bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative modeling of the role of surface traps in CdSe/CdS/ZnS nanocrystal photoluminescence decay dynamics
Authors: Jones Marcus , Lo Shun S. , Scholes Gregory D.
Published: February 2009

Charge carrier trapping is an important phenomenon in nanocrystal (NC) decay dynamics because it reduces photoluminescence (PL) quantum efficiencies and obscures efforts to understand the interaction of NC excitons with their surroundings. Particularly crucial to our understanding of excitation dynamics in, e.g., multiNC assemblies, would be a way of differentiating between processes involving trap states and those that do not. Direct optical measurement of NC trap state processes is not usually possible because they have negligible transition dipole moments; however, they are known to indirectly affect exciton photoluminescence. Here, we develop a framework, based on Marcus electron transfer theory, to determine NC trap state dynamics from time-resolved NC exciton PL measurements. Our results demonstrate the sensitivity of PL to interfacial dynamics, indicating that the technique can be used as an indirect but effective probe of trap distribution changes. We anticipate that this study represents a step toward understanding how excitons in nanocrystals interact with their surroundings: a quality that must be optimized for their efficient application in photovoltaics, photodetectors, or chemical sensors.
Identification of mRNA splicing factors as the endothelial receptor for carbohydrate-dependent lung colonization of cancer cells
Authors: Hatakeyama Shingo , Sugihara Kazuhiro , Nakayama Jun , Akama Tomoya O. , Wong Shuk-Man Annie , Kawashima Hiroto , Zhang Jianing , Smith David F. , Ohyama Chikara , Fukuda Minoru , Fukuda Michiko N.
Published: February 2009

Cell surfaces of epithelial cancer are covered by complex carbohydrates, whose structures function in malignancy and metastasis. However, the mechanism underlying carbohydrate-dependent cancer metastasis has not been defined. Previously, we identified a carbohydrate-mimicry peptide designated I-peptide, which inhibits carbohydrate-dependent lung colonization of sialyl Lewis X-expressing B16-FTIII-M cells in E/P-selectin doubly-deficient mice. We hypothesized that lung endothelial cells express an unknown carbohydrate receptor, designated as I-peptide receptor (IPR), responsible for lung colonization of B16-FTIII-M cells. Here, we visualized IPR by in vivo biotinylation, which revealed that the major IPR is a group of 35-kDa proteins. IPR proteins isolated by I-peptide affinity chromatography were identified by proteomics as Ser/Arg-rich alternative pre-mRNA splicing factors or
Sfrs1
,
Sfrs2
,
Sfrs5
, and
Sfrs7
gene products. Bacterially expressed Sfrs1 protein bound to B16-FTIII-M cells but not to parental B16 cells. Recombinant Sfrs1 protein bound to a series of fucosylated oligosaccharides in glycan array and plate-binding assays. When anti-Sfrs antibodies were injected intravenously into mice, antibodies labeled a subset of lung capillaries. Anti-Sfrs antibodies inhibited homing of I-peptide-displaying phage to the lung colonization of B16-FTIII-M cells in vivo in the mouse. These results strongly suggest that Sfrs proteins are responsible for fucosylated carbohydrate-dependent lung metastasis of epithelial cancers.
Pattern formation by dynamically interacting network motifs
Authors: Lembong Jessica , Yakoby Nir , Shvartsman Stanislav Y.
Published: February 2009

Systematic validation of pattern formation mechanisms revealed by molecular studies of development is essentially impossible without mathematical models. Models can provide a compact summary of a large number of experiments that led to mechanism formulation and guide future studies of pattern formation. Here, we realize this program by analyzing a mathematical model of epithelial patterning by the highly conserved EGFR and BMP signaling pathways in
Drosophila
oogenesis. The model accounts for the dynamic interaction of the feedforward and feedback network motifs that control the expression of Broad, a zinc finger transcription factor expressed in the cells that form the upper part of the respiratory eggshell appendages. Based on the combination of computational analysis and genetic experiments, we show that the model accounts for the key features of wild-type pattern formation, correctly predicts patterning defects in multiple mutants, and guides the identification of additional regulatory links in a complex pattern formation mechanism.
The B-type lamin is required for somatic repression of testis-specific gene clusters
Authors: Shevelyov Y. Y. , Lavrov S. A. , Mikhaylova L. M. , Nurminsky I. D. , Kulathinal R. J. , Egorova K. S. , Rozovsky Y. M. , Nurminsky D. I.
Published: February 2009

Large clusters of coexpressed tissue-specific genes are abundant on chromosomes of diverse species. The genes coordinately misexpressed in diverse diseases are also found in similar clusters, suggesting that evolutionarily conserved mechanisms regulate expression of large multigenic regions both in normal development and in its pathological disruptions. Studies on individual loci suggest that silent clusters of coregulated genes are embedded in repressed chromatin domains, often localized to the nuclear periphery. To test this model at the genome-wide scale, we studied transcriptional regulation of large testis-specific gene clusters in somatic tissues of
Drosophila
. These gene clusters showed a drastic paucity of known expressed transgene insertions, indicating that they indeed are embedded in repressed chromatin. Bioinformatics analysis suggested the major role for the B-type lamin, LamDm
o
, in repression of large testis-specific gene clusters, showing that in somatic cells as many as three-quarters of these clusters interact with LamDm
o
. Ablation of LamDm
o
by using mutants and RNAi led to detachment of testis-specific clusters from nuclear envelope and to their selective transcriptional up-regulation in somatic cells, thus providing the first direct evidence for involvement of the B-type lamin in tissue-specific gene repression. Finally, we found that transcriptional activation of the lamina-bound testis-specific gene cluster in male germ line is coupled with its translocation away from the nuclear envelope. Our studies, which directly link nuclear architecture with coordinated regulation of tissue-specific genes, advance understanding of the mechanisms underlying both normal cell differentiation and developmental disorders caused by lesions in the B-type lamins and interacting proteins.
CXCL14 is an autocrine growth factor for fibroblasts and acts as a multi-modal stimulator of prostate tumor growth
Authors: Augsten Martin , Hägglöf Christina , Olsson Eleonor , Stolz Claudia , Tsagozis Panagiotis , Levchenko Tetyana , Frederick Mitchell J. , Borg Åke , Micke Patrick , Egevad Lars , Östman Arne
Published: February 2009

