bluuebunny/crossref_metadata_2025 huggingface dataset:
Cu–Cu diffusion bonding enhancement at low temperature by surface passivation using self-assembled monolayer of alkane-thiol
Authors: Tan C. S. , Lim D. F. , Singh S. G. , Goulet S. K. , Bergkvist M.
Published: November 2009

Self-assembled monolayer (SAM) of 1-hexanethiol is applied on copper (Cu) surface to retard surface oxidation during exposure in the ambient. This SAM layer can be desorbed effectively with an annealing step in inert N2 ambient to provide a clean Cu surface. Using this passivation method with SAM, wafers covered with thin Cu layer are passivated, stored, desorbed, and bonded at 250 °C. The bonded Cu layer presents clear evidence of substantial interdiffusion and grain growth despite prolonged exposure in the ambient. This method of passivation is proven to be effective and can be further optimized to enable high quality Cu–Cu direct bonding at low temperature for application in three-dimensional integration.
O-Benzylidene Derivatives of D-Arabinose Diethyl and Dipropyl Dithioacetal
Authors: Kuszmann J , Gacsbaitz E
Published: November 2009

Benzylidenation of D-arabinose diethyl and dipropyl dithioacetals with α,α-dimethoxytoluene in the presence of p-toluenesulfonic acid has been studied in detail. Under kinetic control the two terminal dioxolan -type 4,5-O-(R)- and 4,5-O-(S)-benzylidene diastereomers are formed first which are in equilibrium with each other In the thermodynamic phase of the reaction the corresponding dioxan -type 3,5-O-(R)- benzylidene isomer is formed too, but all three monobenzylidene isomers are gradually converted into the four possible dioxolan -type 2,3 : 4,5-di-O benzylidene diastereomers . The dioxan -type 2,4:3,5-di-O-benzylidene isomer was present only in trace amounts. When benzaldehyde was used as reagent in the presence of hydrochloric acid or zinc chloride only the 2,3: 4,5-di-O-benzylidene diastereomers were formed. Partial hydrolysis of the dibenzylidene derivatives yielded the corresponding 2,3-O-benzylidene diastereomers. Structures, including the chirality of the benzylidene groups, were determined by n.m.r. spectroscopy. A mechanism suggested for the reaction was partially supported by equilibration studies.
Synthesis of Sugar-Derived Nitrogen Heterocycles
Authors: Oleary TK , Read RW
Published: November 2009

The synthesis of nitrogen heterocycles through condensation of stereoisomeric butane-1,2,3,4-tetramines with aldehydes, and their structure elucidation through spectroscopic methods are described. Significant differences in the products from each of the amines were observed due to differences in the relative stereochemistry of the amines. Molecular mechanics energy calculations when carried out on all possible products from the condensation of both the threo and erythro tetramines with acetaldehyde revealed minimum energy structures that were consistent with those found experimentally. The products were therefore probably the result of thermodynamic control.
1,2-O-(Ethane-1,2-diyl)-α-D-glucofuranose. Crystal Structure, and the Stereochemistry of Related Bicyclic Acetal Analogues
Authors: Lebuis AM , Lee DS , Perlin AS
Published: November 2009

Crystalline 1,2-O-(ethane-1,2-diyl)-α-D- glucofuranose (9) is orthorhombic, P 21212, with a = 17.702(4), b = 8.892(2), c = 5.6400(9) Ǻ, Z = 4, R = 0.050, and Rw = 0.041. The conformation of the 1,4-dioxan ring in this bicyclic acetal is slightly distorted from 7C1, and that of the glucofuranose ring is intermediate between the 3E and 3T2 conformations. Extensive intermolecular hydrogen-bonding of exocyclic OH(5) and OH(6) dominates the solid state interactions. In aqueous solution, compound (9) retains close to the same stereochemical characteristics as in the crystal, including those of the exocyclic C(4)-C(5)-C(6) segment of the molecule, according to n.m.r. spectroscopic evidence. These findings provide support for the structures assigned to related bicyclic acetals (7) and (8), which differ from (9) in having a methyl substituent at C(8) on their 1,4-dioxan rings, notably in confirming that the configuration at C(8) is R in (7) and S in (8).
MM3(92) Analysis of Inositol Ring Puckering
Authors: Dowd MK , French AD , Reilly PJ
Published: November 2009

The molecular mechanics method MM3(92) was used to study the puckering of the nine inositol isomers. Energy surfaces were generated based on the Cremer-Pople puckering definitions and the geometric plate carree representations of Pickett and Strauss. Chair forms are favoured for all the inositol isomers in agreement with experiment. The lowest energy non-chair form, more than 10 kJ/mol in free energy above the chair, is a skew of muco-inositol , in which all the hydroxyls are oriented either equatorially or pseudo-equatorially. Hydrogen-hydrogen coupling constants are in good agreement with experiment. The predicted order of stability for the isomers is scyllo - > myo - > chiro - > neo- > � epi -> muco - ≈ allo -> cis-inositol. This order generally agrees with Angyal's proposed stability order based on the number and type of gauche and 1,3-diaxial ring substituents. In contrast with recent ab initio calculations and values calculated with Angyal's method, the MM3 � gas-phase free energy of scyllo-inositol was lower than that of myo-inositol by 5.5 kJ/mol. The calculated transition energy for the chair-to-chair conversion of cis-inositol differs by 12.5-17.2 kJ/mol from the experimental value, depending on the strength of the electrostatic field.
Hydrogenolysis of the 4,6-O-Ketals of Glucopyranosides. Configuration-Dependent High Regio- and Stereo-Selectivity of the Diastereoisomeric Acetophenone Derivatives
Authors: Hajko J , Szabovik G , Kerekgyarto J , Kajtar M , Liptak A
Published: November 2009

