bluuebunny/crossref_metadata_2025 huggingface dataset:
CENP-O Class Proteins Form a Stable Complex and Are Required for Proper Kinetochore Function
Authors: Hori Tetsuya , Okada Masahiro , Maenaka Katsumi , Fukagawa Tatsuo
Published: December 2007

We previously identified a multisubunit complex (CENP-H/I complex) in kinetochores from human and chicken cells. We showed that the CENP-H/I complex is divided into three functional classes. In the present study, we investigated CENP-O class proteins, which include CENP-O, -P, -Q, -R, and -50 (U). We created chicken DT40 cell knockouts of each of these proteins, and we found that all knockout lines were viable, but that they showed slow proliferation and mitotic defects. Kinetochore localization of CENP-O, -P, -Q, and -50 was interdependent, but kinetochore localization of these proteins was observed in CENP-R–deficient cells. A coexpression assay in bacteria showed that CENP-O, -P, -Q, and -50 proteins form a stable complex that can associate with CENP-R. Phenotype analysis of knockout cells showed that all proteins except for CENP-R were required for recovery from spindle damage, and phosphorylation of CENP-50 was essential for recovery from spindle damage. We also found that treatment with the proteasome inhibitor MG132 partially rescued the severe mitotic phenotype observed in response to release from nocodazole block in CENP-50–deficient cells. This suggests that CENP-O class proteins are involved in the prevention of premature sister chromatid separation during recovery from spindle damage.
Shugoshin Promotes Sister Kinetochore Biorientation inSaccharomyces cerevisiae
Authors: Kiburz Brendan M. , Amon Angelika , Marston Adele L.
Published: December 2007

Chromosome segregation must be executed accurately during both mitotic and meiotic cell divisions. Sgo1 plays a key role in ensuring faithful chromosome segregation in at least two ways. During meiosis this protein regulates the removal of cohesins, the proteins that hold sister chromatids together, from chromosomes. During mitosis, Sgo1 is required for sensing the absence of tension caused by sister kinetochores not being attached to microtubules emanating from opposite poles. Here we describe a differential requirement for Sgo1 in the segregation of homologous chromosomes and sister chromatids. Sgo1 plays only a minor role in segregating homologous chromosomes at meiosis I. In contrast, Sgo1 is important to bias sister kinetochores toward biorientation. We suggest that Sgo1 acts at sister kinetochores to promote their biorientation.
MKKS Is a Centrosome-shuttling Protein Degraded by Disease-causing Mutations via CHIP-mediated Ubiquitination
Authors: Hirayama Shoshiro , Yamazaki Yuji , Kitamura Akira , Oda Yukako , Morito Daisuke , Okawa Katsuya , Kimura Hiroshi , Cyr Douglas M. , Kubota Hiroshi , Nagata Kazuhiro
Published: December 2007

McKusick–Kaufman syndrome (MKKS) is a recessively inherited human genetic disease characterized by several developmental anomalies. Mutations in the MKKS gene also cause Bardet–Biedl syndrome (BBS), a genetically heterogeneous disorder with pleiotropic symptoms. However, little is known about how MKKS mutations lead to disease. Here, we show that disease-causing mutants of MKKS are rapidly degraded via the ubiquitin–proteasome pathway in a manner dependent on HSC70 interacting protein (CHIP), a chaperone-dependent ubiquitin ligase. Although wild-type MKKS quickly shuttles between the centrosome and cytosol in living cells, the rapidly degraded mutants often fail to localize to the centrosome. Inhibition of proteasome functions causes MKKS mutants to form insoluble structures at the centrosome. CHIP and partner chaperones, including heat-shock protein (HSP)70/heat-shock cognate 70 and HSP90, strongly recognize MKKS mutants. Modest knockdown of CHIP by RNA interference moderately inhibited the degradation of MKKS mutants. These results indicate that the MKKS mutants have an abnormal conformation and that chaperone-dependent degradation mediated by CHIP is a key feature of MKKS/BBS diseases.
Induction of Autophagy during Extracellular Matrix Detachment Promotes Cell Survival
Authors: Fung Christopher , Lock Rebecca , Gao Sizhen , Salas Eduardo , Debnath Jayanta
Published: December 2007

