bluuebunny/crossref_metadata_2025 huggingface dataset:
Surfactants from the gas phase may promote cloud droplet formation
Authors: Sareen Neha , Schwier Allison N. , Lathem Terry L. , Nenes Athanasios , McNeill V. Faye
Published: February 2013

Clouds, a key component of the climate system, form when water vapor condenses upon atmospheric particulates termed cloud condensation nuclei (CCN). Variations in CCN concentrations can profoundly impact cloud properties, with important effects on local and global climate. Organic matter constitutes a significant fraction of tropospheric aerosol mass, and can influence CCN activity by depressing surface tension, contributing solute, and influencing droplet activation kinetics by forming a barrier to water uptake. We present direct evidence that two ubiquitous atmospheric trace gases, methylglyoxal (MG) and acetaldehyde, known to be surface-active, can enhance aerosol CCN activity upon uptake. This effect is demonstrated by exposing acidified ammonium sulfate particles to 250 parts per billion (ppb) or 8 ppb gas-phase MG and/or acetaldehyde in an aerosol reaction chamber for up to 5 h. For the more atmospherically relevant experiments, i.e., the 8-ppb organic precursor concentrations, significant enhancements in CCN activity, up to 7.5% reduction in critical dry diameter for activation, are observed over a timescale of hours, without any detectable limitation in activation kinetics. This reduction in critical diameter enhances the apparent particle hygroscopicity up to 26%, which for ambient aerosol would lead to cloud droplet number concentration increases of 8–10% on average. The observed enhancements exceed what would be expected based on Köhler theory and bulk properties. Therefore, the effect may be attributed to the adsorption of MG and acetaldehyde to the gas–aerosol interface, leading to surface tension depression of the aerosol. We conclude that gas-phase surfactants may enhance CCN activity in the atmosphere.
Radiocarbon dating casts doubt on the late chronology of the Middle to Upper Palaeolithic transition in southern Iberia
Authors: Wood Rachel E. , Barroso-Ruíz Cecilio , Caparrós Miguel , Jordá Pardo Jesús F. , Galván Santos Bertila , Higham Thomas F. G.
Published: February 2013

It is commonly accepted that some of the latest dates for Neanderthal fossils and Mousterian industries are found south of the Ebro valley in Iberia at
ca.
36 ka calBP (calibrated radiocarbon date ranges). In contrast, to the north of the valley the Mousterian disappears shortly before the Proto-Aurignacian appears at
ca.
42 ka calBP. The latter is most likely produced by anatomically modern humans. However, two-thirds of dates from the south are radiocarbon dates, a technique that is particularly sensitive to carbon contaminants of a younger age that can be difficult to remove using routine pretreatment protocols. We have attempted to test the reliability of chronologies of 11 southern Iberian Middle and early Upper Paleolithic sites. Only two, Jarama VI and Zafarraya, were found to contain material that could be reliably dated. In both sites, Middle Paleolithic contexts were previously dated by radiocarbon to less than 42 ka calBP. Using ultrafiltration to purify faunal bone collagen before radiocarbon dating, we obtain ages at least 10 ka
14
C years older, close to or beyond the limit of the radiocarbon method for the Mousterian at Jarama VI and Neanderthal fossils at Zafarraya. Unless rigorous pretreatment protocols have been used, radiocarbon dates should be assumed to be inaccurate until proven otherwise in this region. Evidence for the late survival of Neanderthals in southern Iberia is limited to one possible site, Cueva Antón, and alternative models of human occupation of the region should be considered.
RNA-binding protein Sam68 controls synapse number and local β-actin mRNA metabolism in dendrites
Authors: Klein Matthew E. , Younts Thomas J. , Castillo Pablo E. , Jordan Bryen A.
Published: February 2013

Proper synaptic function requires the spatial and temporal compartmentalization of RNA metabolism via transacting RNA-binding proteins (RBPs). Loss of RBP activity leads to abnormal posttranscriptional regulation and results in diverse neurological disorders with underlying deficits in synaptic morphology and transmission. Functional loss of the 68-kDa RBP Src associated in mitosis (Sam68) is associated with the pathogenesis of the neurological disorder fragile X tremor/ataxia syndrome. Sam68 binds to the mRNA of β-actin (actb), an integral cytoskeletal component of dendritic spines. We show that Sam68 knockdown or disruption of the binding between Sam68 and its actb mRNA cargo in primary hippocampal cultures decreases the amount of actb mRNA in the synaptodendritic compartment and results in fewer dendritic spines. Consistent with these observations, we find that Sam68-KO mice have reduced levels of actb mRNA associated with synaptic polysomes and diminished levels of synaptic actb protein, suggesting that Sam68 promotes the translation of actb mRNA at synapses in vivo. Moreover, genetic knockout of Sam68 or acute knockdown in vivo results in fewer excitatory synapses in the hippocampal formation as assessed morphologically and functionally. Therefore, we propose that Sam68 regulates synapse number in a cell-autonomous manner through control of postsynaptic actb mRNA metabolism. Our research identifies a role for Sam68 in synaptodendritic posttranscriptional regulation of actb and may provide insight into the pathophysiology of fragile X tremor/ataxia syndrome.
Polariton Bose–Einstein condensate at room temperature in an Al(Ga)N nanowire–dielectric microcavity with a spatial potential trap
Authors: Das Ayan , Bhattacharya Pallab , Heo Junseok , Banerjee Animesh , Guo Wei
Published: February 2013

