bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Spikelets on Hippocampal CA1 Pyramidal Cell Activity During Spatial Exploration
Authors: Epsztein Jérôme , Lee Albert K. , Chorev Edith , Brecht Michael
Published: January 2010

Space and Spikelets

In neurons, spikelets are voltage fluctuations of small amplitude with a spike-like waveform. Spikelets are difficult to detect with extracellular techniques traditionally used to record neuronal activity in freely moving animals.

Epsztein
et al.

(p.
474
) used head-anchored whole-cell recordings to analyze spikelet activity during spatial exploration in freely moving rats. A high incidence of spikelets was often followed by action potentials. Like action potentials, spikelets were all-or-none, but had different kinetics and amplitude, and were clearly distinct from excitatory postsynaptic potentials and occurred to a different extent in different cells. In cells with clear place fields, spikelets had similar spatial firing preferences, as did regular action potentials. Thus, spatially modulated spikelets may be involved in information processing in cortical neuronal networks.
Measurement of Universal Thermodynamic Functions for a Unitary Fermi Gas
Authors: Horikoshi Munekazu , Nakajima Shuta , Ueda Masahito , Mukaiyama Takashi
Published: January 2010

Dissecting Fermion Interactions

Electrons, protons, and other building blocks of our universe belong to a class of particles we call fermions. Different interfermion interactions give rise to different forms of matter. In the strongly interacting resonant regime, however, fermionic systems have thermodynamic properties that depend only on the interparticle spacing and scaled temperature.

Horikoshi
et al.

(p.
442
; see the Perspective by

Marwan

) precisely characterize the thermodynamics in this universal regime for a system of ultracold fermionic lithium atoms. Analysis of a large number of trapped-gas density profiles confirms that the results depend neither on trap geometry nor the absolute temperature of the gas. The results are relevant to studies of all strongly interacting fermionic systems, including neutron stars and nuclear matter.
Adjusting the Solar System's Absolute Clock
Authors: Connelly J. N.
Published: January 2010

The recent demonstration that a basic assumption in using isotope decay to measure the age of meteorites is incorrect has profound implications for dating the early solar system.
Epitaxial Growth Writ Large
Authors: Einstein Theodore L. , Stasevich Timothy J.
Published: January 2010

The technological goal of optimizing the controlled deposition of atomic monolayers is simplified by studying models of deposition of larger colloids.
And Then There Were None?
Authors: Roberts Richard G. , Brook Barry W.
Published: January 2010

Direct dating of fossils of the putative last survivors of the Australian megafauna supports claims that they were extinct by 40 thousand years ago and not later.
Unsexing the Brain
Pink Brain, Blue Brain
How Small Differences Grow into Troublesome Gaps—and What We Can Do About It

by Lise Eliot

Houghton Mifflin Harcourt, Boston, 2009. 432 pp. $25. ISBN 9780618393114.
Authors: Henderson A. Scott
Published: January 2010

Using a comprehensive survey of existing research, Eliot counters the overemphasis on sex differences that characterizes most popular comparisons of the development of girls and boys.
African Physicists Set Their Sights on Mammoth Scope
Authors: Bohannon John
Published: January 2010

On the minds of many at a meeting last week in the Senegalese capital was the Square Kilometre Array, a next-generation radio telescope that will probe gas clouds in the early universe with a collecting area 100 times that of the Very Large Array in Socorro, New Mexico. It is planned to be built in either Africa or Australia.
Trends Document China's Prowess
Authors: Mervis Jeffrey
Published: January 2010

A new report shows how a decade of investment in science and technology has moved the world's most populous nation into the front ranks on key global indicators.
Magnetics Point to Magma 'Ocean' at Io
Authors: Kerr Richard A.
Published: January 2010

Space physicists presented evidence at the fall meeting of the American Geophysical Union for a global ocean tens of kilometers beneath the volcano-pocked surface of Io. This one, however, would be mostly molten rock.
Inactivation of Murine Norovirus 1 and
Bacteroides fragilis
Phage B40-8 by Mesophilic and Thermophilic Anaerobic Digestion of Pig Slurry
Authors: Baert Leen , De Gusseme Bart , Boon Nico , Verstraete Willy , Debevere Johan , Uyttendaele Mieke
Published: January 2010

Mesophilic (37°C) and thermophilic (52°C) anaerobic digestion of pig slurry induced at least a 4-log decrease in murine norovirus 1, used as a surrogate virus for porcine norovirus, after 13 and 7 days, respectively.
Bacteroides fragilis
phage B40-8, employed as a universal viral model, was lowered by 2.5 log after 7 days. The viral titer declined due to temperature and matrix effects.
Mechanism of
De Novo
Branched-Chain Amino Acid Synthesis as an Alternative Electron Sink in Hypoxic
Aspergillus nidulans
Cells
Authors: Shimizu Motoyuki , Fujii Tatsuya , Masuo Shunsuke , Takaya Naoki
Published: January 2010

