bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of a vertical tunneling graphene heterojunction field-effect transistor
Authors: Bala Kumar S. , Seol Gyungseon , Guo Jing
Published: July 2012

Vertical tunneling field-effect-transistor (FET) based on graphene heterojunctions with layers of hBN is simulated by self-consistent quantum transport simulations. It is found that the asymmetric p-type and n-type conduction is due to work function difference between the graphene contact and the tunneling channel material. Modulation of the bottom-graphene-contact plays an important role in determining the switching characteristic of the device. Due to the electrostatic short-channel-effects stemming from the vertical-FET structure, the output I-V characteristics do not saturate. The scaling behaviors the vertical-FET as a function of the gate insulator thickness and the thickness of the tunneling channel material are examined.
Study on low-energy sputtering near the threshold energy by molecular dynamics simulations
Authors: Yan C. , Zhang Q. Y.
Published: July 2012

Using molecular dynamics simulation, we have studied the low-energy sputtering at the energies near the sputtering threshold. Different projectile-target combinations of noble metal atoms (Cu, Ag, Au, Ni, Pd, and Pt) are simulated in the range of incident energy from 0.1 to 200 eV. It is found that the threshold energies for sputtering are different for the cases of M1 < M2 and M1 ≥ M2, where M1 and M2 are atomic mass of projectile and target atoms, respectively. The sputtering yields are found to have a linear dependence on the reduced incident energy, but the dependence behaviors are different for the both cases. The two new formulas are suggested to describe the energy dependences of the both cases by fitting the simulation results with the determined threshold energies. With the study on the energy dependences of sticking probabilities and traces of the projectiles and recoils, we propose two different mechanisms to describe the sputtering behavior of low-energy atoms near the threshold energy for the cases of M1 < M2 and M1 ≥ M2, respectively.
Quantification of high-specificity cyclic diguanylate signaling
Authors: Massie Jonathan P. , Reynolds Evan L. , Koestler Benjamin J. , Cong Jian-Ping , Agostoni Marco , Waters Christopher M.
Published: July 2012

Cyclic di-GMP (c-di-GMP) is a second messenger molecule that regulates the transition between sessile and motile lifestyles in bacteria. Bacteria often encode multiple diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that produce and degrade c-di-GMP, respectively. Because of multiple inputs into the c-di-GMP–signaling network, it is unclear whether this system functions via high or low specificity. High-specificity signaling is characterized by individual DGCs or PDEs that are specifically associated with downstream c-di-GMP–mediated responses. In contrast, low-specificity signaling is characterized by DGCs or PDEs that modulate a general signal pool, which, in turn, controls a global c-di-GMP–mediated response. To determine whether c-di-GMP functions via high or low specificity inVibrio cholerae, we correlated the in vivo c-di-GMP concentration generated by seven DGCs, each expressed at eight different levels, to the c-di-GMP–mediated induction of biofilm formation and transcription. There was no correlation between total intracellular c-di-GMP levels and biofilm formation or gene expression when considering all states. However, individual DGCs showed a significant correlation between c-di-GMP production and c-di-GMP–mediated responses. Moreover, the rate of phenotypic change versus c-di-GMP concentration was significantly different between DGCs, suggesting that bacteria can optimize phenotypic output to c-di-GMP levels via expression or activation of specific DGCs. Our results conclusively demonstrate that c-di-GMP does not function via a simple, low-specificity signaling pathway inV. cholerae.
Dynamics of photogenerated holes in surface modified α-Fe
2
O
3
photoanodes for solar water splitting
Authors: Barroso Monica , Mesa Camilo A. , Pendlebury Stephanie R. , Cowan Alexander J. , Hisatomi Takashi , Sivula Kevin , Grätzel Michael , Klug David R. , Durrant James R.
Published: July 2012

This paper addresses the origin of the decrease in the external electrical bias required for water photoelectrolysis with hematite photoanodes, observed following surface treatments of such electrodes. We consider two alternative surface modifications: a cobalt oxo/hydroxo-based (CoO
x
) overlayer, reported previously to function as an efficient water oxidation electrocatalyst, and a Ga
2
O
3
overlayer, reported to passivate hematite surface states. Transient absorption studies of these composite electrodes under applied bias showed that the cathodic shift of the photocurrent onset observed after each of the surface modifications is accompanied by a similar cathodic shift of the appearance of long-lived hematite photoholes, due to a retardation of electron/hole recombination. The origin of the slower electron/hole recombination is assigned primarily to enhanced electron depletion in the Fe
2
O
3
for a given applied bias.
Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages
Authors: Chen Xuefen , Barozzi Iros , Termanini Alberto , Prosperini Elena , Recchiuti Antonio , Dalli Jesmond , Mietton Flore , Matteoli Gianluca , Hiebert Scott , Natoli Gioacchino
Published: July 2012