Hydrogenolysis (reductive cleavage) of the (R) isomers of the acetophenone 4,6-O-derivatives of glucopyranosides with LiAlH4/AlCl3 gives the 4-O-(1'-phenylethyl) ethers with (R) configuration; the corresponding (S) isomers produce the respective (R) 6-O-(1'-phenylethyl ) ethers are produced. The hydrogenolysis of other 4,6-O-ketals affords O 4 ether derivatives; the two diastereoisomeric 4,6-O-s-butylidene derivatives (cyclic ketals ) give O 4-ethers with the opposite absolute configuration. The stereoselectivity of these reactions is explained by the development of a four-centre transition state. The absolute configuration of the ethers has been determined by means of circular dichroism measurements.
Conformational Analysis of C60 Ball-and-Chain Molecules: a Molecular Orbital Study
Authors: Shephard MJ , Paddonrow MN
Published: November 2009

A computational study of the conformational analysis of a series of C60 ball-and-chain bichromophoric molecules (1)-(6) has been carried out by means of the AM1 and HF/3-21G//AM1 theoretical methods. It is found that the AM1 method underestimates both the relative conformational energies and the magnitude of the energy barriers folded and extended conformers. In contrast, the HF/3-21G//AM1 method gives reasonable values for these quantities. The HF/3-21G//AM1 calculated energy differences between the folded and extended conformers of systems (2)-(5) are less than 5 kJ/mol and the barriers to their interconversion are c. 30 kJ/mol. The conformational bias in these systems may be modified by the judicious placement of methyl groups in the region of the hydrocarbon chain closest to the C60 cage. It is found that the length of the chain and the nature of the non-C60. chromophore have little effect on the conformational energetics.
The Crystal Structure of cis-Inositol Monohydrate—Un Objet Retrouvé
Authors: Freeman HC , Langs DA , Nockolds CE , Oh YL
Published: November 2009

cis-Inositol monohydrate, C6H12O6.H2O, crystallizes in the monoclinic space group P 21/n [a 9.900(8), b 9.296(8), c 17.795(15) Ǻ, β 90.5(1)°, Z 8]. The normalized structure factors Eh have an atypical statistical distribution, and attempts to solve the structure by direct methods (triplet relationships) were unsuccessful. The structure was ultimately solved by Patterson and Fourier methods, and was refined by full-matrix least squares [Rw = 0.047 for 1665 independent reflections ≥2σ(Imin)]. The cis-inositol molecules have approximately trigonal symmetry, as expected. The difficulties encountered during the structure analysis are explained by the presence of two nearly identical molecules of high symmetry in the asymmetric unit. The independent molecules are related by translational pseudosymmetry, and their orientations are such that all the C-C and C-O bonds in the structure are approximately parallel to a small number of directions.
Bringing the Hutchinsonian niche into the 21st century: Ecological and evolutionary perspectives
Authors: Holt Robert D.
Published: November 2009

G. Evelyn Hutchinson more than a half century ago proposed that one could characterize the ecological niche of a species as an abstract mapping of population dynamics onto an environmental space, the axes of which are abiotic and biotic factors that influence birth and death rates. If a habitat has conditions within a species' niche, a population should persist without immigration from external sources, whereas if conditions are outside the niche, it faces extinction. Analyses of species' niches are essential to understanding controls on species' geographical range limits and how these limits might shift in our rapidly changing world. Recent developments in ecology and evolutionary biology suggest it is time to revisit and refine Hutchinson's niche concept. After reviewing techniques for quantifying niches, I examine subtleties that arise because of impacts species have on their own environments, the density-dependent modulation of how individuals experience environments, and the interplay of dispersal and temporal heterogeneity in determining population persistence. Moreover, the evolutionary record over all time scales reveals a spectrum of rates of change in species' niches, from rapid niche evolution to profound niche conservatism. Substantial challenges revolving around the evolutionary dimension of the Hutchinsonian niche include quantifying the magnitude of evolved intraspecific and clade-level variation in niches and understanding the factors that govern where along the spectrum of potential evolutionary rates any given lineage lies. A growing body of theory provides elements of a conceptual framework for understanding niche conservatism and evolution, paving the way for an evolutionary theory of the niche.
Precuneus shares intrinsic functional architecture in humans and monkeys
Authors: Margulies Daniel S. , Vincent Justin L. , Kelly Clare , Lohmann Gabriele , Uddin Lucina Q. , Biswal Bharat B. , Villringer Arno , Castellanos F. Xavier , Milham Michael P. , Petrides Michael
Published: November 2009