A spatial potential trap is formed in a 6.0-μm Al(Ga)N nanowire by varying the Al composition along its length during epitaxial growth. The polariton emission characteristics of a dielectric microcavity with the single nanowire embedded in-plane have been studied at room temperature. Excitation is provided at the Al(Ga)N end of the nanowire, and polariton emission is observed from the lowest bandgap GaN region within the potential trap. Comparison of the results with those measured in an identical microcavity with a uniform GaN nanowire and having an identical exciton–photon detuning suggests evaporative cooling of the polaritons as they are transported into the trap in the Al(Ga)N nanowire. Measurement of the spectral characteristics of the polariton emission, their momentum distribution, first-order spatial coherence, and time-resolved measurements of polariton cooling provides strong evidence of the formation of a near-equilibrium Bose–Einstein condensate in the GaN region of the nanowire at room temperature. In contrast, the condensate formed in the uniform GaN nanowire–dielectric microcavity without the spatial potential trap is only in self-equilibrium.
Phosphorylation of
Sox9
is required for neural crest delamination and is regulated downstream of BMP and canonical Wnt signaling
Authors: Liu Jessica A. J. , Wu Ming-Hoi , Yan Carol H. , Chau Bolton K. H. , So Henry , Ng Alvis , Chan Alan , Cheah Kathryn S. E. , Briscoe James , Cheung Martin
Published: February 2013

Coordination of neural crest cell (NCC) induction and delamination is orchestrated by several transcription factors. Among these, Sry-related HMG box-9 (
Sox9
) and
Snail2
have been implicated in both the induction of NCC identity and, together with phoshorylation, NCC delamination. How phosphorylation effects this function has not been clear. Here we show, in the developing chick neural tube, that phosphorylation of
Sox9
on S64 and S181 facilitates its SUMOylation, and the phosphorylated forms of
Sox9
are essential for trunk neural crest delamination. Both phosphorylation and to a lesser extent SUMOylation, of
Sox9
are required to cooperate with
Snail2
to promote delamination. Moreover, bone morphogenetic protein and canonical Wnt signaling induce phosphorylation of
Sox9
, thereby connecting extracellular signals with the delamination of NCCs. Together the data suggest a model in which extracellular signals initiate phosphorylation of
Sox9
and its cooperation with
Snail2
to induce NCC delamination.
Insects groom their antennae to enhance olfactory acuity
Authors: Böröczky Katalin , Wada-Katsumata Ayako , Batchelor Dale , Zhukovskaya Marianna , Schal Coby
Published: February 2013

Grooming, a common behavior in animals, serves the important function of removing foreign materials from body surfaces. When antennal grooming was prevented in the American cockroach,
Periplaneta americana
, field emission gun scanning electron microscopy images revealed that an unstructured substance accumulated on nongroomed antennae, covering sensillar pores, but not on groomed antennae of the same individuals. Gas chromatography analysis of antennal extracts showed that over a 24-h period nongroomed antennae accumulated three to four times more cuticular hydrocarbons than groomed antennae. Moreover, nongroomed antennae accumulated significantly more environmental contaminants from surfaces (stearic acid) and from air (geranyl acetate) than groomed antennae. We hypothesized that the accumulation of excess native cuticular hydrocarbons on the antennae would impair olfactory reception. Electroantennogram experiments and single-sensillum recordings supported this hypothesis: antennae that were prevented from being groomed were significantly less responsive than groomed antennae to the sex pheromone component periplanone-B, as well as to the general odorants geranyl acetate and hexanol. We therefore conclude that antennal grooming removes excess native cuticular lipids and foreign chemicals that physically and/or chemically interfere with olfaction, and thus maintains the olfactory acuity of the antennae. Similar experimental manipulations of the German cockroach (
Blattella germanica
), carpenter ant (
Camponotus pennsylvanicus
), and the housefly (
Musca domestica
), which use different modes of antennal grooming, support the hypothesis that antennal grooming serves a similar function in a wide range of insect taxa.
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response
Authors: Wine Yariv , Boutz Daniel R. , Lavinder Jason J. , Miklos Aleksandr E. , Hughes Randall A. , Hoi Kam Hon , Jung Sang Taek , Horton Andrew P. , Murrin Ellen M. , Ellington Andrew D. , Marcotte Edward M. , Georgiou George
Published: February 2013

We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography–high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique V
H
CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigen-specific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody V
H
clonotypes. Of these 34 CDRH3s, 12 account for ∼60% of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.
Beta-lactam antibiotics modulate T-cell functions and gene expression via covalent binding to cellular albumin
Authors: Mor Felix , Cohen Irun R.
Published: February 2013