Histone deacetylases (HDACs) regulate inflammatory gene expression, as indicated by the potent antiinflammatory activity of pan-HDAC inhibitors. However, the specific contribution of each of the 11 HDAC proteins to the inflammatory gene expression program is unknown. Using an integrated genomic approach, we found that Hdac3-deficient macrophages were unable to activate almost half of the inflammatory gene expression program when stimulated with LPS. A large part of the activation defect was attributable to loss of basal and LPS-inducible expression of IFN-β, which maintains Stat1 protein levels in unstimulated cells and acts in an autocrine/paracrine manner after stimulation to promote a secondary wave of Stat1-dependent gene expression. Loss of Hdac3-mediated repression of nuclear receptors led to hyperacetylation of thousands of genomic sites and associated gene derepression. The up-regulation of the constitutively expressed prostaglandin endoperoxide synthase, Ptgs1 (Cox-1), a nuclear receptor target, had a causative role in the phenotype because its chemical inhibition reverted, albeit partially, the Ifn-β activation defect. These data indicate a central role for Hdac3 in inflammation and may have relevance for the use of selective Hdac inhibitors as antiinflammatory agents.
Laminin receptor specific therapeutic gold nanoparticles (
198
AuNP-EGCg) show efficacy in treating prostate cancer
Authors: Shukla Ravi , Chanda Nripen , Zambre Ajit , Upendran Anandhi , Katti Kavita , Kulkarni Rajesh R. , Nune Satish Kumar , Casteel Stan W. , Smith Charles Jeffrey , Vimal Jatin , Boote Evan , Robertson J. David , Kan Para , Engelbrecht Hendrik , Watkinson Lisa D. , Carmack Terry L. , Lever John R. , Cutler Cathy S. , Caldwell Charles , Kannan Raghuraman , Katti Kattesh V.
Published: July 2012

Systemic delivery of therapeutic agents to solid tumors is hindered by vascular and interstitial barriers. We hypothesized that prostate tumor specific epigallocatechin-gallate (EGCg) functionalized radioactive gold nanoparticles, when delivered intratumorally (IT), would circumvent transport barriers, resulting in targeted delivery of therapeutic payloads. The results described herein support our hypothesis. We report the development of inherently therapeutic gold nanoparticles derived from the Au-198 isotope; the range of the
198
Au β-particle (approximately 11 mm in tissue or approximately 1100 cell diameters) is sufficiently long to provide cross-fire effects of a radiation dose delivered to cells within the prostate gland and short enough to minimize the radiation dose to critical tissues near the periphery of the capsule. The formulation of biocompatible
198
AuNPs utilizes the redox chemistry of prostate tumor specific phytochemical EGCg as it converts gold salt into gold nanoparticles and also selectively binds with excellent affinity to Laminin67R receptors, which are over expressed in prostate tumor cells. Pharmacokinetic studies in PC-3 xenograft SCID mice showed approximately 72% retention of
198
AuNP-EGCg in tumors 24 h after intratumoral administration. Therapeutic studies showed 80% reduction of tumor volumes after 28 d demonstrating significant inhibition of tumor growth compared to controls. This innovative nanotechnological approach serves as a basis for designing biocompatible target specific antineoplastic agents. This novel intratumorally injectable
198
AuNP-EGCg nanotherapeutic agent may provide significant advances in oncology for use as an effective treatment for prostate and other solid tumors.
Additional role for the
ccd
operon of F-plasmid as a transmissible persistence factor
Authors: Tripathi Arti , Dewan Pooja C. , Barua Bipasha , Varadarajan Raghavan
Published: July 2012

Toxin-antitoxin (TA) systems are found on both bacterial plasmids and chromosomes, but in most cases their functional role is unclear. Gene knockouts often yield limited insights into functions of individual TA systems because of their redundancy. The well-characterized F-plasmid–based CcdAB TA system is important for F-plasmid maintenance. We have isolated several point mutants of the toxin CcdB that fail to bind to its cellular target, DNA gyrase, but retain binding to the antitoxin, CcdA. Expression of such mutants is shown to result in release of the WT toxin from a functional preexisting TA complex as well as derepression of the TA operon. One such inactive, active-site mutant of CcdB was used to demonstrate the contribution of CcdB to antibiotic persistence. Transient activation of WT CcdB either by coexpression of the mutant or by antibiotic/heat stress was shown to enhance the generation of drug-tolerant persisters in a process dependent on Lon protease and RecA. An F-plasmid containing a
ccd
locus can, therefore, function as a transmissible persistence factor.
Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction
Authors: Scian Michele , Lin Jasper C. , Le Trong Isolde , Makhatadze George I. , Stenkamp Ronald E. , Andersen Niels H.
Published: July 2012

To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data, including the structural basis for the increase in fold stability associated with motif cyclization and the manner in which a polar serine side chain is accommodated in the hydrophobic interior. A hexameric oligomer of the cyclic peptide is found in both crystal forms and indicates that under appropriate conditions, this minimized system may also serve as a model for protein–protein interactions.
Dual blockade of lipid and cyclin-dependent kinases induces synthetic lethality in malignant glioma
Authors: Cheng Christine K. , Gustafson W. Clay , Charron Elizabeth , Houseman Benjamin T. , Zunder Eli , Goga Andrei , Gray Nathanael S. , Pollok Brian , Oakes Scott A. , James C. David , Shokat Kevan M. , Weiss William A. , Fan Qi-Wen
Published: July 2012

