bluuebunny/crossref_metadata_2025 huggingface dataset:
Fowlpox Virus Encodes a Bcl-2 Homologue That Protects Cells from Apoptotic Death through Interaction with the Proapoptotic Protein Bak
Authors: Banadyga Logan , Gerig Jenna , Stewart Tara , Barry Michele
Published: August 2007

Poxviruses are renowned for encoding numerous immunomodulatory proteins capable of undermining potent immune defenses. One effective barrier against infection is apoptosis, a process controlled at the mitochondria by pro- and antiapoptotic members of the highly conserved Bcl-2 family of proteins. Although poxviruses are known to encode an array of effective inhibitors of apoptosis, members of the
Avipoxvirus
genus, which includes fowlpox virus, encode proteins with Bcl-2 homology. Here, we show that FPV039, a fowlpox virus protein with limited Bcl-2 homology, inhibited apoptosis in response to a variety of cytotoxic stimuli, including virus infection itself. Similar to other antiapoptotic Bcl-2 proteins, FPV039 localized predominantly to the mitochondria in both human and chicken cells and protected human cells from tumor necrosis factor alpha-induced loss of the mitochondrial membrane potential. In addition, coimmunoprecipitation revealed that FPV039 interacted constitutively with the proapoptotic Bcl-2 protein, Bak, in both human and chicken cells. Concordantly, FPV039 also inhibited apoptosis induced by the transient overexpression of Bak. To confirm these results in the context of virus infection, we generated a recombinant vaccinia virus lacking F1L, the endogenous apoptotic inhibitor in vaccinia virus, and expressing FPV039. In the context of vaccinia virus infection, FPV039 retained the ability to localize to the mitochondria and interacted with Bak. Moreover, FPV039 prevented the activation of Bak and protected infected cells from apoptosis induced by staurosporine and virus infection. Together, our data indicate that FPV039 is a functional Bcl-2 homologue that inhibits apoptosis by neutralizing the proapoptotic Bcl-2 family member Bak.
Pathogenic Potential of Borna Disease Virus Lacking the Immunodominant CD8 T-Cell Epitope
Authors: Richter Kirsten , Baur Karen , Ackermann Andreas , Schneider Urs , Hausmann Jürgen , Staeheli Peter
Published: August 2007

Borna disease virus (BDV) is a highly neurotropic, noncytolytic virus. Experimentally infected B10.BR mice remain healthy unless specific antiviral T cells that infiltrate the infected brain are triggered by immunization. In contrast, infected MRL mice spontaneously mount an antiviral T-cell response that can result in meningoencephalitis and neurological disease. The antiviral T cells may, alternatively, eliminate the virus without inducing disease if they are present in sufficient numbers before the virus replicates to high titers. Since the immune response of H-2kmice is directed mainly against the epitope TELEISSI located in the viral nucleoprotein N, we generated BDV mutants that feature TQLEISSI in place of TELEISSI. We show that adoptive transfer of BDV N-specific CD8 T cells induced neurological disease in B10.BR mice persistently infected with wild-type BDV but not with the mutant virus expressing TQLEISSI. Surprisingly, the mutant virus replicated less well in adult MRL wild-type mice than in mutant mice lacking mature CD8 T cells. Furthermore, when MRL mice were infected with the TQLEISSI-expressing BDV mutant as newborns, neurological disease was observed, although at a lower rate and with slower kinetics than in mice infected with wild-type virus. These results confirm that TELEISSI is the major CD8 T-cell epitope in H-2kmice and suggest that unidentified minor epitopes are present in the BDV proteome which are recognized rather efficiently by antiviral T cells if the dominant epitope is absent.
Cytomegalovirus UL131-128 Products Promote gB Conformational Transition and gB-gH Interaction during Entry into Endothelial Cells
Authors: Patrone Marco , Secchi Massimiliano , Bonaparte Eleonora , Milanesi Gabriele , Gallina Andrea
Published: August 2007

Herpesviruses use gB and gH-gL glycoproteins to execute fusion. Other virus-specific glycoproteins are required for receptor binding and fusion activation. The human cytomegalovirus (HCMV) UL131-128 proteins are essential for the infection of leukocytes, endothelial cells (ECs), and many epithelial cell lines. Here we show that UL131-128 play a role in a chain of events involving gB and gH during HCMV entry into ECs. An HCMV strain bearing the wild-type (wt) UL131-128 locus exhibited a gB transition from a protease-resistant to protease-sensitive form, a conformational change that was suppressed by a thiourea inhibitor of fusion (WY1768); in contrast, gH was susceptible to proteolysis throughout entry. Moreover, gB and gH transiently interacted, and a lipid mixing assay showed that the wt strain had carried out fusion by 60 min postinfection. However, these events were greatly altered when UL131-128-defective strains were used for infection or when there was an excess of soluble pUL128 during wt infection: the gB conformational change became WY1768 resistant, the gB-gH complex was no longer observed, and fusion was prevented. Both gB and gH in this case showed late protease resistance, related to their endocytic uptake. Our data point to the involvement of UL131-128 proteins in driving gB through a WY1768-sensitive fold transition, thus promoting a short-lived gB-gH complex and fusion; they also suggest that HCMV fuses with the EC plasma membrane and that endocytosis ensues only when the virus cannot trigger UL131-128-dependent steps.
Human Transcriptome Subtraction by Using Short Sequence Tags To Search for Tumor Viruses in Conjunctival Carcinoma
Authors: Feng Huichen , Taylor Jennifer L. , Benos Panayiotis V. , Newton Robert , Waddell Keith , Lucas Sebastien B. , Chang Yuan , Moore Patrick S.
Published: August 2007

