bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the German Version of the Exercise Dependence Scale
Authors: Müller Astrid , Claes Laurence , Smits Dirk , Gefeller Olaf , Hilbert Anja , Herberg Antonia , Müller Verena , Hofmeister Dirk , de Zwaan Martina
Published: July 2012

This study evaluated the psychometric properties of the German version of the 21-item Exercise Dependence Scale (EDS-G), which was administered in a large representative German sample (N = 1,611). In order to examine convergent validity, we also asked participants to answer the Eating Disorder Examination-Questionnaire (EDE-Q). To investigate the discriminant validity, clients of fitness centers (N = 129), sport students (N = 85), and medical students (N = 129) filled out the EDS-G. In this German population-based sample, the seven-factor structure suggested by the original authors as well as a higher-order model (7 + 1 factor model) were supported. The total EDS-G scale showed an excellent internal reliability and was positively related to the EDE-Q total and subscale scores. The EDS-G scores differentiated between samples with varying degrees of exercise. In summary, the results indicate that the EDS-G is a psychometrically sound and potentially valid brief measure for the assessment of exercise dependence symptoms.
A General Linear Framework for Modeling Continuous Responses With Error in Persons and Items
Authors: Ferrando Pere J.
Published: July 2012

This study develops a general linear model intended for personality and attitude items with (approximately) continuous responses that is based on a double source of measurement error: items and persons. Two restricted sub-models are then obtained from the general model by placing restrictions on the item and person parameters. And it follows that the standard unidimensional factor-analytic model is one of these sub-models. Procedures for (a) calibrating the items, (b) obtaining individual estimates of location and fluctuation, (c) assessing model-data fit, and (d) assessing measurement precision are discussed for all the models considered, and illustrated with two empirical examples in the personality domain.
A Multiple-Process Latent Transition Model of Poverty and Health
Authors: Sacker Amanda , Worts Diana , McDonough Peggy
Published: July 2012

Health researchers often use the life-course perspective, exploring how long-range experiences in one life domain may influence, and be influenced by, those in another. We develop a multiple-process latent transition model (MPLTM) to estimate changes in health and poverty dynamics simultaneously, using repeated measures of self-rated health and income for working-aged adults from the British Household Panel Survey. We apply the model to quantify concurrent and longitudinal effects to assess whether changes in these two processes are related or independent. Model extensions add time-invariant (cohort, gender) and time-varying (weeks nonemployed in previous year) covariates. We find both concurrent and bidirectional longitudinal relationships between poverty and health, with nonemployment appearing to mediate longitudinal health-to-poverty effects and confound longitudinal poverty-to-health effects. The MPLTM can provide quantitative estimates of complex interlocking processes that are often difficult to measure and assess.
The Relationship Between Psychological Empowerment and Innovative Behavior
Authors: Singh Manjari , Sarkar Anita
Published: July 2012

Past studies have established the importance of psychological empowerment in fostering innovative behavior. This paper broadens the conceptual understanding by exploring the mechanisms of this linkage through dimensional analysis. The study also examines the mediating role of job involvement in this relationship. In this study of 401 women primary school teachers in India, the dimensions of psychological empowerment were self-rated whereas innovative behavior and job involvement were assessed by colleagues. Our findings show partial mediation for the meaning dimension and complete mediation for the non-work domain control dimension. Self-determination at job and organization levels have a direct effect on employees’ innovative behavior but no effect through job involvement. Competence and impact has no direct or indirect effect on innovative behavior.
Study of a coincident observation between the ROCSAT‐1 density irregularity and Ascension Island scintillation
Authors: Liu Y. H. , Chao C. K. , Su S.‐Y. , Liu C. H.
Published: July 2012

A coincident observation that occurred on 24 March 2000 between the irregularity structure measured by ROCSAT‐1 and the scintillation experiment at the Ascension Island has been studied. The study of scintillation statistics is carried out first, and the results show that the Nakagami distribution can portray the normalized intensity of the L‐band scintillation at various S4 values, up to S4 equal to 1.4. Moreover, the departure of frequency dependence on S4 predicted by the weak scintillation is noticed due to multiple forward scattering effects. The coincident feature between the characteristics of irregularity structure and the scintillation variation are then studied. The causal relationship between the fluctuation of ion density and the scintillation variation is obtained. A numerical simulation using the parabolic wave equation has been carried out with the ROCSAT‐1 data in space to compare with the ground scintillation observation. The results show the reasonable scintillation level at the coincident time to indicate a direct relationship between the irregularity structure and the scintillation in both temporal and amplitudinal variations. Finally, some assumptions and limitations of the simulation model are discussed.
EISCAT observations of pump‐enhanced plasma temperature and optical emission excitation rate as a function of power flux
Authors: Bryers C. J. , Kosch M. J. , Senior A. , Rietveld M. T. , Yeoman T. K.
Published: July 2012