Malignant glioma, the most common primary brain tumor, is generally incurable. Although phosphatidylinositol-3-kinase (PI3K) signaling features prominently in glioma, inhibitors generally block proliferation rather than induce apoptosis. Starting with an inhibitor of both lipid and protein kinases that induced prominent apoptosis and that failed early clinical development because of its broad target profile and overall toxicity, we identified protein kinase targets, the blockade of which showed selective synthetic lethality when combined with PI3K inhibitors. Prioritizing protein kinase targets for which there are clinical inhibitors, we demonstrate that cyclin-dependent kinase (CDK)1/2 inhibitors, siRNAs against CDK1/2, and the clinical CDK1/2 inhibitor roscovitine all cooperated with the PI3K inhibitor PIK-90, blocking the antiapoptotic protein Survivin and driving cell death. In addition, overexpression of CDKs partially blocked some of the apoptosis caused by PIK-75. Roscovitine and PIK-90, in combination, were well tolerated in vivo and acted in a synthetic-lethal manner to induce apoptosis in human glioblastoma xenografts. We also tested clinical Akt and CDK inhibitors, demonstrating induction of apoptosis in vitro and providing a preclinical rationale to test this combination therapy in patients.
Modeling an autism risk factor in mice leads to permanent immune dysregulation
Authors: Hsiao Elaine Y. , McBride Sara W. , Chow Janet , Mazmanian Sarkis K. , Patterson Paul H.
Published: July 2012

Increasing evidence highlights a role for the immune system in the pathogenesis of autism spectrum disorder (ASD), as immune dysregulation is observed in the brain, periphery, and gastrointestinal tract of ASD individuals. Furthermore, maternal infection (maternal immune activation, MIA) is a risk factor for ASD. Modeling this risk factor in mice yields offspring with the cardinal behavioral and neuropathological symptoms of human ASD. In this study, we find that offspring of immune-activated mothers display altered immune profiles and function, characterized by a systemic deficit in CD4
+
TCRβ
+
Foxp3
+
CD25
+
T regulatory cells, increased IL-6 and IL-17 production by CD4
+
T cells, and elevated levels of peripheral Gr-1
+
cells. In addition, hematopoietic stem cells from MIA offspring exhibit altered myeloid lineage potential and differentiation. Interestingly, repopulating irradiated control mice with bone marrow derived from MIA offspring does not confer MIA-related immunological deficits, implicating the peripheral environmental context in long-term programming of immune dysfunction. Furthermore, behaviorally abnormal MIA offspring that have been irradiated and transplanted with immunologically normal bone marrow from either MIA or control offspring no longer exhibit deficits in stereotyped/repetitive and anxiety-like behaviors, suggesting that immune abnormalities in MIA offspring can contribute to ASD-related behaviors. These studies support a link between cellular immune dysregulation and ASD-related behavioral deficits in a mouse model of an autism risk factor.
Regulation of miRNA abundance by RNA binding protein TOUGH in
Arabidopsis
Authors: Ren Guodong , Xie Meng , Dou Yongchao , Zhang Shuxin , Zhang Chi , Yu Bin
Published: July 2012

MicroRNAs (miRNAs) are regulators of gene expression in plants and animals. The biogenesis of miRNAs is precisely controlled to secure normal development of organisms. Here we report that TOUGH (TGH) is a component of the DCL1–HYL1–SERRATE complex that processes primary transcripts of miRNAs [i.e., primary miRNAs (pri-miRNAs)] into miRNAs in
Arabidopsis
. Lack of TGH impairs multiple DCL activities in vitro and reduces the accumulation of miRNAs and siRNAs in vivo. TGH is an RNA-binding protein, binds pri-miRNAs and precursor miRNAs in vivo, and contributes to pri-miRNA–HYL1 interaction. These results indicate that TGH might regulate abundance of miRNAs through promoting DCL1 cleavage efficiency and/or recruitment of pri-miRNAs.
Geospatial revolution and remote sensing LiDAR in Mesoamerican archaeology
Authors: Chase Arlen F. , Chase Diane Z. , Fisher Christopher T. , Leisz Stephen J. , Weishampel John F.
Published: July 2012

The application of light detection and ranging (LiDAR), a laser-based remote-sensing technology that is capable of penetrating overlying vegetation and forest canopies, is generating a fundamental shift in Mesoamerican archaeology and has the potential to transform research in forested areas world-wide. Much as radiocarbon dating that half a century ago moved archaeology forward by grounding archaeological remains in time, LiDAR is proving to be a catalyst for an improved spatial understanding of the past. With LiDAR, ancient societies can be contextualized within a fully defined landscape. Interpretations about the scale and organization of densely forested sites no longer are constrained by sample size, as they were when mapping required laborious on-ground survey. The ability to articulate ancient landscapes fully permits a better understanding of the complexity of ancient Mesoamerican urbanism and also aids in modern conservation efforts. The importance of this geospatial innovation is demonstrated with newly acquired LiDAR data from the archaeological sites of Caracol, Cayo, Belize and Angamuco, Michoacán, Mexico. These data illustrate the potential of technology to act as a catalytic enabler of rapid transformational change in archaeological research and interpretation and also underscore the value of on-the-ground archaeological investigation in validating and contextualizing results.
Rational design of a fluorescent NADPH derivative imaging constitutive nitric-oxide synthases upon two-photon excitation
Authors: Li Yun , Wang Huan , Tarus Bogdan , Perez Miguel Romero , Morellato Laurence , Henry Etienne , Berka Vladimir , Tsai Ah-Lim , Ramassamy Booma , Dhimane Hamid , Dessy Chantal , Tauc Patrick , Boucher Jean-Luc , Deprez Eric , Slama-Schwok Anny
Published: July 2012