Digital transcript subtraction (DTS) was developed to subtract in silico known human sequences from expression library data sets, leaving candidate nonhuman sequences for further analysis. This approach requires precise discrimination between human and nonhuman cDNA sequences. Database comparisons show high likelihood that small viral sequences can be successfully distinguished from human sequences. DTS analysis of 9,026 20-bp tags from an expression library of BCBL-1 cells infected with Kaposi's sarcoma-associated herpesvirus (KSHV) resolved all but three candidate sequences. Two of these sequences belonged to KSHV transcripts, and the third belonged to an unannotated human expression sequence tag. Overall, 0.24% of transcripts from this cell line were of viral origin. DTS analysis of 241,122 expression tags from three squamous cell conjunctival carcinomas revealed that only 21 sequences did not align with sequences from human databases. All 21 candidates amplify human transcripts and have secondary evidence for being of human origin. This analysis shows that it is unlikely that distinguishable viral transcripts are present in conjunctival carcinomas at 20 transcripts per million or higher, which is the equivalent of approximately 4 transcripts per cell. DTS is a simple screening method to discover novel viral nucleic acids. It provides, for the first time, quantitative evidence against some classes of viral etiology when no viral transcripts are found, thereby reducing the uncertainty involved in new pathogen discovery.
Rescue of Influenza C Virus from Recombinant DNA
Authors: Crescenzo-Chaigne Bernadette , van der Werf Sylvie
Published: August 2007

The rescue of influenza viruses by reverse genetics has been described only for the influenza A and B viruses. Based on a similar approach, we developed a reverse-genetics system that allows the production of influenza C viruses entirely from cloned cDNA. The complete sequences of the 3′ and 5′ noncoding regions of type C influenza virus C/Johannesburg/1/66 necessary for the cloning of the cDNA were determined for the seven genomic segments. Human embryonic kidney cells (293T) were transfected simultaneously with seven plasmids that direct the synthesis of each of the seven viral RNA segments of the C/JHB/1/66 virus under the control of the human RNA polymerase I promoter and with four plasmids encoding the viral nucleoprotein and the PB2, PB1, and P3 proteins of the viral polymerase complex. This strategy yielded between 103and 104PFU of virus per ml of supernatant at 8 to 10 days posttransfection. Additional viruses with substitutions introduced in the hemagglutinin-esterase-fusion protein were successfully produced by this method, and their growth phenotype was evaluated. This efficient system, which does not require helper virus infection, should be useful in viral mutagenesis studies and for generation of expression vectors from type C influenza virus.
Lethal Mutagenesis of Poliovirus Mediated by a Mutagenic Pyrimidine Analogue
Authors: Graci Jason D. , Harki Daniel A. , Korneeva Victoria S. , Edathil Jocelyn P. , Too Kathleen , Franco David , Smidansky Eric D. , Paul Aniko V. , Peterson Blake R. , Brown Daniel M. , Loakes David , Cameron Craig E.
Published: August 2007

Lethal mutagenesis is the mechanism of action of ribavirin against poliovirus (PV) and numerous other RNA viruses. However, there is still considerable debate regarding the mechanism of action of ribavirin against a variety of RNA viruses. Here we show by using T7 RNA polymerase-mediated production of PV genomic RNA, PV polymerase-catalyzed primer extension, and cell-free PV synthesis that a pyrimidine ribonucleoside triphosphate analogue (rPTP) with ambiguous base-pairing capacity is an efficient mutagen of the PV genome. The in vitro incorporation properties of rPTP are superior to ribavirin triphosphate. We observed a log-linear relationship between virus titer reduction and the number of rPMP molecules incorporated. A PV genome encoding a high-fidelity polymerase was more sensitive to rPMP incorporation, consistent with diminished mutational robustness of high-fidelity PV. The nucleoside (rP) did not exhibit antiviral activity in cell culture, owing to the inability of rP to be converted to rPMP by cellular nucleotide kinases. rP was also a poor substrate for herpes simplex virus thymidine kinase. The block to nucleoside phosphorylation could be bypassed by treatment with the P nucleobase, which exhibited both antiviral activity and mutagenesis, presumably a reflection of rP nucleotide formation by a nucleotide salvage pathway. These studies provide additional support for lethal mutagenesis as an antiviral strategy, suggest that rPMP prodrugs may be highly efficacious antiviral agents, and provide a new tool to determine the sensitivity of RNA virus genomes to mutagenesis as well as interrogation of the impact of mutational load on the population dynamics of these viruses.
Torque Teno Virus (SANBAN Isolate) ORF2 Protein Suppresses NF-κB Pathways via Interaction with IκB Kinases
Authors: Zheng Hong , Ye Linbai , Fang Xiaonan , Li Baozong , Wang Yuhua , Xiang Xiaoxiao , Kong Lingbao , Wang Wei , Zeng Yinchun , Ye Li , Wu Zhenghui , She Yinglong , Zhou Xiaolin
Published: August 2007

