bluuebunny/crossref_metadata_2025 huggingface dataset:
Foldable structures and the natural design of pollen grains
Authors: Katifori Eleni , Alben Silas , Cerda Enrique , Nelson David R. , Dumais Jacques
Published: April 2010

Upon release from the anther, pollen grains of angiosperm flowers are exposed to a dry environment and dehydrate. To survive this process, pollen grains possess a variety of physiological and structural adaptations. Perhaps the most striking of these adaptations is the ability of the pollen wall to fold onto itself to prevent further desiccation. Roger P. Wodehouse coined the term harmomegathy for this folding process in recognition of the critical role it plays in the survival of the pollen grain. There is still, however, no quantitative theory that explains how the structure of the pollen wall contributes to harmomegathy. Here we demonstrate that simple geometrical and mechanical principles explain how wall structure guides pollen grains toward distinct folding pathways. We found that the presence of axially elongated apertures of high compliance is critical for achieving a predictable and reversible folding pattern. Moreover, the intricate sculpturing of the wall assists pollen closure by preventing mirror buckling of the surface. These results constitute quantitative structure-function relationships for pollen harmomegathy and provide a framework to elucidate the functional significance of the very diverse pollen morphologies observed in angiosperms.
Inhibition of Mac-1 (CD11b/CD18) enhances tumor response to radiation by reducing myeloid cell recruitment
Authors: Ahn G-One , Tseng Diane , Liao Cho-Hwa , Dorie Mary Jo , Czechowicz Agnieszka , Brown J. Martin
Published: April 2010

Despite recent advances in radiotherapy, loco-regional failures are still the leading cause of death in many cancer patients. We have previously reported that bone marrow-derived CD11b+myeloid cells are recruited to tumors grown in irradiated tissues, thereby restoring the vasculature and tumor growth. In this study, we examined whether neutralizing CD11b monoclonal antibodies could inhibit the recruitment of myeloid cells into irradiated tumors and inhibit their regrowth. We observed a significant enhancement of antitumor response to radiation in squamous cell carcinoma xenografts in mice when CD11b antibodies are administered systemically. Histological examination of tumors revealed that CD11b antibodies reduced infiltration of myeloid cells expressing S100A8 and matrix metalloproteinase-9. CD11b antibodies further inhibited bone marrow-derived cell adhesion and transmigration to C166 endothelial cell monolayers and chemotactic stimuli, respectively, to levels comparable to those from CD11b knockout or CD18 hypomorphic mice. Given the clinical availability of humanized CD18 antibodies, we tested two murine tumor models in CD18 hypomorphic or CD11b knockout mice and found that tumors were more sensitive to irradiation when grown in CD18 hypomorphic mice but not in CD11b knockout mice. When CD18 hypomorphism was partially rescued by reconstitution with the wild-type bone marrow, the resistance of the tumors to irradiation was restored. Our study thus supports the rationale of using clinically available Mac-1 (CD11b/CD18) antibodies as an adjuvant therapy to radiotherapy.
Bounded uncertainty and climate change economics
Authors: Costello Christopher J. , Neubert Michael G. , Polasky Stephen A. , Solow Andrew R.
Published: April 2010

It has been argued recently that the combination of risk aversion and an uncertainty distribution of future temperature change with a heavy upper tail invalidates mainstream economic analyses of climate change policy. A simple model is used to explore the effect of imposing an upper bound on future temperature change. The analysis shows that imposing even a high bound reverses the earlier argument and that the optimal policy, as measured by the willingness to pay to avoid climate change, is relatively insensitive to this bound over a wide range.
Semiautomated model building for RNA crystallography using a directed rotameric approach
Authors: Keating Kevin S. , Pyle Anna Marie
Published: April 2010

Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conformers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the
Coot
model building program is under development.
The Hippo–Salvador pathway restrains hepatic oval cell proliferation, liver size, and liver tumorigenesis
Authors: Lee Kwang-Pyo , Lee Joo-Hyeon , Kim Tae-Shin , Kim Tack-Hoon , Park Hee-Dong , Byun Jin-Seok , Kim Min-Chul , Jeong Won-Il , Calvisi Diego F. , Kim Jin-Man , Lim Dae-Sik
Published: April 2010

Loss of Hippo signaling in
Drosophila
leads to tissue overgrowth as a result of increased cell proliferation and decreased cell death. YAP (a homolog of
Drosophila
Yorkie and target of the Hippo pathway) was recently implicated in control of organ size, epithelial tissue development, and tumorigenesis in mammals. However, the role of the mammalian Hippo pathway in such regulation has remained unclear. We now show that mice with liver-specific ablation of WW45 (a homolog of
Drosophila
Salvador and adaptor for the Hippo kinase) manifest increased liver size and expansion of hepatic progenitor cells (oval cells) and eventually develop hepatomas. Moreover, ablation of WW45 increased the abundance of YAP and induced its localization to the nucleus in oval cells, likely accounting for their increased proliferative capacity, but not in hepatocytes. Liver tumors that developed in mice heterozygous for
WW45
deletion or with liver-specific WW45 ablation showed a mixed pathology combining characteristics of hepatocellular carcinoma and cholangiocarcinoma and seemed to originate from oval cells. Together, our results suggest that the mammalian Hippo–Salvador pathway restricts the proliferation of hepatic oval cells and thereby controls liver size and prevents the development of oval cell–derived tumors.
Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA
Authors: Larson Greger , Liu Ranran , Zhao Xingbo , Yuan Jing , Fuller Dorian , Barton Loukas , Dobney Keith , Fan Qipeng , Gu Zhiliang , Liu Xiao-Hui , Luo Yunbing , Lv Peng , Andersson Leif , Li Ning
Published: April 2010