We report the structure-based design and synthesis of a unique NOS inhibitor, called nanoshutter NS1, with two-photon absorption properties. NS1 targets the NADPH site of NOS by a nucleotide moiety mimicking NADPH linked to a conjugated push–pull chromophore with nonlinear absorption properties. Because NS1 could not provide reducing equivalents to the protein and competed with NADPH binding, it efficiently inhibited NOS catalysis. NS1 became fluorescent once bound to NOS with an excellent signal-to-noise ratio because of two-photon excitation avoiding interference from the flavin–autofluorescence and because free NS1 was not fluorescent in aqueous solutions. NS1 fluorescence enhancement was selective for constitutive NOS in vitro, in particular for endothelial NOS (eNOS). Molecular dynamics simulations suggested that two variable residues among NOS isoforms induced differences in binding of NS1 and in local solvation around NS1 nitro group, consistent with changes of NS1 fluorescence yield. NS1 colocalized with eNOS in living human umbilical vein endothelial cells. Thus, NS1 constitutes a unique class of eNOS probe with two-photon excitation in the 800–950-nm range, with great perspectives for eNOS imaging in living tissues.
Prostaglandin E2deficiency uncovers a dominant role for thromboxane A2in house dust mite-induced allergic pulmonary inflammation
Authors: Liu Tao , Laidlaw Tanya M. , Feng Chunli , Xing Wei , Shen Shiliang , Milne Ginger L. , Boyce Joshua A.
Published: July 2012

Prostaglandin E2(PGE2) is an abundant lipid inflammatory mediator with potent but incompletely understood anti-inflammatory actions in the lung. Deficient PGE2generation in the lung predisposes to airway hyperresponsiveness and aspirin intolerance in asthmatic individuals. PGE2-deficientptges−/−mice develop exaggerated pulmonary eosinophilia and pulmonary arteriolar smooth-muscle hyperplasia compared with PGE2-sufficient controls when challenged intranasally with a house dust mite extract. We now demonstrate that both pulmonary eosinophilia and vascular remodeling in the setting of PGE2deficiency depend on thromboxane A2and signaling through the T prostanoid (TP) receptor. Deletion of TP receptors fromptges−/−mice reduces inflammation, vascular remodeling, cytokine generation, and airway reactivity to wild-type levels, with contributions from TP receptors localized to both hematopoietic cells and tissue. TP receptor signaling ex vivo is controlled heterologously by E prostanoid (EP)1and EP2receptor-dependent signaling pathways coupling to protein kinases C and A, respectively. TP-dependent up-regulation of intracellular adhesion molecule-1 expression is essential for the effects of PGE2deficiency. Thus, PGE2controls the strength of TP receptor signaling as a major bronchoprotective mechanism, carrying implications for the pathobiology and therapy of asthma.
Dopamine receptor D
3
regulates endocytic sorting by a Prazosin-sensitive interaction with the coatomer COPI
Authors: Zhang Xin , Wang Wenchao , Bedigian Anne V. , Coughlin Margaret L. , Mitchison Timothy J. , Eggert Ulrike S.
Published: July 2012

Macromolecules enter cells by endocytosis and are sorted to different cellular destinations in early/sorting endosomes. The mechanism and regulation of sorting are poorly understood, although transitions between vesicular and tubular endosomes are important. We found that the antihypertensive drug Prazosin inhibits endocytic sorting by an off-target perturbation of the G protein-coupled receptor dopamine receptor D
3
(DRD3). Prazosin is also a potent cytokinesis inhibitor, likely as a consequence of its effects on endosomes. Prazosin stabilizes a normally transient interaction between DRD3 and the coatomer COPI, a complex involved in membrane transport, and shifts endosomal morphology entirely to tubules, disrupting cargo sorting. RNAi depletion of DRD3 alone also inhibits endocytic sorting, indicating a noncanonical role for a G protein-coupled receptor. Prazosin is a powerful tool for rapid and reversible perturbation of endocytic dynamics.
Lipid interaction of the C terminus and association of the transmembrane segments facilitate atlastin-mediated homotypic endoplasmic reticulum fusion
Authors: Liu Tina Y. , Bian Xin , Sun Sha , Hu Xiaoyu , Klemm Robin W. , Prinz William A. , Rapoport Tom A. , Hu Junjie
Published: July 2012

The homotypic fusion of endoplasmic reticulum (ER) membranes is mediated by atlastin (ATL), which consists of an N-terminal cytosolic domain containing a GTPase module and a three-helix bundle followed by two transmembrane (TM) segments and a C-terminal tail (CT). Fusion depends on a GTP hydrolysis-induced conformational change in the cytosolic domain. Here, we show that the CT and TM segments also are required for efficient fusion and provide insight into their mechanistic roles. The essential feature of the CT is a conserved amphipathic helix. A synthetic peptide corresponding to the helix, but not to unrelated amphipathic helices, can act
in trans
to restore the fusion activity of tailless ATL. The CT promotes vesicle fusion by interacting directly with and perturbing the lipid bilayer without causing significant lysis. The TM segments do not serve as mere membrane anchors for the cytosolic domain but rather mediate the formation of ATL oligomers. Point mutations in either the C-terminal helix or the TMs impair ATL’s ability to generate and maintain ER morphology in vivo. Our results suggest that protein–lipid and protein–protein interactions within the membrane cooperate with the conformational change of the cytosolic domain to achieve homotypic ER membrane fusion.
Initial steps in the opening of a Shaker potassium channel
Authors: Hoshi Toshinori , Armstrong Clay M.
Published: July 2012