Although branched-chain amino acids are synthesized as building blocks of proteins, we found that the fungus
Aspergillus nidulans
excretes them into the culture medium under hypoxia. The transcription of predicted genes for synthesizing branched-chain amino acids was upregulated by hypoxia. A knockout strain of the gene encoding the large subunit of acetohydroxy acid synthase (AHAS), which catalyzes the initial reaction of the synthesis, required branched-chain amino acids for growth and excreted very little of them. Pyruvate, a substrate for AHAS, increased the amount of hypoxic excretion in the wild-type strain. These results indicated that the fungus responds to hypoxia by synthesizing branched-chain amino acids via a
de novo
mechanism. We also found that the small subunit of AHAS regulated hypoxic branched-chain amino acid production as well as cellular AHAS activity. The AHAS knockout resulted in higher ratios of NADH/NAD
+
and NADPH/NADP
+
under hypoxia, indicating that the branched-chain amino acid synthesis contributed to NAD
+
and NADP
+
regeneration. The production of branched-chain amino acids and the hypoxic induction of involved genes were partly repressed in the presence of glucose, where cells produced ethanol and lactate and increased levels of lactate dehydrogenase activity. These indicated that hypoxic branched-chain amino acid synthesis is a unique alternative mechanism that functions in the absence of glucose-to-ethanol/lactate fermentation and oxygen respiration.
Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse
Proteobacteria
Authors: Craig Jeffrey W. , Chang Fang-Yuan , Kim Jeffrey H. , Obiajulu Steven C. , Brady Sean F.
Published: January 2010

The small-molecule biosynthetic diversity encoded within the genomes of uncultured bacteria is an attractive target for the discovery of natural products using functional metagenomics. Phenotypes commonly associated with the production of small molecules, such as antibiosis, altered pigmentation, or altered colony morphology, are easily identified from screens of arrayed metagenomic library clones. However, functional metagenomic screening methods are limited by their intrinsic dependence on a heterologous expression host. Toward the goal of increasing the small-molecule biosynthetic diversity found in functional metagenomic studies, we report the phenotypic screening of broad-host-range environmental DNA libraries in six different proteobacteria:
Agrobacterium tumefaciens
,
Burkholderia graminis
,
Caulobacter vibrioides
,
Escherichia coli
,
Pseudomonas putida
, and
Ralstonia metallidurans
. Clone-specific small molecules found in culture broth extracts from pigmented and antibacterially active clones, as well as the genetic elements responsible for the biosynthesis of these metabolites, are described. The host strains used in this investigation provided access to unique sets of clones showing minimal overlap, thus demonstrating the potential advantage conferred on functional metagenomics through the use of multiple diverse host species.
Genotyping of
Giardia duodenalis
Cysts by New Real-Time PCR Assays for Detection of Mixed Infections in Human Samples
Authors: Almeida Andre , Pozio Edoardo , Cacciò Simone M.
Published: January 2010

Of the seven genetic groups, or assemblages, currently recognized in the
Giardia duodenalis
species complex, only assemblages A and B are associated with human infection, but they also infect other mammals. Recent investigations have suggested the occurrence of genetic exchanges among isolates of
G. duodenalis
, and the application of assemblage-specific PCR has shown both assemblages A and B in a significant number of human infections. In this work, three real-time quantitative (qPCR) assays were developed to target the
G. duodenalis
triose phosphate isomerase, glutamate dehydrogenase, and open reading frame C4 sequences. Primers were designed to allow the specific amplification of the DNA of assemblage A or B and to generate products distinguishable by their melting curves or, after qPCR, by their sequences, sizes, or restriction patterns. The assays showed full specificity and detected DNA from a single trophozoite (4 to 8 target copies). We applied these assays, as well as a TaqMan assay that targets the β-
giardin
gene, to genomic DNA extracted from 30 human stools and to
Giardia
cysts purified by immunomagnetic capture from the same samples. Simultaneous detection of both assemblages was observed in a large number of DNAs extracted from stools, and experiments on the cysts purified from the same samples showed that this was essentially attributable to mixed infections, as only one assemblage was detected when dilutions of cysts were tested. In a few cases, detection of both assemblages was observed even when single cysts were tested. This result, which suggests the presence of recombinants, needs to be confirmed using more accurate methods for cyst separation and enumeration. The assays described in this study can be used to detect
Giardia
cysts infectious to humans in samples from animals and in water and food.
Comparison of Two Optical-Density-Based Methods and a Plate Count Method for Estimation of Growth Parameters of
Bacillus cereus
Authors: Biesta-Peters Elisabeth G. , Reij Martine W. , Joosten Han , Gorris Leon G. M. , Zwietering Marcel H.
Published: January 2010

Quantitative microbiological models predicting proliferation of microorganisms relevant for food safety and/or food stability are useful tools to limit the need for generation of biological data through challenge testing and shelf-life testing. The use of these models requires quick and reliable methods for the generation of growth data and estimation of growth parameters. Growth parameter estimation can be achieved using methods based on plate counting and methods based on measuring the optical density. This research compares the plate count method with two optical density methods, namely, the 2-fold dilution (2FD) method and the relative rate to detection (RRD) method. For model organism
Bacillus cereus
F4810/72, the plate count method and both optical density methods gave comparable estimates for key growth parameters. Values for the maximum specific growth rate (
μ
max
) derived by the 2FD method and by the RRD method were of the same order of magnitude, but some marked differences between the two approaches were apparent. Whereas the 2FD method allowed the derivation of values for lag time (λ) from the data, this was not possible with the RRD method. However, the RRD method gave many more data points per experiment and also gave more data points close to the growth boundary. This research shows that all three proposed methods can be used for parameter estimation but that the choice of method depends on the objectives of the research.
Functional Analysis of the Three TATA Binding Protein Homologs in
Methanosarcina acetivorans
Authors: Reichlen Matthew J. , Murakami Katsuhiko S. , Ferry James G.
Published: January 2010