We analyze optical emissions and enhanced electron temperatures induced by high power HF radio waves as a function of power flux using the EISCAT heater with a range of effective radiated powers. The UHF radar was used to measure the electron temperatures and densities. The Digital All Sky Imager was used to record the 630.0 nm optical emission intensities. We quantify the HF flux loss due to self‐absorption in the D‐region (typically 3–11 dB) and refraction in the F‐region to determine the flux which reaches the upper‐hybrid resonance height. We find a quasi‐linear relationship between the HF flux and both the temperature enhancement and the optical emission excitation rate with a threshold at ∼37.5 μWm−2. On average ∼70% of the HF flux at the upper‐hybrid resonance height goes in to heating the electrons for fluxes above the threshold compared to ∼40% for fluxes below the threshold.
Ice‐cloud particle habit classification using principal components
Authors: Lindqvist H. , Muinonen K. , Nousiainen T. , Um J. , McFarquhar G. M. , Haapanala P. , Makkonen R. , Hakkarainen H.
Published: July 2012

A novel automatic classification method is proposed for identifying the habits of large ice‐cloud particles and deriving the shape distribution of particle ensembles. This IC‐PCA (Ice‐crystal Classification with Principal Component Analysis) tool is based on a principal component analysis of selected physical and statistical features of ice‐crystal perimeters. The method is developed and tested using image data obtained with a Cloud Particle Imager, but can be applied to other silhouette data as well. For three randomly selected test cases of 222, 200, and 201 crystals from tropical, midlatitude, and arctic ice clouds, the combined classification accuracy of the IC‐PCA is 81.1%. Since previous, semiautomatic classification methods are more time‐consuming and include a subjective phase, the automatic and objective IC‐PCA offers a notable improvement in retrieving the shapes of the individual crystals. As the habit distributions of ice‐cloud particles can be applied to computations of radiative impact of cirrus, it is also demonstrated how classification uncertainties propagate into the radiative transfer computations by using the arctic test case as an example. Computations of shortwave radiative fluxes show that the flux differences between clouds of manually and automatically classified crystals can be as large as 10 Wm−2 but also that two manual classifications of the same image data result in even larger differences, implying the need for a systematic and repeatable classification method.
Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years
Authors: de Rezende Júlia Rosa , Kjeldsen Kasper Urup , Hubert Casey R J , Finster Kai , Loy Alexander , Jørgensen Bo Barker
Published: July 2012

Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 104 per cm3 at the surface and decreased exponentially to 100 per cm3 at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments.
Carbon Nanotube-Based Materials for Fuel Cell Applications
Authors: Liu Jilei , Lai Linfei , Sahoo Nanda Gopal , Zhou Weijiang , Shen Zexiang , Chan Siew Hwa
Published: July 2012

Carbon nanotubes (CNTs) have attracted extensive research interest due to their unique structure and properties such as high surface area, extraordinary mechanical properties, high electronic conductivity and chemical stability. These remarkable characteristics of CNTs, along with the inherent benefits of a carbon material, make CNTs promising candidates for fuel cell applications. In this review, we summarize and compare the recent research and development on CNT-based fuel cells, particularly focussing on CNTs as a catalytic support for enhanced electro-catalytic activity, metal-free electro-catalysts for the oxygen reduction reaction and fillers in the polymer electrolyte membrane in fuel cells.
Solea senegalensis vasa transcripts: molecular characterisation, tissue distribution and developmental expression profiles
Authors: Pacchiarini Tiziana , Cross Ismael , Leite Ricardo B. , Gavaia Paulo , Ortiz-Delgado Juan B. , Pousão-Ferreira Pedro , Rebordinos Laureana , Sarasquete Carmen , Cabrita Elsa
Published: July 2012

The Vasa protein is an RNA helicase belonging the DEAD (Asp-Glu-Ala-Asp)-box family. The crucial role played by the vasa gene in the germ-cell lineage of both vertebrates and invertebrates has made this gene a useful molecular marker for germinal cells and a useful tool in surrogate broodstock production using primordial germ cell transplantation. With the aim of establishing a novel approach to improving Solea senegalensis broodstock management, the vasa gene in this species was characterised. Four S. senegalensis vasa transcripts were isolated: Ssvasa1, Ssvasa2, Ssvasa3 and Ssvasa4. Their phylogenetic relationship with other vasa homologues was determined confirming the high degree of conservation of this helicase throughout evolution. Our qPCR results showed that S. senegalensis vasa transcripts are prevalently expressed in gonads, with ovary-specific expression for Ssvasa3 and Ssvasa4. During embryonic and larval development, a switch between the longest and the shortest transcripts was observed. While Ssvasa1 and Ssvasa2 were maternally supplied, Ssvasa3 and Ssvasa4 depended on the de novo expression program of the growing juveniles, suggesting that vasa mRNA could be involved in Senegalese sole gonad differentiation. In situ hybridisation and immunohistochemical analysis performed in 150-days after hatching (DAH) larvae showed vasa product expression in the germinal region of early gonads. In our work we demonstrated the usefulness of Ssvasa mRNAs as molecular markers for primordial germ cells and germinal cells during embryonic development, larval ontogenesis and gonad differentiation. Furthermore, our results confirmed the potential of vasa to help investigate germinal cell biotechnology for Senegalese sole reproduction.
Modification of antisense phosphodiester oligodeoxynucleotides by a 5' cholesteryl moiety increases cellular association and improves efficacy.
Authors: Krieg A M , Tonkinson J , Matson S , Zhao Q , Saxon M , Zhang L M , Bhanja U , Yakubov L , Stein C A
Published: July 2012