Recent work has suggested that beta-lactam antibiotics might directly affect eukaryotic cellular functions. Here, we studied the effects of commonly used beta-lactam antibiotics on rodent and human T cells in vitro and in vivo on T-cell–mediated experimental autoimmune diseases. We now report that experimental autoimmune encephalomyelitis and adjuvant arthritis were significantly more severe in rats treated with cefuroxime and other beta-lactams. T cells appeared to mediate the effect: an anti-myelin basic protein T-cell line treated with cefuroxime or penicillin was more encephalitogenic in adoptive transfer experiments. The beta-lactam ampicillin, in contrast to cefuroxime and penicillin, did not enhance encephalomyelitis, but did inhibit the autoimmune diabetes developing spontaneously in nonobese diabetic mice. Gene expression analysis of human peripheral blood T cells showed that numerous genes associated with T helper 2 (Th2) and T regulatory (Treg) differentiation were down-regulated in T cells stimulated in the presence of cefuroxime; these genes were up-regulated in the presence of ampicillin. The T-cell protein that covalently bound beta-lactam antibiotics was found to be albumin. Human and rodent T cells expressed albumin mRNA and protein, and penicillin-modified albumin was taken up by rat T cells, leading to enhanced encephalitogenicity. Thus, beta-lactam antibiotics in wide clinical use have marked effects on T-cell behavior; beta-lactam antibiotics can function as immunomodulators, apparently through covalent binding to albumin.
L
-acetylcarnitine causes rapid antidepressant effects through the epigenetic induction of mGlu2 receptors
Authors: Nasca Carla , Xenos Dionysios , Barone Ylenia , Caruso Alessandra , Scaccianoce Sergio , Matrisciano Francesco , Battaglia Giuseppe , Mathé Aleksander A. , Pittaluga Anna , Lionetto Luana , Simmaco Maurizio , Nicoletti Ferdinando
Published: February 2013

Epigenetic mechanisms are involved in the pathophysiology of depressive disorders and are unique potential targets for therapeutic intervention. The acetylating agent
L
-acetylcarnitine (LAC), a well-tolerated drug, behaves as an antidepressant by the epigenetic regulation of type 2 metabotropic glutamate (mGlu2) receptors. It caused a rapid and long-lasting antidepressant effect in Flinders Sensitive Line rats and in mice exposed to chronic unpredictable stress, which, respectively, model genetic and environmentally induced depression. In both models, LAC increased levels of acetylated H3K27 bound to the
Grm2
promoter and also increased acetylation of NF-ĸB-p65 subunit, thereby enhancing the transcription of
Grm2
gene encoding for the mGlu2 receptor in hippocampus and prefrontal cortex. Importantly, LAC reduced the immobility time in the forced swim test and increased sucrose preference as early as 3 d of treatment, whereas 14 d of treatment were needed for the antidepressant effect of chlorimipramine. Moreover, there was no tolerance to the action of LAC, and the antidepressant effect was still seen 2 wk after drug withdrawal. Conversely, NF-ĸB inhibition prevented the increase in mGlu2 expression induced by LAC, whereas the use of a histone deacetylase inhibitor supported the epigenetic control of mGlu2 expression. Finally, LAC had no effect on mGlu2 knockout mice exposed to chronic unpredictable stress, and a single injection of the mGlu2/3 receptor antagonist LY341495 partially blocked LAC action. The rapid and long-lasting antidepressant action of LAC strongly suggests a unique approach to examine the epigenetic hypothesis of depressive disorders in humans, paving the way for more efficient antidepressants with faster onset of action.
The compatibility of agricultural intensification in a global hotspot of smallholder agrobiodiversity (Bolivia)
Authors: Zimmerer Karl S.
Published: February 2013

Integrating the conservation of biodiversity by smallholder farmers with agricultural intensification is increasingly recognized as a leading priority of sustainability and food security amid global environmental and socioeconomic change. An international research project investigated the smallholder agrobiodiversity of maize (corn) in a global hotspot (Bolivia) undergoing significant intensification. Peach-based intensification was pronounced (300–400%) and prolonged (2000–2010) in study areas. Intensification and maize agrobiodiversity were found to co-occur within smallholder landscapes. Interactions of these field systems did not trigger land-change tipping points leading to landrace extirpation. By 2010 maize landraces in the study areas still demonstrated high levels of taxonomic and ecological biodiversity and contributed significantly to this crop’s agrobiodiversity at national (31%) and hemispheric (3%) scales. Social and ecological resilience and in situ conservation of the maize agrobiodiversity by Bolivian smallholders was enabled through robust linkages to off-farm migration; resource access and asset capabilities among both traditional and nontraditional growers; landrace agroecology and food uses; and innovative knowledge and skills. The smallholders’ resilience resulting from these linkages was integral to the conditional success of the in situ conservation of maize agrobiodiversity. Environment–development interactions both enabled smallholders’ agrobiodiversity resilience and influenced the limits and vulnerability of agrobiodiversity. Scientific policy recommendations regarding land-use planning and sustainability analysis are targeted to specific Río+20 priorities for agrobiodiversity.
Spindle checkpoint deficiency is tolerated by murine epidermal cells but not hair follicle stem cells
Authors: Foijer Floris , DiTommaso Tia , Donati Giacomo , Hautaviita Katta , Xie Stephanie Z. , Heath Emma , Smyth Ian , Watt Fiona M. , Sorger Peter K. , Bradley Allan
Published: February 2013