The roles of three TATA binding protein (TBP) homologs (TBP1, TBP2, and TBP3) in the archaeon
Methanosarcina acetivorans
were investigated by using genetic and molecular approaches. Although
tbp2
and
tbp3
deletion mutants were readily obtained, a
tbp1
mutant was not obtained, and the growth of a conditional
tbp1
expression strain was tetracycline dependent, indicating that TBP1 is essential. Transcripts of
tbp1
were 20-fold more abundant than transcripts of
tbp2
and 100- to 200-fold more abundant than transcripts of
tbp3
, suggesting that TBP1 is the primary TBP utilized during growth. Accordingly,
tbp1
is strictly conserved in the genomes of
Methanosarcina
species. Δ
tbp3
and Δ
tbp2
strains exhibited an extended lag phase compared with the wild type, although the lag phase for the Δ
tbp2
strain was less pronounced when this strain was transitioning from growth on methylotrophic substrates to growth on acetate. Acetate-adapted Δ
tbp3
cells exhibited growth rates, final growth yields, and lag times that were significantly reduced compared with those of the wild type when the organisms were cultured with growth-limiting concentrations of acetate, and the acetate-adapted Δ
tbp2
strain exhibited a final growth yield that was reduced compared with that of the wild type when the organisms were cultured with growth-limiting acetate concentrations. DNA microarray analyses identified 92 and 77 genes with altered transcription in the Δ
tbp2
and Δ
tbp3
strains, respectively, which is consistent with a role for TBP2 and TBP3 in optimizing gene expression. Together, the results suggest that TBP2 and TBP3 are required for efficient growth under conditions similar to the conditions in the native environment of
M. acetivorans
.
Heavy Involvement of Stringent Transcription Control Depending on the Adenine or Guanine Species of the Transcription Initiation Site in Glucose and Pyruvate Metabolism inBacillus subtilis
Authors: Tojo Shigeo , Kumamoto Kanako , Hirooka Kazutake , Fujita Yasutaro
Published: January 2010

InBacillussubtiliscells, the GTP level decreases and the ATP level increases upon a stringent response. This reciprocal change in the concentrations of the substrates of RNA polymerase affects the rate of transcription initiation of certain stringent genes depending on the purine species at their transcription initiation sites. DNA microarray analysis suggested that not only therrnandilv-leugenes encoding rRNAs and the enzymes for synthesis of branched-chain amino acids, respectively, but also many genes, including genes involved in glucose and pyruvate metabolism, might be subject to this kind of stringent transcription control. Actually, theptsGHIandpdhABCDoperons encoding the glucose-specific phosphoenolpyruvate:sugar phosphotransferase system and the pyruvate dehydrogenase complex were found to be negatively regulated, likerrn, whereas thepycAgene encoding pyruvate carboxylase and thealsSDoperon for synthesis of acetoin from pyruvate were positively regulated, likeilv-leu. Replacement of the guanine at position 1 and/or position 2 ofptsGHIand at position 1 ofpdhABCD(transcription initiation base at position 1) by adenine changed the negative stringent control of these operons in the positive direction. The initiation bases for transcription ofpdhABCDandpycAwere newly determined. Then the promoter sequences of these stringent operons were aligned, and the results suggested that the presence of a guanine(s) and the presence of an adenine(s) at position 1 and/or position 2 might be indispensable for negative and positive stringent control, respectively. Such stringent transcription control that affects the transcription initiation rate through reciprocal changes in the GTP and ATP levels likely occurs for numerous genes ofB. subtilis.
Inactivation of Genes Encoding Plastoglobulin-Like Proteins in
Synechocystis
sp. PCC 6803 Leads to a Light-Sensitive Phenotype
Authors: Cunningham Francis X. , Tice Ashley B. , Pham Christina , Gantt Elisabeth
Published: January 2010

Plastoglobulins (PGL) are the predominant proteins of lipid globules in the plastids of flowering plants. Genes encoding proteins similar to plant PGL are also present in algae and cyanobacteria but in no other organisms, suggesting an important role for these proteins in oxygenic photosynthesis. To gain an understanding of the core and fundamental function of PGL, the two genes that encode PGL-like polypeptides in the cyanobacterium
Synechocystis
sp. PCC 6803 (
pgl1
and
pgl2
) were inactivated individually and in combination. The resulting mutants were able to grow under photoautotrophic conditions, dividing at rates that were comparable to that of the wild-type (WT) under low-light (LL) conditions (10 microeinsteins·m
−2
·s
−1
) but lower than that of the WT under moderately high-irradiance (HL) conditions (150 microeinsteins·m
−2
·s
−1
). Under HL, each Δ
pgl
mutant had less chlorophyll, a lower photosystem I (PSI)/PSII ratio, more carotenoid per unit of chlorophyll, and very much more myxoxanthophyll (a carotenoid symptomatic of high light stress) per unit of chlorophyll than the WT. Large, heterogeneous inclusion bodies were observed in cells of mutants inactivated in
pgl2
or both
pgl2
and
pgl1
under both LL and HL conditions. The mutant inactivated in both
pgl
genes was especially sensitive to the light environment, with alterations in pigmentation, heterogeneous inclusion bodies, and a lower PSI/PSII ratio than the WT even for cultures grown under LL conditions. The WT cultures grown under HL contained 2- to 3-fold more PGL1 and PGL2 per cell than cultures grown under LL conditions. These and other observations led us to conclude that the PGL-like polypeptides of
Synechocystis
play similar but not identical roles in some process relevant to the repair of photooxidative damage.
Binding of Complement Regulators to Invasive Nontypeable
Haemophilus influenzae
Isolates Is Not Increased Compared to Nasopharyngeal Isolates, but Serum Resistance Is Linked to Disease Severity
Authors: Hallström Teresia , Resman Fredrik , Ristovski Mikael , Riesbeck Kristian
Published: January 2010