Phosphodiester oligodeoxynucleotides bearing a 5' cholesteryl (chol) modification bind to low density lipoprotein (LDL), apparently by partitioning the chol-modified oligonucleotides into the lipid layer. Both HL60 cells and primary mouse spleen T and B cells incubated with fluorescently labeled chol-modified oligonucleotide showed substantially increased cellular association by flow cytometry and increased internalization by confocal microscopy compared to an identical molecule not bearing the chol group. Cellular internalization of chol-modified oligonucleotide occurred at least partially through the LDL receptor; it was increased in mouse spleen cells by cell culture in lipoprotein-deficient medium and/or lovastatin, and it was decreased by culture in high serum medium. To determine whether chol-modified oligonucleotides are more potent antisense agents, we titered antisense unmodified phosphodiester and chol-modified oligonucleotides targeted against a mouse immunosuppressive protein. Murine spleen cells cultured with 20 microM phosphodiester antisense oligonucleotides had a 2-fold increase in RNA synthesis, indicating the expected lymphocyte activation. Antisense chol-modified oligonucleotides showed an 8-fold increase in relative potency: they caused a 2-fold increase in RNA synthesis at just 2.5 microM. The increased efficacy was blocked by heparin and was further increased by cell culture in 1% (vs. 10%) fetal bovine serum, suggesting that the effect may, at least in part, be mediated via the LDL receptor. Antisense chol-modified oligonucleotides are sequence specific and have increased potency as compared to unmodified oligonucleotides.
Sequence of a 189-kb segment of the chromosome of
Rhodobacter capsulatus
SB1003
Authors: Vlček Čestmir , Paces Václav , Maltsev Natalia , Pačes Jan , Haselkorn Robert , Fonstein Michael
Published: July 2012

Cosmids from the 1A3–1A10 region of the complete miniset were individually subcloned by using the vector M13 mp18. Sequences of each cosmid were assembled from about 400 DNA fragments generated from the ends of these phage subclones and merged into one 189-kb contig. About 160 ORFs identified by the CodonUse program were subjected to similarity searches. The biological functions of 80 ORFs could be assigned reliably by using the WIT and Magpie genome investigation tools. Eighty percent of these recognizable ORFs were organized in functional clusters, which simplified assignment decisions and increased the strength of the predictions. A set of 26 genes for cobalamin biosynthesis, genes for polyhydroxyalkanoic acid metabolism, DNA replication and recombination, and DNA gyrase were among those identified. Most of the ORFs lacking significant similarity with reference databases also were grouped. There are two large clusters of these ORFs, one located between 45 and 67 kb of the map, and the other between 150 and 183 kb. Nine of the loosely identified ORFs (of 15) of the first of these clusters match ORFs from phages or transposons. The other cluster also has four ORFs of possible phage origin.
Relative numbers of cortical and brainstem inputs to the lateral geniculate nucleus
Authors: Erişir Alev , Van Horn Susan C. , Sherman S. Murray
Published: July 2012

Terminals of a morphological type known as RD (for
r
ound vesicles and
d
ense mitochondria, which we define here as the aggregate of types formerly known as RSD and RLD, where “S” is small and “L” is large) constitute at least half of the synaptic inputs to the feline lateral geniculate nucleus, which represents the thalamic relay of retinal input to cortex. It had been thought that the vast majority of these RD terminals were of cortical origin, making the corticogeniculate pathway by far the largest source of input to geniculate relay cells. However, another source of RD terminals recently identified derives from cholinergic cells of the brainstem parabrachial region. (These cells also contain NO.) We used techniques of electron microscopy to determine quantitatively the relative contribution of cortex and brainstem to the population of RD terminals. We identified corticogeniculate terminals by orthograde transport of biocytin injected into the visual cortex and identified brainstem terminals by immunocytochemical labeling for choline acetyltransferase or brain NO synthase (the synthesizing enzymes for acetylcholine and NO, respectively). We estimated the relative numbers of corticogeniculate and brainstem terminals with a two-step algorithm: First, we determined the relative probability of sampling each terminal type in our material, and then we calculated what mixture of identified corticogeniculate and brainstem terminals was needed to recreate the size distribution of the parent RD terminal population. We conclude that brainstem terminals comprise roughly one-half of the RD population. Thus, the cortical input is perhaps half as large and the brainstem input is an order of magnitude larger than had been thought. This further suggests that the brainstem inputs might play a surprisingly complex and subtle role in the control of the geniculocortical relay.
A subunit of human nuclear RNase P has ATPase activity
Authors: Li Yong , Altman Sidney
Published: July 2012