Since the first discovery of Torque teno virus (TTV) in 1997, many researchers focused on its epidemiology and transcriptional regulation, but the function of TTV-encoded proteins remained unknown. The function of the TTV open reading frame (ORF) in the nuclear factor κB (NF-κB) pathway has not yet been established. In this study, we found for the first time that the TTV ORF2 protein could suppress NF-κB activity in a dose-dependent manner in the canonical NF-κB pathway. By Western blot analysis, we proved that the TTV ORF2 protein did not alter the level of NF-κB expression but prevented the p50 and p65 subunits from entering the nucleus due to the inhibition of IκBα protein degradation. Further immunoprecipitation assays showed that the TTV ORF2 protein could physically interact with IKKβ as well as IKKα, but not IKKγ. Luciferase assays and Western blot experiments showed that the TTV ORF2 protein could also suppress NF-κB activity in the noncanonical NF-κB pathway and block the activation and translocation of p52. Finally, we found that the TTV ORF2 protein inhibited the transcription of NF-κB-mediated downstream genes (interleukin 6 [IL-6], IL-8, and COX-2) through down-regulation of NF-κB. Together, these data indicate that the TTV ORF2 protein suppresses the canonical and noncanonical NF-κB pathways, suggesting that the TTV ORF2 protein may be involved in regulating the innate and adaptive immunity of organisms, contributing to TTV pathogenesis, and even be related to some diseases.
Pathogenesis of Avian Influenza (H7) Virus Infection in Mice and Ferrets: Enhanced Virulence of Eurasian H7N7 Viruses Isolated from Humans
Authors: Belser Jessica A. , Lu Xuihua , Maines Taronna R. , Smith Catherine , Li Yan , Donis Ruben O. , Katz Jacqueline M. , Tumpey Terrence M.
Published: August 2007

Before 2003, only occasional case reports of human H7 influenza virus infections occurred as a result of direct animal-to-human transmission or laboratory accidents; most of these infections resulted in conjunctivitis. An increase in isolation of avian influenza A H7 viruses from poultry outbreaks and humans has raised concerns that additional zoonotic transmissions of influenza viruses from poultry to humans may occur. To better understand the pathogenesis of H7 viruses, we have investigated their ability to cause disease in mouse and ferret models. Mice were infected intranasally with H7 viruses of high and low pathogenicity isolated from The Netherlands in 2003 (Netherlands/03), the northeastern United States in 2002-2003, and Canada in 2004 and were monitored for morbidity, mortality, viral replication, and proinflammatory cytokine production in respiratory organs. All H7 viruses replicated efficiently in the respiratory tracts of mice, but only Netherlands/03 isolates replicated in systemic organs, including the brain. Only A/NL/219/03 (NL/219), an H7N7 virus isolated from a single fatal human case, was highly lethal for mice and caused severe disease in ferrets. Supporting the apparent ocular tropism observed in humans following infection with viruses of the H7 subtype, both Eurasian and North American lineage H7 viruses were detected in the mouse eye following ocular inoculation, whereas an H7N2 virus isolated from the human respiratory tract was not. Therefore, in general, the relative virulence and cell tropism of the H7 viruses in these animal models correlated with the observed virulence in humans.
Fusion Induced by a Class II Viral Fusion Protein, Semliki Forest Virus E1, Is Dependent on the Voltage of the Target Cell
Authors: Markosyan Ruben M. , Kielian Margaret , Cohen Fredric S.
Published: August 2007

Cells expressing the low pH-triggered class II viral fusion protein E1 of Semliki Forest virus (SFV) were fused to target cells. Fusion was monitored by electrical capacitance and aqueous dye measurements. Electrical voltage-clamp measurements showed that SFV E1-induced cell-cell fusion occurred quickly after acidification for a trans-negative potential across the target membrane (i.e., negative potential inside the target cell) but that a trans-positive potential eliminated all fusion. Use of an ionophore to control potentials for a large population of cells confirmed the dependence of fusion on voltage polarity. In contrast, fusion induced by the class I fusion proteins of human immunodeficiency virus, avian sarcoma leukosis virus, and influenza virus was independent of the voltage polarity across the target cell. Initial pore size and pore growth were also independent of voltage polarity for the class I proteins. An intermediate of SFV E1-induced fusion was created by transient acidification at low temperature. Membranes were hemifused at this intermediate state, and raising the temperature at neutral pH allowed full fusion to occur. Capacitance measurements showed that maintaining a trans-positive potential definitely blocked fusion at steps following the creation of the hemifusion intermediate and may have inhibited fusion at prior steps. It is proposed that the trans-negative voltage across the endosomal membrane facilitates fusion after low-pH-induced conformational changes of SFV E1 have occurred.
Severe Acute Respiratory Syndrome Coronavirus Gene 7 Products Contribute to Virus-Induced Apoptosis
Authors: Schaecher Scott R. , Touchette Erin , Schriewer Jill , Buller R. Mark , Pekosz Andrew
Published: August 2007