The structural model of a K
V
(K
+
-selective, voltage-gated) channel in the open state is known (Protein Data Bank ID code 2R9R). Each subunit of the channel has four negatively charged residues distributed in the transmembrane segments S1, S2, and S3 that bind to and facilitate the movement within the membrane of the positively charged, voltage-sensing residues of S4. When extrapolated to the closed state, the two outermost negatively charged residues are exposed to extracellular fluid and not bound to S4 residues, all of which have theoretically been driven inward by voltage. If this closed state model is correct, these residues are available to bind external cations. We examined the effects of La
3+
on voltage-gated Shaker K
+
channels. Addition of the trivalent cation La
3+
(50 μM) extracellularly markedly prolongs the lag that precedes channel opening and slows the subsequent rise of K
+
current (I
K
) at all voltages. Decay kinetics of I
K
at negative voltages are unaltered. Gating current (I
g
) recorded from a nonconducting mutant shows that La
3+
reduces the initial amplitude of I
g
nearly twofold. We postulate that, in the resting state, La
3+
binds to the unoccupied, outermost negative residues, hindering outward S4 motion, thus increasing the lag on activation and slowing the rise of I
K
. In the activated state, La
3+
is displaced by outward movement of arginine residues in S4; La
3+
, therefore, is not present to affect channel closing. The results give strong support to the closed state model of the K
V
channel and a clear explanation of the effect of multivalent cations on cellular excitability.
Role of the irreplaceable residues in the LacY alternating access mechanism
Authors: Zhou Yonggang , Jiang Xiaoxu , Kaback H. Ronald
Published: July 2012

Few side chains in the galactoside/H
+
symporter LacY (lactose permease of
Escherichia coli
) are irreplaceable for an alternating access mechanism in which sugar binding induces closing of the cytoplasmic cavity and reciprocal opening of a periplasmic cavity. In this study, each irreplaceable residue was mutated individually, and galactoside-induced opening or closing of periplasmic or cytoplasmic cavities was probed by site-directed alkylation. Mutation of Glu126 (helix IV) or Arg144 (helix V), which are essential for sugar binding, completely blocks sugar-induced periplasmic opening as expected. Remarkably, however, replacement of Glu269 (helix VIII), His322 (helix X), or Tyr236 (helix VII) causes spontaneous opening of the periplasmic cavity in the absence of sugar and decreased closing of the cytoplasmic cavity in the presence of galactoside. In contrast, mutation of Arg302 (helix IX) or Glu325 (helix X) has no such effect, and sugar binding induces normal opening and closing of periplasmic and cytoplasmic cavities. Possibly, Glu269, His322, and Tyr236 act in concert to coordinate opening and closing of the cavities by binding water, which also acts as a cofactor in H
+
translocation. Mutation of the triad results in loss of the bound water, which destabilizes LacY, and the cavities open and close in an uncoordinated manner. Thus, the triad mutants exhibit poor affinity for sugar, and galactoside/H
+
symport is abolished as well.
Estimating Oocyte Growth Rate and Its Potential Relationship to Spawning Frequency in Teleosts with Indeterminate Fecundity
Authors: Ganias Konstantinos , Nunes Cristina , Vavalidis Theocharis , Rakka Maria , Stratoudakis Yorgos
Published: July 2012

We present a method for estimating the interspawning interval (ISI) in batch-spawning teleosts with indeterminate fecundity based on the rate of oocyte growth and the size of oocytes at the beginning and end of the spawning cycle. The method is accompanied by a number of prerequisites, which are tested and subsequently applied to wild collections of Atlantic sardine Sardina pilchardus (also known as European pilchard). The rate of oocyte growth and oocyte size at the end of vitellogenesis were shown to exhibit rather constant values in Atlantic sardine; thus, the ISI could be simply estimated as a factor of oocyte size at the beginning of the spawning cycle (Ob). Given that vitellogenesis in Atlantic sardine ceases at final oocyte maturation, Ob was estimated by measuring the size of oocytes of the subsequent batch in females with hydrated oocytes. The resulting average ISI was very close to inverse values of the spawning fraction estimated through the postovulatory follicle method, which indicated the validity of the ISI method. Applications of the ISI method require fewer samples of adult females compared with the postovulatory follicle method, are histology independent, and could be combined with oocyte counts to provide batch fecundity measurements. These modifications in spawning frequency and batch fecundity estimation could help to decrease both cost and labor in daily egg production method surveys.
Assessment of Testis Development during Induced Spermatogenesis in the European Eel Anguilla anguilla
Authors: Tomkiewicz Jonna , Kofoed Tanja M. N. , Pedersen Jes S.
Published: July 2012

