bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of biochar in modifying the environmental fate, bioavailability, and efficacy of pesticides in soils: a review
Authors: Kookana Rai S.
Published: September 2010

The role of biochar in sequestration of carbon, reducing the emission of greenhouse gases, and improving the soil fertility is increasingly being recognised and is leading to the recommendations of biochar amendment of soils. However, the implications of such amendments to the environmental fate and efficacy of pesticides are not well understood. The published work on the role of black carbon (which includes charcoal, soot, and other pyrolytic carbon materials) in the environmental fate and effect of organic contaminants is reviewed here, together with the studies on bioavailability and efficacy of some herbicides in soils amended with freshly produced biochars. Biochars, due to their unique properties especially their highly carbonaceous and aromatic nature and high specific surface area, have been reported to be up to >2000 times more effective than soil in sorbing pesticides. The incorporation of relatively small amounts of fresh biochars in soil (0.05% by wt) has also been shown to inhibit the microbial degradation of organic compounds including pesticides as well as reduce their plant availability and efficacy. Based on limited published research on biochars and related research on black carbon reviewed here, biochar amendments to soils are likely to reduce the bioavailability and efficacy of pesticides. Furthermore, these amendments can influence the potential accumulation and ecotoxicological impact of pesticides and other organic contaminants in the soil environment. The implications of heterogeneity and ageing of biochars applied to soils for sorption and desorption processes and in turn for other environmental fate processes need to be understood to seek the appropriate balance between carbon sequestration and pesticide efficacy. While biochar amendment of soil holds appeal from a carbon accounting and soil conditioning perspective, further research is urgently required to determine how biochar influences the efficacy and environmental fate of agrochemicals such as pesticides.
Influence of biochar use on sugarcane growth, soil parameters, and groundwater quality
Authors: Chen Yan , Shinogi Yoshiyuki , Taira Masahiko
Published: September 2010

This study deals with the influence of biochar use on sugarcane growth and nitrate-nitrogen percolation losses, as well as chemical and physical properties of Shimajiri maji soil. Two varieties of biochars, biosolids and bagasse (residues of sugarcane stalks after juice extraction), were mixed with Shimajiri maji soil. Changes in nitrate-nitrogen concentration in percolating water, specific gravity, and available soil moisture before sugarcane planting and after harvest were investigated. Indices of sugarcane growth (stem diameter and length), Brix, and yield of estimated available sugar in each plot were estimated.
Results indicated that bagasse charcoal reduced soil dry density and increased available moisture of Shimajiri maji soil. Maintaining suitable soil water content increased yields and sugar content of sugarcane, while nitrate-nitrogen concentration in percolating water also decreased. Hence, bagasse charcoal use may reduce nitrogen loads in Shimajiri maji soil.
Retention capacity of biochar-amended New Zealand dairy farm soil for an estrogenic steroid hormone and its primary metabolite
Authors: Sarmah Ajit K. , Srinivasan Prakash , Smernik Ronald J. , Manley-Harris Merilyn , Antal Michael Jerry , Downie Adriana , van Zwieten Lukas
Published: September 2010

We examined the retention ability of a New Zealand dairy farm soil amended with 3 types of biochar produced from a variety of feedstocks for a steroid hormone (oestradiol, E2) and its primary transformation product (estrone, E1). Biochars produced from corn cob (CC), pine sawdust (PSD) and green waste (GW) were characterised by scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, and solid-state 13C nuclear magnetic resonance spectroscopy. Batch sorption studies were performed on soil amended with each biochar (0.5% and 1% by weight) using a complex solvent extraction scheme, and isotherms were fitted to the Freundlich model.
All isotherms were highly non-linear, with N values in the range 0.46–0.83 (E2) and 0.66–0.88 (E1) in soil amended with different percentages of biochars. Overall, addition of all 3 biochars was found to increase the soil sorption affinity for the hormones, with E2 sorption being the highest in the soil amended with 1% PSD biochar. There was no marked difference in hormone sorption ability in the other 2 treatments (soil treated with 1% CC biochar and 1% GW biochar). Overall, the effective distribution coefficient (Kdeff) values for E2 at the lowest equilibrium concentration (Cw 0.5 mg/L) ranged from 35 to 311 L/kg in soil amended with the 3 types of biochar. Addition of 0.5% of PSD biochar resulted in ~560% increase in the Kdeff value for E2, while at 1% addition of PSD biochar, uptake of E2 was nearly 1400% higher than the control. For E1, the percentage increase in Kdeff was comparatively smaller than E2; however, it still ranged from 40 to 280%, and 60 to >320% at addition of 0.5% and 1% PSD biochar, respectively, compared with the control soil. Highest treatment temperature and associated greater surface area, low ash content, higher carbon content, and the abundance of polar functional groups (e.g. –OH, C=O) may explain why the soil amended with PSD biochar exhibited high sorptive capacity for the hormones.
Producing biochars with enhanced surface activity through alkaline pretreatment of feedstocks
Authors: Hina K. , Bishop P. , Arbestain M. Camps , Calvelo-Pereira R. , Maciá-Agulló J. A. , Hindmarsh J. , Hanly J. A. , Macías F. , Hedley M. J.
Published: September 2010