The spindle assembly checkpoint (SAC) ensures correct chromosome segregation during mitosis by preventing aneuploidy, an event that is detrimental to the fitness and survival of normal cells but oncogenic in tumor cells. Deletion of SAC genes is incompatible with early mouse development, and RNAi-mediated depletion of SAC components in cultured cells results in rapid death. Here we describe the use of a conditional KO of mouseMad2, an essential component of the SAC signaling cascade, as a means to selectively induce chromosome instability and aneuploidy in the epidermis of the skin. We observe that SAC inactivation is tolerated by interfollicular epidermal cells but results in depletion of hair follicle bulge stem cells. Eventually, a histologically normal epidermis develops within ∼1 mo after birth, albeit without any hair. Mad2-deficient cells in this epidermis exhibited abnormal transcription of metabolic genes, consistent with aneuploid cell state. Hair follicle bulge stem cells were completely absent, despite the continued presence of rudimentary hair follicles. These data demonstrate that different cell lineages within a single tissue respond differently to chromosome instability: some proliferating cell lineages can survive, but stem cells are highly sensitive.
NADPH oxidases regulate septin-mediated cytoskeletal remodeling during plant infection by the rice blast fungus
Authors: Ryder Lauren S. , Dagdas Yasin F. , Mentlak Thomas A. , Kershaw Michael J. , Thornton Christopher R. , Schuster Martin , Chen Jisheng , Wang Zonghua , Talbot Nicholas J.
Published: February 2013

The rice blast fungusMagnaporthe oryzaeinfects plants with a specialized cell called an appressorium, which uses turgor to drive a rigid penetration peg through the rice leaf cuticle. Here, we show that NADPH oxidases (Nox) are necessary for septin-mediated reorientation of the F-actin cytoskeleton to facilitate cuticle rupture and plant cell invasion. We report that the Nox2–NoxR complex spatially organizes a heteroligomeric septin ring at the appressorium pore, required for assembly of a toroidal F-actin network at the point of penetration peg emergence. Maintenance of the cortical F-actin network during plant infection independently requires Nox1, a second NADPH oxidase, which is necessary for penetration hypha elongation. Organization of F-actin in appressoria is disrupted by application of antioxidants, whereas latrunculin-mediated depolymerization of appressorial F-actin is competitively inhibited by reactive oxygen species, providing evidence that regulated synthesis of reactive oxygen species by fungal NADPH oxidases directly controls septin and F-actin dynamics.
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly
Authors: Park Chungoo , Chen Xiaoshu , Yang Jian-Rong , Zhang Jianzhi
Published: February 2013

Significance

The expression level of a gene is a leading determinant of its rate of protein sequence evolution, but the underlying mechanisms are unclear. We show that as the mRNA concentration increases, natural selection for mRNA folding intensifies, resulting in larger fractions of mutations deleterious to mRNA folding and lower rates of protein evolution. Counterintuitively, selection for mRNA folding also impacts the nonsynonymous-to-synonymous nucleotide substitution rate ratio, requiring a revision of the current interpretation of this ratio as a measure of protein-level selection. These findings demonstrate a prominent role of selection at the mRNA level in molecular evolution.
An essential role for chloroplast heat shock protein 90 (Hsp90C) in protein import into chloroplasts
Authors: Inoue Hitoshi , Li Ming , Schnell Danny J.
Published: February 2013

Chloroplast heat shock protein 90 (Hsp90C) represents a highly conserved subfamily of the Hsp90 family of molecular chaperones whose function has not been defined. We identified Hsp90C as a component that interacts with import intermediates of nuclear-encoded preproteins during posttranslational import into isolated chloroplasts. Hsp90C was specifically coprecipitated with a complex of protein import components, including Tic110, Tic40, Toc75, Tic22, and the stromal chaperones, Hsp93 and Hsp70. Radicicol, an inhibitor of Hsp90 ATPase activity, reversibly inhibited the import of a variety of preproteins during translocation across the inner envelope membrane, indicating that Hsp90C functions in membrane translocation into the organelle. Hsp90C is encoded by a single gene in
Arabidopsis thaliana
, and insertion mutations in the Hsp90C gene are embryo lethal, indicating an essential function for the chaperone in plant viability. On the basis of these results, we propose that Hsp90C functions within a chaperone complex in the chloroplast stroma to facilitate membrane translocation during protein import into the organelle.
Enhancer-like long-range transcriptional activation by λ CI-mediated DNA looping
Authors: Cui Lun , Murchland Iain , Shearwin Keith E. , Dodd Ian B.
Published: February 2013

How distant enhancer elements regulate the assembly of a transcription complex at a promoter remains poorly understood. Here, we use long-range gene regulation by the bacteriophage λ CI protein as a powerful system to examine this process in vivo. A 2.3-kb DNA loop, formed by CI bridging its binding sites at
OR
and
OL
, is known already to enhance repression at the lysogenic promoter
PRM
, located at
OR
. Here, we show that CI looping also activates
PRM
by allowing the C-terminal domain of the α subunit of the RNA polymerase bound at
PRM
to contact a DNA site adjacent to the distal CI sites at
OL
. Our results establish
OL
as a multifaceted enhancer element, able to activate transcription from long distances independently of orientation and position. We develop a physicochemical model of our in vivo data and use it to show that the observed activation is consistent with a simple recruitment mechanism, where the α–C-terminal domain to DNA contact need only provide ∼2.7 kcal/mol of additional binding energy for RNA polymerase. Structural modeling of this complete enhancer–promoter complex reveals how the contact is achieved and regulated, and suggests that distal enhancer elements, once appropriately positioned at the promoter, can function in essentially the same way as proximal promoter elements.
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
Authors: Sigova Alla A. , Mullen Alan C. , Molinie Benoit , Gupta Sumeet , Orlando David A. , Guenther Matthew G. , Almada Albert E. , Lin Charles , Sharp Phillip A. , Giallourakis Cosmas C. , Young Richard A.
Published: February 2013