Autophagy has been proposed to promote cell death during lumen formation in three-dimensional mammary epithelial acini because numerous autophagic vacuoles are observed in the dying central cells during morphogenesis. Because these central cells die due to extracellular matrix (ECM) deprivation (anoikis), we have directly interrogated how matrix detachment regulates autophagy. Detachment induces autophagy in both nontumorigenic epithelial lines and in primary epithelial cells. RNA interference-mediated depletion of autophagy regulators (ATGs) inhibits detachment-induced autophagy, enhances apoptosis, and reduces clonogenic recovery after anoikis. Remarkably, matrix-detached cells still exhibit autophagy when apoptosis is blocked by Bcl-2 overexpression, and ATG depletion reduces the clonogenic survival of Bcl-2–expressing cells after detachment. Finally, stable reduction of ATG5 or ATG7 in MCF-10A acini enhances luminal apoptosis during morphogenesis and fails to elicit long-term luminal filling, even when combined with apoptotic inhibition mediated by Bcl-2 overexpression. Thus, autophagy promotes epithelial cell survival during anoikis, including detached cells harboring antiapoptotic lesions.
Market Power and Market Failure The Decline of the European Fertilizer Industry and the Expansion of Norsk Hydro
Authors: Lie Einar
Published: December 2007

During the 1980s, the fertilizer industry in Western Europe underwent some radical changes. Reduced profitability and overcapacity forced a number of smaller producers to close down, and most of the major firms in the business either withdrew from the market or reduced their capacity. The exception was the Norwegian industrial conglomerate Norsk Hydro, which expanded rapidly and established itself as the largest producer in Europe and later globally.

The article discusses the strategy behind Hydro's expansion in relation to the changing structure of the fertilizer market, which historically was characterized by tacit and explicit agreements on prices and market shares between the major producers. Hydro's strategy and growth are analyzed in relation to some theoretical contributions from the study of transnationalisation of enterprises. A main argument is that Hydro's expansion was not driven by advantages in cost structure or organizational capabilities, nor did the expansion create such advantages. The Norwegian company expanded in foreignmarkets partly because it had less to lose from a counterattack than competitors in largermarkets and partly because of strategic disadvantages. Contrary to most of its large European competitors, Hydro failed to identify the long term threats to the stability and profitability of the Western European market.
Comparison of the functional responses of invasive and native amphipods
Authors: Bollache Loic , Dick Jaimie T.A , Farnsworth Keith D , Montgomery W. Ian
Published: December 2007

While we can usually understand the impacts of invasive species on recipient communities, invasion biology lacks methodologies that are potentially more predictive. Such tools should ideally be straightforward and widely applicable. Here, we explore an approach that compares the functional responses (FRs) of invader and native amphipod crustaceans.
Dikerogammarus villosus
is a Ponto-Caspian amphipod currently invading Europe and poised to invade North America. Compared with other amphipods that it actively replaces in freshwaters,
D. villosus
exhibited significantly greater predation, consuming significantly more prey with a higher type II FR. This corroborates the known dramatic field impacts of
D. villosus
on invaded communities. In another species, FRs were nearly identical in invasive and native ranges. We thus propose that if FRs of other taxa and trophic groups follow such general patterns, this methodology has potential in predicting future invasive species impacts.
Dispersion equations for steady waves in an anisotropic elastic plate or a layered plate
Authors: Ting T.C.T
Published: December 2007

Steady waves propagating in a plate that consists of one or more layers of general anisotropic elastic material are studied. The surface of the plate can be a traction-free (F), rigid (R) or slippery surface (S). The interface between any two layers in the plate can be perfectly bonded (b) or in sliding contact (s). The thickness of the layers need not be the same. The purpose of this paper is to present dispersion equations for all possible combinations of the boundary and interface conditions. If the thickness
h
of one of the layers is very small, the dispersion equation allows us to expand the solution in an infinite series in the power of
h
from which an approximate solution can be obtained by keeping the terms up to
O
(
h

n

) for any
n
. The special case of a sandwich plate that consists of a centre layer and two identical outside layers is studied. In the literature, the dispersion equations for a sandwich plate were studied for special elastic materials. The results presented here are for elastic materials of general anisotropy.
On the theory of advective effects on biological dynamics in the sea. III. The role of turbulence in biological–physical interactions
Authors: Goodman Louis , Robinson Allan R
Published: December 2007

A nonlinear model for biological and physical dynamical interactions in a laminar upwelling flow field in parts I and II of this study is extended to turbulent flow. In the previous studies, a prescription for obtaining quadrature solutions to the fundamental biodynamical equations was developed. In this study, we use a probability density function approach on these solutions to obtain statistics of the biodynamical state variables and their self-interaction for the case of turbulent advection. To illustrate the theory, a simple nutrient (
N
), phytoplankton (
P
) problem is considered, that of upwelling into a surface turbulent layer. Biological interaction is modelled as bilinear, representing the uptake of
N
by
P
in a uniform light euphotic zone. A random walk model is used to obtain the appropriate probability density function for the advective turbulent field. The mean quantities,