Surface-activated biochars not only represent a useful carbon sink, but can also act as useful filtering materials to extract plant nutrients (e.g. NH4+) from wastes (e.g. animal or municipal waste streams) and added thereafter to soils. Biochars produced by low-temperature pyrolysis of fibrous debarking waste from pine (PI) and eucalyptus (EU) were pre-treated with either diluted (L) or undiluted (S) alkaline tannery waste (L-PI, S-PI, L-EU, S-EU). Biochars produced from untreated feedstock were used as controls. Samples were characterised by FT-IR, solid-state CP MAS 13C NMR, XPS, SEM microphotographs, and BET specific surface area. Elemental composition, carbon recovery, yield, surface charge, and NH4+ sorption/desorption properties were also studied.
Carbon recovery was lower in biochars prepared from L-EU and S-EU (43 and 42%, respectively) than in control EU (45%) but these biochars showed greater changes in their chemical characteristics than those made from L-PI and S-PI, which showed minimal decrease in recovered carbon. The specific surface area of the biochars decreased with treatments, although acidic surface groups increased. In subsequent sorption experiments, treated biochars retained more NH4+ from a 40 mg N/L waste stream (e.g. 61% retention in control EU and 83% in S-EU). Desorption was low, especially in treated biochars relative to untreated biochars (0.1–2% v. 14–27%). The results suggest that surface activated biochars can be obtained with negligible impairment to the carbon recovered.
Disruption of theArabidopsisCGI-58 homologue produces Chanarin–Dorfman-like lipid droplet accumulation in plants
Authors: James Christopher N. , Horn Patrick J. , Case Charlene R. , Gidda Satinder K. , Zhang Daiyuan , Mullen Robert T. , Dyer John M. , Anderson Richard G. W. , Chapman Kent D.
Published: September 2010

CGI-58is the defective gene in the human neutral lipid storage disease called Chanarin-Dorfman syndrome. This disorder causes intracellular lipid droplets to accumulate in nonadipose tissues, such as skin and blood cells. Here, disruption of the homologousCGI-58gene inArabidopsis thalianaresulted in the accumulation of neutral lipid droplets in mature leaves. Mass spectroscopy of isolated lipid droplets fromcgi-58loss-of-function mutants showed they contain triacylglycerols with common leaf-specific fatty acids. Leaves of maturecgi-58plants exhibited a marked increase in absolute triacylglycerol levels, more than 10-fold higher than in wild-type plants. Lipid levels in the oil-storing seeds ofcgi-58loss-of-function plants were unchanged, and unlike mutations in β-oxidation, thecgi-58seeds germinated and grew normally, requiring no rescue with sucrose. We conclude that the participation ofCGI-58in neutral lipid homeostasis of nonfat-storing tissues is similar, although not identical, between plant and animal species. This unique insight may have implications for designing a new generation of technologies that enhance the neutral lipid content and composition of crop plants.
Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase
Authors: Bandaria Jigar N. , Dutta Samrat , Nydegger Michael W. , Rock William , Kohen Amnon , Cheatum Christopher M.
Published: September 2010

The potential for femtosecond to picosecond time-scale motions to influence the rate of the intrinsic chemical step in enzyme-catalyzed reactions is a source of significant controversy. Among the central challenges in resolving this controversy is the difficulty of experimentally characterizing thermally activated motions at this time scale in functionally relevant enzyme complexes. We report a series of measurements to address this problem using two-dimensional infrared spectroscopy to characterize the time scales of active-site motions in complexes of formate dehydrogenase with the transition-state-analog inhibitor azide (

). We observe that the frequency–frequency time correlation functions (FFCF) for the ternary complexes with NAD
+
and NADH decay completely with slow time constants of 3.2 ps and 4.6 ps, respectively. This result suggests that in the vicinity of the transition state, the active-site enzyme structure samples a narrow and relatively rigid conformational distribution indicating that the transition-state structure is well organized for the reaction. In contrast, for the binary complex, we observe a significant static contribution to the FFCF similar to what is seen in other enzymes, indicating the presence of the slow motions that occur on time scales longer than our measurement window.
Oleoyl serine, an endogenous
N
-acyl amide, modulates bone remodeling and mass
Authors: Smoum Reem , Bar Arik , Tan Bo , Milman Garry , Attar-Namdar Malka , Ofek Orr , Stuart Jordyn M. , Bajayo Alon , Tam Joseph , Kram Vardit , O'Dell David , Walker Michael J. , Bradshaw Heather B. , Bab Itai , Mechoulam Raphael
Published: September 2010

Bone mass is determined by a continuous remodeling process, whereby the mineralized matrix is being removed by osteoclasts and subsequently replaced with newly formed bone tissue produced by osteoblasts. Here we report the presence of endogenous amides of long-chain fatty acids with amino acids or with ethanolamine (
N
-acyl amides) in mouse bone. Of these compounds,
N
-oleoyl-
l
-serine (OS) had the highest activity in an osteoblast proliferation assay. In these cells, OS triggers a Gi-protein-coupled receptor and Erk1/2. It also mitigates osteoclast number by promoting osteoclast apoptosis through the inhibition of Erk1/2 phosphorylation and receptor activator of nuclear-κB ligand (RANKL) expression in bone marrow stromal cells and osteoblasts. In intact mice, OS moderately increases bone volume density mainly by inhibiting bone resorption. However, in a mouse ovariectomy (OVX) model for osteoporosis, OS effectively rescues bone loss by increasing bone formation and markedly restraining bone resorption. The differential effect of exogenous OS in the OVX vs. intact animals is apparently a result of an OVX-induced decrease in skeletal OS levels. These data show that OS is a previously unexplored lipid regulator of bone remodeling. It represents a lead to antiosteoporotic drug discovery, advantageous to currently available therapies, which are essentially either proformative or antiresorptive.
Impact of natural genetic variation on the transcriptome of autotetraploid
Arabidopsis thaliana
Authors: Yu Zheng , Haberer Georg , Matthes Michaela , Rattei Thomas , Mayer Klaus F. X. , Gierl Alfons , Torres-Ruiz Ramon A.
Published: September 2010