Human nuclear RNase P purified from HeLa cells has ATPase activity.
This activity is associated with one of the protein subunits of the
enzyme, Rpp20. Thus, human nuclear RNase P, which contains several
proteins and one essential RNA, has at least one other enzymatic
activity in addition to cleavage of phosphoester bonds in RNA. The
amino acid sequence of Rpp20 has a signature motif found in an
ATPase-containing subunit of a family of protein complexes (ABC
transporters) that mediate a variety of trans-membrane traffic, as well
as a segment, DIxxN, that resembles the DEAD box motif of many ATPases:
together, these might represent an ATPase signature motif.
Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in
Saccharomyces cerevisiae
Authors: Barillà Daniela , Lee Barbara A. , Proudfoot Nick J.
Published: July 2012

The carboxyl-terminal domain (CTD) of the largest subunit of RNA
polymerase II plays an important role in transcription and processing
of the nascent transcript by interacting with both transcription and
RNA processing factors. We show here that the
cleavage/polyadenylation factor IA of
Saccharomyces
cerevisiae
directly contacts CTD. First by affinity
chromatography experiments with yeast extracts we demonstrate that the
Rna15p, Rna14p, and Pcf11p subunits of this complex are associated with
phosphorylated CTD. This interaction is confirmed for Rna15p by yeast
two-hybrid analysis. Second, Pcf11p, but not Rna15p, is shown to
directly contact phosphorylated CTD based on
in vitro
binding studies with recombinant proteins. These findings establish a
direct interaction of cleavage/polyadenylation factor IA with the
CTD. Furthermore, a quantitative analysis of transcription run-on
performed on temperature-sensitive mutant strains reveals that the lack
of either functional Rna14p or Pcf11p affects transcription termination
more severely than the absence of a functional Rna15p. Moreover, these
data reinforce the concept that CTD phosphorylation acts as a
regulatory mechanism in the maturation of the primary transcript.
Direct evidence for the participation of gap junction-mediated intercellular communication in the transmission of damage signals from α-particle irradiated to nonirradiated cells
Authors: Azzam Edouard I. , de Toledo Sonia M. , Little John B.
Published: July 2012

It has generally been considered that important biological effects
of ionizing radiation arise as a direct consequence of DNA damage
occurring in irradiated cells. We have examined this hypothesis by
exposing cells to very low fluences of α-particles, similar to those
emitted by radon gas, such that as few as 1% of the cells in a
population are traversed by a particle and thus receive any radiation
exposure. By using the endpoints of changes in gene expression and
induction of DNA damage, we show that nonirradiated “bystander”
cells participate in the overall response of confluent
density-inhibited populations of cultured fibroblast and epithelial
cells. By
in situ
immunofluorescence techniques and the
use of cells genetically compromised in their ability to perform gap
junction intercellular communication, we present direct evidence for
the involvement of connexin43-mediated intercellular communication in
the transmission of damage signals to nonirradiated cells. Induction of
the stress-inducible p21
Waf1
protein in aggregates of
neighboring cells far exceeding the fraction of cells whose nucleus has
been traversed occurred in gap junction-competent cells only. These
changes in p21
Waf1
expression correlated with both the
induction of DNA damage (as measured by micronucleus formation) as well
as increased Ser-15 phosphorylation of p53.
Genetic architecture of thermal adaptation in
Escherichia coli
Authors: Riehle Michelle M. , Bennett Albert F. , Long Anthony D.
Published: July 2012

Elucidating the genetic basis of adaptation on a genomewide scale
has evaded biologists, but complete genome sequences and DNA
high-density array technology make genomewide surveys more tractable.
Six lines of
Escherichia coli
adapted for 2,000
generations to a stressful high temperature of 41.5°C were examined
on a genomewide scale for duplication/deletion events by using DNA
high-density arrays. A total of five duplication and deletion events
were detected. These five events occurred in three of the six lines,
whereas the remaining three lines contained no detectable events. Three
of the duplications were at 2.85 Mb of the
E. coli
chromosome, providing evidence for the replicability of the adaptation
to high temperature. Four candidate genes previously shown to play
roles in stress and starvation survival were identified in the region
of common duplication. Expression of the two candidate genes examined
is elevated over expression levels in the ancestral lines or the lines
without the duplication. In the two cases where the duplication at 2.85
Mb has been further characterized, the timing of the genome
reorganization is coincident with significant increases in relative
fitness. In both of these cases, the model for the origin of the
duplication is a complex recombination event involving insertion
sequences and repeat sequences. These results provide additional
evidence for the idea that gene duplication plays an integral role
in adaptation, specifically as a means for gene amplification.
Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (
Hordeum vulgare
subspecies
spontaneum
)
Authors: Lin Jing-Zhong , Brown Anthony H. D. , Clegg Michael T.
Published: July 2012

Patterns of nucleotide sequence diversity in the
predominantly self-fertilizing species
Hordeum vulgare
subspecies
spontaneum
(wild barley) are compared between
the putative alcohol dehydrogenase 3 locus (denoted
“
adh3
”) and alcohol dehydrogenase 1
(
adh1
), two related but unlinked loci. The data consist
of a sequence sample of 1,873 bp of “
adh3
” drawn
from 25 accessions that span the species range. There were 104
polymorphic sites in the sequenced region of
“
adh3
.” The data reveal a strong geographic
pattern of diversity at “
adh3
” despite geographic
uniformity at
adh1
. Moreover, levels of nucleotide
sequence diversity differ by nearly an order of magnitude between the
two loci. Genealogical analysis resolved two distinct clusters of
“
adh3
” alleles (dimorphic sequence types) that
coalesce roughly 3 million years ago. One type consists of accessions
from the Middle East, and the other consists of accessions
predominantly from the Near East. The two “
adh3
”
sequence types are characterized by a high level of differentiation
between clusters (≈2.2%), which induces an overall excess of
intermediate frequency variants in the pooled sample. Finally, there is
evidence of intralocus recombination in the “
adh3
”
data, despite the high level of self-fertilization characteristic of
wild barley.
A model for the emergence of cooperation, interdependence, and structure in evolving networks
Authors: Jain Sanjay , Krishna Sandeep
Published: July 2012