The aim of the present study was to analyze the importance of nontypeable
Haemophilus influenzae
(NTHi) isolated from patients with sepsis (invasive isolates) compared to nasopharyngeal isolates from patients with upper respiratory tract infection for resistance to complement-mediated attack in human serum and to correlate this result with disease severity. We studied and characterized cases of invasive NTHi disease in detail. All patients with invasive NTHi isolates were adults, and 35% had a clinical presentation of severe sepsis according to the ACCP/SCCM classification of sepsis grading. Moreover, 41% of the patients had evidence of immune deficiency. The different isolates were analyzed for survival in human serum and for binding of
125
I-labeled, purified human complement inhibitors C4b-binding protein (C4BP), factor H, and vitronectin, in addition to binding of regulators directly from serum. No significant differences were found when blood-derived and nasopharyngeal isolates were compared, suggesting that interactions with the complement system are equally important for NTHi strains, irrespective of isolation site. Interestingly, a correlation between serum resistance and invasive disease severity was found. The ability to resist the attack of the complement system seems to be important for NTHi strains infecting the respiratory tract as well as the bloodstream.
Clinical Characteristics, Outcomes, and Microbiologic Features Associated with Methicillin-Resistant
Staphylococcus aureus
Bacteremia in Pediatric Patients Treated with Vancomycin
Authors: Welsh Kerry J. , Abbott April N. , Lewis Evan M. , Gardiner Jeanelle M. , Kruzel Mark C. , Lewis Cole T. , Mohr John F. , Wanger Audrey , Armitige Lisa Y.
Published: January 2010

Vancomycin is the first-line therapy for methicillin-resistant
Staphylococcus aureus
(MRSA) bacteremia, but its efficacy in adult patients has been questioned. Less is known about the outcomes of MRSA bacteremia treated with vancomycin in pediatric patients. This study reviews the outcomes and clinical characteristics of MRSA bacteremia in children treated with vancomycin and characterizes the microbiologic and molecular features of the bloodstream isolates. A retrospective cohort study was conducted among pediatric patients with MRSA bacteremia treated with vancomycin for >5 days from 1 August 2005 to 31 May 2007 in a large tertiary care center. MRSA bloodstream isolates were characterized by antimicrobial susceptibility testing, PCR analysis of virulence genes, and Diversilab typing. Clinical records were reviewed for outcomes and comorbidities. A total of 22 pediatric patients with MRSA bacteremia were identified. Eleven cases (50.0%) were considered vancomycin treatment failures. Features significantly associated with vancomycin treatment failure were prematurity (
P
= 0.02) and isolates positive for Panton-Valentine leukocidin (PVL) (
P
= 0.008). Features typically associated with community-associated MRSA strains were identified in hospital-associated isolates. A dominant clone was not responsible for the high number of treatment failures. Further studies are needed to determine if vancomycin should be the first-line treatment for MRSA bacteremia in premature infants and for PVL-positive isolates.
Protection against Lethal Vaccinia Virus Challenge by Using an Attenuated Matrix Protein Mutant Vesicular Stomatitis Virus Vaccine Vector Expressing Poxvirus Antigens
Authors: Braxton Cassandra L. , Puckett Shelby H. , Mizel Steven B. , Lyles Douglas S.
Published: January 2010

Recombinant vesicular stomatitis viruses (VSV) are excellent candidate vectors for vaccination against human diseases. The neurovirulence of VSV in animal models requires the attenuation of the virus for use in humans. Previous efforts have focused on attenuating virus replication. Studies presented here test an alternative approach for attenuation that uses a matrix (M) protein mutant (rM51R) VSV as a vaccine vector against respiratory infection. This mutant is attenuated for viral virulence by its inability to suppress the innate immune response. The ability of rM51R VSV vectors to protect against lethal respiratory challenge was tested using a vaccinia virus intranasal challenge model. Mice immunized intranasally with rM51R vectors expressing vaccinia virus antigens B5R and L1R were protected against lethal vaccinia virus challenge. A single immunization with the vectors provided protection against vaccinia virus-induced mortality; however, a prime-boost strategy reduced the severity of the vaccinia virus-induced disease progression. Antibody titers measured after the prime and boost were low despite complete protection against lethal challenge. However, immunized animals had higher antibody titers during the challenge, suggesting that memory B-cell responses may be important for the protection. Depletion experiments demonstrated that B cells but not CD8 T cells were involved in the protection mediated by rM51R vaccine vectors that express B5R and L1R. These results demonstrate the potential of M protein mutant VSVs as candidate vaccine vectors against human diseases.
Simian Virus 40 Infection Triggers a Balanced Network That Includes Apoptotic, Survival, and Stress Pathways
Authors: Butin-Israeli Veronika , Drayman Nir , Oppenheim Ariella
Published: January 2010