Polyploidy, the presence of more than two complete sets of chromosomes in an organism, has significantly shaped the genomes of angiosperms during evolution. Two forms of polyploidy are often considered: allopolyploidy, which originates from interspecies hybrids, and autopolyploidy, which originates from intraspecies genome duplication events. Besides affecting genome organization, polyploidy generates other genetic effects. Synthetic allopolyploid plants exhibit considerable transcriptome alterations, part of which are likely caused by the reunion of previously diverged regulatory hierarchies. In contrast, autopolyploids have relatively uniform genomes, suggesting lower alteration of gene expression. To evaluate the impact of intraspecies genome duplication on the transcriptome, we generated a series of unique
Arabidopsis thaliana
autotetraploids by using different ecotypes.
A. thaliana
autotetraploids show transcriptome alterations that strongly depend on their parental genome composition and include changed expression of both new genes and gene groups previously described from allopolyploid
Arabidopsis
. Alterations in gene expression are stable, nonstochastic, developmentally specific, and associated with changes in DNA methylation. We propose that
Arabidopsis
possesses an inherent and heritable ability to sense and respond to elevated, yet balanced chromosome numbers. The impact of natural variation on alteration of autotetraploid gene expression stresses its potential importance in the evolution and breeding of plants.
O-linked β-
N
-acetylglucosamine transferase is indispensable in the failing heart
Authors: Watson Lewis J. , Facundo Heberty T. , Ngoh Gladys A. , Ameen Mohamed , Brainard Robert E. , Lemma Kewakebt M. , Long Bethany W. , Prabhu Sumanth D. , Xuan Yu-Ting , Jones Steven P.
Published: September 2010

The failing heart is subject to elevated metabolic demands, adverse remodeling, chronic apoptosis, and ventricular dysfunction. The interplay among such pathologic changes is largely unknown. Several laboratories have identified a unique posttranslational modification that may have significant effects on cardiovascular function. The O-linked β-
N
-acetylglucosamine (O-GlcNAc) posttranslational modification (O-GlcNAcylation) integrates glucose metabolism with intracellular protein activity and localization. Because O-GlcNAc is derived from glucose, we hypothesized that altered O-GlcNAcylation would occur during heart failure and figure prominently in its pathophysiology. After 5 d of coronary ligation in WT mice, cardiac O-GlcNAc transferase (OGT; which adds O-GlcNAc to proteins) and levels of O-GlcNAcylation were significantly (
P
< 0.05) elevated in the surviving remote myocardium. We used inducible, cardiac myocyte-specific Cre recombinase transgenic mice crossed with loxP-flanked OGT mice to genetically delete cardiomyocyte OGT (cmOGT KO) and ascertain its role in the failing heart. After tamoxifen induction, cardiac O-GlcNAcylation of proteins and OGT levels were significantly reduced compared with WT, but not in other tissues. WT and cardiomyocyte OGT KO mice underwent nonreperfused coronary ligation and were followed for 4 wk. Although OGT deletion caused no functional change in sham-operated mice, OGT deletion in infarcted mice significantly exacerbated cardiac dysfunction compared with WT. These data provide keen insights into the pathophysiology of the failing heart and illuminate a previously unrecognized point of integration between metabolism and cardiac function in the failing heart.
Allosteric inhibition of complement function by a staphylococcal immune evasion protein
Authors: Chen Hui , Ricklin Daniel , Hammel Michal , Garcia Brandon L. , McWhorter William J. , Sfyroera Georgia , Wu You-Qiang , Tzekou Apostolia , Li Sheng , Geisbrecht Brian V. , Woods Virgil L. , Lambris John D.
Published: September 2010

The complement system is a major target of immune evasion by
Staphylococcus aureus
. Although many evasion proteins have been described, little is known about their molecular mechanisms of action. Here we demonstrate that the extracellular fibrinogen-binding protein (Efb) from
S. aureus
acts as an allosteric inhibitor by inducing conformational changes in complement fragment C3b that propagate across several domains and influence functional regions far distant from the Efb binding site. Most notably, the inhibitor impaired the interaction of C3b with complement factor B and, consequently, formation of the active C3 convertase. As this enzyme complex is critical for both activation and amplification of the complement response, its allosteric inhibition likely represents a fundamental contribution to the overall immune evasion strategy of
S. aureus
.
Induced pluripotent stem cell models of the genomic imprinting disorders Angelman and Prader–Willi syndromes
Authors: Chamberlain Stormy J. , Chen Pin-Fang , Ng Khong Y. , Bourgois-Rocha Fany , Lemtiri-Chlieh Fouad , Levine Eric S. , Lalande Marc
Published: September 2010