,

, as well as the biological interaction term

are calculated. The term

has two contributions,

, and the turbulence-induced interaction term,

. It is shown that the often neglected turbulence-induced coupling term

is of the order

and opposite in sign. This results in, over a wide range of Peclet numbers, the mean interaction term

being significantly smaller than either of its constituent terms,

and

.
Thermopiezoelectricity without energy dissipation
Authors: Ieşan D
Published: December 2007

In this paper, we use the Green–Naghdi theory of thermomechanics of continua to derive a linear theory of thermopiezoelectricity of a body with inner structure. This theory permits propagation of thermal waves at finite speed. We establish a uniqueness result and a continuous dependence of the solutions upon initial data and body supplies. Some applications (the problem of a concentrated heat source, the problem of an impulsive body force, the deformation of a thick-walled spherical shell) are presented.
A Sequential Algorithm for Possibility-Based Design Optimization
Authors: Zhou Jun , Mourelatos Zissimos P.
Published: December 2007

Deterministic optimal designs that are obtained without taking into account uncertainty/variation are usually unreliable. Although reliability-based design optimization accounts for variation, it assumes that statistical information is available in the form of fully defined probabilistic distributions. This is not true for a variety of engineering problems where uncertainty is usually given in terms of interval ranges. In this case, interval analysis or possibility theory can be used instead of probability theory. This paper shows how possibility theory can be used in design and presents a computationally efficient sequential optimization algorithm. After the fundamentals of possibility theory and fuzzy measures are described, a double-loop, possibility-based design optimization algorithm is presented where all design constraints are expressed possibilistically. The algorithm handles problems with only uncertain or a combination of random and uncertain design variables and parameters. In order to reduce the high computational cost, a sequential algorithm for possibility-based design optimization is presented. It consists of a sequence of cycles composed of a deterministic design optimization followed by a set of worst-case reliability evaluation loops. Two examples demonstrate the accuracy and efficiency of the proposed sequential algorithm.
An Analytical Contact Model for Design of Compliant Fingers
Authors: Lan Chao-Chieh , Lee Kok-Meng
Published: December 2007

A compliant gripper gains its dextral manipulation by the flexural motion of its fingers. It is a preferable device as compared to grippers with multijoint actuations because of reduced fabrication complexity and increased structural reliability. The prediction of contact forces and deflected shape are essential to the design of a compliant finger. A formulation based on nonlinear constrained minimization is presented to analyze contact problems of compliant fingers. The deflections by flexural and shear deformations are both considered. For a planar finger, this formulation further reduces the domain of discretization by one dimension. Hence, it offers a simpler formulation and is computationally more efficient than other methods such as finite element analysis. This method is rather generic and can facilitate design analysis and optimization of compliant fingers. We illustrate some of these attractive features with two types of compliant fingers, one for object handling and the other for snap-fit assembly applications.
Designing Synchronous Belt Transmissions With Variable Velocity Ratio
Authors: Innocenti Carlo , Paganelli Davide
Published: December 2007

The paper presents a new procedure to design a two-pulley synchronous belt transmission connecting, with no belt tensioner, two parallel-axis shafts with a variable velocity ratio. The procedure takes into account the limited number of choices for pitch and length of off-the-shelf synchronous belts, which translates into the need of fine-adjusting either the center distance or the law of motion. Different from other approaches reported in the technical literature, the suggested method is based on the numerical solution of a set of functional equations. A numerical example shows the application of the proposed method to a case study.
Ginsenoside Rg1 and Aluminum Hydroxide Synergistically Promote Immune Responses to Ovalbumin in BALB/c Mice
Authors: Sun Jianhua , Song Xiaoming , Hu Songhua
Published: December 2007