Many long noncoding RNA (lncRNA) species have been identified in mammalian cells, but the genomic origin and regulation of these molecules in individual cell types is poorly understood. We have generated catalogs of lncRNA species expressed in human and murine embryonic stem cells and mapped their genomic origin. A surprisingly large fraction of these transcripts (>60%) originate from divergent transcription at promoters of active protein-coding genes. The divergently transcribed lncRNA/mRNA gene pairs exhibit coordinated changes in transcription when embryonic stem cells are differentiated into endoderm. Our results reveal that transcription of most lncRNA genes is coordinated with transcription of protein-coding genes.
AMPKα2 exerts its anti-inflammatory effects through PARP-1 and Bcl-6
Authors: Gongol Brendan , Marin Traci , Peng I-Chen , Woo Brian , Martin Marcy , King Stephanie , Sun Wei , Johnson David A. , Chien Shu , Shyy John Y.-J.
Published: February 2013

B-cell lymphoma–6 protein (Bcl-6) is a corepressor for inflammatory mediators such as vascular cell adhesion molecule–1 and monocyte chemotactic protein–1 and –3, which function to recruit monocytes to vascular endothelial cells upon inflammation. Poly [ADP ribose] polymerase 1 (PARP-1) is proinflammatory, in part through its binding at theBcl-6intron 1 to suppress Bcl-6 expression. We investigated the mechanisms by which PARP-1 dissociates from theBcl-6intron 1, ultimately leading to attenuation of endothelial inflammation. Analysis of the PARP-1 primary sequence suggested that phosphorylation of PARP-1 Serine 177 (Ser-177) by AMP-activated protein kinase (AMPK) is responsible for the induction of Bcl-6. Our results show that AMPK activation with treatment of 5-aminoimidazole-4-carboxamide ribonucleotide, metformin, or pulsatile shear stress induces PARP-1 dissociation from theBcl-6intron 1, increases Bcl-6 expression, and inhibits expression of inflammatory mediators. Conversely, AMPKα suppression or knockdown produces the opposite effects. The results demonstrate an anti-infamatory pathway linking AMPK, PARP-1, and Bcl-6 in endothelial cells.
Male-specific lethal complex in
Drosophila
counteracts histone acetylation and does not mediate dosage compensation
Authors: Sun Lin , Fernandez Harvey R. , Donohue Ryan C. , Li Jilong , Cheng Jianlin , Birchler James A.
Published: February 2013

Significance

A popular hypothesis to explain dosage compensation of the X chromosome in male
Drosophila
is that a histone acetylase is brought to the chromosome by the MSL complex and increases H4 lysine16 acetylation, which mediates the increased expression. We investigated the properties of the MSL complex with a series of specific gene-targeting and global gene-expression experiments. The data indicate that the MSL complex does not mediate dosage compensation directly, but rather, its activity overrides the high level of histone acetylation and counteracts the potential overexpression of X-linked genes to achieve the proper twofold up-regulation in males.
Anti-KIT monoclonal antibody inhibits imatinib-resistant gastrointestinal stromal tumor growth
Authors: Edris Badreddin , Willingham Stephen B. , Weiskopf Kipp , Volkmer Anne K. , Volkmer Jens-Peter , Mühlenberg Thomas , Montgomery Kelli D. , Contreras-Trujillo Humberto , Czechowicz Agnieszka , Fletcher Jonathan A. , West Robert B. , Weissman Irving L. , van de Rijn Matt
Published: February 2013

Gastrointestinal stromal tumor (GIST) is the most common sarcoma of the gastrointestinal tract and arises from the interstitial cells of Cajal. It is characterized by expression of the receptor tyrosine kinase CD117 (KIT). In 70–80% of GIST cases, oncogenic mutations in
KIT
are present, leading to constitutive activation of the receptor, which drives the proliferation of these tumors. Treatment of GIST with imatinib, a small-molecule tyrosine kinase inhibitor, inhibits KIT-mediated signaling and initially results in disease control in 70–85% of patients with KIT-positive GIST. However, the vast majority of patients eventually develop resistance to imatinib treatment, leading to disease progression and posing a significant challenge in the clinical management of these tumors. Here, we show that an anti-KIT monoclonal antibody (mAb), SR1, is able to slow the growth of three human GIST cell lines in vitro. Importantly, these reductions in cell growth were equivalent between imatinib-resistant and imatinib-sensitive GIST cell lines. Treatment of GIST cell lines with SR1 reduces cell-surface KIT expression, suggesting that mAb-induced KIT down-regulation may be a mechanism by which SR1 inhibits GIST growth. Furthermore, we also show that SR1 treatment enhances phagocytosis of GIST cells by macrophages, indicating that treatment with SR1 may enhance immune cell-mediated tumor clearance. Finally, using two xenotransplantation models of imatinib-sensitive and imatinib-resistant GIST, we demonstrate that SR1 is able to strongly inhibit tumor growth in vivo. These results suggest that treatment with mAbs targeting KIT may represent an alternative, or complementary, approach for treating GIST.
Innate immunity receptor CD36 promotes cerebral amyloid angiopathy
Authors: Park Laibaik , Zhou Joan , Zhou Ping , Pistick Rose , El Jamal Sleiman , Younkin Linda , Pierce Joseph , Arreguin Andrea , Anrather Josef , Younkin Steven G. , Carlson George A. , McEwen Bruce S. , Iadecola Costantino
Published: February 2013