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent “catalytic” and “inhibitory” interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of “keystone” species, followed by recoveries.
Evolution of hematopoiesis: Three members of the PU.1 transcription factor family in a cartilaginous fish,
Raja eglanteria
Authors: Anderson Michele K. , Sun Xiao , Miracle Ann L. , Litman Gary W. , Rothenberg Ellen V.
Published: July 2012

T lymphocytes and B lymphocytes are present in jawed vertebrates,
including cartilaginous fishes, but not in jawless vertebrates or
invertebrates. The origins of these lineages may be understood in terms
of evolutionary changes in the structure and regulation of
transcription factors that control lymphocyte development, such as
PU.1. The identification and characterization of three members of the
PU.1 family of transcription factors in a cartilaginous fish,
Raja eglanteria
, are described here. Two of these genes
are orthologs of mammalian PU.1 and Spi-C, respectively, whereas the
third gene, Spi-D, is a different family member. In addition, a
PU.1-like gene has been identified in a jawless vertebrate,
Petromyzon marinus
(sea lamprey). Both DNA-binding and
transactivation domains are highly conserved between mammalian and
skate PU.1, in marked contrast to lamprey Spi, in which similarity is
evident only in the DNA-binding domain. Phylogenetic analysis of
sequence data suggests that the appearance of Spi-C may predate the
divergence of the jawed and jawless vertebrates and that Spi-D arose
before the divergence of the cartilaginous fish from the lineage
leading to the mammals. The tissue-specific expression patterns of
skate PU.1 and Spi-C suggest that these genes share regulatory as well
as structural properties with their mammalian orthologs.
The
Bithorax Complex
of
Drosophila melanogaster
: Underreplication and morphology in polytene chromosomes
Authors: Moshkin Yuri M. , Alekseyenko Artyom A. , Semeshin Valery F. , Spierer Anne , Spierer Pierre , Makarevich Grigoryi F. , Belyaeva Elena S. , Zhimulev Igor F.
Published: July 2012

The level of polyteny of the
Drosophila
salivary
gland chromosomes was determined throughout the chromosome region
89E1–4, the locus of the
Bithorax Complex
. A zone of
underreplication spans the 300 kb of DNA from the
Ubx
to
Abd-B
loci. From the centromere proximal end of the
complex, a 70-kb-long gradual decrease of polytenization starts with
the
Ubx
transcription unit and, after a floor
corresponding to the
abd-A
locus, raises gradually back
to the maximum over 70 kb in the region of the
Abd-B
transcription unit. In flies carrying the mutation
Suppressor of
DNA Underreplication
[
Su(UR)ES
], the
underreplication of the
Bithorax Complex
is fully
suppressed. In the wild type, the
Bithorax Complex
forms
a weak point featuring thinner bands separated by clefts or
constrictions. In
Su(UR)ES
strain in contrast, the
89E1–4 band looks like a single solid band consisting of homogenous
dense material. We speculate that the wild-type Su(UR)ES protein
hampers DNA replication of silenced domains and leads to their
underreplication in salivary gland polytene chromosomes.
A mechanism for combinatorial regulation of electrical activity: Potassium channel subunits capable of functioning as Src homology 3-dependent adaptors
Authors: Nitabach Michael N. , Llamas D. Alberto , Araneda Ricardo C. , Intile Joanne L. , Thompson Ian J. , Zhou Yi I. , Holmes Todd C.
Published: July 2012

It is an open question how ion channel subunits that lack
protein–protein binding motifs become targeted and covalently modified
by cellular signaling enzymes. Here, we show that Src-family protein
tyrosine kinases (PTKs) bind to heteromultimeric
Shaker
-family voltage-gated potassium (Kv) channels by
interactions between the Src homology 3 (SH3) domain and the
proline-rich SH3 domain ligand sequence in the
Shaker
-family subunit Kv1.5. Once bound to Kv1.5,
Src-family PTKs phosphorylate adjacent subunits in the Kv channel
heteromultimer that lack proline-rich SH3 domain ligand sequences. This
SH3-dependent tyrosine phosphorylation contributes to significant
suppression of voltage-evoked currents flowing through the
heteromultimeric channel. These results demonstrate that Kv1.5 subunits
function as SH3-dependent adaptor proteins that marshal Src-family
kinases to heteromultimeric potassium channel signaling complexes, and
thereby confer functional sensitivity upon coassembled channel subunits
that are themselves not bound directly to Src-family kinases by
allowing their phosphorylation. This is a mechanism for information
transfer between subunits in heteromultimeric ion channels that is
likely to underlie the generation of combinatorial signaling diversity
in the control of cellular electrical excitability.
TheArabidopsis-accelerated cell death geneACD2encodes red chlorophyll catabolite reductase and suppresses the spread of disease symptoms
Authors: Mach Jennifer M. , Castillo Andrea R. , Hoogstraten Rebecca , Greenberg Jean T.
Published: July 2012