Angelman syndrome (AS) and Prader–Willi syndrome (PWS) are neurodevelopmental disorders of genomic imprinting. AS results from loss of function of the ubiquitin protein ligase E3A (
UBE3A
) gene, whereas the genetic defect in PWS is unknown. Although induced pluripotent stem cells (iPSCs) provide invaluable models of human disease, nuclear reprogramming could limit the usefulness of iPSCs from patients who have AS and PWS should the genomic imprint marks be disturbed by the epigenetic reprogramming process. Our iPSCs derived from patients with AS and PWS show no evidence of DNA methylation imprint erasure at the
cis
-acting PSW imprinting center. Importantly, we find that, as in normal brain, imprinting of
UBE3A
is established during neuronal differentiation of AS iPSCs, with the paternal
UBE3A
allele repressed concomitant with up-regulation of the
UBE3A
antisense transcript. These iPSC models of genomic imprinting disorders will facilitate investigation of the AS and PWS disease processes and allow study of the developmental timing and mechanism of
UBE3A
repression in human neurons.
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in
Escherichia coli
and
Mycobacterium tuberculosis
Authors: Chandrasekaran Sriram , Price Nathan D.
Published: September 2010

Prediction of metabolic changes that result from genetic or environmental perturbations has several important applications, including diagnosing metabolic disorders and discovering novel drug targets. A cardinal challenge in obtaining accurate predictions is the integration of transcriptional regulatory networks with the corresponding metabolic network. We propose a method called probabilistic regulation of metabolism (PROM) that achieves this synthesis and enables straightforward, automated, and quantitative integration of high-throughput data into constraint-based modeling, making it an ideal tool for constructing genome-scale regulatory-metabolic network models for less-studied organisms. PROM introduces probabilities to represent gene states and gene–transcription factor interactions. By using PROM, we constructed an integrated regulatory-metabolic network for the model organism,
Escherichia coli
, and demonstrated that our method based on automated inference is more accurate and comprehensive than the current state of the art, which is based on manual curation of literature. After validating the approach, we used PROM to build a genome-scale integrated metabolic-regulatory model for
Mycobacterium tuberculosis
, a critically important human pathogen. This study incorporated data from more than 1,300 microarrays, 2,000 transcription factor–target interactions regulating 3,300 metabolic reactions, and 1,905 KO phenotypes for
E. coli
and
M. tuberculosis
. PROM identified KO phenotypes with accuracies as high as 95%, and predicted growth rates quantitatively with correlation of 0.95. Importantly, PROM represents the successful integration of a top-down reconstructed, statistically inferred regulatory network with a bottom-up reconstructed, biochemically detailed metabolic network, bridging two important classes of systems biology models that are rarely combined quantitatively.
FERONIA receptor-like kinase regulates RHO GTPase signaling of root hair development
Authors: Duan Qiaohong , Kita Daniel , Li Chao , Cheung Alice Y. , Wu Hen-Ming
Published: September 2010

Plant RHO GTPases (RAC/ROPs) mediate multiple extracellular signals ranging from hormone to stress and regulate diverse cellular processes important for polarized cell growth, differentiation, development, reproduction, and responses to the environment. They shuttle between the GDP-bound inactive state and the GTP-bound activated state and their activation is predominantly mediated by a family of guanine nucleotide exchange factors (GEFs) referred to as ROPGEFs. Using the
Arabidopsis
ROPGEF1 as bait, we identified members of a receptor-like kinase (RLK) family as potential upstream regulators for RAC/ROP signaling. NADPH oxidase-derived reactive oxygen species (ROS) are emerging as important regulators for growth and development and play a crucial role in mediating RAC/ROP-regulated root hair development, a polarized cell growth process. We therefore screened T-DNA insertion mutants in these RLKs for root hair defects and found that mutations in one of them, At3g51550 encoding the FERONIA (FER) receptor-like kinase, induced severe root hair defects. We show that the
fer
phenotypes correlated with reduced levels of active RAC/ROPs and NADPH oxidase-dependent, auxin-regulated ROS accumulation in roots and root hairs and that up-regulating RAC/ROP signaling in
fer
countered the mutant phenotypes. Taken together, these observations strongly support FER as an upstream regulator for the RAC/ROP-signaled pathway that controls ROS-mediated root hair development. Moreover, FER was pulled down by ROP2 GTPase in a guanine nucleotide-regulated manner implying a dynamic signaling complex involving FER, a ROPGEF, and a RAC/ROP.
Structural basis for the autoprocessing of zinc metalloproteases in the thermolysin family
Authors: Gao Xiang , Wang Jue , Yu Da-Qi , Bian Fei , Xie Bin-Bin , Chen Xiu-Lan , Zhou Bai-Cheng , Lai Lu-Hua , Wang Zhi-Xin , Wu Jia-Wei , Zhang Yu-Zhong
Published: September 2010

Thermolysin-like proteases (TLPs), a large group of zinc metalloproteases, are synthesized as inactive precursors. TLPs with a long propeptide (∼200 residues) undergo maturation following autoprocessing through an elusive molecular mechanism. We report the first two crystal structures for the autoprocessed complexes of a typical TLP, MCP-02. In the autoprocessed complex, Ala205 shifts upward by 33 Å from the previously covalently linked residue, His204, indicating that, following autocleavage of the peptide bond between His204 and Ala205, a large conformational change from the zymogen to the autoprocessed complex occurs. The eight N-terminal residues (residues Ala205-Gly212) of the catalytic domain form a new β-strand, nestling into two other β-strands. Simultaneously, the apparent
T

m

of the autoprocessed complex increases 20 °C compared to that of the zymogen. The stepwise degradation of the propeptide begins with two sequential cuttings at Ser49-Val50 and Gly57-Leu58, which lead to the disassembly of the propeptide and the formation of mature MCP-02. Our findings give new insights into the molecular mechanism of TLP maturation.
Dissemination of invasiveSalmonellavia bacterial-induced extrusion of mucosal epithelia
Authors: Knodler Leigh A. , Vallance Bruce A. , Celli Jean , Winfree Seth , Hansen Bryan , Montero Marinieve , Steele-Mortimer Olivia
Published: September 2010