This study explored the role of secreted fibroblast-derived factors in prostate cancer growth. Analyses of matched normal and tumor tissue revealed up-regulation of CXCL14 in cancer-associated fibroblasts of a majority of prostate cancer. Fibroblasts over-expressing CXCL14 promoted the growth of prostate cancer xenografts, and increased tumor angiogenesis and macrophage infiltration. Mechanistic studies demonstrated that autocrine CXCL14-stimulation of fibroblasts stimulate migration and ERK-dependent proliferation of fibroblasts. CXCL14-stimulation of monocyte migration was also demonstrated. Furthermore, CXCL14-producing fibroblasts, but not recombinant CXCL14, enhanced in vitro proliferation and migration of prostate cancer cells and in vivo angiogenesis. These studies thus identify CXCL14 as a novel autocrine stimulator of fibroblast growth and migration, with multi-modal tumor-stimulatory activities. In more general terms, our findings suggest autocrine stimulation of fibroblasts as a previously unrecognized mechanism for chemokine-mediated stimulation of tumor growth, and suggest a novel mechanism whereby cancer-associated fibroblasts achieve their pro-tumorigenic phenotype.
Odorant receptors at the growth cone are coupled to localized cAMP and Ca
2+
increases
Authors: Maritan Micol , Monaco Giovanni , Zamparo Ilaria , Zaccolo Manuela , Pozzan Tullio , Lodovichi Claudia
Published: February 2009

A distinctive feature in the topographic organization of the olfactory system in mammals is the dual function of the odorant receptor (OR): it detects odors in the nasal epithelium and plays an instructive role in the axonal convergence of olfactory sensory neurons (OSN) into the olfactory bulb (OB). The latter function is supported by genetic experiments and by the expression of the OR not only on the cilia, but also on the axon termini of the OSN. The signaling pathway coupled to the OR on the cilia is well known and is recognized to involve cAMP and Ca
2+
, whereas, until now, nothing was known on the functional characteristics of the OR on the axon termini-growth cone. Here, by analyzing the spatiotemporal dynamics of cAMP and Ca
2+
in living OSN
in vitro
and
in situ
, we found that the OR at the growth cone is capable of binding odors and is coupled to cAMP synthesis and Ca
2+
influx through cyclic nucleotide gated (CNG) channels. Furthermore we found that selective odor activation of the OR on the growth cone is followed by nuclear translocation of protein kinase A catalytic subunit. These results define the functional properties of the OR on the growth cone and suggest a potential role of OR activation in axonal convergence and sensory map formation.
Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus
Authors: Baskin Carole R. , Bielefeldt-Ohmann Helle , Tumpey Terrence M. , Sabourin Patrick J. , Long James P. , García-Sastre Adolfo , Tolnay Airn-E. , Albrecht Randy , Pyles John A. , Olson Pam H. , Aicher Lauri D. , Rosenzweig Elizabeth R. , Murali-Krishna Kaja , Clark Edward A. , Kotur Mark S. , Fornek Jamie L. , Proll Sean , Palermo Robert E. , Sabourin Carol L. , Katze Michael G.
Published: February 2009

The mechanisms responsible for the virulence of the highly pathogenic avian influenza (HPAI) and of the 1918 pandemic influenza virus in humans remain poorly understood. To identify crucial components of the early host response during these infections by using both conventional and functional genomics tools, we studied 34 cynomolgus macaques (
Macaca fascicularis
) to compare a 2004 human H5N1 Vietnam isolate with 2 reassortant viruses possessing the 1918 hemagglutinin (HA) and neuraminidase (NA) surface proteins, known conveyors of virulence. One of the reassortants also contained the 1918 nonstructural (NS1) protein, an inhibitor of the host interferon response. Among these viruses, HPAI H5N1 was the most virulent. Within 24 h, the H5N1 virus produced severe bronchiolar and alveolar lesions. Notably, the H5N1 virus targeted type II pneumocytes throughout the 7-day infection, and induced the most dramatic and sustained expression of type I interferons and inflammatory and innate immune genes, as measured by genomic and protein assays. The H5N1 infection also resulted in prolonged margination of circulating T lymphocytes and notable apoptosis of activated dendritic cells in the lungs and draining lymph nodes early during infection. While both 1918 reassortant viruses also were highly pathogenic, the H5N1 virus was exceptional for the extent of tissue damage, cytokinemia, and interference with immune regulatory mechanisms, which may help explain the extreme virulence of HPAI viruses in humans.
Two-slit diffraction with highly charged particles: Niels Bohr's consistency argument that the electromagnetic field must be quantized
Authors: Baym Gordon , Ozawa Tomoki
Published: February 2009