Deposition of amyloid-β (Aβ) in cerebral arteries, known as cerebral amyloid angiopathy (CAA), occurs both in the setting of Alzheimer’s disease and independent of it, and can cause cerebrovascular insufficiency and cognitive deficits. The mechanisms leading to CAA have not been established, and no therapeutic targets have been identified. We investigated the role of CD36, an innate immunity receptor involved in Aβ trafficking, in the neurovascular dysfunction, cognitive deficits, and amyloid accumulation that occurs in mice expressing the Swedish mutation of the amyloid precursor protein (Tg2576). We found that Tg2576 mice lacking CD36 have a selective reduction in Aβ1-40 and CAA. This reduced vascular amyloid deposition was associated with preservation of the Aβ vascular clearance receptor LRP-1, and protection from the deleterious effects of Aβ on cerebral arterioles. These beneficial vascular effects were reflected by marked improvements in neurovascular regulation and cognitive performance. Our data suggest that CD36 promotes vascular amyloid deposition and the resulting cerebrovascular damage, leading to neurovascular dysfunction and cognitive deficits. These findings identify a previously unrecognized role of CD36 in the mechanisms of vascular amyloid deposition, and suggest that this scavenger receptor is a putative therapeutic target for CAA and related conditions.
Inhibition of neural crest formation by Kctd15 involves regulation of transcription factor AP-2
Authors: Zarelli Valeria E. , Dawid Igor B.
Published: February 2013

The neural crest develops in vertebrate embryos within a discrete domain at the neural plate boundary and eventually gives rise to a migrating population of cells that differentiate into a multitude of derivatives. We have shown that the broad-complex, tramtrack and bric a brac (BTB) domain-containing factor potassium channel tetramerization domain containing 15 (Kctd15) inhibits neural crest formation, and we proposed that its function is to delimit the neural crest domain. Here we report that Kctd15 is a highly effective inhibitor of transcription factor activating enhancer binding protein 2 (AP-2) in zebrafish embryos and in human cells; AP-2 is known to be critical for several steps of neural crest development. Kctd15 interacts with AP-2α but does not interfere with its nuclear localization or binding to cognate sites in the genome. Kctd15 binds specifically to the activation domain of AP-2α and efficiently inhibits transcriptional activation by a hybrid protein composed of the regulatory protein Gal4 DNA binding and AP-2α activation domains. Mutation of one proline residue in the activation domain to an alanine (P59A) yields a protein that is highly active but largely insensitive to Kctd15. These results indicate that Kctd15 acts in the embryo at least in part by specifically binding to the activation domain of AP-2α, thereby blocking the function of this critical factor in the neural crest induction hierarchy.
Gibberellins accumulate in the elongating endodermal cells of
Arabidopsis
root
Authors: Shani Eilon , Weinstain Roy , Zhang Yi , Castillejo Cristina , Kaiserli Eirini , Chory Joanne , Tsien Roger Y. , Estelle Mark
Published: February 2013

Plant hormones are small-molecule signaling compounds that are collectively involved in all aspects of plant growth and development. Unlike animals, plants actively regulate the spatial distribution of several of their hormones. For example, auxin transport results in the formation of auxin maxima that have a key role in developmental patterning. However, the spatial distribution of the other plant hormones, including gibberellic acid (GA), is largely unknown. To address this, we generated two bioactive fluorescent GA compounds and studied their distribution in
Arabidopsis thaliana
roots. The labeled GAs specifically accumulated in the endodermal cells of the root elongation zone. Pharmacological studies, along with examination of mutants affected in endodermal specification, indicate that GA accumulation is an active and highly regulated process. Our results strongly suggest the presence of an active GA transport mechanism that would represent an additional level of GA regulation.
Biomechanics of DNA structures visualized by 4D electron microscopy
Authors: Lorenz Ulrich J. , Zewail Ahmed H.
Published: February 2013

We present a technique for in situ visualization of the biomechanics of DNA structural networks using 4D electron microscopy. Vibrational oscillations of the DNA structure are excited mechanically through a short burst of substrate vibrations triggered by a laser pulse. Subsequently, the motion is probed with electron pulses to observe the impulse response of the specimen in space and time. From the frequency and amplitude of the observed oscillations, we determine the normal modes and eigenfrequencies of the structures involved. Moreover, by selective “nano-cutting” at a given point in the network, it was possible to obtain Young’s modulus, and hence the stiffness, of the DNA filament at that position. This experimental approach enables nanoscale mechanics studies of macromolecules and should find applications in other domains of biological networks such as origamis.
The Multiple Pronunciations of Japanese Kanji: A Masked Priming Investigation
Authors: Verdonschot Rinus Gerardus , La Heij Wido , Tamaoka Katsuo , Kiyama Sachiko , You Wen-Ping , Schiller Niels Olaf
Published: February 2013