Salmonella entericais an intracellular bacterial pathogen that resides and proliferates within a membrane-bound vacuole in epithelial cells of the gut and gallbladder. Although essential to disease, howSalmonellaescapes from its intracellular niche and spreads to secondary cells within the same host, or to a new host, is not known. Here, we demonstrate that a subpopulation ofSalmonellahyperreplicating in the cytosol of epithelial cells serves as a reservoir for dissemination. These bacteria are transcriptionally distinct from intravacuolarSalmonella. They are induced for the invasion-associated type III secretion system and possess flagella; hence, they are primed for invasion. Epithelial cells laden with these cytosolic bacteria are extruded out of the monolayer, releasing invasion-primed and -competentSalmonellainto the lumen. This extrusion mechanism is morphologically similar to the process of cell shedding required for turnover of the intestinal epithelium. In contrast to the homeostatic mechanism, however, bacterial-induced extrusion is accompanied by an inflammatory cell death characterized by caspase-1 activation and the apical release of IL-18, an important cytokine regulator of gut inflammation. Although epithelial extrusion is obviously beneficial toSalmonellafor completion of its life cycle, it also provides a mechanistic explanation for the mucosal inflammation that is triggered duringSalmonellainfection of the gastrointestinal and biliary tracts.
Transcranial magnetic stimulation of posterior parietal cortex affects decisions of hand choice
Authors: Oliveira Flavio T. P. , Diedrichsen Jörn , Verstynen Timothy , Duque Julie , Ivry Richard B.
Published: September 2010

Deciding which hand to use for an action is one of the most frequent decisions people make in everyday behavior. Using a speeded reaching task, we provide evidence that hand choice entails a competitive decision process between simultaneously activated action plans for each hand. We then show that single-pulse transcranial magnetic stimulation to the left posterior parietal cortex biases this competitive process, leading to an increase in ipsilateral, left hand reaches. Stimulation of the right posterior parietal cortex did not alter hand choice, suggesting a hemispheric asymmetry in the representations of reach plans. These results are unique in providing causal evidence that the posterior parietal cortex is involved in decisions of hand choice.
Characterization and structure of DhpI, a phosphonate
O
-methyltransferase involved in dehydrophos biosynthesis
Authors: Lee Jin-Hee , Bae Brian , Kuemin Michael , Circello Benjamin T. , Metcalf William W. , Nair Satish K. , van der Donk Wilfred A.
Published: September 2010

Phosphonate natural products possess a range of biological activities as a consequence of their ability to mimic phosphate esters or tetrahedral intermediates formed in enzymatic reactions involved in carboxyl group metabolism. The dianionic form of these compounds at pH 7 poses a drawback with respect to their ability to mimic carboxylates and tetrahedral intermediates. Microorganisms producing phosphonates have evolved two solutions to overcome this hurdle: biosynthesis of monoanionic phosphinates containing two P-C bonds or esterification of the phosphonate group. The latter solution was first discovered for the antibiotic dehydrophos that contains a methyl ester of a phosphonodehydroalanine group. We report here the expression, purification, substrate scope, and structure of the
O
-methyltransferase from the dehydrophos biosynthetic gene cluster. The enzyme utilizes
S
-adenosylmethionine to methylate a variety of phosphonates including 1-hydroxyethylphosphonate, 1,2-dihydroxyethylphosphonate, and acetyl-1-aminoethylphosphonate. Kinetic analysis showed that the best substrates are tripeptides containing as C-terminal residue a phosphonate analog of alanine suggesting the enzyme acts late in the biosynthesis of dehydrophos. These conclusions are corroborated by the X-ray structure that reveals an active site that can accommodate a tripeptide substrate. Furthermore, the structural studies demonstrate a conformational change brought about by substrate or product binding. Interestingly, the enzyme has low substrate specificity and was used to methylate the clinical antibiotic fosfomycin and the antimalaria clinical candidate fosmidomycin, showing its promise for applications in bioengineering.
A phosphorylation-regulated amphipathic helix controls the membrane translocation and function of the yeast phosphatidate phosphatase
Authors: Karanasios Eleftherios , Han Gil-Soo , Xu Zhi , Carman George M. , Siniossoglou Symeon
Published: September 2010

Regulation of membrane lipid composition is crucial for many aspects of cell growth and development. Lipins, a novel family of phosphatidate (PA) phosphatases that generate diacylglycerol (DAG) from PA, are emerging as essential regulators of fat metabolism, adipogenesis, and organelle biogenesis. The mechanisms that govern lipin translocation onto membranes are largely unknown. Here we show that recruitment of the yeast lipin (Pah1p) is regulated by PA levels onto the nuclear/endoplasmic reticulum (ER) membrane. Recruitment requires the transmembrane protein phosphatase complex Nem1p-Spo7p. Once dephosphorylated, Pah1p can bind to the nuclear/ER membrane independently of Nem1p-Spo7p via a short amino-terminal amphipathic helix. Dephosphorylation enhances the activity of Pah1p, both in vitro and in vivo, but only in the presence of a functional helix. The helix is required for both phospholipid and triacylglycerol biosynthesis. Our data suggest that dephosphorylation of Pah1p by the Nem1p-Spo7p complex enables the amphipathic helix to anchor Pah1p onto the nuclear/ER membrane allowing the production of DAG for lipid biosynthesis.
Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes
Authors: Danchin Etienne G. J. , Rosso Marie-Noëlle , Vieira Paulo , de Almeida-Engler Janice , Coutinho Pedro M. , Henrissat Bernard , Abad Pierre
Published: September 2010