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (
Sus scrofa
) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.
Linking global climate and temperature variability to widespread amphibian declines putatively caused by disease
Authors: Rohr Jason R. , Raffel Thomas R.
Published: April 2010

The role of global climate change in the decline of biodiversity and the emergence of infectious diseases remains controversial, and the effect of climatic variability, in particular, has largely been ignored. For instance, it was recently revealed that the proposed link between climate change and widespread amphibian declines, putatively caused by the chytrid fungus
Batrachochytrium dendrobatidis
(
Bd
), was tenuous because it was based on a temporally confounded correlation. Here we provide temporally unconfounded evidence that global El Niño climatic events drive widespread amphibian losses in genus
Atelopus
via increased regional temperature variability, which can reduce amphibian defenses against pathogens. Of 26 climate variables tested, only factors associated with temperature variability could account for the spatiotemporal patterns of declines thought to be associated with
Bd
. Climatic predictors of declines became significant only after controlling for a pattern consistent with epidemic spread (by temporally detrending the data). This presumed spread accounted for 59% of the temporal variation in amphibian losses, whereas El Niño accounted for 59% of the remaining variation. Hence, we could account for 83% of the variation in declines with these two variables alone. Given that global climate change seems to increase temperature variability, extreme climatic events, and the strength of Central Pacific El Niño episodes, climate change might exacerbate worldwide enigmatic declines of amphibians, presumably by increasing susceptibility to disease. These results suggest that changes to temperature variability associated with climate change might be as significant to biodiversity losses and disease emergence as changes to mean temperature.
A hyperactive quantitative trait locus allele of
Arabidopsis BRX
contributes to natural variation in root growth vigor
Authors: Beuchat Julien , Li Shuwei , Ragni Laura , Shindo Chikako , Kohn Michael H. , Hardtke Christian S.
Published: April 2010

Quantitative trait loci analysis of natural
Arabidopsis thaliana
accessions is increasingly exploited for gene isolation. However, to date this has mostly revealed deleterious mutations. Among them, a loss-of-function allele identified the root growth regulator
BREVIS RADIX (BRX)
. Here we present evidence that
BRX
and the paralogous
BRX-LIKE (BRXL)
genes are under selective constraint in monocotyledons as well as dicotyledons. Unexpectedly, however, whereas none of the
Arabidopsis
orthologs except
AtBRXL1
could complement
brx
null mutants when expressed constitutively, nearly all monocotyledon
BRXLs
tested could. Thus, BRXL proteins seem to be more diversified in dicotyledons than in monocotyledons. This functional diversification was correlated with accelerated rates of sequence divergence in the N-terminal regions. Population genetic analyses of 30 haplotypes are suggestive of an adaptive role of
AtBRX
and
AtBRXL1
. In two accessions, Lc-0 and Lov-5, seven amino acids are deleted in the variable region between the highly conserved C-terminal, so-called BRX domains. Genotyping of 42 additional accessions also found this deletion in Kz-1, Pu2-7, and Ws-0. In segregating recombinant inbred lines, the Lc-0 allele

(AtBRX
Lc-0
)

conferred significantly enhanced root growth. Moreover, when constitutively expressed in the same regulatory context,

AtBRX
Lc-0

complemented
brx
mutants more efficiently than an allele without deletion. The same was observed for AtBRXL1, which compared with AtBRX carries a 13 amino acid deletion that encompasses the deletion found in AtBRX
Lc-0
. Thus, the

AtBRX
Lc-0

allele seems to contribute to natural variation in root growth vigor and provides a rare example of an experimentally confirmed, hyperactive allelic variant.
Costs and constraints from time-delayed feedback in small gene regulatory motifs
Authors: Grönlund Andreas , Lötstedt Per , Elf Johan
Published: April 2010

The multistep character of transcription, translation, and protein modification inevitably leads to time delays between sensing gene regulatory signals and responding with changed concentrations of functional proteins. However, the interplay between the time-delayed and the stochastic nature of gene regulation has been poorly investigated. Here we present an extension of the linear noise approximation which makes it possible to estimate second moments—variances and covariances—of fluctuations around stationary states in time-delayed systems. The usefulness of the method is exemplified by analyzing two ubiquitous regulatory motifs. In the first system, we show that there is an optimal combination of transcriptional repression and direct product inhibition in determining the activity of an enzyme system. In particular, we demonstrate that direct product inhibition is necessary to avoid deleterious fluctuations in a system when the gene regulatory response is delayed. The second system is an anabolic motif where the substrate fluxes are balanced by time-delayed regulation responding to the substrate concentrations. The extended linear noise approximation makes it possible to show analytically that increased association rate between the substrates leads to a lower product flux because of increasing unbalance in substrate pools.
A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus
Authors: Yu Xiao , Li Bo , Fu Yanping , Jiang Daohong , Ghabrial Said A. , Li Guoqing , Peng Youliang , Xie Jiatao , Cheng Jiasen , Huang Junbin , Yi Xianhong
Published: April 2010