The combined adjuvant effect of ginsenoside Rg1 and aluminum hydroxide (alum) on immune responses to ovalbumin (OVA) in mice was investigated. BALB/c mice were subcutaneously (s.c.) inoculated twice with OVA alone or in combination with Rg1, alum, or Rg1 plus alum. Samples were collected 2 weeks after the boosting for the measurement of anti-OVA immunoglobulin G (IgG) isotypes in sera and gamma interferon (IFN-γ) and interleukin-5 (IL-5) produced in singular splenocyte cultures. Delayed-type hypersensitivity (DTH) responses were measured in mice immunized as described above. After 10 days, the mice were injected s.c. with OVA at the footpads. Thereafter, the thickness of the footpads was measured once daily for 5 days. The results indicated that alum enhanced mainly Th2 (IgG1 and IL-5) responses (P< 0.05), while Rg1 enhanced both Th1 (IgG1 and IL-5) and Th2 (IgG2a, IFN-γ, and DTH) responses (P< 0.05). The highest immune responses were found in the mice injected with OVA solution containing both alum and Rg1. In addition, the hemolytic activity of Rg1 was much lower than that of Quil A. Therefore, Rg1 deserves further studies in order to tailor desired immune responses when a mixed Th1/Th2 immune response is needed.
Rapid Detection and Molecular Serotyping of Adenovirus by Use of PCR Followed by Electrospray Ionization Mass Spectrometry
Authors: Blyn Lawrence B. , Hall Thomas A. , Libby Brian , Ranken Raymond , Sampath Rangarajan , Rudnick Karl , Moradi Emily , Desai Anjali , Metzgar David , Russell Kevin L. , Freed Nikki E. , Balansay Melinda , Broderick Michael P. , Osuna Miguel A. , Hofstadler Steven A. , Ecker David J.
Published: December 2007

We have developed a PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) assay for the rapid detection, identification, and serotyping of human adenoviruses. The assay employs a high-performance mass spectrometer to “weigh” the amplicons obtained from PCR using primers designed to amplify known human adenoviruses. Masses are converted to base compositions and, by comparison against a database of the genetic sequences, the serotype present in a sample is determined. The performance of the assay was demonstrated with quantified viral standards and environmental and human clinical samples collected from a military training facility. Over 500 samples per day can be analyzed with sensitivities greater than 100 genomes per reaction. This approach can be applied to many other families of infectious agents for rapid and sensitive analysis.
Utility of Real-Time PCR for Diagnosis of Legionnaires’ Disease in Routine Clinical Practice
Authors: Diederen Bram M. W. , Kluytmans Jan A. J. W. , Vandenbroucke-Grauls Christina M. , Peeters Marcel F.
Published: December 2007

The main aim of our study was to determine the added value of PCR for the diagnosis of Legionnaires’ disease (LD) in routine clinical practice. The specimens were samples submitted for routine diagnosis of pneumonia from December 2002 to November 2005. Patients were evaluated if, in addition to PCR, the results of at least one of the following diagnostic tests were available: (i) culture for
Legionella
spp. on buffered charcoal yeast extract agar or (ii) detection of
Legionella pneumophila
antigen in urine specimens. Of the 151 evaluated patients, 37 (25%) fulfilled the European Working Group on Legionella Infections criteria for a confirmed case of LD (the “gold standard”). An estimated sensitivity, specificity, and overall percent agreement of 86% (32 of 37; 95% confidence interval [CI] = 72 to 95%), 95% (107 of 112; 95% CI = 90 to 98%), and 93% (139 of 149), respectively, were found for 16S rRNA-based PCR, and corresponding values of 92% (34 of 37; 95% CI = 78 to 98%), 98% (110 of 112; 95% CI = 93 to 100%), and 97% (144 of 149), respectively, were found for the
mip
gene-based PCR. A total of 35 patients were diagnosed by using the urinary antigen test, and 34 were diagnosed by the 16S rRNA-based PCR. With the
mip
gene PCR one more case of LD (
n
= 36; not significant) was detected. By combining urinary antigen test and the
mip
gene PCR, LD was diagnosed in an additional 4 (11%) patients versus the use of the urinary antigen test alone. The addition of a
L. pneumophila
-specific
mip
gene PCR to a urinary antigen test is useful in patients with suspected LD who produce sputum and might allow the early detection of a significant number of additional patients.
eapGene as Novel Target for Specific Identification ofStaphylococcus aureus
Authors: Hussain Muzaffar , von Eiff Christof , Sinha Bhanu , Joost Insa , Herrmann Mathias , Peters Georg , Becker Karsten
Published: December 2007