The proteins encoded by gene 7 of the severe acute respiratory syndrome coronavirus (SARS-CoV) have been demonstrated to have proapoptotic activity when expressed from cDNA but appear to be dispensable for virus replication. Recombinant SARS-CoVs bearing deletions in gene 7 were used to assess the contribution of gene 7 to virus replication and apoptosis in several transformed cell lines, as well as to replication and pathogenesis in golden Syrian hamsters. Deletion of gene 7 had no effect on SARS-CoV replication in transformed cell lines, nor did it alter the induction of early apoptosis markers such as annexin V binding and activation of caspase 3. However, viruses with gene 7 disruptions were not as efficient as wild-type virus in inducing DNA fragmentation, as judged by terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) staining, indicating that the gene 7 products do contribute to virus-induced apoptosis. Disruption of gene 7 did not affect virus replication or morbidity in golden Syrian hamsters, suggesting that the gene 7 products are not required for acute infection in vivo. The data indicate that open reading frames 7a and 7b contribute to but are not solely responsible for the apoptosis seen in SARS-CoV-infected cells.
Critical Role for Arginine Methylation in Adenovirus-Infected Cells
Authors: Iacovides Demetris C. , O'Shea Clodagh C. , Oses-Prieto Juan , Burlingame Alma , McCormick Frank
Published: August 2007

During the late stages of adenovirus infection, the 100K protein (100K) inhibits the translation of cellular messages in the cytoplasm and regulates hexon trimerization and assembly in the nucleus. However, it is not known how it switches between these two functions. Here we show that 100K is methylated on arginine residues at its C terminus during infection and that this region is necessary for binding PRMT1 methylase. Methylated 100K is exclusively nuclear. Mutation of the third RGG motif (amino acids 741 to 743) prevents localization to the nucleus during infection, suggesting that methylation of that sequence is important for 100K shuttling. Treatment of infected cells with methylation inhibitors inhibits expression of late structural proteins. These data suggest that arginine methylation of 100K is necessary for its localization to the nucleus and is a critical cellular function necessary for productive adenovirus infection.
Neonatal volume guarantee ventilation: effects of spontaneous breathing, triggered and untriggered inflations
Authors: McCallion N , Lau R , Morley C J , Dargaville P A
Published: August 2007

Background:

During volume guarantee (VG) ventilation the peak inflating pressure (PIP) for each ventilator inflation is adjusted to ensure the expired tidal volume (VTe) is close to the set VTe. Differences in the PIP between inflations triggered by the infant’s inspirations and untriggered inflations are seen.

Aim:

To investigate the effects of triggered and untriggered inflations on PIP and VTe.

Methods:

Neonates were ventilated with the Dräger Babylog 8000 using assist control (synchronous intermittent positive pressure ventilation) and VG modes. Continuous recordings of ventilator pressures and tidal volumes were made at 200 Hz for 10 minutes.

Results:

In 10 infants, 6540 inflations were analysed, of which 4052 (62%) were triggered. Triggered inflations had a significantly lower mean (SD) PIP than untriggered inflations: 12.9 (4.9) vs 17.0 (3.3) cm H2O, (p<0.001). Despite this, there was no significant difference in the VTe of each type of inflation (103% and 101% of the set VTe, respectively). When a triggered inflation was immediately preceded or followed by an untriggered inflation the PIP changed by about 5 cm H2O. Between adjacent inflations of the same type, the change in PIP was less than 3 cm H2O: for triggered inflations it was 0.11 (1.50) cm H2O and for untriggered inflations 0.06 (1.53) cm H2O.

Conclusion:

During VG ventilation with the Dräger Babylog 8000 the PIP was 4 cm H2O lower during triggered inflations than untriggered inflations, although the expired tidal volumes were similar.
TRANSMEMBRANE STRUCTURE PREDICTIONS WITH HYDROPATHY INDEX/CHARGE TWO-DIMENSIONAL TRAJECTORIES OF STOCHASTIC DYNAMICAL SYSTEMS
Authors: KABURAGI TAKASHI , MURAMATSU DAIGO , MATSUMOTO TAKASHI
Published: August 2007

A novel algorithm is proposed for predicting transmembrane protein secondary structure from two-dimensional vector trajectories consisting of a hydropathy index and formal charge of a test amino acid sequence using stochastic dynamical system models. Two prediction problems are discussed. One is the prediction of transmembrane region counts; another is that of transmembrane regions, i.e. predicting whether or not each amino acid belongs to a transmembrane region. The prediction accuracies, using a collection of well-characterized transmembrane protein sequences and benchmarking sequences, suggest that the proposed algorithm performs reasonably well. An experiment was performed with a glutamate transporter homologue from Pyrococcus horikoshii. The predicted transmembrane regions of the five human glutamate transporter sequences and observations based on the computed likelihood are reported.
ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES
Authors: KUNDROTAS PETRAS , GEORGIEVA PAULINA , SHOSHEVA ALEXANDRA , CHRISTOVA PETYA , ALEXOV EMIL
Published: August 2007

In this study, we address the issue of performing meaningful pKa calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pKa values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pKa calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pKa values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pKa calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pKa fluctuations among the models or have pKa values shifted by several pH units with respect to the pKa calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pKa calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pKa values for highly conserved titratable residues within large sets of homologous proteins.
Geochronology and the geological record
Authors: Snelling N.J.
Published: August 2007

Some history

By about the middle of the nineteeth century natural scientists had come to the conclusion that geological time was to be measured in hundreds of millions of years. Darwin in the first edition of
The Origin of Species
published in 1859 estimated that 300 million years had elapsed since the end of the Mesozoic Era; Lyell concluded in 1867 that about 240 million years had elapsed since the beginning of the Ordovician Period. Despite the temptation to point out the obvious discrepancy in these particular estimates and to suggest that they were no more than educated guesses it must be remembered that they reflected the most careful marshalling of a vast number of verifiable observations. Indeed they can now be seen to be remarkably realistic and in marked contrast to the estimates based on more theoretical considerations such as ocean salinity, sediment thickness, the cooling of the Earth or the Sun's energy source.

