cell–matrix adhesions, highlighting the structure–function relationships between the numerous components of cell adhesions that mediate or modulate numerous cell adhesive, migratory, and regulatory processes. We will discuss the mechanisms underlying the scaffolding and sensing processes generated at integrin-mediated adhesions, considering them along two major multiscale conceptual trajectories: molecular complexity and time—that is, a hierarchy of complexity that spans the range from molecules to multimolecular complexes in mature adhesions, as well as the temporal progression of structures during the assembly and maturation of matrix adhesions, from initial cell–matrix recognition to the formation, maturation, and reorganization of cytoskeleton-associated matrix adhesions.     

Arf GTPase-activating Protein AGAP2 Regulates Focal Adhesion Kinase Activity and Focal Adhesion Remodeling

Focal adhesions are specialized sites of cell attachment to the extracellular matrix where integrin receptors link extracellular matrix to the actin cytoskeleton, and they are constantly remodeled during cell migration. Focal adhesion kinase (FAK) is an important regulator of focal adhesion remodeling. AGAP2 is an Arf GTPase-activating protein that regulates endosomal trafficking and is overexpressed in different human cancers. Here we examined the regulation of the FAK activity and the focal adhesion remodeling by AGAP2. Our results show that FAK binds the pleckstrin homology domain of AGAP2, and the binding is independent of FAK activation following epidermal growth factor receptor stimulation. Overexpression of AGAP2 augments the activity of FAK, and concordantly, the knockdown of AGAP2 expression with RNA interference attenuates the FAK activity stimulated by epidermal growth factor or platelet-derived growth factor receptors. AGAP2 is localized to the focal adhesions, and its overexpression results in dissolution of the focal adhesions, whereas knockdown of its expression stabilizes them. The AGAP2-induced dissolution of the focal adhesions is independent of its GTPase-activating protein activity but may involve its N-terminal G protein-like domain. Our results indicate that AGAP2 regulates the FAK activity and the focal adhesion disassembly during cell migration.Focal adhesions are macromolecular structures that connect actin cytoskeleton to the extracellular matrix and play an important role in cell migration (1). Components of focal adhesions include signaling proteins such as focal adhesion kinase (FAK),³ c-Src, and paxillin, as well as structural proteins such as talin and vinculin (2, 3). Focal adhesions are constantly formed and disassembled (i.e. remodeled) at the leading edge of migrating cells, and they are disassembled at the trailing edge during the cell migration (4, 5). Available evidence demonstrates that the remodeling of focal adhesions is regulated by FAK (6) and Arf-directed GTPase-activating proteins (Arf GAPs) (7).FAK is a member of the Src family nonreceptor tyrosine kinases whose activities are regulated by intra-molecular phosphorylation (8). Autophosphorylation of FAK on tyrosine residue 397 provides docking sites for Src homology 2 domain-containing proteins, including c-Src. After binding to FAK, c-Src phosphorylates FAK on Tyr-576 and Tyr-577 to activate fully the intrinsic kinase activity of FAK (9). Cellular functions of FAK are many and include cell migration, survival, and proliferation; and activation of FAK occurs upon integrin clustering or stimulation of cell surface receptors such as the epidermal growth factor (EGF) or platelet-derived growth factor (PDGF) receptors. FAK activation following integrin clustering results in recruitment of structural and signaling proteins that collectively contribute to the formation of the focal adhesions (10). In FAK null cells, focal adhesions are formed but cannot disassemble (11), suggesting that FAK is required for the focal adhesion disassembly.ADP-ribosylation factors (Arfs) are GTP-binding proteins that lack detectable intrinsic GTPase activities. Therefore, hydrolysis of GTP bound to Arf is mediated by Arf GAPs (12, 13). The AZAP family of Arf GAPs are multidomain proteins that contain a catalytic core of pleckstrin homology (PH), Arf GAP, and ankyrin repeat domains (14), and each subgroup possesses characteristic domain(s). For example, ASAPs have a BAR (Bin, Amphiphysin, Rvs) domain at their N termini and a Src homology 3 domain at their C termini; ARAPs have a Rho GAP domain and five PH domains; and AGAPs have a G protein-like domain (GLD) at their N termini and their PH domains are split, i.e. there is an insert of 80–100 amino acids between the β5 strand and β6 strand. The Arf GAPs regulate membrane trafficking and remodeling of the actin cytoskeleton (7, 15), but the molecular mechanisms underlying the contribution of individual Arf GAPs to membrane trafficking and actin remodeling are being defined. We have reported that AGAP2 binds the clathrin adaptor protein AP-1 and regulates the AP-1/Rab4-dependent endosomal trafficking (16). Studies from other groups have indicated that AGAP2 is overexpressed in different human cancers, including glioblastoma, and that AGAP2 enhances the invasion of glioblastoma cells (17, 18).In this study, we tested the hypothesis that AGAP2 regulates focal adhesion remodeling and cell migration. We find that AGAP2 forms a complex with FAK, increases the FAK activity, and provokes the focal adhesion disassembly that may lead to increased cell migration. Some Arf GAPs have been shown to regulate focal adhesions, and each Arf GAP seems to regulate the focal adhesions by a distinct mechanism. Our results introduce a new way to regulate the focal adhesions by the Arf GAP AGAP2, i.e. through the regulation of FAK activity. These observations support the idea that various Arf GAPs function coordinately to provide temporal and spatial regulation of the focal adhesions during cell migration.     

Leaching of BTEX from Aged Crude Oil Contaminated Model Soils: Experimental and Modeling Results

It is generally assumed that soil properties such as organic matter content, porosity, and mineral surface area have a significant effect on the bioavailability and leachability of aged petroleum hydrocarbons. In order to test this hypothesis, nine model soils or sorbents (i.e., fine and coarse quartz sand, montmorillonite and kaolinite clay, peat, 60Å and 150Å silica gel, a loam soil, and non-porous glass beads) were spiked with a crude oil, aged for 27 months in the laboratory, and transferred to glass columns for the performance of continuous flow leaching experiments. The column effluents were periodically sampled for 43 days and analyzed for BTEX. A one-dimensional flow model for predicting the dissolution and dispersion of individual hydrocarbons from a multi-component NAPL such as crude oil was used to fit the leaching data (i.e., the BTEX concentration versus time curves) by adjusting the equilibrium oil-leachate partitioning coefficient (K ^ol ) for each respective hydrocarbon. The Peclet number, which is a measure of dispersion and a required modeling parameter, was measured in separate chloride tracer experiments for each soil column.

Results demonstrate that soil properties did not significantly affect the leaching kinetics of BTEX from the columns. Instead, BTEX leaching curves could be successfully fitted with the one-dimensional NAPL dissolution flow model for all sorbents with the exception of montmorillonite clay. The fitting parameter K ^ol for each hydrocarbon was found to be similar to the K ^ol values that were independently measured for the same crude oil by Rixey et al. (Journal of Hazardous Materials B, 65: 137–156, 1999 Rixey, W. G., Garg, S. and Nie, Y. 1999. Comparison of the fixed-bed and batch leaching characteristics of aromatic compounds in residually trapped crude oils and oily wastes. J. Hazard. Mat. B, 64: 137–156. [CSA][CROSSREF] [Google Scholar]). In addition, the fitted K ^ol values were very similar for BTEX leaching from aged compared to freshly spiked loam soil. These findings indicate that leaching of BTEX in the aged soils that are contaminated with crude oil at the high concentrations commonly found in the environment (i.e., > 20,000 mg/kg) was not affected by soil properties or aging but rather was governed by the equilibrium dissolution of these hydrocarbons from the crude oil NAPL that is coating the soil particles.