The cell surface-associated extracellular adherence protein (Eap) mediates adherence ofStaphylococcus aureusto host extracellular matrix components and inhibits inflammation, wound healing, and angiogenesis. A well-characterized collection ofS. aureusand non-S. aureusstaphylococcal isolates (n= 813) was tested for the presence of the Eap-encoding gene (eap) by PCR to investigate the use of theeapgene as a specific diagnostic tool for identification ofS. aureus. Whereas all 597S. aureusisolates wereeappositive, this gene was not detectable in 216 non-S. aureusstaphylococcal isolates comprising 47 different species and subspecies of coagulase-negative staphylococci and non-S. aureuscoagulase-positive or coagulase-variable staphylococci. Furthermore, non-S. aureusisolates did not express Eap homologs, as verified on the transcriptional and protein levels. Based on these data, the sensitivity and specificity of the newly developed PCR targeting theeapgene were both 100%. Thus, the unique occurrence of Eap inS. aureusoffers a promising tool particularly suitable for molecular diagnostics of this pathogen.
Molecular Method for
Bartonella
Species Identification in Clinical and Environmental Samples
Authors: García-Esteban Coral , Gil Horacio , Rodríguez-Vargas Manuela , Gerrikagoitia Xeider , Barandika Jesse , Escudero Raquel , Jado Isabel , García-Amil Cristina , Barral Marta , García-Pérez Ana L. , Bhide Mangesh , Anda Pedro
Published: December 2007

A new, efficient molecular method for detection of
Bartonella
, based on the 16S-23S rRNA intergenic spacer and 16S rRNA amplification by multiplex PCR combined with reverse line blotting, was designed. This assay could simultaneously detect 20 different known species and other
Bartonella
species not described previously.
New mRNAs Are Preferentially Translated during Vesicular Stomatitis Virus Infection
Authors: Whitlow Zackary W. , Connor John H. , Lyles Douglas S.
Published: December 2007

During vesicular stomatitis virus (VSV) infection, host protein synthesis is inhibited, while synthesis of viral proteins increases. VSV infection causes inhibition of host transcription and RNA transport. Therefore, most host mRNAs in the cytoplasm of infected cells were synthesized before infection. However, viral mRNAs are synthesized throughout infection and are newer than preexisting host mRNAs. To determine if the timing of appearance of mRNAs in the cytoplasm affected their translation during VSV infection, we transfected reporter mRNAs into cells at various times relative to the time of infection and measured their rate of translation in mock- and VSV-infected cells. We found that translation of mRNAs transfected during infection was not inhibited but that translation of mRNAs transfected prior to infection was inhibited during VSV infection. Based on these data, we conclude that the timing of viral mRNA appearance in the cytoplasm is responsible, at least in part, for the preferential translation of VSV mRNAs. A time course measuring translation efficiencies of viral and host mRNAs showed that the translation efficiencies of viral mRNAs increased between 4 and 8 h postinfection, while translation efficiencies of host mRNAs decreased. The increased translation efficiency of viral mRNAs occurred in cells infected with an M protein mutant virus that is defective in host shutoff, demonstrating that the enhanced translation of viral mRNA is genetically separable from inhibition of translation of host mRNA.
Vaccination of Macaques with Adjuvanted Formalin-Inactivated Influenza A Virus (H5N1) Vaccines: Protection against H5N1 Challenge without Disease Enhancement
Authors: Ruat Caroline , Caillet Catherine , Bidaut Alexandre , Simon James , Osterhaus Albert D. M. E.
Published: December 2007

We investigated the ability of adjuvanted, inactivated split-virion influenza A virus (H5N1) vaccines to protect against infection and demonstrated that the disease exacerbation phenomenon seen with adjuvanted formaldehyde-inactivated respiratory syncytial virus and measles virus investigational vaccines did not occur with these H5N1 vaccines. Macaques were vaccinated twice with or without an aluminum hydroxide or oil-in-water emulsion adjuvanted vaccine. Three months later, animals were challenged with homologous wild-type H5N1. No signs of vaccine-induced disease exacerbation were seen. With either adjuvant, vaccination induced functional and cross-reactive antibodies and protected the lungs and upper respiratory tract. Without an adjuvant, the vaccine provided partial protection. Best results were obtained with the emulsion adjuvant.
The Vaccinia Virus B5 Protein Requires A34 for Efficient Intracellular Trafficking from the Endoplasmic Reticulum to the Site of Wrapping and Incorporation into Progeny Virions
Authors: Earley Amalia K. , Chan Winnie M. , Ward Brian M.
Published: December 2007