The infection process by simian virus 40 (SV40) and entry of its genome into nondividing cells are only partly understood. Infection begins by binding to GM1 receptors at the cell surface, cellular entry via caveolar invaginations, and trafficking to the endoplasmic reticulum, where the virus disassembles. To gain a deeper insight into the contribution of host functions to this process, we studied cellular signaling elicited by the infecting virus. Signaling proteins were detected by Western blotting and immunofluorescence staining. The study was assisted by a preliminary proteomic screen. The contribution of signaling proteins to the infection process was evaluated using specific inhibitors. We found that CV-1 cells respond to SV40 infection by activating poly(ADP-ribose) polymerase 1 (PARP-1)-mediated apoptotic signaling, which is arrested by the Akt-1 survival pathway and stress response. A single key regulator orchestrating the three pathways is phospholipase C-gamma (PLCγ). The counteracting apoptotic and survival pathways are robustly balanced as the infected cells neither undergo apoptosis nor proliferate. Surprisingly, we have found that the apoptotic pathway, including activation of PARP-1 and caspases, is absolutely required for the infection to proceed. Thus, SV40 hijacks the host defense to promote its infection. Activities of PLCγ and Akt-1 are also required, and their inhibition abrogates the infection. Notably, this signaling network is activated hours before T antigen is expressed. Experiments with recombinant empty capsids, devoid of DNA, indicated that the major capsid protein VP1 alone triggers this early signaling network. The emerging robust signaling network reflects a delicate evolutionary balance between attack and defense in the host-virus relationship.
Bicaudal D1-Dependent Trafficking of Human Cytomegalovirus Tegument Protein pp150 in Virus-Infected Cells
Authors: Indran Sabarish V. , Ballestas Mary E. , Britt William J.
Published: January 2010

Human cytomegalovirus (HCMV) virion assembly takes place in the nucleus and cytoplasm of infected cells. The HCMV virion tegument protein pp150 (ppUL32) is an essential protein of HCMV and has been suggested to play a role in the cytoplasmic phase of HCMV assembly. To further define its role in viral assembly and to identify host cell proteins that interact with pp150 during viral assembly, we utilized yeast two-hybrid analyses to detect an interaction between pp150 and Bicaudal D1 (BicD1), a protein thought to play a role in trafficking within the secretory pathway. BicD1 is known to interact with the dynein motor complex and the Rab6 GTPase. The interaction between pp150 and BicD1 was confirmed by coimmunoprecipitation and fluorescence resonance energy transfer. Depletion of BicD1 with short hairpin RNA (shRNA) caused decreased virus yield and a defect in trafficking of pp150 to the cytoplasmic viral assembly compartment (AC), without altering trafficking to the AC of another essential tegument protein, pp28, or the viral glycoprotein complex gM/gN. The C terminus of BicD1 has been previously shown to interact with the GTPase Rab6, suggesting a potential role for Rab6-mediated vesicular trafficking in HCMV assembly. Finally, overexpression of the N terminus of truncated BicD1 acts in a dominant-negative manner and leads to disruption of the AC and a decrease in the assembly of infectious virus. This phenotype was similar to that observed following overexpression of dynamitin (p50) and provided additional evidence that morphogenesis of the AC and virus assembly were dynein dependent.
Experimental Verification of a Traceback Phenomenon in Prion Infection
Authors: Kobayashi Atsushi , Sakuma Nobuyuki , Matsuura Yuichi , Mohri Shirou , Aguzzi Adriano , Kitamoto Tetsuyuki
Published: January 2010

The clinicopathological phenotypes of sporadic Creutzfeldt-Jakob disease (sCJD) correlate with the allelotypes (M or V) of the polymorphic codon 129 of the human prion protein (PrP) gene and the electrophoretic mobility patterns of abnormal prion protein (PrPSc). Transmission of sCJD prions to mice expressing human PrP with a heterologous genotype (referred to as cross-sequence transmission) results in prolonged incubation periods. We previously reported that cross-sequence transmission can generate a new prion strain with unique transmissibility, designated a traceback phenomenon. To verify experimentally the traceback of sCJD-VV2 prions, we inoculated sCJD-VV2 prions into mice expressing human PrP with the 129M/M genotype. These 129M/M mice showed altered neuropathology and a novel PrPSctype after a long incubation period. We then passaged the brain homogenate from the 129M/M mouse inoculated with sCJD-VV2 prions into other 129M/M or 129V/V mice. Despite cross-sequence transmission, 129V/V mice were highly susceptible to these prions compared to the 129M/M mice. The neuropathology and PrPSctype of the 129V/V mice inoculated with the 129M/M mouse-passaged sCJD-VV2 prions were identical to those of the 129V/V mice inoculated with sCJD-VV2 prions. Moreover, we generated for the first time a type 2 PrPSc-specific antibody in addition to type 1 PrPSc-specific antibody and discovered that drastic changes in the PrPScsubpopulation underlie the traceback phenomenon. Here, we report the first direct evidence of the traceback in prion infection.
Novel Function of CD81 in Controlling Hepatitis C Virus Replication
Authors: Zhang Yong-Yuan , Zhang Bai-Hua , Ishii Koji , Liang T. Jake
Published: January 2010