Towards the end of the nineteenth century the geologists' views regarding the age of the Earth came under particularly strong attack from W. Thomson (later Lord Kelvin) whose arguments were based on the energy source of the Sun and the cooling history of the Earth, and who concluded that the Earth was probably younger than about 100 million years. That geologists found Thomson's estimates thoroughly unpalatable is very clear from the literature of the time but his calculations were apparently irrefutable. However, the impasse was soon to be resolved following the discovery of the phenomenon of radioactivity
Precambrian geochronology and the geological record
Authors: Moorbath S. , Taylor P. N.
Published: August 2007

Rb-Sr, Sm-Nd and Pb/Pb whole-rock isochron methods and the U-Pb zircon method have been widely applied to dating Precambrian igneous and meta-igneous rocks. Application of these methods in regional geochronological studies provides reliable constraints on the age and temporal evolution of rock units, even when some parent-daughter systems have suffered disturbance in metamorphic and/or metasomatic events which significantly post-date primary rock formation. Initial isotopic compositions of Sr, Nd and Pb aid geological interpretation of isochron age data, constrain crustal residence time of the protoliths and can be used to assess the relative contributions of mantle and crust in magma genesis.

Precambrian sediments can be indirectly dated by reference to age data on interbedded volcanics, or by age-bracketing between dated basement rocks and dated cross-cutting intrusives. Significant progress has also been made in the direct dating of sedimentary rocks. Published isotopic age determinations on early Precambrian sediments containing biogenic remains are briefly reviewed. Provided that stratigraphical and geochronological correlations are correct, it appears that stromatohtic limestones were being deposited by
c.
3400 - 3300 Ma ago, and that true microfossils occur in rocks dated at
c.
3200 - 3000 Ma. Evidence relating to possible biogenic markers in sediments reliably dated at
c.
3800 - 3700 Ma is not yet definitive.
The Ordovician, Silurian and Devonian periods
Authors: McKerrow W. S. , Lambert R. St. J. , Cocks L. R. M.
Published: August 2007

A reassessment of published age determinations, including some recent dates on Middle Devonian, Late Silurian, basal Caradoc and middle Arenig rocks, enables the construction of a more precise time-scale. The most accurate points on our scale are: basal Frasnian, 368 ± 8 Ma; early Ludlow, 421 ± 2 Ma; end of early Llandovery, 431 ± 6 Ma; early Caradoc, 450 ± 7; middle Arenig, 482 ± 5 Ma. Interpolations from these data indicate that the base of the Devonian is 412 ± 5 Ma, and the base of the Silurian is 435 ± 7 Ma. The end of the Devonian is less precise, we estimated it to be at 354 + 10, -5 Ma (depending on stratigraphic and sedimentological estimates for the duration of the Frasnian and Famennian stages). The base of the Tremadoc is perhaps 513 ± 10 Ma. Dating by K/Ar,
40
Ar/
39
Ar, U/Pb and Sm/Nd all show good agreement, but some Rb/Sr isochrons on acid volcanic rocks lie off our time-scale line. Most fission track dates on zircons from bentonites have very large errors; a few with the smallest errors are shown on our graph, but none of them have been precise enough to use in the construction of the time-scale.
Geochronology of the Carboniferous, Permian and Triassic
Authors: Forster S. C. , Warrington G.
Published: August 2007

Criteria concerning sample and analytical data and stratigraphic control have been used in a critical assessment of the suitability, for use in construction of a Phancrozoic time-scale, of radiometric data relevant to the Carboniferous, Permian and Triassic periods. Few of the age determinations available in 1982 satisfy these criteria and many of those used previously as a basis for time-scales for this part of the Phanerozoic are considred unacceptable by present standards. On the basis of this review, ages of 365 ± 5 Ma, 290 ± Ma and 250 © 5 Ma. respectively, are proposed for the beginning of the Carboniferous. Permain and Triassic periods, and 205 © 5 Ma for the end of the Triassic. Radiometric ages are related. where possible, to the principal chronostratigraphic divisions of the rock successions representing those periods.
Jurassic to Paleogene: Part 2 Paleogene geochronology and chronostratigraphy
Authors: Berggren W. A. , Kent Dennis V. , Flynn John J.
Published: August 2007

We present a revised Paleogene geochronology based upon a best fit to selected high temperature radiometric dates on a number of identified magnetic polarity chrons (within the late Cretaceous, Paleogene and Neogene) which minimizes apparent accelerations in sea-floor spreading. An assessment of first order correlations of calcareous plankton biostratigraphic datum events to magnetic polarity stratigraphy yields the following estimated magnetobiochronology of major chronostratigraphic boundaries: Cretaceous-Tertiary boundary (Chron C29R), 66.4 Ma; Paleocene-Eocene (Chron C24R), 57.8 Ma; Eocene-Oligocene (Chron C13R), 36.6 Ma; Oligocene-Miocene (Chron C6CN), 23.7 Ma.