In a study of reproduction in male European eels Anguilla anguilla, we induced spermatogenesis through hormone injection and established a spermatogenic maturity index (SMI) as a novel quantification of testis development. Eels in the experiments were sacrificed weekly and testis tissue was sampled for histological analysis of spermatogenesis. Testis development was followed over 18 weeks, during which the males continued to develop spermatocytes and produce spermatozoa. The SMI describes testis development from estimation of the area fractions of various tissue categories characterized by progressive gamete development stages in histological sections of the testes. The index weighs the volume fractions of the different tissues (somatic cells and germ cell stages) and describes development on a scale of 0 to 1. The method improves the existing histological classification, providing a quantitative measure that reflects the spermatogenic process and can be correlated with morphological and physiological parameters. In this study, the SMI reacted immediately to the onset of spermatogenesis and increased linearly over time, tracking the development of spermatocysts and spermatozoa. In week 7, the SMI reached a stable level of around 0.75, where it remained, with limited fluctuations, until the end of the experiment. This reflected the composition of different germ cell stages in the testis tissue with a continuous generation of spermatocysts and production of spermatozoa. In comparison, the gonadosomatic index showed a delayed response to the onset of spermatogenesis and fluctuated substantially during the sperm production period. The properties of the SMI made it a useful index for describing spermatogenesis in male European eels during this experiment and a promising tool for quantifying testis development and describing male reproductive strategy in other fish species.
Reproductive Timing in Marine Fishes: Variability, Temporal Scales, and Methods
Authors: Lowerre-Barbieri Susan K. , Ganias Konstantinos , Saborido-Rey Fran , Murua Hilario , Hunter John R.
Published: July 2012

Reproductive timing can be defined as the temporal pattern of reproduction over a lifetime. Although reproductive timing is highly variable in marine fishes, certain traits are universal, including sexual maturity, undergoing one or more reproductive cycles, participating in one or more spawning events within a reproductive cycle, release of eggs or offspring, aging, and death. These traits commonly occur at four temporal scales: lifetime, annual, intraseasonal, and diel. It has long been known that reproductive timing affects reproductive success, especially in terms of the onset of sexual maturity and the match or mismatch between seasonal spawning and offspring survival. However, a comprehensive understanding of variability in reproductive timing over species, populations, and temporal scales is lacking. In addition, there is a need to assess how variability in reproductive timing affects a population's resilience. Because natural selection occurs at the individual level, this necessitates an understanding of within-population (i.e., individual) variability in reproductive timing and how fishing may impact it through age truncation and size-specific selectivity or fisheries-induced evolution. In this paper, we review the temporal aspects of reproductive strategies and the four most-studied reproductive timing characteristics in fishes: sexual maturity, spawning seasonality, spawning frequency, and diel periodicity. For each characteristic, we synthesize how it has traditionally been measured, advances in understanding the underlying physiology, its role in equilibrium-based fish population dynamics, and its importance to reproductive success. We then provide a review of emerging methodology—with an emphasis on ovarian histology—to improve our ability to assess variability in reproductive timing both among populations and within populations.
Retention of Coastal Cod Eggs in a Fjord Caused by Interactions between Egg Buoyancy and Circulation Pattern
Authors: Myksvoll Mari S. , Sundby Svein , Ådlandsvik Bjørn , Vikebø Frode B.
Published: July 2012

Norwegian coastal cod form a stationary population of Atlantic cod Gadus morhua consisting of several genetically separated subpopulations. A small-scale differentiation in marine populations with pelagic eggs and larvae is made possible by local retention of early life stages in coastal environments. A numerical model was used to simulate the circulation in a fjord system in northern Norway over 2 years with different river runoff patterns. The dispersal of cod eggs was calculated with a particle-tracking model that used three-dimensional currents. The observed thickness of the low-salinity surface layer was well reproduced by the model, but the surface salinity was generally lower in the model than in the observations. The cod eggs attained a subsurface vertical distribution, avoiding the surface and causing retention. Interannual variations in river runoff can cause small changes in the vertical distribution of cod eggs and larger changes in the vertical current structure. Retention in the fjord system was strong in both years, but some eggs were subjected to offshore transport over a limited time period. The timing of offshore transport depended on the precipitation and temperatures in adjacent drainage areas. A possible match between maximized spawning and offshore transport may have a negative effect on local recruitment.
A mechanistic description of gating of the human cardiac ryanodine receptor in a regulated minimal environment
Authors: Mukherjee Saptarshi , Thomas N. Lowri , Williams Alan J.
Published: July 2012

Cardiac muscle contraction, triggered by the action potential, is mediated by the release of Ca2+ from the sarcoplasmic reticulum through ryanodine receptor (RyR)2 channels. In situ, RyR2 gating is modulated by numerous physiological and pharmacological agents, and altered RyR2 function underlies the occurrence of arrhythmias in both inherited and acquired diseases. To understand fully the mechanisms underpinning the regulation of RyR2 in the normal heart and how these systems are altered in pathological conditions, we must first gain a detailed knowledge of the fundamental processes of RyR2 gating. In this investigation, we provide key novel mechanistic insights into the physical reality of RyR2 gating revealed by new experimental and analytical approaches. We have examined in detail the single-channel gating kinetics of the purified human RyR2 when activated by cytosolic Ca2+ in a stringently regulated environment where the modulatory influence of factors external to the channel were minimized. The resulting gating schemes are based on an accurate description of single-channel kinetics using hidden Markov model analysis and reveal several novel aspects of RyR2 gating behavior: (a) constitutive gating is observed as unliganded opening events; (b) binding of Ca2+ to the channel stabilizes it in different open states; (c) RyR2 exists in two preopening closed conformations in equilibrium, one of which binds Ca2+ more readily than the other; (d) the gating of RyR2 when bound to Ca2+ can be described by a kinetic scheme incorporating bursts; and (e) analysis of flicker closing events within bursts reveals gating activity that is not influenced by ligand binding. The gating schemes generated in this investigation provide a framework for future studies in which the mechanisms of action of key physiological regulatory factors, disease-linked mutations, and potential therapeutic compounds can be described precisely.
Relative transmembrane segment rearrangements during BK channel activation resolved by structurally assigned fluorophore–quencher pairing
Authors: Pantazis Antonios , Olcese Riccardo
Published: July 2012