English words with an inconsistent grapheme-to-phoneme conversion or with more than one pronunciation (“homographic heterophones”; e.g., “lead”–/l∊d/, /lid/) are read aloud more slowly than matched controls, presumably due to competition processes. In Japanese kanji, the majority of the characters have multiple readings for the same orthographic unit: the native Japanese reading (KUN) and the derived Chinese reading (ON). This leads to the question of whether reading these characters also shows processing costs. Studies examining this issue have provided mixed evidence. The current study addressed the question of whether processing of these kanji characters leads to the simultaneous activation of their KUN and ON reading, This was measured in a direct way in a masked priming paradigm. In addition, we assessed whether the relative frequencies of the KUN and ON pronunciations (“dominance ratio”, measured in compound words) affect the amount of priming. The results of two experiments showed that: (a) a single kanji, presented as a masked prime, facilitates the reading of the (katakana transcriptions of) their KUN and ON pronunciations; however, (b) this was most consistently found when the dominance ratio was around 50% (no strong dominance towards either pronunciation) and when the dominance was towards the ON reading (high-ON group). When the dominance was towards the KUN reading (high-KUN group), no significant priming for the ON reading was observed. Implications for models of kanji processing are discussed.
Iron uptake controls the generation of Leishmania infective forms through regulation of ROS levels
Authors: Mittra Bidyottam , Cortez Mauro , Haydock Andrew , Ramasamy Gowthaman , Myler Peter J. , Andrews Norma W.
Published: February 2013

During its life cycle, Leishmania undergoes extreme environmental changes, alternating between insect vectors and vertebrate hosts. Elevated temperature and decreased pH, conditions encountered after macrophage invasion, can induce axenic differentiation of avirulent promastigotes into virulent amastigotes. Here we show that iron uptake is a major trigger for the differentiation of Leishmania amazonensis amastigotes, independently of temperature and pH changes. We found that iron depletion from the culture medium triggered expression of the ferrous iron transporter LIT1 (Leishmania iron transporter 1), an increase in iron content of the parasites, growth arrest, and differentiation of wild-type (WT) promastigotes into infective amastigotes. In contrast, LIT1-null promastigotes showed reduced intracellular iron content and sustained growth in iron-poor media, followed by cell death. LIT1 up-regulation also increased iron superoxide dismutase (FeSOD) activity in WT but not in LIT1-null parasites. Notably, the superoxide-generating drug menadione or H2O2 was sufficient to trigger differentiation of WT promastigotes into fully infective amastigotes. LIT1-null promastigotes accumulated superoxide radicals and initiated amastigote differentiation after exposure to H2O2 but not to menadione. Our results reveal a novel role for FeSOD activity and reactive oxygen species in orchestrating the differentiation of virulent Leishmania amastigotes in a process regulated by iron availability.
Signaling through C5a receptor and C3a receptor diminishes function of murine natural regulatory T cells
Authors: Kwan Wing-hong , van der Touw William , Paz-Artal Estela , Li Ming O. , Heeger Peter S.
Published: February 2013

Thymus-derived (natural) CD4+ FoxP3+ regulatory T cells (nT reg cells) are required for immune homeostasis and self-tolerance, but must be stringently controlled to permit expansion of protective immunity. Previous findings linking signals transmitted through T cell–expressed C5a receptor (C5aR) and C3a receptor (C3aR) to activation, differentiation, and expansion of conventional CD4+CD25− T cells (T conv cells), raised the possibility that C3aR/C5aR signaling on nT reg cells could physiologically modulate nT reg cell function and thereby further impact the induced strength of T cell immune responses. In this study, we demonstrate that nT reg cells express C3aR and C5aR, and that signaling through these receptors inhibits nT reg cell function. Genetic and pharmacological blockade of C3aR/C5aR signal transduction in nT reg cells augments in vitro and in vivo suppression, abrogates autoimmune colitis, and prolongs allogeneic skin graft survival. Mechanisms involve C3a/C5a-induced phosphorylation of AKT and, as a consequence, phosphorylation of the transcription factor Foxo1, which results in lowered nT reg cell Foxp3 expression. The documentation that C3a/C3aR and C5a/C5aR modulate nT reg cell function via controlling Foxp3 expression suggests targeting this pathway could be exploited to manipulate pathogenic or protective T cell responses.
Characterization of the Bull's Eye Rot of Apple in Chile
Authors: Soto-Alvear Sylvana , Lolas Mauricio , Rosales Inés M. , Chávez Eduardo R. , Latorre Bernardo A.
Published: February 2013