Lateral gene transfer from prokaryotes to animals is poorly understood, and the scarce documented examples generally concern genes of uncharacterized role in the receiver organism. In contrast, in plant-parasitic nematodes, several genes, usually not found in animals and similar to bacterial homologs, play essential roles for successful parasitism. Many of these encode plant cell wall-degrading enzymes that constitute an unprecedented arsenal in animals in terms of both abundance and diversity. Here we report that independent lateral gene transfers from different bacteria, followed by gene duplications and early gain of introns, have shaped this repertoire. We also show protein immunolocalization data that suggest additional roles for some of these cell wall-degrading enzymes in the late stages of these parasites’ life cycle. Multiple functional acquisitions of exogenous genes that provide selective advantage were probably crucial for the emergence and proficiency of plant parasitism in nematodes.
Glatiramer acetate triggers PI3Kδ/Akt and MEK/ERK pathways to induce IL-1 receptor antagonist in human monocytes
Authors: Carpintero Rakel , Brandt Karim J. , Gruaz Lyssia , Molnarfi Nicolas , Lalive Patrice H. , Burger Danielle
Published: September 2010

Glatiramer acetate (GA), an immunomodulator used in multiple sclerosis (MS) therapy, induces the production of secreted IL-1 receptor antagonist (sIL-1Ra), a natural inhibitor of IL-1β, in human monocytes, and in turn enhances sIL-1Ra circulating levels in MS patients. GA is a mixture of peptides with random Glu, Lys, Ala, and Tyr sequences of high polarity and hydrophilic nature that is unlikely to cross the blood–brain barrier. In contrast, sIL-1Ra crosses the blood–brain barrier and, in turn, may mediate GA anti-inflammatory activities within the CNS by counteracting IL-1β activities. Here we identify intracellular signaling pathways induced by GA that control sIL-1Ra expression in human monocytes. By using kinase knockdown and specific inhibitors, we demonstrate that GA induces sIL-1Ra production via the activation of PI3Kδ, Akt, MEK1/2, and ERK1/2, demonstrating that both PI3Kδ/Akt and MEK/ERK pathways rule sIL-1Ra expression in human monocytes. The pathways act in parallel upstream glycogen synthase kinase-3α/β (GSK3α/β), the knockdown of which enhances sIL-1Ra production. Together, our findings demonstrate the existence of signal transduction triggered by GA, further highlighting the mechanisms of action of this drug in MS.
Right-handed double-helix ultrashort DNA yields chiral nematic phases with both right- and left-handed director twist
Authors: Zanchetta Giuliano , Giavazzi Fabio , Nakata Michi , Buscaglia Marco , Cerbino Roberto , Clark Noel A. , Bellini Tommaso
Published: September 2010

Concentrated solutions of duplex-forming DNA oligomers organize into various mesophases among which is the nematic (
N
∗
), which exhibits a macroscopic chiral helical precession of molecular orientation because of the chirality of the DNA molecule. Using a quantitative analysis of the transmission spectra in polarized optical microscopy, we have determined the handedness and pitch of this chiral nematic helix for a large number of sequences ranging from 8 to 20 bases. The B-DNA molecule exhibits a right-handed molecular double-helix structure that, for long molecules, always yields
N
∗
phases with left-handed pitch in the μm range. We report here that ultrashort oligomeric duplexes show an extremely diverse behavior, with both left- and right-handed
N
∗
helices and pitches ranging from macroscopic down to 0.3 μm. The behavior depends on the length and the sequence of the oligomers, and on the nature of the end-to-end interactions between helices. In particular, the
N
∗
handedness strongly correlates with the oligomer length and concentration. Right-handed phases are found only for oligomers shorter than 14 base pairs, and for the sequences having the transition to the
N
∗
phase at concentration larger than 620 mg/mL. Our findings indicate that in short DNA, the intermolecular double-helical interactions switch the preferred liquid crystal handedness when the columns of stacked duplexes are forced at high concentrations to separations comparable to the DNA double-helix pitch, a regime still to be theoretically described.
Endoplasmic reticulum stress-induced transcription factor, CHOP, is crucial for dendritic cell IL-23 expression
Authors: Goodall Jane C. , Wu Changxin , Zhang Yongsheng , McNeill Louise , Ellis Lou , Saudek Vladimir , Gaston J. S. Hill
Published: September 2010

The endoplasmic reticulum (ER) stress response detects malfunctions in cellular physiology, and microbial pattern recognition receptors recognize external threats posed by infectious agents. This study has investigated whether proinflammatory cytokine expression by monocyte-derived dendritic cells is affected by the induction of ER stress. Activation of ER stress, in combination with Toll-like receptor (TLR) agonists, markedly enhanced expression of mRNA of the unique p19 subunit of IL-23, and also significantly augmented secretion of IL-23 protein. These effects were not seen for IL-12 secretion. The IL-23 gene was found to be a target of the ER stress-induced transcription factor C/EBP homologous protein (CHOP), which exhibited enhanced binding in the context of both ER stress and TLR stimulation. Knockdown of CHOP in U937 cells significantly reduced the synergistic effects of TLR and ER stress on
IL-23p19
expression, but did not affect expression of other LPS-responsive genes. The integration of ER stress signals and the requirement for CHOP in the induction of IL-23 responses was also investigated in a physiological setting: infection of myeloid cells with
Chlamydia trachomatis
resulted in the expression of CHOP mRNA and induced the binding of CHOP to the
IL-23
promoter. Furthermore, knockdown of CHOP significantly reduced the expression of IL-23 in response to this intracellular bacterium. Therefore, the effects of pathogens and other environmental factors on ER stress can profoundly affect the nature of innate and adaptive immune responses.
Parallel information processing channels created in the retina
Authors: Schiller Peter H.
Published: September 2010