Voltage-activated proteins can sense, and respond to, changes in the electric field pervading the cell membrane by virtue of a transmembrane helix bundle, the voltage-sensing domain (VSD). Canonical VSDs consist of four transmembrane helices (S1–S4) of which S4 is considered a principal component because it possesses charged residues immersed in the electric field. Membrane depolarization compels the charges, and by extension S4, to rearrange with respect to the field. The VSD of large-conductance voltage- and Ca-activated K+ (BK) channels exhibits two salient inconsistencies from the canonical VSD model: (1) the BK channel VSD possesses an additional nonconserved transmembrane helix (S0); and (2) it exhibits a “decentralized” distribution of voltage-sensing charges, in helices S2 and S3, in addition to S4. Considering these unique features, the voltage-dependent rearrangements of the BK VSD could differ significantly from the standard model of VSD operation. To understand the mode of operation of this unique VSD, we have optically tracked the relative motions of the BK VSD transmembrane helices during activation, by manipulating the quenching environment of site-directed fluorescent labels with native and introduced Trp residues. Having previously reported that S0 and S4 diverge during activation, in this work we demonstrate that S4 also diverges from S1 and S2, whereas S2, compelled by its voltage-sensing charged residues, moves closer to S1. This information contributes spatial constraints for understanding the BK channel voltage-sensing process, revealing the structural rearrangements in a non-canonical VSD.
The work function of n-ZnO deduced from heterojunctions with Si prepared by ALD
Authors: Quemener V , Alnes M , Vines L , Rauwel P , Nilsen O , Fjellvåg H , Monakhov E V , Svensson B G
Published: July 2012

Highly doped n-type ZnO films have been grown on n-type and p-type Si substrates by atomic layer deposition (ALD). Transmission electron microscopy shows columnar growth of the ZnO films with randomly oriented grains and a very thin interfacial layer of SiO
x
(x ⩽ 2) with a thickness below 0.4 nm to the Si substrate. Current–voltage and capacitance–voltage measurements performed at temperatures from 50 to 300 K reveal a strong rectifying behaviour on both types of substrates with an ideality factor close to unity between 180 and 280 K. Using the classical approach of thermionic emission, the barrier heights of the ZnO/n-Si and ZnO/p-Si junctions have been deduced and consistent values are obtained yielding a work function of n-type ZnO close to 4.65 eV.
Elastic photoelectron scattering effects in the XPS analysis of stratified samples
Authors: Jablonski A
Published: July 2012

Two theoretical models describing photoelectron transport in multilayer samples were developed: (i) the Monte Carlo simulation strategy, in which the photoelectron elastic scattering events are accounted for, and (ii) the common x-ray electron spectroscopy (XPS) formalism adjusted to multilayer systems, in which the photoelectron elastic scattering events are ignored. Calculations were performed for Au/Ni and Si/Au multilayer systems with layers of different thicknesses. The emission depth distribution function (EMDDF) calculated for a layer deposited at a surface turns out to be identical to that for the bulk of the layer material; however, it may differ considerably when the layer is buried at a certain depth. The EMDDFs for buried layers are found to be considerably affected by elastic photoelectron scattering, however, in a different way from the EMDDF of the bulk material. The XPS depth profiles calculated for multilayer materials in the considered geometry are noticeably affected by elastic photoelectron collisions. However, in contrast with Auger electron spectroscopy depth profiling, the shape of the profile due to a given layer is not affected by the structure beneath that layer.
Laser lift-off initiated by direct induced ablation of different metal thin films with ultra-short laser pulses
Authors: Heise Gerhard , Domke Matthias , Konrad Jan , Sarrach Sebastian , Sotrop Jürgen , Huber Heinz P
Published: July 2012

Molybdenum thin films on glass substrates play an important role as contact layer for thin film solar cells. They can be ablated by picosecond laser pulses irradiated from the substrate side at low laser fluences of less than 1 J cm−2, while structured trenches remain free from thermal damage and residues. The fluence for that so-called direct induced ablation from the substrate side is in contrast to metal side ablation reduced by approximately one order of magnitude and is far below the thermodynamic limit for heating, melting and evaporating the complete layer. For an extended investigation of the direct induced laser ablation and the underlying mechanism, further thin film materials, chromium, titanium and platinum, with thicknesses between 200 nm and 1 µm were examined. Finally, a simple thermo-dynamical model is able to connect the observed ablation energetics with the mechanical ductility and stress limit of the metal thin films.
42 salt forms of tyramine: structural comparison and the occurrence of hydrate formation
Authors: Briggs Naomi E. B. , Kennedy Alan R. , Morrison Catriona A.
Published: July 2012

The single-crystal diffraction structures of 38 salt forms of the base tyramine (4-hydroxyphenethylamine) are reported for the first time. Together with literature examples, these structures are discussed with respect to cation conformation, cation packing, hydrogen bonding and hydrate formation. It is found that isostructural cation packing can occur even with structurally different anions, with different hydration states and with different hydrogen bonding. Hydrate formation is found to be more likely both (i) when there is an increase in the total number of potential hydrogen bond acceptor and donor atoms; and (ii) when the ratio of potential hydrogen bond donor to acceptor atoms is low.
Optimizing dendritic cell vaccine for immunotherapy in multiple myeloma: tumour lysates are more potent tumour antigens than idiotype protein to promote anti-tumour immunity
Authors: Hong S , Li H , Qian J , Yang J , Lu Y , Yi Q
Published: July 2012