Evidence from macaque monkey tracing studies suggests connectivity-based subdivisions within the precuneus, offering predictions for similar subdivisions in the human. Here we present functional connectivity analyses of this region using resting-state functional MRI data collected from both humans and macaque monkeys. Three distinct patterns of functional connectivity were demonstrated within the precuneus of both species, with each subdivision suggesting a discrete functional role: (
i
) the anterior precuneus, functionally connected with the superior parietal cortex, paracentral lobule, and motor cortex, suggesting a sensorimotor region; (
ii
) the central precuneus, functionally connected to the dorsolateral prefrontal, dorsomedial prefrontal, and multimodal lateral inferior parietal cortex, suggesting a cognitive/associative region; and (
iii
) the posterior precuneus, displaying functional connectivity with adjacent visual cortical regions. These functional connectivity patterns were differentiated from the more ventral networks associated with the posterior cingulate, which connected with limbic structures such as the medial temporal cortex, dorsal and ventromedial prefrontal regions, posterior lateral inferior parietal regions, and the lateral temporal cortex. Our findings are consistent with predictions from anatomical tracer studies in the monkey, and provide support that resting-state functional connectivity (RSFC) may in part reflect underlying anatomy. These subdivisions within the precuneus suggest that neuroimaging studies will benefit from treating this region as anatomically (and thus functionally) heterogeneous. Furthermore, the consistency between functional connectivity networks in monkeys and humans provides support for RSFC as a viable tool for addressing cross-species comparisons of functional neuroanatomy.
Toward a quantitative theory of intrinsically disordered proteins and their function
Authors: Liu Jintao , Faeder James R. , Camacho Carlos J.
Published: November 2009

A large number of proteins are sufficiently unstable that their full 3D structure cannot be resolved. The origins of this intrinsic disorder are not well understood, but its ubiquitous presence undercuts the principle that a protein's structure determines its function. Here we present a quantitative theory that makes predictions regarding the role of intrinsic disorder in protein structure and function. In particular, we discuss the implications of analytical solutions of a series of fundamental thermodynamic models of protein interactions in which disordered proteins are characterized by positive folding free energies. We validate our predictions by assigning protein function by using the gene ontology classification—in which “protein binding”, “catalytic activity”, and “transcription regulator activity” are the three largest functional categories—and by performing genome-wide surveys of both the amount of disorder in these functional classes and binding affinities for both prokaryotic and eukaryotic genomes. Specifically, without assuming any a priori structure–function relationship, the theory predicts that both catalytic and low-affinity binding (
K
d
≳10
−7
M) proteins prefer ordered structures, whereas only high-affinity binding proteins (found mostly in eukaryotes) can tolerate disorder. Relevant to both transcription and signal transduction, the theory also explains how increasing disorder can tune the binding affinity to maximize the specificity of promiscuous interactions. Collectively, these studies provide insight into how natural selection acts on folding stability to optimize protein function.
DAB2IP coordinates both PI3K-Akt and ASK1 pathways for cell survival and apoptosis
Authors: Xie Daxing , Gore Crystal , Zhou Jian , Pong Rey-Chen , Zhang Haifeng , Yu Luyang , Vessella Robert L. , Min Wang , Hsieh Jer-Tsong
Published: November 2009

In metastatic prostate cancer (PCa) cells, imbalance between cell survival and death signals such as constitutive activation of phosphatidylinositol 3-kinase (PI3K)-Akt and inactivation of apoptosis-stimulated kinase (ASK1)-JNK pathways is often detected. Here, we show that DAB2IP protein, often down-regulated in PCa, is a potent growth inhibitor by inducing G
0
/G
1
cell cycle arrest and is proapoptotic in response to stress. Gain of function study showed that DAB2IP can suppress the PI3K-Akt pathway and enhance ASK1 activation leading to cell apoptosis, whereas loss of DAB2IP expression resulted in PI3K-Akt activation and ASK1-JNK inactivation leading to accelerated PCa growth in vivo. Moreover, glandular epithelia from DAB2IP
−/−
animal exhibited hyperplasia and apoptotic defect. Structural functional analyses of DAB2IP protein indicate that both proline-rich (PR) and PERIOD-like (PER) domains, in addition to the critical role of C2 domain in ASK1 activity, are important for modulating PI3K-Akt activity. Thus, DAB2IP is a scaffold protein capable of bridging both survival and death signal molecules, which implies its role in maintaining cell homeostasis.
Reprogramming erythroid cells for lysosomal enzyme production leads to visceral and CNS cross-correction in mice with Hurler syndrome
Authors: Wang Daren , Zhang Wei , Kalfa Theodosia A. , Grabowski Gregory , Davies Stella , Malik Punam , Pan Dao
Published: November 2009

Restricting transgene expression to maturing erythroid cells can reduce the risk for activating oncogenes in hematopoietic stem cells (HSCs) and their progeny, yet take advantage of their robust protein synthesis machinery for high-level protein production. This study sought to evaluate the feasibility and efficacy of reprogramming erythroid cells for production of a lysosomal enzyme, α-L-iduronidase (IDUA). An erythroid-specific hybrid promoter provided inducible IDUA expression and release during in vitro erythroid differentiation in murine erythroleukemia cells, resulting in phenotypical cross-correction in an enzyme-deficient lymphoblastoid cell line derived from patients with mucopolysaccharidosis type I (MPS I). Stable and higher than normal plasma IDUA levels were achieved in vivo in primary and secondary MPS I chimeras for at least 9 months after transplantation of HSCs transduced with the erythroid-specific IDUA-containing lentiviral vector (LV). Moreover, long-term metabolic correction was demonstrated by normalized urinary glycosaminoglycan accumulation in all treated MPS I mice. Complete normalization of tissue pathology was observed in heart, liver, and spleen. Notably, neurological function and brain pathology were significantly improved in MPS I mice by erythroid-derived, higher than normal peripheral IDUA protein. These data demonstrate that late-stage erythroid cells, transduced with a tissue-specific LV, can deliver a lysosomal enzyme continuously at supraphysiological levels to the bloodstream and can correct the disease phenotype in both viscera and CNS of MPS I mice. This approach provides a paradigm for the utilization of RBC precursors as a depot for efficient and potentially safer systemic delivery of nonsecreted proteins by ex vivo HSC gene transfer.
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
Authors: Hudson Brian P. , Quispe Joel , Lara-González Samuel , Kim Younggyu , Berman Helen M. , Arnold Eddy , Ebright Richard H. , Lawson Catherine L.
Published: November 2009