The mechanisms of hepatitis C virus (HCV) replication remain poorly understood, and the cellular factors required for HCV replication are yet to be completely defined. CD81 is known to mediate HCV entry. Our study uncovered an unexpected novel function of CD81 in the HCV life cycle that is important for HCV RNA replication. HCV replication occurred efficiently in infected cells with high levels of CD81 expression. In HCV-infected or RNA-transfected cells with low levels of CD81 expression, initial viral protein synthesis occurred normally, but efficient replication failed to proceed. The aborted replication could be restored by the transient transfection of a CD81 expression plasmid. CD81-dependent replication was demonstrated with both an HCV infectious cell culture and HCV replicon cells of genotypes 1b and 2a. We also showed that CD81 expression is positively correlated with the kinetics of HCV RNA synthesis but inversely related to the kinetics of viral protein production, suggesting that CD81 may control viral replication by directing viral RNA template function to RNA replication. Thus, CD81 may be necessary for the efficient replication of the HCV genome in addition to its role in viral entry.
Structure of the Dimerization Domain of the Rabies Virus Phosphoprotein
Authors: Ivanov Ivan , Crépin Thibaut , Jamin Marc , Ruigrok Rob W. H.
Published: January 2010

The crystal structure of the dimerization domain of rabies virus phosphoprotein was determined. The monomer consists of two α-helices that make a helical hairpin held together mainly by hydrophobic interactions. The monomer has a hydrophilic and a hydrophobic face, and in the dimer two monomers pack together through their hydrophobic surfaces. This structure is very different from the dimerization domain of the vesicular stomatitis virus phosphoprotein and also from the tetramerization domain of the Sendai virus phosphoprotein, suggesting that oligomerization is conserved but not structure.
A V3 Loop-Dependent gp120 Element Disrupted by CD4 Binding Stabilizes the Human Immunodeficiency Virus Envelope Glycoprotein Trimer
Authors: Xiang Shi-Hua , Finzi Andrés , Pacheco Beatriz , Alexander Kevin , Yuan Wen , Rizzuto Carlo , Huang Chih-Chin , Kwong Peter D. , Sodroski Joseph
Published: January 2010

Human immunodeficiency virus (HIV-1) entry into cells is mediated by a trimeric complex consisting of noncovalently associated gp120 (exterior) and gp41 (transmembrane) envelope glycoproteins. The binding of gp120 to receptors on the target cell alters the gp120-gp41 relationship and activates the membrane-fusing capacity of gp41. Interaction of gp120 with the primary receptor, CD4, results in the exposure of the gp120 third variable (V3) loop, which contributes to binding the CCR5 or CXCR4 chemokine receptors. We show here that insertions in the V3 stem or polar substitutions in a conserved hydrophobic patch near the V3 tip result in decreased gp120-gp41 association (in the unliganded state) and decreased chemokine receptor binding (in the CD4-bound state). Subunit association and syncytium-forming ability of the envelope glycoproteins from primary HIV-1 isolates were disrupted more by V3 changes than those of laboratory-adapted HIV-1 envelope glycoproteins. Changes in the gp120 β2, β19, β20, and β21 strands, which evidence suggests are proximal to the V3 loop in unliganded gp120, also resulted in decreased gp120-gp41 association. Thus, a gp120 element composed of the V3 loop and adjacent beta strands contributes to quaternary interactions that stabilize the unliganded trimer. CD4 binding dismantles this element, altering the gp120-gp41 relationship and rendering the hydrophobic patch in the V3 tip available for chemokine receptor binding.
Pipeline plough performance in sand waves. Part 2: kinematic calculation method
Authors: Bransby Mark Fraser , Brown Michael John , Lauder Keith , Hatherley Andrew
Published: January 2010

Offshore pipelines can be buried in the seabed by ploughing a trench, placing the pipe at its base, and then backfilling. The presence of sand waves or megaripples on the seabed surface can affect the progress of the plough and prevent the plough from generating a level trench with a uniform trench depth. A calculation method has been presented that makes assumptions about the motion of the plough to predict the kinematics of ploughs through regions of nonuniform seabeds. Results from the calculation methodology are compared with those from small-scale model tests with good agreement, and the detailed kinematics of ploughs are then examined. The calculation method suggests that as a plough moves through a sand-wave field, the oscillation of the plough about the skids results in the trench base being formed alternately by the share tip and heel. The new method allows prediction of likely offshore plough performance given known plough geometry, sand wavelength, and wave amplitude and may be used as a tool for assessing the feasibility of pipeline ploughing in zones of sand waves or megaripples.
Évolution de la microtexture d’une matrice kaolinitique sur chemin triaxial axisymétrique
Authors: Hattab Mahdia , Bouziri-Adrouche Soumia , Fleureau Jean-Marie
Published: January 2010

L’objectif de cette recherche est de comprendre comment évolue la microtexture d’une matrice kaolinitique lorsque celle-ci est soumise à un chemin triaxial de révolution. L’approche consiste à réaliser un essai triaxial sur des éprouvettes du matériau saturé faiblement surconsolidé, puis à suivre l’évolution de la microstructure (orientation des particules et porosité) le long du chemin de chargement par des observations au microscope électronique à balayage. À l’état initial, le matériau est consolidé de façon uniaxiale, et les observations montrent une anisotropie microstructurale avec orientation privilégiée des particules suivant le plan horizontal perpendiculaire à la direction du chargement. Sur chemin isotrope, l’analyse montre une réorientation progressive des particules vers une isotropie structurale. Cette évolution se poursuit en début de chargement triaxial pour tendre ensuite vers une orientation privilégiée des particules selon un plan incliné en fin de chargement. L’évolution de la porosité est examinée à partir de mesures par porosimétrie au mercure, illustrées par des images seuillées de photos MEB. Celles-ci suggèrent l’existence d’une double porosité à l’état initial, qui semble se maintenir lors du chargement isotrope, puis évoluer vers une porosité unimodale, avec une légère diminution de la taille des pores, sur le chemin triaxial.
Variation in the phenology of bud flushing in white and red spruce
Authors: Blum Barton M.
Published: January 2010