We analyze Niels Bohr's proposed two-slit interference experiment with highly charged particles which argues that the consistency of elementary quantum mechanics requires that the electromagnetic field must be quantized. In the experiment a particle's path through the slits is determined by measuring the Coulomb field that it produces at large distances; under these conditions the interference pattern must be suppressed. The key is that, as the particle's trajectory is bent in diffraction by the slits, it must radiate and the radiation must carry away phase information. Thus, the radiation field must be a quantized dynamical degree of freedom. However, if one similarly tries to determine the path of a massive particle through an inferometer by measuring the Newtonian gravitational potential the particle produces, the interference pattern would have to be finer than the Planck length and thus indiscernible. Unlike for the electromagnetic field, Bohr's argument does not imply that the gravitational field must be quantized.
Phosphorylation of Rap1GAP, a striatally enriched protein, by protein kinase A controls Rap1 activity and dendritic spine morphology
Authors: McAvoy Thomas , Zhou Ming-ming , Greengard Paul , Nairn Angus C.
Published: February 2009

Protein kinase A (PKA)-dependent signaling cascades play an important role in mediating the effects of dopamine and other neurotransmitters in striatal medium spiny neurons. We have identified a prominent striatal PKA substrate as Rap1-GTPase activating protein (Rap1GAP), a negative regulator of Rap1 signaling. Although present throughout the brain, Rap1GAP is enriched in striatal medium spiny neurons and is phosphorylated by PKA at Ser-441 and Ser-499 in response to activation of D1 dopamine receptors. Phosphorylation of Rap1GAP is associated with inhibition of GAP activity, as demonstrated by increased Rap1 activity in striatal neurons. Phosphorylation of Rap1GAP is also associated with increased dendritic spine head size in cultured neurons. These findings suggest that phosphorylation of Rap1GAP by PKA plays an important role in striatal neurons by modulating Rap1 actions.
Role of COX-2 in epithelial–stromal cell interactions and progression of ductal carcinoma in situ of the breast
Authors: Hu Min , Peluffo Guillermo , Chen Haiyan , Gelman Rebecca , Schnitt Stuart , Polyak Kornelia
Published: February 2009

Epithelial–stromal cell interactions have an important role in breast tumor progression, but the molecular mechanisms underlying these effects are just beginning to be understood. We previously described that fibroblasts promote, whereas normal myoepithelial cells inhibit, the progression of ductal carcinoma in situ (DCIS) to invasive breast carcinomas by using a xenograft model of human DCIS. Here, we report that the tumor growth and progression-promoting effects of fibroblasts are at least in part due to increased COX-2 expression in tumor epithelial cells provoked by their interaction with fibroblasts. Up-regulation of COX-2 in DCIS xenografts resulted in increased VEGF and MMP14 expression, which may contribute to the larger weight and invasive histology of COX-2-expressing tumors. Administration of celecoxib, a selective COX-2 inhibitor, to tumor-bearing mice decreased xenograft tumor weight and inhibited progression to invasion. Coculture of fibroblasts with DCIS epithelial cells enhanced their motility and invasion, and this change was associated with increased MMP14 expression and MMP9 protease activity. We identified the NF-κB pathway as one of the mediators of stromal fibroblast-derived signals regulating COX-2 expression in tumor epithelial cells. Inhibition of NF-κB and COX-2 activity and down-regulation of MMP9 expression attenuated the invasion-promoting effects of fibroblasts. These findings support a role for COX-2 in promoting the progression of DCIS to invasive breast carcinomas, and suggest that therapeutic targeting of the NF-κB and prostaglandin signaling pathways might be used for the treatment and prevention of breast cancer.
Dual involvement of G-substrate in motor learning revealed by gene deletion
Authors: Endo Shogo , Shutoh Fumihiro , Dinh Tung Le , Okamoto Takehito , Ikeda Toshio , Suzuki Michiyuki , Kawahara Shigenori , Yanagihara Dai , Sato Yamato , Yamada Kazuyuki , Sakamoto Toshiro , Kirino Yutaka , Hartell Nicholas A. , Yamaguchi Kazuhiko , Itohara Shigeyoshi , Nairn Angus C. , Greengard Paul , Nagao Soichi , Ito Masao
Published: February 2009

In this study, we generated mice lacking the gene for G-substrate, a specific substrate for cGMP-dependent protein kinase uniquely located in cerebellar Purkinje cells, and explored their specific functional deficits. G-substrate–deficient Purkinje cells in slices obtained at postnatal weeks (PWs) 10–15 maintained electrophysiological properties essentially similar to those from WT littermates. Conjunction of parallel fiber stimulation and depolarizing pulses induced long-term depression (LTD) normally. At younger ages, however, LTD attenuated temporarily at PW6 and recovered thereafter. In parallel with LTD, short-term (1 h) adaptation of optokinetic eye movement response (OKR) temporarily diminished at PW6. Young adult G-substrate knockout mice tested at PW12 exhibited no significant differences from their WT littermates in terms of brain structure, general behavior, locomotor behavior on a rotor rod or treadmill, eyeblink conditioning, dynamic characteristics of OKR, or short-term OKR adaptation. One unique change detected was a modest but significant attenuation in the long-term (5 days) adaptation of OKR. The present results support the concept that LTD is causal to short-term adaptation and reveal the dual functional involvement of G-substrate in neuronal mechanisms of the cerebellum for both short-term and long-term adaptation.
Hedgehog signal transduction by Smoothened: Pharmacologic evidence for a 2-step activation process
Authors: Rohatgi Rajat , Milenkovic Ljiljana , Corcoran Ryan B. , Scott Matthew P.
Published: February 2009