Mycoviruses are viruses that infect fungi and have the potential to control fungal diseases of crops when associated with hypovirulence. Typically, mycoviruses have double-stranded (ds) or single-stranded (ss) RNA genomes. No mycoviruses with DNA genomes have previously been reported. Here, we describe a hypovirulence-associated circular ssDNA mycovirus from the plant pathogenic fungus
Sclerotinia sclerotiorum
. The genome of this ssDNA virus, named Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), is 2166 nt, coding for a replication initiation protein (Rep) and a coat protein (CP). Although phylogenetic analysis of Rep showed that SsHADV-1 is related to geminiviruses, it is notably distinct from geminiviruses both in genome organization and particle morphology. Polyethylene glycol-mediated transfection of fungal protoplasts was successful with either purified SsHADV-1 particles or viral DNA isolated directly from infected mycelium. The discovery of an ssDNA mycovirus enhances the potential of exploring fungal viruses as valuable tools for molecular manipulation of fungi and for plant disease control and expands our knowledge of global virus ecology and evolution.
Low beta diversity of Maastrichtian dinosaurs of North America
Authors: Vavrek Matthew J. , Larsson Hans C. E.
Published: April 2010

Beta diversity is an important component of large-scale patterns of biodiversity, but its explicit examination is more difficult than that of alpha diversity. Only recently have data sets large enough been presented to begin assessing global patterns of species turnover, especially in the fossil record. We present here an analysis of beta diversity of a Maastrichtian (71–65 million years old) assemblage of dinosaurs from the Western Interior of North America, a region that covers ≈1.5 × 10
6
km
2
, borders an epicontinental sea, and spans ≈20° of latitude. Previous qualitative analyses have suggested regional groupings of these dinosaurs and generally concluded that there were multiple distinct faunal regions. However, these studies did not directly account for sampling bias, which may artificially decrease similarity and increase turnover between regions. Our analysis used abundance-based data to account for sampling intensity and was unable to support any hypothesis of multiple distinct faunas; earlier hypothesized faunal delineations were likely a sampling artifact. Our results indicate a low beta diversity and support a single dinosaur community within the entire Western Interior region of latest Cretaceous North America. Homogeneous environments are a known driver of low modern beta diversities, and the warm equable climate of the late Cretaceous modulated by the epicontenental seaway is inferred to be an underlying influence on the low beta diversity of this ancient ecosystem.
In vivo magnetomotive optical molecular imaging using targeted magnetic nanoprobes
Authors: John Renu , Rezaeipoor Robabeh , Adie Steven G. , Chaney Eric J. , Oldenburg Amy L. , Marjanovic Marina , Haldar Justin P. , Sutton Bradley P. , Boppart Stephen A.
Published: April 2010

Dynamic magnetomotion of magnetic nanoparticles (MNPs) detected with magnetomotive optical coherence tomography (MM-OCT) represents a new methodology for contrast enhancement and therapeutic interventions in molecular imaging. In this study, we demonstrate in vivo imaging of dynamic functionalized iron oxide MNPs using MM-OCT in a preclinical mammary tumor model. Using targeted MNPs, in vivo MM-OCT images exhibit strong magnetomotive signals in mammary tumor, and no significant signals were measured from tumors of rats injected with nontargeted MNPs or saline. The results of in vivo MM-OCT are validated by MRI, ex vivo MM-OCT, Prussian blue staining of histological sections, and immunohistochemical analysis of excised tumors and internal organs. The MNPs are antibody functionalized to target the human epidermal growth factor receptor 2 (
HER2 neu
) protein. Fc-directed conjugation of the antibody to the MNPs aids in reducing uptake by macrophages in the reticulo-endothelial system, thereby increasing the circulation time in the blood. These engineered magnetic nanoprobes have multifunctional capabilities enabling them to be used as dynamic contrast agents in MM-OCT and MRI.
Globular cluster x-ray sources
Authors: Pooley David
Published: April 2010