We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the
Escherichia coli
catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions −78 to +20 of a Class I CAP-dependent promoter with a CAP site at position −61.5 and a premelted transcription bubble. A 20-Å electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbon-sandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP α subunit C-terminal domain (αCTD), interactions of αCTD with σ
70
region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNA-bend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP β′, β, and σ
70
subunits.
Deficits in spatial memory correlate with modified γ-aminobutyric acid type A receptor tyrosine phosphorylation in the hippocampus
Authors: Tretter Verena , Revilla-Sanchez Raquel , Houston Catriona , Terunuma Miho , Havekes Robbert , Florian Cédrick , Jurd Rachel , Vithlani Mansi , Michels Guido , Couve Andrés , Sieghart Werner , Brandon Nicholas , Abel Ted , Smart Trevor G. , Moss Stephen J.
Published: November 2009

Fast synaptic inhibition in the brain is largely mediated by γ-aminobutyric acid receptors (GABA
A
R). While the pharmacological manipulation of GABA
A
R function by therapeutic agents, such as benzodiazepines can have profound effects on neuronal excitation and behavior, the endogenous mechanisms neurons use to regulate the efficacy of synaptic inhibition and their impact on behavior remains poorly understood. To address this issue, we created a knock-in mouse in which tyrosine phosphorylation of the GABA
A
Rs γ2 subunit, a posttranslational modification that is critical for their functional modulation, has been ablated. These animals exhibited enhanced GABA
A
R accumulation at postsynaptic inhibitory synaptic specializations on pyramidal neurons within the CA3 subdomain of the hippocampus, primarily due to aberrant trafficking within the endocytic pathway. This enhanced inhibition correlated with a specific deficit in spatial object recognition, a behavioral paradigm dependent upon CA3. Thus, phospho-dependent regulation of GABA
A
R function involving just two tyrosine residues in the γ2 subunit provides an input-specific mechanism that not only regulates the efficacy of synaptic inhibition, but has behavioral consequences.
Identification of CCR4 and other essential thyroid hormone receptor co-activators by modified yeast synthetic genetic array analysis
Authors: Govindan Manjapra , Meng Xianwang , Denis Clyde L. , Webb Paul , Baxter John D. , Walfish Paul G.
Published: November 2009

Identification of thyroid hormone receptor (TR) co-regulators has enhanced our understanding of thyroid hormone (TH) action. However, it is likely that many other co-regulators remained unidentified, and unbiased methods are required to discover these proteins. We have previously demonstrated that the yeast
Saccharomyces cerevisiae
is an excellent system in which to study TR action, and that defined TR signaling complexes in a eukaryotic background devoid of complicating influences of mammalian cell co-regulators can be constructed and analyzed for endogenous yeast genes, many of which are conserved in mammals. Here, a modified synthetic genetic array analysis was performed by crossing a yeast strain that expressed TRβ1 and the co-activator GRIP1/SRC2 with 384 yeast strains bearing deletions of known genes. Eight genes essential for TH action were isolated, of which 4 are conserved in mammals. Examination of one, the yeast CCR4 and its human homolog CCR4/NOT6 (hCCR4), confirmed that (
i
) transfected CCR4 potentiates a TH response in cultured cells more efficiently than established TR co-activators and (
ii
) knockdown of CCR4 expression strongly inhibited a TH response (>80%). TH treatment promoted rapid and sustained hCCR4 recruitment to the TH-responsive deiodinase 1 promoter and TR co-localizes with hCCR4 in the nucleus and interacts with hCCR4 in 2-hybrid and pull-down assays. These findings indicate that a modified yeast synthetic genetic array strategy is a feasible method for unbiased identification of conserved genes essential for TR and other nuclear receptor hormone functions in mammals.
Intramolecular amide bonds stabilize pili on the surface of bacilli
Authors: Budzik Jonathan M. , Poor Catherine B. , Faull Kym F. , Whitelegge Julian P. , He Chuan , Schneewind Olaf
Published: November 2009

Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of
Bacillus cereus
. The BcpA precursor encompasses 2 Ig folds (CNA
2
and CNA
3
) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA
1
, is formed only after pilin subunits have been incorporated into pili. We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.
Her6 regulates the neurogenetic gradient and neuronal identity in the thalamus
Authors: Scholpp Steffen , Delogu Alessio , Gilthorpe Jonathan , Peukert Daniela , Schindler Simone , Lumsden Andrew
Published: November 2009