The Eocene is seen to have expanded chronologically (~ 21 m.y.) at the expense of the Paleocene (~ 9 m.y.) and is indeed the longest of the Cenozoic epochs. In addition, magnetobiostratigraphic correlations require adjustments in apparent correlations with standard marine stage boundaries in some cases (particularly in the Oligocene). Finally, we present a correlation between standard Paleogene marine and terrestrial stratigraphies.
The Neogene: Part 1
Authors: Jenkins D. G. , Bowen D. Q. , Adams C. G. , Shackleton N. J. , Brassell S. C.
Published: August 2007

The Neogene is taken to include the Miocene, Pliocene, Pleistocene and Holocene, and a well established sequence of marine stages now exists from the early Miocene Aquitanian to the Calabrian in the early Pleistocene. Up-to-date reviews are provided for the classification of continental Pleistocene deposits, oxygen and carbon isotope stratigraphy, organic geochemical stratigraphy and the letter classification of the East Indies Neogene. Major boundaries of the Miocene have been narrowed down to durations of about 1 Ma or less and to progressively shorter durations for the Pleistocene to Holocene boundaries. Future work will have to identify and date these boundaries in stratotype sections. Authors contributions are identified by initials at the end of each section.
A Global Review of the Distribution, Taxonomy, and Impacts of Introduced Seaweeds
Authors: Williams Susan L. , Smith Jennifer E.
Published: August 2007

We reviewed over 407 global seaweed introduction events and have increased the total number of introduced seaweed species to 277. Using binomial tests we show that several algal families contain more successful invaders than would be expected by chance, highlighting groups that should be targeted for management. Hull-fouling and aquaculture are the most significant sources of seaweed invaders and should be carefully regulated. The ecological effects of introduced seaweeds have been studied in only 6% of the species, but these studies show mostly negative effects or changes to the native biota. Herbivores generally prefer native to introduced seaweeds, and are unlikely to control spread, as they can do in other habitats. Undisturbed marine communities can be at least initially resistant to most introduced seaweeds aside from the siphonous green species; however, disturbances and eutrophication can facilitate invasion. Major research gaps include community-level ecological studies and economic assessments.
Functional Versus Morphological Diversity in Macroevolution
Authors: Wainwright Peter C.
Published: August 2007

Studies of the evolution of phenotypic diversity have gained momentum among neontologists interested in the uneven distribution of diversity across the tree of life. Potential morphological diversity in a lineage is a function of the number of independent parameters required to describe the form, and innovations such as structural duplication and functional decoupling can enhance the potential for diversity in a given clade. The functional properties of organisms are determined by underlying parts, but any property that is determined by three or more parts expresses many-to-one mapping of form to function, in which many morphologies will have the same functional property. This ubiquitous feature of organismal design results in surfaces of morphological variation that are neutral with respect to the functional property, and enhances the potential for simultaneously optimizing two or more functions of the system.
Human adipose-derived adult stem cells upregulate palladin during osteogenesis and in response to cyclic tensile strain
Authors: Wall Michelle E. , Rachlin Andrew , Otey Carol A. , Loboa Elizabeth G.
Published: August 2007

Cell morphology may be an important stimulus during differentiation of human adipose-derived adult stem (hADAS) cells, but there are limited studies that have investigated the role of the cytoskeleton or associated proteins in hADAS cells undergoing differentiation. Palladin is an actin-associated protein that plays an integral role in focal adhesion and cytoskeleton organization. In this study we show that palladin was expressed by hADAS cells and was modulated during osteogenic differentiation and in response to cyclic tensile strain. Human ADAS cells expressed the 90- and 140-kDa palladin isoforms and upregulated expression of both isoforms after culture in conditions that promoted osteogenesis. Palladin mRNA expression levels were also increased in hADAS cells subjected to cyclic tensile strain. Knockdown of the palladin gene during osteogenesis resulted in decreased actin stress fibers and decreased protein levels of Eps8, an epidermal growth factor receptor tyrosine kinase that colocalizes with actin. Silencing the palladin gene, however, did not affect hADAS cells' commitment down the osteogenic lineage.
Electrophysiological properties of human adipose tissue-derived stem cells
Authors: Bai Xiaowen , Ma Junyi , Pan Zhizhong , Song Yao-Hua , Freyberg Susanne , Yan Yasheng , Vykoukal Daynene , Alt Eckhard
Published: August 2007

Human adipose tissue-derived stem cells (hASCs) represent a potentially valuable cell source for clinical therapeutic applications. The present study was designed to investigate properties of ionic channel currents present in undifferentiated hASCs and their impact on hASCs proliferation. The functional ion channels in hASCs were analyzed by whole-cell patch-clamp recording and their mRNA expression levels detected by RT-PCR. Four types of ion channels were found to be present in hASCs: most of the hASCs (73%) showed a delayed rectifier-like K+ current ( IKDR); Ca2+-activated K+ current ( IKCa) was detected in examined cells; a transient outward K+ current ( Ito) was recorded in 19% of the cells; a small percentage of cells (8%) displayed a TTX-sensitive transient inward sodium current ( INa.TTX). RT-PCR results confirmed the presence of ion channels at the mRNA level: Kv1.1, Kv2.1, Kv1.5, Kv7.3, Kv11.1, and hEAG1, possibly encoding IKDR; MaxiK, KCNN3, and KCNN4 for IKCa; Kv1.4, Kv4.1, Kv4.2, and Kv4.3 for Ito and hNE-Na for INa.TTX. The IKDR was inhibited by tetraethyl ammonium (TEA) and 4-aminopyridine (4-AP), which significantly reduced the proliferation of hASCs in a dose-dependent manner ( P < 0.05), as suggested by bromodeoxyurindine (BrdU) incorporation. Other selective potassium channel blockers, including linopiridine, iberiotoxin, clotrimazole, and apamin also significantly inhibited IKDR. TTX completely abolished INa.TTX. This study demonstrates for the first time that multiple functional ion channel currents such as IKDR, IKCa, Ito, and INa.TTX are present in undifferentiated hASCs and their potential physiological function in these cells as a basic understanding for future in vitro experiments and in vivo clinical investigations.
Ca2+/calmodulin-dependent protein kinase kinase is involved in AMP-activated protein kinase activation by α-lipoic acid in C2C12 myotubes
Authors: Shen Qingwu W. , Zhu Mei J. , Tong Junfeng , Ren Jun , Du Min
Published: August 2007