Globular clusters and x-ray astronomy have a long and fruitful history.
Uhuru
and
OSO-7
revealed highly luminous (> 10
36
 ergs
-1
) x-ray sources in globular clusters, and
Einstein
and
ROSAT
revealed a larger population of low-luminosity (< 10
33
 ergs
-1
) x-ray sources. It was realized early on that the high-luminosity sources were low-mass x-ray binaries in outburst and that they were orders of magnitude more abundant per unit mass in globular clusters than in the rest of the galaxy. However, the low-luminosity sources proved difficult to classify. Many ideas were put forth—low-mass x-ray binaries in quiescence (qLMXBs), cataclysmic variables (CVs), active main-sequence binaries (ABs), and millisecond pulsars (MSPs)—but secure identifications were scarce. In
ROSAT
observations of 55 clusters, about 25 low-luminosity sources were found.
Chandra
has now observed over 80 Galactic globular clusters, and these observations have revealed over 1,500 x-ray sources. The superb angular resolution has allowed for many counterpart identifications, providing clues to the nature of this population. It is a heterogeneous mix of qLMXBs, CVs, ABs, and MSPs, and it has been shown that the qLMXBs and CVs are both, in part, overabundant like the luminous LMXBs. The number of x-ray sources in a cluster correlates very well with its encounter frequency. This points to dynamical formation scenarios for the x-ray sources and shows them to be excellent tracers of the complicated internal dynamics. The relation between the encounter frequency and the number of x-ray sources has been used to suggest that we have misunderstood the dynamical states of globular clusters.
Supermassive black-hole growth over cosmic time: Active galaxy demography, physics, and ecology from
Chandra
surveys
Authors: Brandt W. N. , Alexander D. M.
Published: April 2010

Extragalactic X-ray surveys over the past decade have dramatically improved understanding of the majority populations of active galactic nuclei (AGNs) over most of the history of the universe. Here we briefly highlight some of the exciting discoveries about AGN demography, physics, and ecology, with a focus on results from
Chandra
. We also discuss some key unresolved questions and future prospects.
X-ray studies of supernova remnants: A different view of supernova explosions
Authors: Badenes Carles
Published: April 2010

The unprecedented spatial and spectral resolutions of
Chandra
have revolutionized our view of the X-ray emission from supernova remnants. The excellent datasets accumulated on young, ejecta-dominated objects like Cas A or Tycho present a unique opportunity to study at the same time the chemical and physical structure of the explosion debris and the characteristics of the circumstellar medium sculpted by the progenitor before the explosion. Supernova remnants can thus put strong constraints on fundamental aspects of both supernova explosion physics and stellar evolution scenarios for supernova progenitors. This view of the supernova phenomenon is completely independent of, and complementary to, the study of distant extragalactic supernovae at optical wavelengths. The calibration of these two techniques has recently become possible thanks to the detection and spectroscopic follow-up of supernova light echoes. In this paper, I review the most relevant results on supernova remnants obtained during the first decade of
Chandra
and the impact that these results have had on open issues in supernova research.
Chandra’s first decade of discovery
Authors: Swartz Douglas A. , Wolk Scott J. , Fruscione Antonella
Published: April 2010

We review some of the many scientific results reported at a symposium held in September 2009 celebrating the 10th anniversary of National Aeronautics and Space Administration's (NASA's) Chandra X-ray Observatory. These results were contributed by scientists who were among the more than 300 symposium participants. We highlight those results that most emphasize the unique imaging and spectroscopic capabilities of Chandra.
Ecological processes can synchronize marine population dynamics over continental scales
Authors: Gouhier Tarik C. , Guichard Frédéric , Menge Bruce A.
Published: April 2010

Determining the relative importance of local and regional processes for the distribution of population abundance is a fundamental but contentious issue in ecology. In marine systems, classical theory holds that the influence of demographic processes and dispersal is confined to local populations whereas the environment controls regional patterns of abundance. Here, we use spatial synchrony to compare the distribution of population abundance of the dominant mussel
Mytilus californianus
observed along the West Coast of the United States to that predicted by dynamical models undergoing different dispersal and environmental treatments to infer the relative influence of local and regional processes. We reveal synchronized fluctuations in the abundance of mussel populations across a whole continent despite limited larval dispersal and strong environmental forcing. We show that dispersal among neighboring populations interacts with local demographic processes to generate characteristic patterns of spatial synchrony that can govern the dynamic distribution of mussel abundance over 1,800 km of coastline. Our study emphasizes the importance of dispersal and local dynamics for the distribution of abundance at the continental scale. It further highlights potential limits to the use of “climate envelope” models for predicting the response of large-scale ecosystems to global climate change.
Interleukin-23 production in dendritic cells is negatively regulated by protein phosphatase 2A
Authors: Chang JiHoon , Voorhees Timothy J. , Liu Yusen , Zhao Yongge , Chang Cheong-Hee
Published: April 2010