During vertebrate brain development, the onset of neuronal differentiation is under strict temporal control. In the mammalian thalamus and other brain regions, neurogenesis is regulated also in a spatially progressive manner referred to as a neurogenetic gradient, the underlying mechanism of which is unknown. Here we describe the existence of a neurogenetic gradient in the zebrafish thalamus and show that the progression of neurogenesis is controlled by dynamic expression of the bHLH repressor
her6
. Members of the Hes/Her family are known to regulate proneural genes, such as Neurogenin and Ascl. Here we find that Her6 determines not only the onset of neurogenesis but also the identity of thalamic neurons, marked by proneural and neurotransmitter gene expression: loss of Her6 leads to premature Neurogenin1-mediated genesis of glutamatergic (excitatory) neurons, whereas maintenance of Her6 leads to Ascl1-mediated production of GABAergic (inhibitory) neurons. Thus, the presence or absence of a single upstream regulator of proneural gene expression, Her6, leads to the establishment of discrete neuronal domains in the thalamus.
Production of hyperpolarized [1,4-
13
C
2
]malate from [1,4-
13
C
2
]fumarate is a marker of cell necrosis and treatment response in tumors
Authors: Gallagher Ferdia A. , Kettunen Mikko I. , Hu De-En , Jensen Pernille R. , Zandt René in ‘t , Karlsson Magnus , Gisselsson Anna , Nelson Sarah K. , Witney Timothy H. , Bohndiek Sarah E. , Hansson Georg , Peitersen Torben , Lerche Mathilde H. , Brindle Kevin M.
Published: November 2009

Dynamic nuclear polarization of
13
C-labeled cell substrates has been shown to massively increase their sensitivity to detection in NMR experiments. The sensitivity gain is sufficiently large that if these polarized molecules are injected intravenously, their spatial distribution and subsequent conversion into other cell metabolites can be imaged. We have used this method to image the conversion of fumarate to malate in a murine lymphoma tumor in vivo after i.v. injection of hyperpolarized [1,4-
13
C
2
]fumarate. In isolated lymphoma cells, the rate of labeled malate production was unaffected by coadministration of succinate, which competes with fumarate for transport into the cell. There was, however, a correlation with the percentage of cells that had lost plasma membrane integrity, suggesting that the production of labeled malate from fumarate is a sensitive marker of cellular necrosis. Twenty-four hours after treating implanted lymphoma tumors with etoposide, at which point there were significant levels of tumor cell necrosis, there was a 2.4-fold increase in hyperpolarized [1,4-
13
C
2
]malate production compared with the untreated tumors. Therefore, the formation of hyperpolarized
13
C-labeled malate from [1,4-
13
C
2
]fumarate appears to be a sensitive marker of tumor cell death in vivo and could be used to detect the early response of tumors to treatment. Given that fumarate is an endogenous molecule, this technique has the potential to be used clinically.
MRPS18–2 protein immortalizes primary rat embryonic fibroblasts and endows them with stem cell-like properties
Authors: Kashuba Elena , Pavan Yenamandra Surya , Deoram Darekar Suhas , Yurchenko Mariya , Kashuba Vladimir , Klein George , Szekely Laszlo
Published: November 2009

We report that the overexpression of mitochondrial ribosomal protein MRPS18–2 (S18–2) can immortalize primary rat embryonic fibroblasts (REFs). The immortalized cells (18IM) lose contact inhibition, form foci, and are capable of anchorage-independent growth. Concurrently, mesodermal markers, such as vimentin, smooth muscle actin, and Fut4, disappear completely. 18IM cells express embryonic stem cell markers, such as SSEA-1, Sox2, and Oct3/4. In confluent cultures, a portion of cells also express ectoderm- and endoderm-specific pan-keratin, ectoderm-specific beta-III-tubulin, mesoderm-specific MHC class II, and become stainable for fat with Oil red O. None of these changes was detected in c-myc+Ha-ras (MR)-transformed cells. In immunodeficient mice, 18IM cells formed small transiently growing tumors that have down-regulated SSEA-1 and showed pan-keratin staining. We conclude that S18–2 can immortalize REFs and induces them to express stem cell traits.
Taxonomy, botany and plant development.
Authors: Subhadrabandhu S. , Stern R. A.
Published: November 2009

This chapter briefly covers the taxonomy, biological development (including flowering and fruiting), and morphology of litchi (Litchi chinensis) and longan.
Distribution, biology and integrated management of the pea leaf weevil,
Sitona lineatus
L. (Coleoptera: Curculionidae), with an analysis of research needs.
Authors: Vankosky M. , Dosdall L. M. , Cárcamo H. A.
Published: November 2009