-α-Lipoic acid (ALA) widely exists in foods and is an antidiabetic agent. ALA stimulates glucose uptake and increases insulin sensitivity by the activation of AMP-activated protein kinase (AMPK) in skeletal muscle, but the underlying mechanism for AMPK activation is unknown. Here, we investigated the mechanism through which ALA activates AMPK in C2C12 myotubes. Incubation of C2C12 myotubes with 200 and 500 μM ALA increased the activity and phosphorylation of the AMPK α-subunit at Thr172. Phosphorylation of the AMPK substrate, acetyl CoA carboxylase (ACC), at Ser79was also increased. No difference in ATP, AMP, and the calculated AMP-to-ATP ratio was observed among the different treatment groups. Since the upstream AMPK kinase, LKB1, requires an alteration of the AMP-to-ATP ratio to activate AMPK, this data showed that LKB1 might not be involved in the activation of AMPK induced by ALA. Treatment of ALA increased the intracellular Ca2+concentration measured by fura-2 fluorescent microscopy ( P < 0.05), showing that ALA may activate AMPK through enhancing Ca2+/calmodulin-dependent protein kinase kinase (CaMKK) signaling. Indeed, chelation of intracellular free Ca2+by loading cells with 25 μM BAPTA-AM for 30 min abolished the ALA-induced activation of AMPK and, in turn, phosphorylation of ACC at Ser79. Furthermore, inhibition of CaMKK using its selective inhibitor, STO-609, abolished ALA-stimulated AMPK activation, with an accompanied reduction of ACC phosphorylation at Ser79. In addition, ALA treatment increased the association of AMPK with CaMKK. To further show the role of CaMKK in AMPK activation, short interfering RNA was used to silence CaMKK, which abolished the ALA-induced AMPK activation. These data show that CaMKK is the kinase responsible for ALA-induced AMPK activation in C2C12 myotubes.
Polyamine homeostasis in arginase knockout mice
Authors: Deignan Joshua L. , Livesay Justin C. , Shantz Lisa M. , Pegg Anthony E. , O'Brien William E. , Iyer Ramaswamy K. , Cederbaum Stephen D. , Grody Wayne W.
Published: August 2007

The role of ornithine decarboxylase (ODC) in polyamine metabolism has long been established, but the exact source of ornithine has always been unclear. The arginase enzymes are capable of producing ornithine for the production of polyamines and may hold important regulatory functions in the maintenance of this pathway. Utilizing our unique set of arginase single and double knockout mice, we analyzed polyamine levels in the livers, brains, kidneys, and small intestines of the mice at 2 wk of age, the latest timepoint at which all of them are still alive, to determine whether tissue polyamine levels were altered in response to a disruption of arginase I (AI) and II (AII) enzymatic activity. Whereas putrescine was minimally increased in the liver and kidneys from the AII knockout mice, spermidine and spermine were maintained. ODC activity was not greatly altered in the knockout animals and did not correlate with the fluctuations in putrescine. mRNA levels of ornithine aminotransferase (OAT), antizyme 1 (AZ1), and spermidine/spermine- N1-acetyltransferase (SSAT) were also measured and only minor alterations were seen, most notably an increase in OAT expression seen in the liver of AI knockout and double knockout mice. It appears that putrescine catabolism may be affected in the liver when AI is disrupted and ornithine levels are highly reduced. These results suggest that endogenous arginase-derived ornithine may not directly contribute to polyamine homeostasis in mice. Alternate sources such as diet may provide sufficient polyamines for maintenance in mammalian tissues.
Chronic intermittent hypoxia causes hepatitis in a mouse model of diet-induced fatty liver
Authors: Savransky Vladimir , Bevans Shannon , Nanayakkara Ashika , Li Jianguo , Smith Philip L. , Torbenson Michael S. , Polotsky Vsevolod Y.
Published: August 2007