IL-12 and IL-23 are produced by activated antigen-presenting cells but the two induce distinct immune responses by promoting Th1 and Th17 cell differentiation, respectively. IL-23 is a heterodimeric cytokine consisting of two subunits: p40 that is shared with IL-12 and p19 unique to IL-23. In this study, we showed that the production of IL-23 but not IL-12 was negatively regulated by protein phosphatase 2A (PP2A) in dendritic cells (DC). PP2A inhibits IL-23 production by suppressing the expression of the IL-23p19 gene. Treating DC with okadaic acid that inhibits the PP2A activity or knocking down the catalytic subunit of PP2A with siRNA enhanced IL-23 but not IL-12 production. Unlike PP2A, MAP kinase phosphatase-1 or CYLD did not show an effect on IL-23 production supporting the specificity of PP2A. PP2A-mediated inhibition requires a newly made protein that is likely responsible for bringing PP2A and IKKβ together upon LPS stimulation, which then results in the termination of IKK phosphorylation. Thus, our results uncovered an important role of the protein phosphatase in the regulation of IL-23 production and identified PP2A as a previously uncharacterized inhibitor of IL-23p19 expression in DC.
Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of
Populus
Authors: Drost Derek R. , Benedict Catherine I. , Berg Arthur , Novaes Evandro , Novaes Carolina R. D. B. , Yu Qibin , Dervinis Christopher , Maia Jessica M. , Yap John , Miles Brianna , Kirst Matias
Published: April 2010

A fundamental goal of systems biology is to identify genetic elements that contribute to complex phenotypes and to understand how they interact in networks predictive of system response to genetic variation. Few studies in plants have developed such networks, and none have examined their conservation among functionally specialized organs. Here we used genetical genomics in an interspecific hybrid population of the model hardwood plant
Populus
to uncover transcriptional networks in xylem, leaves, and roots. Pleiotropic eQTL hotspots were detected and used to construct coexpression networks a posteriori, for which regulators were predicted based on
cis
-acting expression regulation. Networks were shown to be enriched for groups of genes that function in biologically coherent processes and for
cis
-acting promoter motifs with known roles in regulating common groups of genes. When contrasted among xylem, leaves, and roots, transcriptional networks were frequently conserved in composition, but almost invariably regulated by different loci. Similarly, the genetic architecture of gene expression regulation is highly diversified among plant organs, with less than one-third of genes with eQTL detected in two organs being regulated by the same locus. However, colocalization in eQTL position increases to 50% when they are detected in all three organs, suggesting conservation in the genetic regulation is a function of ubiquitous expression. Genes conserved in their genetic regulation among all organs are primarily
cis
regulated (~92%), whereas genes with eQTL in only one organ are largely
trans
regulated.
Trans
-acting regulation may therefore be the primary driver of differentiation in function between plant organs.
Phosphoproteome dynamics reveal heat-shock protein complexes specific to the
Leishmania donovani
infectious stage
Authors: Morales Miguel A. , Watanabe Reiko , Dacher Mariko , Chafey Philippe , Osorio y Fortéa José , Scott David A. , Beverley Stephen M. , Ommen Gabi , Clos Joachim , Hem Sonia , Lenormand Pascal , Rousselle Jean-Claude , Namane Abdelkader , Späth Gerald F.
Published: April 2010

Leishmania
is exposed to a sudden increase in environmental temperature during the infectious cycle that triggers stage differentiation and adapts the parasite phenotype to intracellular survival in the mammalian host. The absence of classical promoter-dependent mechanisms of gene regulation and constitutive expression of most of the heat-shock proteins (HSPs) in these human pathogens raise important unresolved questions as to regulation of the heat-shock response and stage-specific functions of
Leishmania
HSPs. Here we used a gel-based quantitative approach to assess the
Leishmania donovani
phosphoproteome and revealed that 38% of the proteins showed significant stage-specific differences, with a strong focus of amastigote-specific phosphoproteins on chaperone function. We identified STI1/HOP-containing chaperone complexes that interact with ribosomal client proteins in an amastigote-specific manner. Genetic analysis of STI1/HOP phosphorylation sites in conditional

sti1
−/−

null mutant parasites revealed two phosphoserine residues essential for parasite viability. Phosphorylation of the major
Leishmania
chaperones at the pathogenic stage suggests that these proteins may be promising drug targets via inhibition of their respective protein kinases.
Noncanonical interactions between serum transferrin and transferrin receptor evaluated with electrospray ionization mass spectrometry
Authors: Leverence Rachael , Mason Anne B. , Kaltashov Igor A.
Published: April 2010

The primary route of iron acquisition in vertebrates is the transferrin receptor (TfR) mediated endocytotic pathway, which provides cellular entry to the metal transporter serum transferrin (Tf). Despite extensive research efforts, complete understanding of Tf-TfR interaction mechanism is still lacking owing to the complexity of this system. Electrospray ionization mass spectrometry (ESI MS) is used in this study to monitor the protein/receptor interaction and demonstrate the ability of metal-free Tf to associate with TfR at neutral pH. A set of Tf variants is used in a series of competition and displacement experiments to bracket TfR affinity of apo-Tf at neutral pH (0.2–0.6 μM). Consistent with current models of endosomal iron release from Tf, acidification of the protein solution results in a dramatic change of binding preferences, with apo-Tf becoming a preferred receptor binder. Contrary to the current models implying that the apo-Tf/TfR complex dissociates almost immediately upon exposure to the neutral environment at the cell surface, our data indicate that this complex remains intact. Iron-loaded Tf displaces apo-Tf from TfR, making it available for the next cycle of iron binding, transport and delivery to tissues. However, apo-Tf may still interfere with the cellular uptake of engineered Tf molecules whose TfR affinity is affected by various modifications (e.g., conjugation to cytotoxic molecules). This work also highlights the great potential of ESI MS as a tool capable of providing precise details of complex protein-receptor interactions under conditions that closely mimic the environment in which these encounters occur in physiological systems.
Natural immunity to pluripotency antigen OCT4 in humans
Authors: Dhodapkar Kavita M. , Feldman Darren , Matthews Phillip , Radfar Soroosh , Pickering Roxana , Turkula Stefan , Zebroski Henry , Dhodapkar Madhav V.
Published: April 2010