The pea leaf weevil,
Sitona lineatus
L. (Coleoptera, Curculionidae), is a significant pest of field pea (
Pisum sativum
L.) and broad bean (
Vicia faba
L.) crops throughout Europe, Asia, Africa and North America and it has recently become an established pest in the Canadian prairies. The geographical expansion and current distribution of
S. lineatus
, its life history, economic impact and control strategies are reviewed. Primary hosts of the pea leaf weevil, on which pre-imaginal development can occur, are identified, in addition to its secondary hosts, which provide nourishment for adults when not in their reproductive phase. The importance of pheromones and host plant volatile compounds for mate finding and host plant location is reviewed. Research on control strategies for
S. lineatus
is summarized, but to date surprisingly little effort has been expended to develop and implement integrated pest management (IPM) programmes, even though combining insecticide use with host plant resistance, cultural and biological control strategies promises to enhance its management. The development of an effective population monitoring system for pea leaf weevil, scientifically derived economic threshold values, and designing an IPM programme for
S. lineatus
comprise the most critical research needs for improving the sustainable management of this insect.
Pedestal and scrape-off layer dynamics in ELMy H-mode plasmas in JET
Authors: Beurskens M.N.A. , Alfier A. , Alper B. , Balboa I. , Flanagan J. , Fundamenski W. , Giovannozzi E. , Kempenaars M. , Loarte A. , Lomas P. , de La Luna E. , Nunes I. , Pasqualotto R. , Pitts R.A. , Saibene G. , Walsh M. , Wiesen S.
Published: November 2009

Pedestal and scrape-off layer (SOL) dynamics due to edge localized modes (ELMs) have been studied on JET with improved diagnostic capability. The new high resolution Thomson scattering system enables detailed measurement of the space and time evolution of the T
e and n
e pedestal profiles. The pedestal and SOL dynamics for type I ELMy H-mode plasmas have been studied for a wide range of plasma conditions. During a short period of <200 µs after the ELM event radial profiles of filaments in the SOL electron density and temperature have been observed. After that period the SOL density is increased and remains high for several milliseconds. During the same period the electron temperature shows no increase compared with the pre-ELM values. This SOL dynamics has been observed for a wide range of plasma parameters and is independent of plasma pedestal collisionality. For the first time on JET the convective and conductive ELM energy losses have been quantified using the new kinetic profile measurements. The findings provide detailed confirmation of earlier observations based on different measurements and analysis. The pedestal region perturbed by the ELM is the same for both density and temperature and the ELM effect extends up to about 20% of minor radius. The convective energy losses do not vary significantly and are ∼5% of the pedestal stored energy (W
ped) over a large range of pedestal collisionality
from below
to above
whereas the conductive losses strongly decrease from ∼20% of W
ped to 5% of W
ped with increasing
. The experimental observations are compared with a simple model based on losses being driven by parallel transport.
Physical performance analysis and progress of the development of the negative ion RF source for the ITER NBI system
Authors: Fantz U. , Franzen P. , Kraus W. , Berger M. , Christ-Koch S. , Falter H. , Fröschle M. , Gutser R. , Heinemann B. , Martens C. , McNeely P. , Riedl R. , Speth E. , Stäbler A. , Wünderlich D.
Published: November 2009

For heating and current drive the neutral beam injection (NBI) system for ITER requires a 1 MeV deuterium beam for up to 1 h pulse length. In order to inject the required 17 MW the large area source (1.9 m × 0.9 m) has to deliver 40 A of negative ion current at the specified source pressure of 0.3 Pa. In 2007, the IPP RF driven negative hydrogen ion source was chosen by the ITER board as the new reference source for the ITER NBI system due to, in principle, its maintenance free operation and the progress in the RF source development. The performance analysis of the IPP RF sources is strongly supported by an extensive diagnostic program and modelling of the source and beam extraction. The control of the plasma chemistry and the processes in the plasma region near the extraction system are the most critical topics for source optimization both for long pulse operation as well as for the source homogeneity. The long pulse stability has been demonstrated at the test facility MANITU which is now operating routinely at stable pulses of up to 10 min with parameters near the ITER requirements. A quite uniform plasma illumination of a large area source (0.8 m × 0.8 m) has been demonstrated at the ion source test facility RADI. The new test facility ELISE presently planned at IPP is being designed for long pulse plasma operation and short pulse, but large-scale extraction from a half-size ITER source which is an important intermediate step towards ITER NBI.
Mirror stabilization experiments in the Hanbit device
Authors: England A.C. , Lee D.K. , Lee S.G. , Kwon M. , Yoon S.W. , Yasaka Y. , Sugimoto N. , Katanuma I. , Yashiro K. , Imai T.
Published: November 2009

The Hanbit magnetic mirror device has been involved in a series of experiments on stabilization of the MHD flute type mode. We undertook investigations to see whether a divertor and the kinetic stabilizer (KS) of Post et al can stabilize the MHD instability. The Hanbit divertor configuration used one of the central cell coils with reversed current as the divertor coil and two other coils with increased current to compensate the field droop. The divertor eliminated the m = −1 instability when the null point was inside the vacuum tank. The KS used microwave produced plasmas on field lines in the cusp tank region. Two coils on the cusp tank were configured to produce expanding field lines with a large positive radius of curvature. A 5 kW 2.45 GHz magnetron was used to produce an electron cyclotron resonance heated plasma pressure in this region. A reduction in instability duration was observed for high power plasmas. However, for low power plasmas that terminate violently with an m = −1 instability, the KS action made the duration of the instability longer.
The importance of parallel nonlinearity in the self-interaction of geodesic acoustic mode
Authors: Zhang H.S. , Qiu Z. , Chen L. , Lin Z.
Published: November 2009