The Hedgehog (Hh) signaling pathway controls growth, cell fate decisions, and morphogenesis during development. Damage to Hh transduction machinery can lead to birth defects and cancer. The transmembrane protein Smoothened (Smo) relays the Hh signal and is an important drug target in cancer. Smo enrichment in primary cilia is thought to drive activation of target genes. Using small-molecule agonists and antagonists to dissect Smo function, we find that Smo enrichment in cilia is not sufficient for signaling and a distinct second step is required for full activation. This 2-step mechanism—localization followed by activation—has direct implications for the design and use of anticancer therapeutics targeted against Smo.
Oceanic acidification affects marine carbon pump and triggers extended marine oxygen holes
Authors: Hofmann Matthias , Schellnhuber Hans-Joachim
Published: February 2009

Rising atmospheric CO
2
levels will not only drive future global mean temperatures toward values unprecedented during the whole Quaternary but will also lead to massive acidification of sea water. This constitutes by itself an anthropogenic planetary-scale perturbation that could significantly modify oceanic biogeochemical fluxes and severely damage marine biota. As a step toward the quantification of such potential impacts, we present here a simulation-model-based assessment of the respective consequences of a business-as-usual fossil-fuel-burning scenario where a total of 4,075 Petagrams of carbon is released into the atmosphere during the current millennium. In our scenario, the atmospheric
p
CO
2
level peaks at ≈1,750 μatm in the year 2200 while the sea-surface pH value drops by >0.7 units on global average, inhibiting the growth of marine calcifying organisms. The study focuses on quantifying 3 major concomitant effects. The first one is a significant (climate-stabilizing) negative feedback on rising
p
CO
2
levels as caused by the attenuation of biogenic calcification. The second one is related to the biological carbon pump. Because mineral ballast, notably CaCO
3
, is found to play a dominant role in carrying organic matter through the water column, a reduction of its export fluxes weakens the strength of the biological carbon pump. There is, however, a third effect with severe consequences: Because organic matter is oxidized in shallow waters when mineral-ballast fluxes weaken, oxygen holes (hypoxic zones) start to expand considerably in the oceans in our model world—with potentially harmful impacts on a variety of marine ecosystems.
Massively parallel sequencing identifies the gene
Megf8
with ENU-induced mutation causing heterotaxy
Authors: Zhang Zhen , Alpert Deanne , Francis Richard , Chatterjee Bishwanath , Yu Qing , Tansey Terry , Sabol Steven L. , Cui Cheng , Bai Yongli , Koriabine Maxim , Yoshinaga Yuko , Cheng Jan-Fang , Chen Feng , Martin Joel , Schackwitz Wendy , Gunn Teresa M. , Kramer Kenneth L. , De Jong Pieter J. , Pennacchio Len A. , Lo Cecilia W.
Published: February 2009

Forward genetic screens with ENU (
N
-ethyl-
N
-nitrosourea) mutagenesis can facilitate gene discovery, but mutation identification is often difficult. We present the first study in which an ENU- induced mutation was identified by massively parallel DNA sequencing. This mutation causes heterotaxy and complex congenital heart defects and was mapped to a 2.2-Mb interval on mouse chromosome 7. Massively parallel sequencing of the entire 2.2-Mb interval identified 2 single-base substitutions, one in an intergenic region and a second causing replacement of a highly conserved cysteine with arginine (C193R) in the gene
Megf8. Megf8
is evolutionarily conserved from human to fruit fly, and is observed to be ubiquitously expressed. Morpholino knockdown of
Megf8
in zebrafish embryos resulted in a high incidence of heterotaxy, indicating a conserved role in laterality specification.

Megf8
C193R

mouse mutants show normal breaking of symmetry at the node, but Nodal signaling failed to be propagated to the left lateral plate mesoderm. Videomicroscopy showed nodal cilia motility, which is required for left–right patterning, is unaffected. Although this protein is predicted to have receptor function based on its amino acid sequence, surprisingly confocal imaging showed it is translocated into the nucleus, where it is colocalized with Gfi1b and Baf60C, two proteins involved in chromatin remodeling. Overall, through the recovery of an ENU-induced mutation, we uncovered
Megf8
as an essential regulator of left–right patterning.
Oxidant regulated inter-subunit disulfide bond formation between ASIC1a subunits
Authors: Zha Xiang-ming , Wang Runping , Collier Dan M. , Snyder Peter M. , Wemmie John A. , Welsh Michael J.
Published: February 2009

The acid-sensing ion channel-1a (ASIC1a) is composed of 3 subunits and is activated by a decrease in extracellular pH. It plays an important role in diseases associated with a reduced pH and production of oxidants. Previous work showed that oxidants reduce ASIC1a currents. However, the effects on channel structure and composition are unknown. We found that ASIC1a formed inter-subunit disulfide bonds and the oxidant H
2
O
2
increased this link between subunits. Cys-495 in the ASIC1a C terminus was particularly important for inter-subunit disulfide bond formation, although other C-terminal cysteines contributed. Inter-subunit disulfide bonds also produced some ASIC1a complexes larger than trimers. Inter-subunit disulfide bond formation reduced the proportion of ASIC1a located on the cell surface and contributed to the H
2
O
2
-induced decrease in H
+
-gated current. These results indicate that channel function is controlled by disulfide bond formation between intracellular residues on distinct ASIC1a subunits. They also suggest a mechanism by which the redox state can dynamically regulate membrane protein activity by forming intracellular bridges.
Connexin 32 increases the proliferative response of Schwann cells to neuregulin-1 (Nrg1)
Authors: Freidin Mona , Asche Samantha , Bargiello Thaddeus A. , Bennett Michael V. L. , Abrams Charles K.
Published: February 2009