OCT4 is a transcription factor critical for the pluripotency of human embryonal stem (ES) and induced pluipotency stem (IPS) cells. OCT4 is commonly expressed in germ-cell tumors as well as putative cancer stem cells in several tumors, and is a key determinant of oncogenic fate in germ-cell tumors. The capacity of the human immune system to recognize this critical stem-cell gene is not known, but has implications for preventing tumors with ES/IPS-based therapies and targeting stem-cell pathways in cancer. Here we show that OCT4-specific T cells can be readily detected in freshly isolated T cells from most (>80%) healthy donors. The reactivity to OCT4-derived peptides resides primarily in the CD45RO
+
memory T-cell compartment and consists predominantly of CD4
+
T cells. T cells reactive against OCT4-derived peptides can be readily expanded in culture using peptide-loaded dendritic cells. In contrast to healthy donors, immunity to OCT4 was detected in only 35% of patients with newly diagnosed germ-cell tumors. However, chemotherapy of germ-cell tumors led to the induction of anti-OCT4 immunity in vivo in patients lacking such responses at baseline. These data demonstrate the surprising lack of immune tolerance to this critical pluripotency antigen in humans. Harnessing natural immunity to this antigen may allow immune-based targeting of pluripotency-related pathways for prevention of cancers, including those in the setting of ES/IPS-based therapies.
Acute manipulation of Golgi phosphoinositides to assess their importance in cellular trafficking and signaling
Authors: Szentpetery Zsofia , Várnai Peter , Balla Tamas
Published: April 2010

Phosphoinositides are essential lipid regulators of trafficking and signaling pathways of all eukaryotic cells. Phosphatidylinositol 4-phosphate (PtdIns4
P
) is an intermediate in the synthesis of several important phosphoinositide species but also serves as a regulatory molecule in its own right. Phosphatidylinositol 4-kinases are most abundant in the Golgi but are also found in the plasma membrane and in endocytic compartments. To investigate the role of Golgi PtdIns4
P
in orchestrating trafficking events, we used a unique drug-inducible molecular approach to rapidly deplete PtdIns4
P
from Golgi membranes by a recruitable Sac1 phosphatase enzyme. The utility of the system was shown by the rapid loss of Golgi localization of PH domains known to bind PtdIns4
P
after Sac1 recruitment to the Golgi. Acute PtdIns4
P
depletion prevented the exit of cargo from the Golgi destined to both the plasma membrane and the late endosomes and led to the loss of some but not all clathrin adaptors from the Golgi membrane. Rapid PtdIns4
P
depletion in the Golgi also impaired but did not eliminate the replenishment of the plasma membrane PtdIns(4,5)
P
2
during phospholipase C activation revealing a hitherto unrecognized contribution of Golgi PtdIns4
P
to this process. This unique approach will allow further studies on the role of phosphoinositides in endocytic compartments that have evaded detection using the conventional long-term manipulations of inositide kinase and phosphatase activities.
Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in
Nostoc punctiforme
, a group II chromatic adapter
Authors: Hirose Yuu , Narikawa Rei , Katayama Mitsunori , Ikeuchi Masahiko
Published: April 2010

Responding to green and red light, certain cyanobacteria change the composition of their light-harvesting pigments, phycoerythrin (PE) and phycocyanin (PC). Although this phenomenon—complementary chromatic adaptation—is well known, the green light–sensing mechanism for PE accumulation is unclear. The filamentous cyanobacterium
Nostoc punctiforme
ATCC

29133 (
N. punctiforme
) regulates PE synthesis in response to green and red light (group II chromatic adaptation). We disrupted the green/red-perceiving histidine-kinase gene (
ccaS
) or the cognate response regulator gene (
ccaR
), which are clustered with several PE and PC genes (
cpeC
-
cpcG2-cpeR1
operon) in
N. punctiforme
. Under green light, wild-type cells accumulated a significant amount of PE upon induction of
cpeC
-
cpcG2
-
cpeR1
expression, whereas they accumulated little PE with suppression of
cpeC
-
cpcG2
-
cpeR1
expression under red light. Under both green and red light, the
ccaS
mutant constitutively accumulated some PE with constitutively low
cpeC
-
cpcG2
-
cpeR1
expression, whereas the
ccaR
mutant accumulated little PE with suppression of
cpeC
-
cpcG2
-
cpeR1
expression. The results of an electrophoretic mobility shift assay suggest that CcaR binds to the promoter region of
cpeC
-
cpcG2
-
cpeR1
, which contains a conserved direct-repeat motif. Taken together, the results suggest that CcaS phosphorylates CcaR under green light and that phosphorylated CcaR then induces
cpeC
-
cpcG2
-
cpeR1
expression, leading to PE accumulation. In contrast, CcaS probably represses
cpeC
-
cpcG2
-
cpeR1
expression by dephosphorylation of CcaR under red light. We also found that the
cpeB-cpeA
operon is partially regulated by green and red light, suggesting that the green light-induced regulatory protein CpeR1 activates
cpeB-cpeA
expression together with constitutively induced CpeR2.
Transcription factor Late SV40 Factor (LSF) functions as an oncogene in hepatocellular carcinoma
Authors: Yoo Byoung Kwon , Emdad Luni , Gredler Rachel , Fuller Christine , Dumur Catherine I. , Jones Kimberly H. , Jackson-Cook Colleen , Su Zao-zhong , Chen Dong , Saxena Utsav H. , Hansen Ulla , Fisher Paul B. , Sarkar Devanand
Published: April 2010