Gyrokinetic theory and simulation find that the nonlinear self-interactions of the long wavelength geodesic acoustic mode (GAM) in toroidal plasmas cannot efficiently generate the second harmonic due to a cancellation between the perpendicular convective nonlinearity and the parallel nonlinearity, which is neglected in most of gyrokinetic theory and simulation. Other mechanisms beyond conventional GAM theory are required to explain recent experimental observations of the excitation of the GAM second harmonic.
Horizontal and vertical movements of swordfish in the Southeast Pacific
Authors: Abascal Francisco J. , Mejuto Jaime , Quintans Manuel , Ramos-Cartelle Ana
Published: November 2009

Abascal, F. J., Mejuto, J., Quintans, M., and Ramos-Cartelle, A. 2010. Horizontal and vertical movements of swordfish in the Southeast Pacific. – ICES Journal of Marine Science, 67: 466–474. In all, 21 swordfish (Xiphias gladius) were tagged with pop-up archival satellite tags in the Southeast Pacific. Despite problems of premature release, the information obtained provided insight into the horizontal and vertical behaviour of the species in the area. A consistent migratory pattern was observed, fish moving northwest by autumn and presumably returning south by early spring. Swordfish typically forage in deep water during the day and stay in the mixed layer at night, although this behaviour is occasionally modified. The maximum depth recorded was 1136 m, and dives deeper than 900 m were found in five of the six tags analysed. There was a significant positive relationship between average depth by night and visible moon fraction.
Dicer1 functions as a haploinsufficient tumor suppressor
Authors: Kumar Madhu S. , Pester Ryan E. , Chen Cindy Y. , Lane Keara , Chin Christine , Lu Jun , Kirsch David G. , Golub Todd R. , Jacks Tyler
Published: November 2009

While the global down-regulation of microRNAs (miRNAs) is a common feature of human tumors, its genetic basis is largely undefined. To explore this question, we analyzed the consequences of conditional Dicer1 mutation (Dicer1 “floxed” or Dicer1fl) on several mouse models of cancer. Here we show Dicer1 functions as a haploinsufficient tumor suppressor gene. Deletion of a single copy of Dicer1 in tumors from Dicer1fl/+ animals led to reduced survival compared with controls. These tumors exhibited impaired miRNA processing but failed to lose the wild-type Dicer1 allele. Moreover, tumors from Dicer1fl/fl animals always maintained one functional Dicer1 allele. Consistent with selection against full loss of Dicer1 expression, enforced Dicer1 deletion caused inhibition of tumorigenesis. Analysis of human cancer genome copy number data reveals frequent deletion of DICER1. Importantly, however, the gene has not been reported to undergo homozygous deletion, suggesting that DICER1 is haploinsufficient in human cancer. These findings suggest Dicer1 may be an important haploinsufficient tumor suppressor gene and, furthermore, that other factors controlling miRNA biogenesis may also function in this manner.
A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development
Authors: He Xin-Jian , Hsu Yi-Feng , Zhu Shihua , Liu Hai-Liang , Pontes Olga , Zhu Jianhua , Cui Xinping , Wang Co-Shine , Zhu Jian-Kang
Published: November 2009

RNA-directed DNA methylation (RdDM) is a conserved mechanism for epigenetic silencing of transposons and other repetitive elements. We report that the rdm4 (RNA-directed DNA Methylation4) mutation not only impairs RdDM, but also causes pleiotropic developmental defects in Arabidopsis. Both RNA polymerase II (Pol II)- and Pol V-dependent transcripts are affected in the rdm4 mutant. RDM4 encodes a novel protein that is conserved from yeast to humans and interacts with Pol II and Pol V in plants. Our results suggest that RDM4 functions in epigenetic regulation and plant development by serving as a transcriptional regulator for RNA Pol V and Pol II, respectively.
Inferring tumor progression from genomic heterogeneity
Authors: Navin Nicholas , Krasnitz Alexander , Rodgers Linda , Cook Kerry , Meth Jennifer , Kendall Jude , Riggs Michael , Eberling Yvonne , Troge Jennifer , Grubor Vladimir , Levy Dan , Lundin Pär , Månér Susanne , Zetterberg Anders , Hicks James , Wigler Michael
Published: November 2009

Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that heterogeneity can be ascribed to a few clonal subpopulations, rather than a series of gradual intermediates. By comparing multiple subpopulations from different anatomic locations, we have inferred pathways of cancer progression and the organization of tumor growth.
Efficient Operation of NAD(P)H Dehydrogenase Requires Supercomplex Formation with Photosystem I via Minor LHCI in Arabidopsis
Authors: Peng Lianwei , Fukao Yoichiro , Fujiwara Masayuki , Takami Tsuneaki , Shikanai Toshiharu
Published: November 2009

In higher plants, the chloroplast NAD(P)H dehydrogenase (NDH) complex mediates photosystem I (PSI) cyclic and chlororespiratory electron transport. We reported previously that NDH interacts with the PSI complex to form a supercomplex (NDH-PSI). In this study, NDH18 and FKBP16-2 (FK506 Binding Protein 16-2), detected in the NDH-PSI supercomplex by mass spectrometry, were shown to be NDH subunits by the analysis of their knockdown lines. On the basis of extensive mutant characterization, we propose a structural model for chloroplast NDH, whereby NDH is divided into four subcomplexes. The subcomplex A and membrane subcomplex are conserved in cyanobacteria, but the subcomplex B and lumen subcomplex are specific to chloroplasts. Two minor light-harvesting complex I proteins, Lhca5 and Lhca6, were required for the full-size NDH-PSI supercomplex formation. Similar to crr pgr5 double mutants that completely lack cyclic electron flow activity around PSI, the lhca6 pgr5 double mutant exhibited a severe defect in growth. Consistent with the impaired NDH activity, photosynthesis was also severely affected in mature leaves of lhca6 pgr5. We conclude that chloroplast NDH became equipped with the novel subcomplexes and became associated with PSI during the evolution of land plants, and this process may have facilitated the efficient operation of NDH.
Rice MicroRNA Effector Complexes and Targets
Authors: Wu Liang , Zhang Qingqing , Zhou Huanyu , Ni Fangrui , Wu Xueying , Qi Yijun
Published: November 2009