Variation in bud flushing date as related to degree-day accumulation was determined among seed sources, families, and individual white spruce (Piceaglauca (Moench) Voss) trees in both a provenance study plantation and a progeny test of select trees on the Penobscot Experimental Forest in north central Maine. The primary purpose was to determine the feasibility of improving resistance to spruce budworm defoliation by selection for late bud flushing. Comparisons with native red spruce indicate that while some improvement in late flushing may be possible, it is unlikely that late flushing dates comparable with the mean for native red spruce can be achieved for white spruce.
Comparing site quality indices and productivity in ponderosa pine stands of western Montana
Authors: McLeod Scott D. , Running Steven W.
Published: January 2010

Four indices of site quality were compared with volume growth of pure, ideal ponderosa pine (Pinusponderosa Laws.) stands in western Montana. Indices based on quantifying the biophysical factors or physiological processes that control productivity (available water index and a relative index of seasonal photosynthesis from computer simulations) worked as well as those based on tree or stand measurements (site index and leaf area index). The following correlations of mean annual stem volume increment were found: with leaf area index, R2 = 0.93; with available water index, R2 = 0.95; with site index, R2 = 0.98; with gross photosynthesis R2 = 0.96. The available water and photosynthesis indices were also highly correlated to site index (R2 > 0.95). However, the tree-dependent site quality indices varied by stand density. Leaf area index and volume growth increased with stand density while site index decreased. Simulations indicated that depletion of soil water effectively halted transpiration and photosynthesis by midsummer and illustrated that even with adequate water, cold spring and fall temperatures ultimately defined the length of the growing season and hence site quality. We conclude that an ecosystem process model can provide an index to site quality independent of tree or stand measurements.
Quantitative estimation of fungal colonization of wood using an enzyme-linked immunosorbent assay
Authors: Breuil Colette , Seifert Keith A. , Yamada Jane , Rossignol Lynne , Saddler John N.
Published: January 2010

An enzyme-linked immunosorbent assay was developed for the quantitative detection of the sap-staining fungus Ophiostoma sp. C28 in artificially inoculated wood. The fungus can be detected in wood samples as small as 1 mg dry weight and at concentrations much lower than those at which staining becomes visible.
THE HEAT CAPACITIES FROM ANALYTICAL DISTRIBUTION FUNCTIONS
Authors: EMAMPOUR JALAL S. , MORSALI ALI , BEYRAMABADI S. ALI
Published: January 2010

The heat capacities and Joule–Thomson coefficients have been evaluated using three known analytical expressions for radial distribution functions (RDFs). Using such approach not only tests the power of distribution functions theory in predicting the heat capacities and Joule–Thomson coefficients, but also specifies better expressions in determining these properties. To calculate these quantities, the variation of RDF with density and temperature is required. Therefore, we should have analytical expressions which explicitly present RDF as a function of temperature, density, and interparticle distance. It is shown that if an expression is used which properly presents RDFs as a function of interparticle distance, density, and temperature, it is possible to calculate heat capacities and Joule–Thomson coefficients from distribution function theory.
THEORETICAL INVESTIGATION ON THE REACTION MECHANISM OF CuI-CATALYZED FORMATION OF ETHYL 2-PHENYLACETOACETATE
Authors: LI LAI-CAI , ZHANG YING , TIAN AN-MIN , WONG NING-BEW
Published: January 2010

The reaction mechanism of CuI -catalyzed formation of ethyl 2-phenylacetoacetate by arylation of ethyl acetoacetate has been investigated by density functional theory (DFT) using Becke's three-parameter nonlocal exchange functional and the Lee, Yang, and Parr nonlocal correlation functional (B3LYP). The geometries of the reactants, intermediates, transition states, and products have been optimized and verified by means of vibration frequency calculations. According to our assumption, this reaction can be divided into two stages. The rate-determining step is found to be the 3 → 4-TS procedure, which is the first procedure of stage 1. The low energy barrier of 39.85 kcal/mol indicates that this reaction can be carried out, which is in accordance with the experimental facts. For comparison, we have investigated the reaction mechanism of the same chemical reaction without CuI catalyst, whose energy barrier of rate-determining step is 212.76 kcal/mol higher than that with CuI catalyst. This fact suggests that CuI catalyst accelerates the reaction by remarkably lowering the energy barrier. The solvation effects on the barriers of the reaction are important. But the energetic order in DMSO solvent seems to be almost the same as that in gas-phase, which indicates that our conclusion achieved in gas-phase is believable. Our findings reveal the microscopic catalytic mechanism of CuI and are in agreement with the experimental facts.
Mitochondria-produced superoxide mediates angiotensin II-induced inhibition of neuronal potassium current
Authors: Yin Jing-Xiang , Yang Rui-Fang , Li Shumin , Renshaw Alex O. , Li Yu-Long , Schultz Harold D. , Zimmerman Matthew C.
Published: January 2010