accelerated cell death 2(acd2) mutants ofArabidopsishave spontaneous spreading cell death lesions and constitutive activation of defenses in the absence of pathogen infection. Lesion formation inacd2plants can be triggered by the bacterial toxin coronatine through a light-dependent process. Coronatine-triggered and spontaneous lesion spreading inacd2plants also requires protein translation, indicating that cell death occurs by an active process. We have cloned theACD2gene; its predicted product shows significant and extensive similarity to red chlorophyll catabolite reductase, which catalyzes one step in the breakdown of the porphyrin component of chlorophyll [Wüthrich, K. L., Bovet, L., Hunziger, P. E., Donnison, I. S. & Hörtensteiner, S. (2000)Plant J.21, 189–198]. Consistent with this, ACD2 protein contains a predicted chloroplast transit peptide, is processedin vivo, and purifies with the chloroplast fraction in subcellular fractionation experiments. At some stages of development, ACD2 protein also purifies with the mitochondrial fraction. We hypothesize that cell death inacd2plants is caused by the accumulation of chlorophyll breakdown products. Such catabolites might be specific triggers for cell death or they might induce cellular damage through their ability to absorb light and emit electrons that generate free radicals. In response to infection byPseudomonas syringae, transgenic plants expressing excess ACD2 protein show reduced disease symptoms but not reduced growth of bacteria. Thus, breakdown products of chlorophyll may act to amplify the symptoms of disease, including cell death and yellowing. We suggest that economically important plants overexpressing ACD2 might also show increased tolerance to pathogens and might be useful for increasing crop yields.
Expression pattern of
Drosophila ret
suggests a common ancestral origin between the metamorphosis precursors in insect endoderm and the vertebrate enteric neurons
Authors: Hahn Mounou , Bishop J. Michael
Published: July 2012

The
RET
gene, encoding a receptor tyrosine kinase,
is unusual among human protooncogenes in that its mutant alleles are
implicated in a developmental defect involving enteric neurons as well
as in tumorigenesis. The cells affected in both types of disorders are
derived from the neural crest. Targeted disruption of mouse
ret
has revealed an additional role in kidney
development. Here we report the analysis of a
ret
homolog in
Drosophila melanogaster
, an arthropod with no
neural crest.
Drosophila ret
(
D-ret
)
encodes a protein of 1,235 amino acids that has all of the domains
identified in the vertebrate
ret
, including a cadherin
motif. During embryogenesis,
D-ret
mRNA is first
detected in the yolk sac at the late gastrula stage. In the
postgastrula,
D-ret
is expressed in the foregut neurons,
excretory system, peripheral ganglia, and the central nervous system.
Thus, despite the wide divergence of early embryonic fate maps between
vertebrates and invertebrates,
D-ret
is expressed in
cells that are presumed to be the functional equivalents of the
ret-
expressing cells in vertebrates. Unexpectedly,
D-ret
is also expressed in the imaginal islands of the
endodermal gut. These cells are proliferation-competent precursors for
adult midgut that are diffusely embedded in the growth-arrested
juvenile gut. These
ret
-expressing nonneuronal cells are
strikingly analogous to vertebrate enteric neurons in their topography,
but not in their cell fate. Our finding suggests a previously
unrecognized phylogenetic relationship between the
ret
-expressing cells in vertebrates and the precursor
reserves of metamorphosing insects.
Reprogramming of telomerase activity and rebuilding of telomere length in cloned cattle
Authors: Betts Dean H. , Bordignon Vilceu , Hill Jonathan R. , Winger Quinton , Westhusin Mark E. , Smith Lawrence C. , King W. Allan
Published: July 2012

Nuclear reprogramming requires the removal of epigenetic
modifications imposed on the chromatin during cellular differentiation
and division. The mammalian oocyte can reverse these alterations to a
state of totipotency, allowing the production of viable cloned
offspring from somatic cell nuclei. To determine whether nuclear
reprogramming is complete in cloned animals, we assessed the telomerase
activity and telomere length status in cloned embryos, fetuses, and
newborn offspring derived from somatic cell nuclear transfer. In this
report, we show that telomerase activity was significantly
(
P
< 0.05) diminished in bovine fibroblast donor
cells compared with embryonic stem-like cells, and surprisingly was
16-fold higher in fetal fibroblasts compared with adult fibroblasts
(
P
< 0.05). Cell passaging and culture periods
under serum starvation conditions significantly decreased telomerase
activity by approximately 30–50% compared with nontreated early
passage cells (
P
< 0.05). Telomere shortening was
observed during
in vitro
culture of bovine fetal
fibroblasts and in very late passages of embryonic stem-like cells.
Reprogramming of telomerase activity was apparent by the blastocyst
stage of postcloning embryonic development, and telomere lengths were
longer (15–23 kb) in cloned fetuses and offspring than the relatively
short mean terminal restriction fragment lengths (14–18 kb) observed
in adult donor cells. Overall, telomere lengths of cloned fetuses and
newborn calves (≈20 kb) were not significantly different from those
of age-matched control animals (
P
> 0.05). These
results demonstrate that cloned embryos inherit genomic modifications
acquired during the donor nuclei's
in vivo
and
in vitro
period but are subsequently reversed during
development of the cloned animal.
Environmental stress and mutational load in diploid strains of the yeast
Saccharomyces cerevisiae
Authors: Szafraniec Krzysztof , Borts Rhona H. , Korona Ryszard
Published: July 2012