MicroRNAs (miRNAs) are small silencing RNAs with regulatory roles in gene expression. miRNAs interact with Argonaute (AGO) proteins to form effector complexes that cleave target mRNAs or repress translation. Rice (Oryza sativa) encodes four AGO1 homologs (AGO1a, AGO1b, AGO1c, and AGO1d). We used RNA interference (RNAi) to knock down the four AGO1s. The RNAi lines displayed pleiotropic developmental phenotypes and had increased accumulation of miRNA targets. AGO1a, AGO1b, and AGO1c complexes were purified and further characterized. The three AGO1s all have a strong preference for binding small RNAs (sRNAs) with 5′ U and have Slicer activity. We cataloged the sRNAs in each AGO1 complex by deep sequencing and found that all three AGO1s predominantly bound known miRNAs. Most of the miRNAs were evenly distributed in the three AGO1 complexes, suggesting a redundant role for the AGO1s. Intriguingly, a subset of miRNAs were specifically incorporated into or excluded from one of the AGO1s, suggesting functional specialization among the AGO1s. Furthermore, we identified rice miRNA targets at a global level. The validated targets include transcription factors that control major stages of development and also genes involved in a variety of physiological processes, indicating a broad regulatory role for miRNAs in rice.
No so HoT – heads or tails is not able to reliably compare multiple sequence alignments
Authors: Wise Michael J.
Published: November 2009

Most phylogenetic‐tree building applications use multiple sequence alignments as a starting point. A recent meta‐level methodology, called Heads or Tails, aims to reveal the quality of multiple sequence alignments by comparing alignments taken in the forward direction with the alignments of the same sequences when the sequences are reversed. Through an examination of a special case for multiple sequence alignment – pair‐wise alignments, where an optimal algorithm exists – and the use of a modiﬁed global‐alignment application, it is shown that the forward and reverse alignments, even when they are the same, do not capture all the possible variations in the alignments and when the forward and reverse alignments differ there may be other alignments that remain unaccounted for. The implication is that comparing just the forward and (biologically irrelevant) reverse alignments is not sufficient to capture the variability in multiple sequence alignments, and the Heads or Tails methodology is therefore not suitable as a method for investigating multiple sequence alignment accuracy. Part of the reason is the inability of individual multiple sequence alignment applications to adequately sample the space of possible alignments. A further implication is that the Hall [Hall, B.G., 2008. Mol. Biol. Evol. 25, 1576–1580] methodology may create optimal synthetic multiple sequence alignments that extant aligners will be unable to completely recover ab initio due to alternative alignments being possible at particular sites. In general, it is shown that more divergent sequences will give rise to an increased number of alternative alignments, so sequence sets with a higher degree of similarity are preferable to sets with lower similarity as the starting point for phylogenetic tree building.

 © The Willi Hennig Society 2009.
Translational Mini-Review Series on Th17 Cells: Function and regulation of human T helper 17 cells in health and disease
Authors: Crome S Q , Wang A Y , Levings M K
Published: November 2009

OTHER ARTICLES PUBLISHED IN THIS MINI-REVIEW SERIES ON Th17 CELLS Induction of interleukin-17 production by regulatory T cells. Clin Exp Immunol 2009; doi:10.1111/j.1365-2249.2009.04038.x Are T helper 17 cells really pathogenic in autoimmunity? Clin Exp Immunol 2009; doi:10.1111/j.1365-2249.2009.04039.x CD4+ T helper cells: functional plasticity and differential sensitivity to regulatory T cell-mediated regulation. Clin Exp Immunol 2009; doi:10.1111/j.1365-2249.2009.04040.x Development of mouse and human T helper 17 cells. Clin Exp Immunol 2009; doi:10.1111/j.1365-2249.2009.04041.x

T helper (Th) cell have a central role in modulating immune responses. While Th1 and Th2 cells have long been known to regulate cellular and humoral immunity, Th17 cells have been identified only recently as a Th lineage that regulates inflammation via production of distinct cytokines such as interleukin (IL)-17. There is growing evidence that Th17 cells are pathological in many human diseases, leading to intense interest in defining their origins, functions and developing strategies to block their pathological effects. The cytokines that regulate Th17 differentiation have been the focus of much debate, due primarily to inconsistent findings from studies in humans. Evidence from human disease suggests that their in vivo development is driven by specialized antigen-presenting cells. Knowledge of how Th17 cells interact with other immune cells is limited, but recent data suggest that Th17 cells may not be subject to strict cellular regulation by T regulatory cells. Notably, Th17 cells and T regulatory cells appear to share common developmental pathways and both cell types retain significant plasticity. Herein, we will discuss the molecular and cellular regulation of Th17 cells with an emphasis on studies in humans.