Connexin 32 (Cx32), a gap junction protein, is found within the para-nodal region and Schmidt-Lanterman incisures of myelinating Schwann cells (SCs). In developing and regenerating peripheral nerves, pro-myelinating SCs express Cx32 mRNA and protein in conjunction with the expression of myelin specific genes. Neuregulin-1 (Nrg1), a member of the neuregulin family of growth factors, controls SC proliferation and differentiation depending on the cellular environment and the particular stage of SC maturation. Primary cultures of purified SCs from newborn mouse sciatic nerve were used to characterize both the role of Nrg1 in the expression of Cx32 and, conversely, the role of Cx32 in SC responsiveness to Nrg1. Glial growth factor 2, an isoform of Nrg1, up-regulated Cx32 in both proliferating and non-proliferating SCs. However, SCs from Cx32-KO mice exhibited a significantly smaller mitogenic response to glial growth factor 2. Electrical coupling between Cx32-KO SCs did not differ from that between WT SCs, indicating the presence of other connexins. These results suggest a link between Cx32 expression and Nrg1 regulation of SC proliferation that does not involve Cx32-mediated intercellular communication.
Specific synthetic lethal killing of RAD54B-deficient human colorectal cancer cells by FEN1 silencing
Authors: McManus Kirk J. , Barrett Irene J. , Nouhi Yasaman , Hieter Philip
Published: February 2009

Mutations that cause chromosome instability (CIN) in cancer cells produce “sublethal” deficiencies in an essential process (chromosome segregation) and, therefore, may represent a major untapped resource that could be exploited for therapeutic benefit in the treatment of cancer. If second-site unlinked genes can be identified, that when knocked down, cause a synthetic lethal (SL) phenotype in combination with a somatic mutation in a CIN gene, novel candidate therapeutic targets will be identified. To test this idea, we took a cross species SL candidate gene approach by recapitulating a SL interaction observed between rad54 and rad27 mutations in yeast, via knockdown of the highly sequence- and functionally-related proteins RAD54B and FEN1 in a cancer cell line. We show that knockdown of RAD54B, a gene known to be somatically mutated in cancer, causes CIN in mammalian cells. Using high-content microscopy techniques, we demonstrate that RAD54B-deficient human colorectal cancer cells are sensitive to SL killing by reduced FEN1 expression, while isogenic RAD54B proficient cells are not. This conserved SL interaction suggests that extrapolating SL interactions observed in model organisms for homologous genes mutated in human cancers will aid in the identification of novel therapeutic targets for specific killing of cancerous cells exhibiting CIN.
Dysregulated gene expression networks in human acute myelogenous leukemia stem cells
Authors: Majeti Ravindra , Becker Michael W. , Tian Qiang , Lee Tsung-Lu Michael , Yan Xiaowei , Liu Rui , Chiang Jung-Hsien , Hood Leroy , Clarke Michael F. , Weissman Irving L.
Published: February 2009

We performed the first genome-wide expression analysis directly comparing the expression profile of highly enriched normal human hematopoietic stem cells (HSC) and leukemic stem cells (LSC) from patients with acute myeloid leukemia (AML). Comparing the expression signature of normal HSC to that of LSC, we identified 3,005 differentially expressed genes. Using 2 independent analyses, we identified multiple pathways that are aberrantly regulated in leukemic stem cells compared with normal HSC. Several pathways, including Wnt signaling, MAP Kinase signaling, and Adherens Junction, are well known for their role in cancer development and stem cell biology. Other pathways have not been previously implicated in the regulation of cancer stem cell functions, including Ribosome and T Cell Receptor Signaling pathway. This study demonstrates that combining global gene expression analysis with detailed annotated pathway resources applied to highly enriched normal and malignant stem cell populations, can yield an understanding of the critical pathways regulating cancer stem cells.
Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function
Authors: Pavani Sri Rama Prasanna , Thompson Michael A. , Biteen Julie S. , Lord Samuel J. , Liu Na , Twieg Robert J. , Piestun Rafael , Moerner W. E.
Published: February 2009

We demonstrate single-molecule fluorescence imaging beyond the optical diffraction limit in 3 dimensions with a wide-field microscope that exhibits a double-helix point spread function (DH-PSF). The DH-PSF design features high and uniform Fisher information and has 2 dominant lobes in the image plane whose angular orientation rotates with the axial (
z
) position of the emitter. Single fluorescent molecules in a thick polymer sample are localized in single 500-ms acquisitions with 10- to 20-nm precision over a large depth of field (2 μm) by finding the center of the 2 DH-PSF lobes. By using a photoactivatable fluorophore, repeated imaging of sparse subsets with a DH-PSF microscope provides superresolution imaging of high concentrations of molecules in all 3 dimensions. The combination of optical PSF design and digital postprocessing with photoactivatable fluorophores opens up avenues for improving 3D imaging resolution beyond the Rayleigh diffraction limit.
Molecular basis of the interactions between the p73 N terminus and p300: Effects on transactivation and modulation by phosphorylation
Authors: Burge Sarah , Teufel Daniel P. , Townsley Fiona M. , Freund Stefan M. V. , Bycroft Mark , Fersht Alan R.
Published: February 2009