The negative effect of permanent contamination of populations
because of spontaneous mutations does not appear to be very high if
judged from the relatively good health of humans or many wild and
domesticated species. This is partly explained by the fact that, in
diploids, the new mutations are usually located in heterozygous loci
and therefore are masked by wild-type alleles. The expression of
mutations at the phenotypic level may also strongly depend on
environmental factors if, for example, deleterious alleles are more
easily compensated under favorable conditions. The present experiment
uses diploid strains of yeast in which mutations arise at high rates
because a mismatch-repair protein is missing. This mutagenesis resulted
in a number of new alleles that were in heterozygous loci. They had no
detectable effect on fitness when the environment was benign. A very
different outcome was seen when thermal shock was applied, where
fitness of the mutation-contaminated clones was lower and more diverse
than that of the nonmutagenized clones. This shows that the genetic
load conferred by spontaneous mutations can be underestimated or even
overlooked in favorable conditions. Therefore, genetic variation can be
higher and natural selection more intense when environmental conditions
are getting poorer. These conclusions apply, at least, to that
component of variation that directly originates from spontaneous
mutations (as opposed to the variation resulting from the history of
selection).
Brain serotonin dysfunction accounts for aggression in male mice lacking neuronal nitric oxide synthase
Authors: Chiavegatto Silvana , Dawson Valina L. , Mamounas Laura A. , Koliatsos Vassilis E. , Dawson Ted M. , Nelson Randy J.
Published: July 2012

Genetically engineered mice with targeted disruption of the
neuronal nitric oxide synthase (nNOS) gene established the inhibitory
role of nitric oxide (NO) in male impulsive aggressive behavior. This
was later confirmed by using selective nNOS inhibitors in male
wild-type mice. The molecular mechanisms accounting for the aggressive
behavior caused by the lack of neuronally derived NO is not known.
Recent studies suggest that central serotonergic neuronal circuits and
particularly 5-HT
1A
and 5-HT
1B
receptors play a
prominent role in the regulation of aggression. Accordingly, we
investigated whether the aggressiveness caused by the lack of nNOS
might be because of alterations in serotonergic function. We now
demonstrate that the excessive aggressiveness and impulsiveness of nNOS
knockout mice is caused by selective decrements in serotonin (5-HT)
turnover and deficient 5-HT
1A
and 5-HT
1B
receptor function in brain regions regulating emotion. These results
indicate an important role for NO in normal brain 5-HT function and may
have significant implications for the treatment of
psychiatric disorders characterized by aggressiveness and
impulsivity.
Evolution of treatment effects over time: Empirical insight from recursive cumulative metaanalyses
Authors: Ioannidis John P. A. , Lau Joseph
Published: July 2012

Evidence on how much medical interventions work may change
over time. It is important to determine what fluctuations in the
treatment effect reported by randomized trials and their metaanalyses
may be expected and whether extreme fluctuations signal future major
changes. We applied recursive cumulative metaanalysis of randomized
controlled trials to evaluate the relative change in the pooled
treatment effect (odds ratio) over time for 60 interventions in two
medical fields (pregnancy/perinatal medicine,
n
=
45 interventions; myocardial infarction,
n
= 15
interventions). We evaluated the scatter of relative changes for
different numbers of total patients in previous trials. Outlier cases
were noted with changes greater than 2.5 standard deviations of the
expected. With 500 accumulated patients, the pooled odds ratio may
change by 0.6- to 1.7-fold in the immediate future. When 2000 patients
have already been randomized, the respective figures are between 0.74-
and 1.35-fold for pregnancy/perinatal medicine and between 0.83- and
1.21-fold for myocardial infarction studies. Extreme early fluctuations
in the treatment effect were observed in three interventions (magnesium
in myocardial infarction, calcium and antiplatelet agents for
prevention of preeclampsia), where recent mega-trials have contradicted
prior metaanalyses, as well as in four other examples where early large
treatment effects were dissipated when more data appeared. Past
experience may help quantify the uncertainty surrounding the treatment
effects reported in early clinical trials and their metaanalyses. Early
wide oscillations in the evolution of the treatment effect for specific
interventions may sometimes signal further major changes in the future.
A stochastic model for the self-similar heterogeneity of regional organ blood flow
Authors: Kendal Wayne S.
Published: July 2012