In the retina, several parallel channels originate that extract different attributes from the visual scene. This review describes how these channels arise and what their functions are. Following the introduction four sections deal with these channels. The first discusses the “ON” and “OFF” channels that have arisen for the purpose of rapidly processing images in the visual scene that become visible by virtue of either light increment or light decrement; the ON channel processes images that become visible by virtue of light increment and the OFF channel processes images that become visible by virtue of light decrement. The second section examines the midget and parasol channels. The midget channel processes fine detail, wavelength information, and stereoscopic depth cues; the parasol channel plays a central role in processing motion and flicker as well as motion parallax cues for depth perception. Both these channels have ON and OFF subdivisions. The third section describes the accessory optic system that receives input from the retinal ganglion cells of Dogiel; these cells play a central role, in concert with the vestibular system, in stabilizing images on the retina to prevent the blurring of images that would otherwise occur when an organism is in motion. The last section provides a brief overview of several additional channels that originate in the retina.
Suppressor of MEK null (SMEK)/protein phosphatase 4 catalytic subunit (PP4C) is a key regulator of hepatic gluconeogenesis
Authors: Yoon Young-Sil , Lee Min-Woo , Ryu Dongryeol , Kim Jeong Ho , Ma Hui , Seo Woo-Young , Kim Yo-Na , Kim Su Sung , Lee Chul Ho , Hunter Tony , Choi Cheol Soo , Montminy Marc R. , Koo Seung-Hoi
Published: September 2010

Fasting promotes hepatic gluconeogenesis to maintain glucose homeostasis. The cAMP-response element binding protein (CREB)-regulated transcriptional coactivator 2 (CRTC2) is responsible for transcriptional activation of gluconeogenic genes and is critical for conveying the opposing hormonal signals of glucagon and insulin in the liver. Here, we show that suppressor of MEK null 1 (SMEK1) and SMEK2 [protein phosphatase 4 (PP4) regulatory subunits 3a and 3b, respectively] are directly involved in the regulation of hepatic glucose metabolism in mice. Expression of hepatic SMEK1/2 is up-regulated during fasting or in mouse models of insulin-resistant conditions in a Peroxisome Proliferator-Activated Receptor-gamma Coactivator 1α (PGC-1α)-dependent manner. Overexpression of SMEK promotes elevations in plasma glucose with increased hepatic gluconeogenic gene expression, whereas depletion of the SMEK proteins reduces hyperglycemia and enhances CRTC2 phosphorylation; the effect is blunted by S171A CRTC2, which is refractory to salt-inducible kinase (SIK)-dependent inhibition. Taken together, we would propose that mammalian SMEK/PP4C proteins are involved in the regulation of hepatic glucose metabolism through dephosphorylation of CRTC2.
IκBζ is essential for natural killer cell activation in response to IL-12 and IL-18
Authors: Miyake Tohru , Satoh Takashi , Kato Hiroki , Matsushita Kazufumi , Kumagai Yutaro , Vandenbon Alexis , Tani Tohru , Muta Tatsushi , Akira Shizuo , Takeuchi Osamu
Published: September 2010

IκBζ, encoded byNfibiz, is a nuclear IκB-like protein harboring ankyrin repeats. IκBζ has been shown to regulate IL-6 production in macrophages and Th17 development in T cells. However, the role of IκBζ in natural killer (NK) cells has not be understood. In the present study, we found that the expression of IκBζ was rapidly induced in response to IL-18 in NK cells, but not in T cells. Analysis ofNfkbiz−/−mice revealed that IκBζ was essential for the production of IFN-γ production and cytotoxic activity in NK cells in response to IL-12 and/or IL-18 stimulation. IL-12/IL-18–mediated gene induction was profoundly impaired inNfkbiz−/−NK cells. Whereas the phosphorylation of STAT4 was normally induced by IL-12 stimulation, STAT4 was not recruited to theIfnggene regions inNfkbiz−/−NK cells. Acetylation of histone 3 K9 onIfngregions was also abrogated inNfkbiz−/−NK cells. IκBζ was recruited on the proximal promoter region of theIfnggene, and overexpression of IκBζ together with IL-12 activated theIfngpromoter. Furthermore,Nfkbiz−/−mice were highly susceptible to mouse MCMV infection. Taken together, these results demonstrate that IκBζ is essential for the activation of NK cells and antiviral host defense responses.
Proteome of mouse oocytes at different developmental stages
Authors: Wang Shufang , Kou Zhaohui , Jing Zhiyi , Zhang Yu , Guo Xinzheng , Dong Mengqiu , Wilmut Ian , Gao Shaorong
Published: September 2010