Obstructive sleep apnea (OSA) causes chronic intermittent hypoxia (CIH) during sleep. OSA is associated with nonalcoholic steatohepatitis (NASH) in obese individuals and may contribute to progression of nonalcoholic fatty liver disease from steatosis to NASH. The purpose of this study was to examine whether CIH induces inflammatory changes in the liver in mice with diet-induced hepatic steatosis. C57BL/6J mice ( n = 8) on a high-fat, high-cholesterol diet were exposed to CIH for 6 mo and were compared with mice on the same diet exposed to intermittent air (control; n = 8). CIH caused liver injury with an increase in serum ALT (461 ± 58 U/l vs. 103 ± 16 U/l in the control group; P < 0.01) and AST (637 ± 37 U/l vs. 175 ± 13 U/l in the control group; P < 0.001), whereas alkaline phosphatase and total bilirubin levels were unchanged. Histology revealed hepatic steatosis in both groups, with mild accentuation of fat staining in the zone 3 hepatocytes in mice exposed to CIH. Animals exposed to CIH exhibited lobular inflammation and fibrosis in the liver, which were not evident in control mice. CIH caused significant increases in lipid peroxidation in serum and liver tissue; significant increases in hepatic levels of myeloperoxidase and proinflammatory cytokines IL-1β, IL-6, and CXC chemokine MIP-2; a trend toward an increase in TNF-α; and an increase in α1(I)-collagen mRNA. We conclude that CIH induces lipid peroxidation and inflammation in the livers of mice on a high-fat, high-cholesterol diet.
Impaired deglutitive EGJ relaxation in clinical esophageal manometry: a quantitative analysis of 400 patients and 75 controls
Authors: Ghosh Sudip K. , Pandolfino John E. , Rice John , Clarke John O. , Kwiatek Monika , Kahrilas Peter J.
Published: August 2007

Assessing deglutitive esophagogastric junction (EGJ) relaxation is an essential focus of clinical manometry. Our aim was to apply automated algorithmic analyses to high-resolution manometry (HRM) studies to ascertain the optimal method for discriminating normal from abnormal deglutitive EGJ relaxation. All 473 subjects (73 controls) were studied with a 36-channel solid-state HRM assembly during water swallows. Patients were classified as: 1) achalasia, 2) postfundoplication, 3) nonachalasia with normal deglutitive EGJ relaxation, or 4) functional obstruction (preserved peristalsis with incomplete EGJ relaxation). Automated computer programs assessed the adequacy of EGJ relaxation by using progressively complex analysis routines to compensate for esophageal shortening, crural diaphragm contraction, and catheter movement, all potential confounders. The single-sensor method of assessing EGJ relaxation had a sensitivity of only 52% for detecting achalasia. Of the automated HRM analysis paradigms tested, the 4-s integrated relaxation pressure using a cutoff of 15 mmHg performed optimally with 98% sensitivity and 96% specificity in the detection of achalasia. We also identified a heterogeneous group of 26 patients with functional EGJ obstruction attributed to variant achalasia and other diverse pathology. Although further clinical experience will ultimately judge, it is our expectation that applying rigorous methodology such as described herein to the analysis of HRM studies will improve the consistency in the interpretation of clinical manometry and prove useful in guiding clinical management.
Physiological genetics of dietary restriction: uncoupling the body temperature and body weight responses
Authors: Rikke Brad A. , Johnson Thomas E.
Published: August 2007

Numerous physiological and molecular changes accompany dietary restriction (DR), which has been a major impediment to elucidating the causal basis underlying DR's many health benefits. Two major metabolic responses to DR that potentially underlie many of these changes are the body temperature ( Tb) and body weight (BW) responses. These responses also represent an especially difficult challenge to uncouple during DR. We demonstrate in this study, using two recombinant inbred (RI) panels of mice (the LXS and LSXSS) that naturally occurring genetic variation serves as a powerful tool for modulating Tb and BW independently during DR. The correlation coefficient between the two responses was essentially zero, with R = −0.04 in the LXS and −0.03 in the LSXSS, the latter averaged across replicate cohorts. This study is also the first to report that there is highly significant ( P = 10−10) strain variation in the Tb response to DR in the LXS (51 strains tested), with strain means ranging from 2 to 4°C below normal. The results suggest that the strain variation in the Tb response to DR is largely due to differences in the rate of heat loss rather than heat production (i.e., metabolic rate). This variation can thus be used to assess the long-term effects of lower Tb independent of BW or metabolic rate, as well as independent of food intake and motor activity as previously shown. These results also suggest that murine genetic variation may be useful for uncoupling many more responses to DR.
Effect of uremia on HDL composition, vascular inflammation, and atherosclerosis in wild-type mice
Authors: Bang Christian A. , Bro Susanne , Bartels Emil D. , Pedersen Tanja X. , Nielsen Lars B.
Published: August 2007

Wild-type mice normally do not develop atherosclerosis, unless fed cholic acid. Uremia is proinflammatory and increases atherosclerosis 6- to 10-fold in apolipoprotein E-deficient mice. This study examined the effect of uremia on lipoproteins, vascular inflammation, and atherosclerosis in wild-type C57BL/6J mice. Uremia was induced by nephrectomy (NX) and increased plasma urea and creatinine concentrations 2.5- to 4.5-fold; control mice were sham operated. After NX, mice were fed a Western-type diet or the same diet with 0.5% cholic acid. Cholic acid-fed NX mice did not thrive and were killed. In NX mice fed the Western-type diet ( n = 7), the total plasma cholesterol concentration was similar to that in sham mice ( n = 11), but on gel filtration the LDL/HDL cholesterol ratio was increased. HDL from NX mice contained more serum amyloid A and triglycerides and less cholesterol than HDL from sham mice. Plasma concentrations of sICAM-1 and sVCAM-1 and aortic mRNA expression of ICAM-1 and VCAM-1 did not differ between NX and sham mice. Twenty-six weeks after NX, the average oil red O-stained area of the aortic root was similar in NX and sham mice fed the Western-type diet, while it was increased in cholic acid-fed sham mice. The results suggest that moderate uremia neither induces aortic inflammation nor atherosclerosis in C57BL/6J mice despite increased LDL/HDL cholesterol ratio and altered HDL composition.