Hepatocellular carcinoma (HCC) is a highly aggressive cancer with no currently available effective treatment. Understanding of the molecular mechanism of HCC development and progression is imperative for developing novel, effective, and targeted therapies for this lethal disease. In this article, we document that the cellular transcription factor Late SV40 Factor (LSF) plays an important role in HCC pathogenesis. LSF protein was significantly overexpressed in human HCC cells compared to normal hepatocytes. In 109 HCC patients, LSF protein was overexpressed in >90% cases, compared to normal liver, and LSF expression level showed significant correlation with the stages and grades of the disease. Forced overexpression of LSF in less aggressive HCC cells resulted in highly aggressive, angiogenic, and multiorgan metastatic tumors in nude mice. Conversely, inhibition of LSF significantly abrogated growth and metastasis of highly aggressive HCC cells in nude mice. Microarray studies revealed that as a transcription factor, LSF modulated specific genes regulating invasion, angiogenesis, chemoresistance, and senescence. The expression of osteopontin (OPN), a gene regulating every step in tumor progression and metastasis, was robustly up-regulated by LSF. It was documented that LSF transcriptionally up-regulates OPN, and loss-of-function studies demonstrated that OPN plays an important role in mediating the oncogenic functions of LSF. Together, these data establish a regulatory role of LSF in cancer, particularly HCC pathogenesis, and validate LSF as a viable target for therapeutic intervention.
Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation
Authors: Dovey Oliver M. , Foster Charles T. , Cowley Shaun M.
Published: April 2010

Histone deacetylases (HDAC) 1 and 2 are highly similar enzymes that help regulate chromatin structure as the core catalytic components of corepressor complexes. Although tissue-specific deletion of HDAC1 and HDAC2 has demonstrated functional redundancy, germ-line deletion of HDAC1 in the mouse causes early embryonic lethality, whereas HDAC2 does not. To address the unique requirement for HDAC1 in early embryogenesis we have generated conditional knockout embryonic stem (ES) cells in which HDAC1 or HDAC2 genes can be inactivated. Deletion of HDAC1, but not HDAC2, causes a significant reduction in the HDAC activity of Sin3A, NuRD, and CoREST corepressor complexes. This reduced corepressor activity results in a specific 1.6-fold increase in histone H3 K56 acetylation (H3K56Ac), thus providing genetic evidence that H3K56Ac is a substrate of HDAC1. In culture, ES cell proliferation was unaffected by loss of either HDAC1 or HDAC2. Rather, we find that loss of HDAC1 affects ES cell differentiation. ES cells lacking either HDAC1 or HDAC2 were capable of forming embryoid bodies (EBs), which stimulates differentiation into the three primary germ layers. However, HDAC1-deficient EBs were significantly smaller, showed spontaneous rhythmic contraction, and increased expression of both cardiomyocyte and neuronal markers. In summary, our genetic study of HDAC1 and HDAC2 in ES cells, which mimic the embryonic epiblast, has identified a unique requirement for HDAC1 in the optimal activity of HDAC1/2 corepressor complexes and cell fate determination during differentiation.
The basal ganglia communicate with the cerebellum
Authors: Bostan Andreea C. , Dum Richard P. , Strick Peter L.
Published: April 2010

The basal ganglia and cerebellum are major subcortical structures that influence not only movement, but putatively also cognition and affect. Both structures receive input from and send output to the cerebral cortex. Thus, the basal ganglia and cerebellum form multisynaptic loops with the cerebral cortex. Basal ganglia and cerebellar loops have been assumed to be anatomically separate and to perform distinct functional operations. We investigated whether there is any direct route for basal ganglia output to influence cerebellar function that is independent of the cerebral cortex. We injected rabies virus (RV) into selected regions of the cerebellar cortex in cebus monkeys and used retrograde transneuronal transport of the virus to determine the origin of multisynaptic inputs to the injection sites. We found that the subthalamic nucleus of the basal ganglia has a substantial disynaptic projection to the cerebellar cortex. This pathway provides a means for both normal and abnormal signals from the basal ganglia to influence cerebellar function. We previously showed that the dentate nucleus of the cerebellum has a disynaptic projection to an input stage of basal ganglia processing, the striatum. Taken together these results provide the anatomical substrate for substantial two-way communication between the basal ganglia and cerebellum. Thus, the two subcortical structures may be linked together to form an integrated functional network.
Palmitoylation stabilizes unliganded rod opsin
Authors: Maeda Akiko , Okano Kiichiro , Park Paul S.-H. , Lem Janis , Crouch Rosalie K. , Maeda Tadao , Palczewski Krzysztof
Published: April 2010