The transcription factor p73 belongs to the p53 family of proteins and can transactivate a number of target genes in common with p53. Here, we characterized the interaction of the p73 N terminus with four domains of the transcriptional coactivator p300 and with the negative regulator Mdm2 by using biophysical and cellular measurements. We found that, like p53, the N terminus of p73 contained two distinct transactivation subdomains, comprising residues 10–30 and residues 46–67. The p73 N terminus bound weakly to the Taz1, Kix, and IBiD domains of p300 but with submicromolar affinity for Taz2, in contrast to previous reports. We found weaker binding of the p73 N terminus to the p300 domains in vitro correlated with a significant decrease in transactivation activity in a cell line for the QS and T14A mutants, and tighter binding of the phosphomimetic T14D in vitro correlated with an increase in vivo. Further, we found that phosphorylation of T14 increased the affinity of the p73 N terminus for Taz2 10-fold. The phosphomimetic p73α T14D caused increased levels of transactivation.
The Inclusion of Women and Minorities in Smoking Cessation Clinical Trials: A Systematic Review
Authors: Dickerson Daniel L. , Leeman Robert F. , Mazure Carolyn M. , O'Malley Stephanie S.
Published: February 2009

This study assesses the impact of the 1993 NIH Revitalization Act on the inclusion and subgroup analysis of women and minorities in trials of FDA‐approved smoking cessation pharmacotherapy. Female representation, while commensurate with population levels, declined significantly for trials that began recruitment after 1993(M = 47.2% vs. M = 53.9%), and fewer than half reported analyses by gender. Minorities continued to be under‐represented in later trials; however, significant improvement in representation (M = 16.1% vs. M = 10%) and analysis by race occurred. Industry‐sponsored studies had lower minority representation than NIH funded studies. Recommendations are offered to improve subgroup analyses and minority inclusion.
Prediction of Cannabis Use Disorder between Boyhood and Young Adulthood: Clarifying the Phenotype and Environtype
Authors: Kirisci Levent , Tarter Ralph , Mezzich Ada , Ridenour Ty , Reynolds Maureen , Vanyukov Michael
Published: February 2009

Employing a prospective paradigm, this investigation derived the childhood phenotype and the environtype associated with risk for cannabis use disorder. Two hundred and sixteen boys were evaluated between age 10–12 on a comprehensive protocol using self, mother, and teacher reports and followed‐up at ages 19 and 22 to determine the presence of cannabis use disorder. The Transmissible Liability Index (TLI) and Non‐Transmissible Liability Index (NTLI) were derived using item response theory. Logistic regression was conducted to evaluate the accuracy of the indexes, singly and in combination, to predict cannabis use disorder. The TLI and NTLI together predicted with 70% and 75% accuracy cannabis use disorder manifest by age 19 and age 22. Sensitivity was 75% at both ages 19 and 22, whereas specificity was respectively 51% and 64%. The findings pertaining to sensitivity indicate that SUD risk for cannabis use disorder can be screened in childhood; however, the specificity scores demonstrate that a low score on the TLI does not inevitably portend a good prognosis up to 10 years later.
A Preliminary Trial: Double‐Blind Comparison of Nefazodone, Bupropion‐SR, and Placebo in the Treatment of Cannabis Dependence
Authors: Carpenter Kenneth M. , McDowell David , Brooks Daniel J. , Cheng Wendy Y. , Levin Frances R.
Published: February 2009

The present study investigated the efficacy of nefazodone and bupropion‐sustained release for treating cannabis dependence. A double‐blind, placebo‐controlled, piggy back design was employed to assess if nefazodone and bupropion‐sustained release increased the probability of abstinence from cannabis and reduced the severity of cannabis dependence and cannabis withdrawal symptoms during a 13‐week outpatient treatment program. One‐hundred and six participants (Mean = 32 years; females n = 25) were randomized to one of three medication conditions (nefazodone, bupropion‐sustained release, or placebo) and participated in a weekly, individually based coping skills therapy program. Results indicated an increased probability of achieving abstinence over the course of treatment and a decrease in the severity of cannabis dependence and the withdrawal symptom of irritability. There were no significant effects demonstrated for nefazodone and bupropion‐sustained release on cannabis use or cannabis withdrawal symptoms. The results indicate nefazodone and bupropion‐sustained release may have limited efficacy in treating cannabis dependence.
Low Plasma Levels of Docosahexaenoic Acid Are Associated with an Increased Relapse Vulnerability in Substance Abusers
Authors: Buydens‐Branchey Laure , Branchey Marc , Hibbeln Joseph R.
Published: February 2009

Low levels of some polyunsaturated fatty acids (PUFAs) could influence behaviors leading to the abuse of substances through their actions on serotonergic and dopaminergic mechanisms. Because substance abusers tend to have poor dietary habits, the possibility that a deficient intake of n‐3 PUFAs, available from dietary sources only, and subsequent low n‐3 plasma levels would predict their relapse rates was explored. Thirty‐five patients admitted to substance abuse clinics were enrolled and followed for one year. Dietary questionnaires and blood samples were collected at baseline and on a quarterly basis, and relapse rates monitored on a monthly basis. Six patients dropped out shortly after study entry, 11 relapsed in the course of the study and dropped out, 7 relapsed but completed the study, and 11 did not relapse and completed the study. Non‐relapsers were found to have significantly higher levels of docosahexaenoic acid (DHA) calculated as μ g/ml and % TFA, when compared to relapsers (p = .031 and p = .010, respectively) and to relapsers and non‐completers combined (p = .014 and p = .009, respectively). These pilot data suggest, but do not prove, the existence of a relationship between low levels of DHA and relapse vulnerability in some individuals who abuse substances. The study of the efficacy of n‐3 supplements or of dietary modifications on relapse appears warranted.
Alcohol and Injury in the United States General Population: A Risk Function Analysis from the 2005 National Alcohol Survey
Authors: Cherpitel Cheryl J. , Ye Yu
Published: February 2009