The theory of exponential dispersion models was applied to
construct a stochastic model for heterogeneities in regional organ
blood flow as inferred from the deposition of labeled microspheres. The
requirements that the dispersion model be additive (or reproductive),
scale invariant, and represent a compound Poisson distribution, implied
that the relative dispersion (
RD
= standard
deviation/mean) of blood flow should exhibit self-similar scaling in
macroscopic tissue samples of masses
m
and

m
ref

such that

RD(m) =
RD(m
ref
). (m/m
ref
)
1−D

,
where
D
was a constant. Under these circumstances this
empirical relationship was a consequence of a compound Poisson-gamma
distribution that represented macroscopic blood flow. The model also
predicted that blood flow, at the microcirculatory level, should also
be heterogeneous but obey a gamma distribution—a prediction supported
by observation.
AB-polymer networks based on oligo(ɛ-caprolactone) segments showing shape-memory properties
Authors: Lendlein Andreas , Schmidt Annette M. , Langer Robert
Published: July 2012

Although shape-memory metal alloys have wide use in medicine
and other areas, improved properties, particularly easy shaping, high
shape stability, and adjustable transition temperature, are realizable
only by polymer systems. In this paper, a polymer system of
shape-memory polymer networks based on oligo(ɛ-caprolactone)
dimethacrylate as crosslinker and
n
-butyl acrylate as
comonomer was introduced. The influence of two structural parameters,
the molecular weight of oligo(ɛ-caprolactone) dimethacrylate and the
weight content of
n
-butyl acrylate, on macroscopic
properties of polymer networks such as thermal and mechanical
properties has been investigated. Tensile tests above and below melting
temperature showed a decrease in the elastic modulus with increasing
comonomer weight content. The crystallization behavior of the new
materials has been investigated, and key parameters for the programming
procedure of the temporary shape have been evaluated. Shape-memory
properties have been quantified by thermocyclic experiments. All
samples reached uniform deformation properties with recovery rates
above 99% after 3 cycles. Whereas strain recovery increased with
increasing
n
-butyl acrylate content, strain fixity
decreased, reflecting the decreasing degree of crystallinity of the
material.
An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from
Streptomyces
sp. strain CL190
Authors: Kaneda Kazuhide , Kuzuyama Tomohisa , Takagi Motoki , Hayakawa Yoichi , Seto Haruo
Published: July 2012

A gene cluster encoding five enzymes of the mevalonate pathway had
been cloned from
Streptomyces
sp. strain CL190. This
gene cluster contained an additional ORF,
orfD
, encoding
an unknown protein that was detected in some archaebacteria and some
Gram-positive bacteria including
Staphylococcus aureus
.
The recombinant product of
orfD
was purified as a
soluble protein and characterized. The molecular mass of the enzyme was
estimated to be 37 kDa by SDS-polyacrylamide gel electrophoresis and
155 kDa by gel filtration chromatography, suggesting that the enzyme is
most likely to be a tetramer. The purified enzyme contained flavin
mononucleotide (FMN) with the amount per tetramer being 1.4 to 1.6
mol/mol. The enzyme catalyzed the isomerization of isopentenyl
diphosphate (IPP) to produce dimethylallyl diphosphate (DMAPP) in the
presence of both FMN and NADPH. The
Escherichia coli
plasmid expressing
orfD
could complement the disrupted
IPP isomerase gene in
E. coli
. These results indicate
that
orfD
encodes an unusual IPP isomerase showing no
sequence similarity to those of IPP isomerases identified to date.
Based on the difference in enzymatic properties, we classify the IPP
isomerases into two types: Type 2 for FMN- and NAD(P)H-dependent
enzymes, and type 1 for the others. In view of the critical role of
this isomerase in
S. aureus
and of the different
enzymatic properties of mammalian (type 1) and
S. aureus
(type 2) isomerases, this unusual enzyme is considered to be a suitable
molecular target for the screening of antibacterial drugs specific to
S. aureus
.
Caspase-2 pre-mRNA alternative splicing: Identification of an intronic element containing a decoy 3′ acceptor site
Authors: Côté Jocelyn , Dupuis Sophie , Jiang Zhi-Hong , Wu Jane Y.
Published: July 2012

We have established a model system using the caspase-2
pre-mRNA and initiated a study on the role of alternative splicing in
regulation of programmed cell death. A caspase-2 minigene construct has
been made that can be alternatively spliced in transfected cells and in
nuclear extracts. Using this system, we have identified a 100-nt region
in downstream intron 9 that inhibits the inclusion of the 61-bp
alternative exon. This element (In100) can facilitate exon skipping in
the context of competing 3′ or 5′ splice sites, but not in
single-intron splicing units. The In100 element is also active in
certain heterologous pre-mRNAs, although in a highly context-dependent
manner. Interestingly, we found that In100 contains a sequence that
highly resembles a bona fide 3′ splice site. We provide evidence that
this sequence acts as a “decoy” acceptor site that engages in U2
snRNP-dependent but nonproductive splicing complexes with the 5′ splice
site of exon 9, hence conferring competitive advantage to the
exon-skipping splicing event (E8-E10). These results reveal a mechanism
of action for a negative intronic regulatory element and uncover a role
for U2 snRNP in the regulation of alternative splicing.