Reactive oxygen species (ROS), particularly superoxide (O2·−), have been identified as key signaling intermediates in ANG II-induced neuronal activation and sympathoexcitation associated with cardiovascular diseases, such as hypertension and heart failure. Studies of the central nervous system have identified NADPH oxidase as a primary source of O2·− in ANG II-stimulated neurons; however, additional sources of O2·−, including mitochondria, have been mostly overlooked. Here, we tested the hypothesis that ANG II increases mitochondria-produced O2·− in neurons and that increased scavenging of mitochondria-produced O2·− attenuates ANG II-dependent intraneuronal signaling. Stimulation of catecholaminergic (CATH.a) neurons with ANG II (100 nM) increased mitochondria-localized O2·− levels, as measured by MitoSOX Red fluorescence. This response was significantly attenuated in neurons overexpressing the mitochondria-targeted O2·−-scavenging enzyme Mn-SOD. To examine the biological significance of the ANG II-mediated increase in mitochondria-produced O2·−, we used the whole cell configuration of the patch-clamp technique to record the well-characterized ANG II-induced inhibition of voltage-gated K+ current ( IKv) in neurons. Adenovirus-mediated Mn-SOD overexpression or pretreatment with the cell-permeable antioxidant tempol (1 mM) significantly attenuated ANG II-induced inhibition of IKv. In contrast, pretreatment with extracellular SOD protein (400 U/ml) had no effect. Mn-SOD overexpression also inhibited ANG II-induced activation of Ca2+/calmodulin kinase II, a redox-sensitive protein known to modulate IKv. These data indicate that ANG II increases mitochondrial O2·−, which mediates, at least in part, ANG II-induced activation of Ca2+/calmodulin kinase II and inhibition of IKv in neurons.
Role of FAK phosphorylation in hypoxia-induced hMSCS migration: involvement of VEGF as well as MAPKS and eNOS pathways
Authors: Lee Sang Hun , Lee Yu Jin , Song Chang Hun , Ahn Young Keun , Han Ho Jae
Published: January 2010

Here we show that the effect of hypoxia on human umbilical cord blood mesenchymal stem cell (hMSC) migration is via the modulation of focal adhesion kinase (FAK) and its related signaling pathways. Hypoxia increased hMSC migration and cell viability, whereas lactate dehydrogenase (LDH) release was not affected for up to 48 h (data not shown). In addition, hypoxia increased the level of reactive oxygen species (ROS) generation in a time-dependent manner. Hypoxia-induced phosphorylation of p38 mitogen-activated protein kinase (MAPK) and stress-activated protein kinase/c-Jun NH2-terminal kinase (SAPK/JNK) were inhibited by the antioxidant ( N-acetylcysteine, NAC, 10−6 M) and (taurine, 4×10−6 M). Hypoxia-induced endothelial nitric oxide synthase (eNOS) phosphorylation was regulated by p38 MAPK and SAPK/JNK activation. In addition, hypoxia increased the level of hypoxia inducible factor (HIF)-1α expression, which was blocked by inhibition of eNOS. Also, hypoxia-induced expression of Flk-1, vascular endothelial growth factor (VEGF), and its secreted form were inhibited by HIF-1α small interfering RNA (siRNA). In this hypoxic condition, FAK and Src phosphorylation were increased in a time-dependent manner. Inhibition of Src with specific inhibitor (PP2, 10−8 M) blocked hypoxia-induced FAK activation. Subsequently, hypoxia-induced FAK phosphorylation was blocked by VEGF siRNA. Finally, hypoxia-induced increase of hMSC migration was inhibited by FAK siRNA. The results indicate that hypoxia increases migration of hMSCs via VEGF-mediated FAK phospholylation and involves the cooperative activity of the ROS, MAPK, eNOS and HIF-1α pathways.
Laminin regulates mouse embryonic stem cell migration: involvement of Epac1/Rap1 and Rac1/cdc42
Authors: Suh Han Na , Han Ho Jae
Published: January 2010

Laminin is the first extracellular matrix (ECM) component to be expressed in the developing mammalian embryo. However, the roles of laminin or the related signal pathways are not well known in mouse embryonic stem cells (mESCs). Presently, we examined the effect of laminin on mESC migration. Laminin (10 μg/ml) decreased cell aggregation, whereas migration was increased. Laminin bound α6β1 integrin and laminin receptor 1 (LR1), decreasing their mRNA levels. Laminin increased focal adhesion kinase (FAK) and paxillin phosphorylation, cAMP intracellular concentration, and the protein levels of exchange factor directly activated by cAMP (Epac1) and Rap1. These increases were completely blocked by α6β1 integrin and LR1 neutralizing antibody, indicating that laminin-bound LR1 assists laminin-induced α6β1 integrin activity and initiates signal. As a downstream signal molecule, laminin activated small G protein such as Rac1/cdc42 and its effector protein p21-activated kinase (PAK). Subsequently, laminin stimulated E-cadherin complex disruption. Inhibition of each pathway such as those for α6β1 integrin and LR1, FAK, Rap1, and PAK1 blocked laminin-induced migration. We conclude that laminin binds both α6β1 integrin and LR1 and induces signaling FAK/paxillin and cAMP/Epac1/Rap1. These signaling merge at Rac1/cdc42 subsequently activate PAK1. Activated PAK1 enhances E-cadherin complex disruption and finally increases mESCs migration.