A risk function analysis of data is reported from the 2005 National Alcohol Survey on average daily volume of alcohol and frequency of consuming five or more drinks per day with reporting any injury during the preceding year, an injury that was treated, or an injury that was treated in the emergency room (ER). Data suggest the association of alcohol and injury based on ER studies is not representative of all injuries, and should be taken into account in deriving estimates of risk of injury related to alcohol and alcohol‐attributable fractions based on ER studies.
Olanzapine in Cocaine Dependence: A Double‐Blind, Placebo‐Controlled Trial
Authors: Hamilton Joseph D. , Nguyen Quang X. , Gerber Robert M. , Rubio Nancy B.
Published: February 2009

Preclinical and uncontrolled human studies have suggested the possible efficacy of second‐generation antipsychotics, particularly olanzapine, in treating cocaine dependence. We conducted a randomized, double‐blind, placebo‐controlled trial in which 48 cocaine‐dependent subjects received olanzapine or identical‐appearing placebo for 16 weeks. The primary outcome measure was the proportion of cocaine‐negative weekly urine screens during treatment. Secondary measures included scores on a Craving Questionnaire, Addiction Severity Index subscales, and extrapyramidal symptom scales. Olanzapine and placebo did not differ on any outcome measure. Both olanzapine and placebo subjects frequently reported side effects, but no unexpected ones. We conclude that olanzapine appears ineffective for cocaine dependence.
Sexual Risk Behavior Associated with Co‐administration of Methamphetamine and Other Drugs in a Sample of HIV‐Positive Men Who Have Sex with Men
Authors: Semple Shirley J. , Strathdee Steffanie A. , Zians Jim , Patterson Thomas L.
Published: February 2009

This study examined the association between sexual risk behavior and co‐administration of methamphetamine with other drugs in a sample of 341 HIV‐positive MSM. Those who reported methamphetamine co‐administration in the past two months (65%) reported significantly more unprotected anal and oral sex and a greater number of casual, anonymous, and paid sex partners in this timeframe compared to men who used methamphetamine alone. Two primary patterns of co‐administration were identified: 1) drug combinations motivated by sexual performance and enhancement (eg, methamphetamine, poppers, sildenafil); and 2) “party drug” combinations (eg, methamphetamine, GHB, ketamine). Implications for further research and possible applications to risk‐reduction interventions are discussed.
Cautionary Guidelines for the Use of Opioids in Chronic Pain
Authors: Streltzer Jon , Ziegler Penelope , Johnson Brian
Published: February 2009

Guidelines for the use of opioids in the treatment of chronic pain have recently been proposed by the American Academy of Addiction Psychiatry. Older guidelines proposed by American pain organizations had the effect of liberalizing opioid prescription. In recent years, dramatic increases in prescribed opioids have been followed by equally dramatic rises in morbidity and mortality from prescription opioids. In addition, new research has increased knowledge of the long‐term effects of opioids. These new guidelines propose increased caution in regard to opioid prescription for chronic pain.
A Comparison of Substance Use Disorder Severity and Course in American Indian Male and Female Veterans
Authors: Westermeyer Joseph , Canive Jose , Thuras Paul , Thompson James , Crosby Ross D. , Garrard Judith
Published: February 2009

The purpose of this analysis was to compare substance use disorder (SUD) diagnoses, severity, comorbidity, and course in 362 American Indian veterans. The sample was drawn from communities in the north central and southwestern areas of the United States, structured to over‐sample women and to include half‐rural/half‐urban residents. Instruments used in the study included current demography, military history, the Diagnostic Interview Schedule/Quick Version, Michigan Alcoholism Screening Test modified to include alcohol and drugs (MAST/AD), Brief Symptom Inventory, Posttraumatic Checklist, and a treatment algorithm. Univariate analyses showed that women had lower scores on the MAST/AD, reported lower symptom levels on the Posttraumatic Checklist, and were less apt to use VA mental health services, but were more willing to seek mental health treatment if needed (with probabilities of .01 to .001). At borderline probabilities (.02 to .05), women were younger and had more education, whereas men had more drug‐related diagnoses and more combat exposure. On binary logistic regression, women were less apt to have a drug diagnosis and had lower MAST/AD scores; the other differences were not significant. Female American Indian veterans with SUD manifested many of the same gender‐related differences as women in the population at large, but with some exceptions (eg, comorbidity). Trauma, PTSD, and continuing posttraumatic symptoms occurred frequently in both male and female veterans of American Indian heritage. VA facilities should out‐reach to American Indian women, who report a willingness to seek mental health services but may avoid VA care.
Opioid Deaths in Rural Virginia: A Description of the High Prevalence of Accidental Fatalities Involving Prescribed Medications
Authors: Wunsch Martha J. , Nakamoto Kent , Behonick George , Massello William
Published: February 2009