Apple fruit in Chile are primarily produced for export to Asia, Europe, and the United States, which typically requires 15 to 40 days of maritime transportation. Therefore, Chilean apple production must fulfill the sanitization requirements imposed by the receiving countries. Under these circumstances, it was important to clarify the etiology of bull's eye rot that can severely affect ‘Cripps Pink’ apple and other late-harvest cultivars in Chile. Based on morphological characteristics and the partial sequence analysis of the internal transcribed spacer sequences and β-tubulin genes, Neofabraea alba was identified as the causal agent of the bull's eye rot of Chilean apple. These results were further corroborated using species-specific primers. The incidence of bull's eye rot varied considerably; for instance, in 2009, 0.0 to 58.7% in 38 Cripps Pink orchards surveyed in the relatively arid and humid apple-growing areas of Chile, respectively. There was no evidence for the presence of N. malicorticis or N. perennans, which are commonly identified as causal agents of bull's eye rot in other apple-producing countries. Altogether, these data suggest that N. alba might represent the predominant and possibly the only cause of bull's-eye rot of Chilean apple.
Phenotypic Characterization of Multifungicide Resistance in Botrytis cinerea Isolates from Strawberry Fields in Florida
Authors: Amiri A. , Heath S. M. , Peres N. A.
Published: February 2013

Chemical control has always been essential for the management of gray mold, caused by Botrytis cinerea, to ensure sustainable strawberry production. However, lack of knowledge about actual resistance development may have disastrous consequences and lead to severe epidemics such as the one that affected several strawberry fields in 2012 in Florida. In this study, we tested 392 isolates collected from Florida strawberry fields between 2010 and 2012 for their sensitivity to boscalid (Bosc), a succinate dehydrogenase inhibitor (SdhI); pyraclostrobin, a quinone outside inhibitor (QoI); boscalid + pyraclostrobin (Pristine); fenhexamid, a hydroxyanilide (Hyd); pyrimethanil and cyprodinil, anilinopyrimidines; fludioxonil, a phenylpyrrole; and fludioxonil + cyprodinil (Switch). The respective resistance frequencies for boscalid, pyraclostrobin, Pristine, fenhexamid, cyprodinil, and pyrimethanil were 85.4, 86.5, 86.0, 44.4, 52.7, and 59.5%. Overall, 17.8 and 19.8% of isolates showed reduced sensitivity to fludioxonil and Switch, respectively. All fungicides sprayed preventively on detached strawberry fruit failed to control isolates with high levels of resistance to each fungicide except for fludioxonil and Switch. Four phenotypes with multifungicide resistance (MFR) were detected in B. cinerea populations from Florida. Isolates resistant to one fungicide (FR1), two (MFR2), three (MFR3), and four (MFR4) fungicides from different chemical groups represented 5.9, 28.6, 41.8, and 23.7% of the total resistant population, respectively. The MFR3 isolates were predominant and contained two subpopulations, the Bosc-QoI-APR isolates (56.5%) and the Bosc-QoI-HydR isolates (40.6%). In addition to reporting on very highly resistant populations to boscalid and QoI fungicides, we show evidence for a widespread multifungicide resistance to B. cinerea that warrants immediate implementation of novel management strategies to impede the development of more resistant populations.
Identification of New Fungal Pathogens of Coast Live Oak in California
Authors: Lynch Shannon Colleen , Zambino Paul J. , Mayorquin Joey Sal , Wang Danny Ho , Eskalen Akif
Published: February 2013

A decline of coast live oak (Quercus agrifolia) has been observed throughout southern California. In this study, the identity and pathogenicity of non-Botryosphaeriaceae fungal species consistently recovered from necrotic tissues of branch and bleeding trunk canker samples from these locations were assessed. Species were identified morphologically and by comparison of the complete sequence of the internal transcribed spacer (ITS) of the ribosomal DNA to sequences available in GenBank. Phylogenetic analyses were then conducted using ITS and partial sequences of the β-tubulin and mitochondrial small ribosomal subunit genes for unknown species. Fungi recovered and identified included Fusarium solani, Phaeoacremonium mortoniae, Diatrypella verrucaeformis, and a fungus described herein as Cryptosporiopsis querciphila sp. nov. One-year-old coast live oak seedlings were wound inoculated under controlled conditions to test pathogenicity of the fungal species. Each fungal species was successfully reisolated from necrotic tissue at 70 and 100% for P. mortoniae and all other species, and xylem necrosis was significantly different between all treatments and controls (P < 0.0001 at α = 0.05). Isolates of F. solani were the most aggressive tested. These species represent new records of fungal pathogens of coast live oak in California. Results from the pathogenicity test suggest that these fungi play a role in the decline of southern California coast live oak trees.
Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods
Authors: Stadler Tanja , Bonhoeffer Sebastian
Published: February 2013

Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).
The antigenic evolution of influenza: drift or thrift?
Authors: Wikramaratna Paul S. , Sandeman Michi , Recker Mario , Gupta Sunetra
Published: February 2013

It is commonly assumed that antibody responses against the influenza virus are polarized in the following manner: strong antibody responses are directed at highly variable antigenic epitopes, which consequently undergo ‘antigenic drift’, while weak antibody responses develop against conserved epitopes. As the highly variable epitopes are in a constant state of flux, current antibody-based vaccine strategies are focused on the conserved epitopes in the expectation that they will provide some level of clinical protection after appropriate boosting. Here, we use a theoretical model to suggest the existence of epitopes of low variability, which elicit a high degree of both clinical and transmission-blocking immunity. We show that several epidemiological features of influenza and its serological and molecular profiles are consistent with this model of ‘antigenic thrift’, and that identifying the protective epitopes of low variability predicted by this model could offer a more viable alternative to regularly update the influenza vaccine than exploiting responses to weakly immunogenic conserved regions.