S-palmitoylation is a conserved feature in many G protein–coupled receptors (GPCRs) involved in a broad array of signaling processes. The prototypical GPCR, rhodopsin, is S-palmitoylated on two adjacent C-terminal Cys residues at its cytoplasmic surface. Surprisingly, absence of palmitoylation has only a modest effect on in vitro or in vivo signaling. Here, we report that palmitoylation-deficient (

Palm
−/−

) mice carrying two Cys to Thr and Ser mutations in the opsin gene displayed profound light-induced retinal degeneration that first involved rod and then cone cells. After brief bright light exposure, their retinas exhibited two types of deposits containing nucleic acid and invasive phagocytic macrophages. When

Palm
−/−

mice were crossed with

Lrat
−/−

mice lacking lecithin:retinol acyl transferase to eliminate retinoid binding to opsin and thereby rendering the eye insensitive to light, rapid retinal degeneration occurred even in 3- to 4-week-old animals. This rapid degeneration suggests that nonpalmitoylated rod opsin is unstable. Treatment of 2-week-old

Palm
−/−
Lrat
−/−

mice with an artificial chromophore precursor prevented this retinopathy. In contrast, elimination of signaling to G protein in

Palm
−/−
Gnat1
−/−

mice had no effect, indicating that instability of unpalmitoylated opsin lacking chromophore rather than aberrant signal transduction resulted in retinal pathology. Together, these observations provide evidence for a structural role of rhodopsin S-palmitoylation that may apply to other GPCRs as well.
Drosophila
TRPA1 channel mediates chemical avoidance in gustatory receptor neurons
Authors: Kim Sang Hoon , Lee Youngseok , Akitake Bradley , Woodward Owen M. , Guggino William B. , Montell Craig
Published: April 2010

Mammalian sweet, bitter, and umami taste is mediated by a single transduction pathway that includes a phospholipase C (PLC)β and one cation channel, TRPM5. However, in insects such as the fruit fly,
Drosophila melanogaster
, it is unclear whether different tastants, such as bitter compounds, are sensed in gustatory receptor neurons (GRNs) through one or multiple ion channels, as the cation channels required in insect GRNs are unknown. Here, we set out to explore additional sensory roles for the
Drosophila
TRPA1 channel, which was known to function in thermosensation. We found that TRPA1 was expressed in GRNs that respond to aversive compounds. Elimination of TRPA1 had no impact on the responses to nearly all bitter compounds tested, including caffeine, quinine, and strychnine. Rather, we found that TRPA1 was required in a subset of avoidance GRNs for the behavioral and electrophysiological responses to aristolochic acid. TRPA1 did not appear to be activated or inhibited directly by aristolochic acid. We found that elimination of the same PLC that leads to activation of TRPA1 in thermosensory neurons was also required in the TRPA1-expressing GRNs for avoiding aristolochic acid. Given that mammalian TRPA1 is required for responding to noxious chemicals, many of which cause pain and injury, our analysis underscores the evolutionarily conserved role for TRPA1 channels in chemical avoidance.
Understanding gastric forces calculated from high-resolution pill tracking
Authors: Laulicht Bryan , Tripathi Anubhav , Schlageter Vincent , Kucera Pavel , Mathiowitz Edith
Published: April 2010

Although other methods exist for monitoring gastrointestinal motility and contractility, this study exclusively provides direct and quantitative measurements of the forces experienced by an orally ingested pill. We report motive forces and torques calculated from real-time, in vivo measurements of the movement of a magnetic pill in the stomachs of fasted and fed humans. Three-dimensional net force and two-dimensional net torque vectors as a function of time data during gastric residence are evaluated using instantaneous translational and rotational position data. Additionally, the net force calculations described can be applied to high-resolution pill tracking acquired by any modality. The fraction of time pills experience ranges of forces and torques are analyzed and correlate with the physiological phases of gastric digestion. We also report the maximum forces and torques experienced in vivo by pills as a quantitative measure of the amount of force pills experience during the muscular contractions leading to gastric emptying. Results calculated from human data are compared with small and large animal models with a translational research focus. The reported magnitude and direction of gastric forces experienced by pills in healthy stomachs serves as a baseline for comparison with pathophysiological states. Of clinical significance, the directionality associated with force vector data may be useful in determining the muscle groups associated with gastrointestinal dysmotility. Additionally, the quantitative comparison between human and animal models improves insight into comparative gastric contractility that will aid rational pill design and provide a quantitative framework for interpreting gastroretentive oral formulation test results.