In rural Virginia, drug overdose deaths increased 300% from 1997 to 2003. Polydrug deaths predominate (57.9%) in this review of 893 medical examiner cases. Prescription opioids (74.0%), antidepressants (49.0%), and benzodiazepines (39.3%) were more prevalent than illicit drugs. Two‐thirds of decedents were 35–54 years old; 37% were female. When compared to western Virginia metropolitan cases, polydrug abuse was more common, specific medication combinations were found, the death rate per population was higher, and fewer illicit drugs were detected. These rural prescription overdose deaths differ from urban illicit drug deaths, suggesting the need for different strategies in prevention, treatment, and intervention by clinicians and policymakers.
Predictors of Treatment Outcome in Outpatient Cocaine and Alcohol Dependence Treatment
Authors: Ahmadi Jamshid , Kampman Kyle M. , Oslin David M. , Pettinati Helen M. , Dackis Charles , Sparkman Thorne
Published: February 2009

We examined the ability of several baseline variables to predict treatment outcome in a pharmacotherapy trial that included 164 participants who were both cocaine‐ and alcohol‐dependent and were selected for a randomized, double‐blind, placebo‐controlled study. Predictor variables included results from the baseline Addiction Severity Index (ASI), initial Urine Drug Screen results, cocaine and alcohol craving and cocaine and alcohol withdrawal symptoms at the start of treatment. Successful treatment was defined as four continuous weeks of self‐reported cocaine abstinence verified by urine drug screens. In respect to demographic characteristics, there were no significant differences between patients who achieved four weeks of abstinence from cocaine and those who did not. Baseline variables that most consistently predicted cocaine abstinence included initial urine drug screen (UDS) results, the initial Cocaine Selective Severity Assessment (CSSA) scores, and initial self‐reported cocaine use in past 30 days, whereas cocaine craving, cocaine composite scores, alcohol craving, alcohol withdrawal symptoms, and alcohol composite scores did not. The results of this study suggest that cocaine dependence severity in general, and initial UDS results, the CSSA scores and frequency of recent cocaine use in particular, have a significant impact on treatment outcome in the treatment of cocaine‐dependent patients with comorbid alcoholism. Initial UDS results and CSSA scores are very useful predictors of treatment outcome and could be used as stratifying variables in outpatient cocaine and alcohol medication trials.
Risk Factors Related to a Hospital-Associated Cluster ofClostridium difficilePCR Ribotype 027 Infections in Germany During 2007
Authors: Weiss Bettina , Kleinkauf Niels , Eckmanns Tim , Heiden Matthias an der , Neumann Matthias , Michels Harald , Jansen Andreas
Published: February 2009

In 2007,Clostridium difficilepolymerase chain reaction (PCR) ribotype 027 emerged in Germany. We conducted a hospital-based case-control study to identify specific risk factors for infection with this strain. Logistic regression analysis involving 15 case patients and 31 control patients revealed that exposure to fluoroquinolones (matched odds ratio, 36.2;P< .01) or cephalosporins (matched odds ratio, 19.1;P< .01) was independently related to C.difficilePCR ribotype 027 infection.
The Cyclin-dependent Kinase Inhibitor Dacapo Promotes Genomic Stability during Premeiotic S Phase
Authors: Narbonne-Reveau Karine , Lilly Mary
Published: February 2009

The proper execution of premeiotic S phase is essential to both the maintenance of genomic integrity and accurate chromosome segregation during the meiotic divisions. However, the regulation of premeiotic S phase remains poorly defined in metazoa. Here, we identify the p21Cip1/p27Kip1/p57Kip2-like cyclin-dependent kinase inhibitor (CKI) Dacapo (Dap) as a key regulator of premeiotic S phase and genomic stability during Drosophila oogenesis. In dap−/−females, ovarian cysts enter the meiotic cycle with high levels of Cyclin E/cyclin-dependent kinase (Cdk)2 activity and accumulate DNA damage during the premeiotic S phase. High Cyclin E/Cdk2 activity inhibits the accumulation of the replication-licensing factor Doubleparked/Cdt1 (Dup/Cdt1). Accordingly, we find that dap−/−ovarian cysts have low levels of Dup/Cdt1. Moreover, mutations in dup/cdt1 dominantly enhance the dap−/−DNA damage phenotype. Importantly, the DNA damage observed in dap−/−ovarian cysts is independent of the DNA double-strands breaks that initiate meiotic recombination. Together, our data suggest that the CKI Dap promotes the licensing of DNA replication origins for the premeiotic S phase by restricting Cdk activity in the early meiotic cycle. Finally, we report that dap−/−ovarian cysts frequently undergo an extramitotic division before meiotic entry, indicating that Dap influences the timing of the mitotic/meiotic transition.
Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative
Authors: Bickel David R. , Montazeri Zahra , Hsieh Pei-Chun , Beatty Mary , Lawit Shai J. , Bate Nicholas J.
Published: February 2009

Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential equations that describe transcriptional kinetics. Practical approximations of kinetic models would enable inferring causal relationships between genes from expression data of microarray, tag-based and conventional platforms, but conclusions are sensitive to the assumptions made.

Results: The representation of a sufficiently large portion of genome enables computation of an upper bound on how much confidence one may place in influences between genes on the basis of expression data. Information about which genes encode transcription factors is not necessary but may be incorporated if available. The methodology is generalized to cover cases in which expression measurements are missing for many of the genes that might control the transcription of the genes of interest. The assumption that the gene expression level is roughly proportional to the rate of translation led to better empirical performance than did either the assumption that the gene expression level is roughly proportional to the protein level or the Bayesian model average of both assumptions.

Availability:  http://www.oisb.ca points to R code implementing the methods (R Development Core Team 2004).

Contact:  dbickel@uottawa.ca

Supplementary information:  http://www.davidbickel.com