Dendritic cells (DCs) are the most potent antigen-presenting cells and are the mediators of T cell immunity. Many investigators have explored the potential of using DCs as a vaccine for tumour-derived antigens in immunotherapy of B cell malignancies, and the results have been disappointing. To search for better tumour antigens to improve the efficacy of DC-based immunotherapy in myeloma, we evaluated and compared the efficacy of the vaccination of DCs pulsed with idiotype (Id) or tumour lysate in the 5TGM1 myeloma mouse model. Our results showed that Id- or tumour lysate-pulsed DC vaccines protected mice efficiently against developing myeloma, retarded tumour growth, induced tumour regression against established tumour and protected surviving mice from tumour rechallenge. The therapeutic responses were associated with an induction of strong humoral immune responses, including anti-Id or anti-lysate antibodies, and cellular immune responses including myeloma-specific CD8+ cytotoxic T lymphocytes, CD4+ type 1 T helper cells and memory T cells in mice receiving Id- or tumour lysate-pulsed DC vaccines. In addition, our studies showed that tumour lysate-pulsed DCs were more potent vaccines than the Id-pulsed DC vaccines to promote anti-tumour immunity in the model. This information will be important for improving the strategies of DC-based immunotherapy for patients with myeloma and other B cell tumours.
Association of polymorphisms in DNMT1, DNMT3A, DNMT3B, MTHFR and MTRR genes with global DNA methylation levels and prognosis of autoimmune thyroid disease
Authors: Arakawa Y , Watanabe M , Inoue N , Sarumaru M , Hidaka Y , Iwatani Y
Published: July 2012

To clarify the association between factors regulating DNA methylation and the prognosis of autoimmune thyroid diseases (AITDs), we genotyped single nucleotide polymorphisms in genes encoding DNA methyltransferase 1 (DNMT1), DNMT3A, DNMT3B, methylenetetrahydrofolate reductase (MTHFR) and methionine synthase reductase (MTRR), which are enzymes essential for DNA methylation. Subjects for this study included 125 patients with Hashimoto's disease (HD), including 48 patients with severe HD and 49 patients with mild HD; 176 patients with Graves’ disease (GD), including 79 patients with intractable GD and 47 patients with GD in remission; and 83 healthy volunteers (control subjects). The DNMT1+32204GG genotype was more frequent in patients with intractable GD than in patients with GD in remission. Genomic DNA showed significantly lower levels of global methylation in individuals with the DNMT1+32204GG genotype than in those with the AA genotype. The MTRR+66AA genotype was observed to be more frequent in patients with severe HD than in those with mild HD. The DNMT1+14395A/G, DNMT3B−579G/T, MTHFR+677C/T and +1298A/C polymorphisms were not correlated with the development or prognosis of AITD. Our study indicates that the DNMT1+32204GG genotype correlates with DNA hypomethylation and with the intractability of GD, and that the MTRR+66AA genotype may correlate with the severity of HD.
Cryptosporidium parvum antigens induce mouse and human dendritic cells to generate Th1‐enhancing cytokines
Authors: BEDI B. , MEAD J. R.
Published: July 2012

Cryptosporidium parvum is an opportunistic intracellular parasite that causes mild to severe diarrhoea, which can be life‐threatening in an immunocompromised host. To increase our understanding of the mechanisms that play a role in host immune responses, we investigated the effects of C. parvum antigens on the phenotype of mouse and human dendritic cells (DCs). Cryptosporidium parvum antigens induced DC activation as indicated by upregulation of the maturation marker CD209, as well as by the production of the cytokines interleukin‐12 p70, IL‐2, IL‐1beta, IL‐6. In particular, significant increases in the expression of IL‐12 p70 were observed from mouse DCs derived from bone marrow in response to solubilized sporozoite antigen and the recombinant cryptosporidial antigens, Cp40 and Cp23. We observed a small but significant increase in IL‐18 expression following the exposure to Cp40. We found that the induction of Th1 cytokines was MyD88 dependent (MyD88 knockout mouse DCs were unresponsive). Additionally, both sporozoite preparations (solubilized and live) significantly induced IL‐12 production by human monocytic dendritic cells (MoDCs). This finding indicates that solubilized as well as recombinant antigens can induce the maturation of DCs and subsequently initiate an innate immune response.
Orthographic neighborhood effects as a function of word frequency: An event‐related potential study
Authors: Vergara‐Martínez Marta , Swaab Tamara Y.
Published: July 2012

The present study assessed the mechanisms and time course by which orthographic neighborhood size (ON) influences visual word recognition. ERPs were recorded to words that varied in ON and in word frequency while participants performed a semantic categorization task. ON was measured with the Orthographic Levenshtein Distance (OLD20), a richer metric of orthographic similarity than the traditional Coltheart's N metric. The N400 effects of ON (260–500 ms) were larger and showed a different scalp distribution for low than for high frequency words, which is consistent with proposals that suggest lateral inhibitory mechanisms at a lexical level. The ERP ON effects had a shorter duration and different scalp distribution than the effects of word frequency (mainly observed between 380–600 ms) suggesting a transient activation of the subset of orthographically similar words in the lexical network compared to the impact of properties of the single words.