The mammalian oocyte possesses powerful reprogramming factors, which can reprogram terminally differentiated germ cells (sperm) or somatic cells within a few cell cycles. Although it has been suggested that use of oocyte-derived transcripts may enhance the generation of induced pluripotent stem cells, the reprogramming factors in oocytes are undetermined, and even the identified proteins composition of oocytes is very limited. In the present study, 7,000 mouse oocytes at different developmental stages, including the germinal vesicle stage, the metaphase II (MII) stage, and the fertilized oocytes (zygotes), were collected. We successfully identified 2,781 proteins present in germinal vesicle oocytes, 2,973 proteins in MII oocytes, and 2,082 proteins in zygotes through semiquantitative MS analysis. Furthermore, the results of the bioinformatics analysis indicated that different protein compositions are correlated with oocyte characteristics at different developmental stages. For example, specific transcription factors and chromatin remodeling factors are more abundant in MII oocytes, which may be crucial for the epigenetic reprogramming of sperm or somatic nuclei. These results provided important knowledge to better understand the molecular mechanisms in early development and may improve the generation of induced pluripotent stem cells.
Palmitoylated Ras proteins traffic through recycling endosomes to the plasma membrane during exocytosis
Authors: Misaki Ryo , Morimatsu Miki , Uemura Takefumi , Waguri Satoshi , Miyoshi Eiji , Taniguchi Naoyuki , Matsuda Michiyuki , Taguchi Tomohiko
Published: September 2010

Ras proteins regulate cell growth, death, and differentiation, and it is well established that this functional versatility is accomplished through their different subcellular localizations. Palmitoylated H- and N-Ras are believed to localize at the perinuclear Golgi and plasma membrane (PM). Notably, however, recycling endosomes (REs) also localize to a perinuclear region, which is often indistinguishable from the Golgi. In this study, we show that active palmitoylated Ras proteins mainly localize intracellularly at REs and that REs act as a way station along the post-Golgi exocytic pathway to the PM. H-Ras requires two palmitoyl groups for RE targeting. The lack of either or both palmitoyl groups leads to the mislocalization of the mutant proteins to the endoplasmic reticulum, Golgi apparatus, or the PM. Therefore, we demonstrate that palmitoylation directs Ras proteins to the correct intracellular organelles for trafficking and activity.
LIM kinases are required for invasive path generation by tumor and tumor-associated stromal cells
Authors: Scott Rebecca W. , Hooper Steven , Crighton Diane , Li Ang , König Ireen , Munro June , Trivier Elisabeth , Wickman Grant , Morin Pierre , Croft Daniel R. , Dawson John , Machesky Laura , Anderson Kurt I. , Sahai Erik A. , Olson Michael F.
Published: September 2010

LIM kinases 1 and 2 (LIMK1/2) are centrally positioned regulators of actin cytoskeleton dynamics. Using siRNA-mediated knockdown or a novel small molecule inhibitor, we show LIMK is required for path generation by leading tumor cells and nontumor stromal cells during collective tumor cell invasion. LIMK inhibition lowers cofilin phosphorylation, F-actin levels, serum response factor transcriptional activity and collagen contraction, and reduces invasion in three-dimensional invasion assays. Although motility was unaffected, LIMK inhibition impairs matrix protein degradation and invadopodia formation associated with significantly faster recovery times in FRAP assays indicative of reduced F-actin stability. When LIMK is knocked down in MDA-MB-231 cells, they lose the ability to lead strands of collectively invading cells. Similarly, when LIMK activity is blocked in cancer-associated fibroblasts, they are unable to lead the collective invasion of squamous carcinoma cells in an organotypic skin model. These results show that LIMK is required for matrix remodeling activities for path generation by leading cells in collective invasion.
Live imaging of single nuclear pores reveals unique assembly kinetics and mechanism in interphase
Authors: Dultz Elisa , Ellenberg Jan
Published: September 2010

In metazoa, new nuclear pore complexes (NPCs) form at two different cell cycle stages: at the end of mitosis concomitant with the reformation of the nuclear envelope and during interphase. However, the mechanisms of these assembly processes may differ. In this study, we apply high resolution live cell microscopy to analyze the dynamics of single NPCs in living mammalian cells during interphase. We show that nuclear growth and NPC assembly are correlated and occur at a constant rate throughout interphase. By analyzing the kinetics of individual NPC assembly events, we demonstrate that they are initiated by slow accumulation of the membrane nucleoporin Pom121 followed by the more rapid association of the soluble NPC subcomplex Nup107–160. This inverse order of recruitment and the overall much slower kinetics compared with postmitotic NPC assembly support the conclusion that the two processes occur by distinct molecular mechanisms.
Age-dependent susceptibility to a viral disease due to decreased natural killer cell numbers and trafficking
Authors: Fang Min , Roscoe Felicia , Sigal Luis J.
Published: September 2010

Although it is well known that aged hosts are generally more susceptible to viral diseases than the young, specific dysfunctions of the immune system directly responsible for this increased susceptibility have yet to be identified. We show that mice genetically resistant to mousepox (the mouse parallel of human smallpox) lose resistance at mid-age. Surprisingly, this loss of resistance is not a result of intrinsically defective T cell responses. Instead, the primary reason for the loss of resistance results from a decreased number of total and mature natural killer (NK) cells in the blood and an intrinsic impairment in their ability to migrate to the lymph node draining the site of infection, which is essential to curb systemic virus spread. Hence, our work links the age-dependent increase in susceptibility to a viral disease to a specific defect of NK cells, opening the possibility of exploring treatments to improve NK cell function in the aged with the goal of enhancing their resistance to viral diseases.