The glycoproteins encoded by the vaccinia virus A34R and B5R genes are involved in intracellular envelope virus formation and are highly conserved among orthopoxviruses. A recombinant virus that has the A34R gene deleted and the B5R gene replaced with a B5R gene fused to the enhanced green fluorescent protein (B5R-GFP) gene was created (vB5R-GFP/ΔA34R) to investigate the role of A34 during virion morphogenesis. Cells infected with vB5R-GFP/ΔA34R displayed GFP fluorescence throughout the cytoplasm, which differed markedly from that seen in cells infected with a normal B5R-GFP-expressing virus (vB5R-GFP). Immunofluorescence and subcellular fractionation demonstrated that B5-GFP localizes with the endoplasmic reticulum in the absence of A34. Expression of either full-length A34 or a construct consisting of the lumenal and transmembrane domains restored normal trafficking of B5-GFP to the site of wrapping in the juxtanuclear region. Coimmunoprecipitation studies confirmed that B5 and A34 interact through their luminal domains, and further analysis revealed that in the absence of A34, B5 is not efficiently incorporated into virions released from the cell.
Mechanisms of Zoonotic Severe Acute Respiratory Syndrome Coronavirus Host Range Expansion in Human Airway Epithelium
Authors: Sheahan Timothy , Rockx Barry , Donaldson Eric , Sims Amy , Pickles Raymond , Corti Davide , Baric Ralph
Published: December 2007

In 2003, severe acute respiratory syndrome coronavirus (SARS-CoV) emerged and caused over 8,000 human cases of infection and more than 700 deaths worldwide. Zoonotic SARS-CoV likely evolved to infect humans by a series of transmission events between humans and animals for sale in China. Using synthetic biology, we engineered the spike protein (S) from a civet strain, SZ16, into our epidemic strain infectious clone, creating the chimeric virus icSZ16-S, which was infectious but yielded progeny viruses incapable of propagating in vitro. After introducing a K479N mutation within the S receptor binding domain (RBD) of SZ16, the recombinant virus (icSZ16-S K479N) replicated in Vero cells but was severely debilitated in growth. The in vitro evolution of icSZ16-S K479N on human airway epithelial (HAE) cells produced two viruses (icSZ16-S K479N D8 and D22) with enhanced growth on HAE cells and on delayed brain tumor cells expressing the SARS-CoV receptor, human angiotensin I converting enzyme 2 (hACE2). The icSZ16-S K479N D8 and D22 virus RBDs contained mutations in ACE2 contact residues, Y442F and L472F, that remodeled S interactions with hACE2. Further, these viruses were neutralized by a human monoclonal antibody (MAb), S230.15, but the parent icSZ16-S K479N strain was eight times more resistant than the mutants. These data suggest that the human adaptation of zoonotic SARS-CoV strains may select for some variants that are highly susceptible to select MAbs that bind to RBDs. The epidemic, icSZ16-S K479N, and icSZ16-S K479N D22 viruses replicate similarly in the BALB/c mouse lung, highlighting the potential use of these zoonotic spike SARS-CoVs to assess vaccine or serotherapy efficacy in vivo.
Hepatitis B Surface Antigen Levels and Sequences of Natural Hepatitis B Virus Variants Influence the Assembly and Secretion of Hepatitis D Virus
Authors: Shih Hsuan Hui , Jeng King-Song , Syu Wan-Jr , Huang Yi-Hsiang , Su Chien-Wei , Peng Wei-Li , Sheen I-Jane , Wu Jaw-Ching
Published: December 2007

Various domains of hepatitis B surface antigen (HBsAg) are essential for the assembly and secretion of hepatitis D virus (HDV). This study investigated the influences of the levels and sequences of HBsAg of naturally occurring HBV variants on the assembly and secretion of HDV. Six hepatitis B virus (HBV)-producing plasmids (three genotype B and three genotype C) and six HBsAg expression plasmids that expressed various HBsAg levels were constructed from the sera of HDV-infected patients. These plasmids were cotransfected with six expression plasmids of HDV of genotype 1, 2, or 4 into the Huh-7 hepatoma cell line. Serum HBsAg and HBV DNA levels were correlated with HDV RNA levels and outcomes of chronic hepatitis D (CHD) patients. The secretion of genotype 1, 2, or 4 HDV generally correlated with HBsAg levels but not with HBV genotypes or HBV DNA levels. Swapping and residue mutagenesis experiments of HBsAg-coding sequences revealed that the residue Pro-62 in the cytosolic domain-I affects the assembly and secretion of genotype 2 and 4 HDV and not those of genotype 1. The pre-S2 N-terminal deletion HBV mutant adversely affects secretion of the three HDV genotypes. In patients, serum HDV RNA levels correlated with HBsAg levels but not with HBV DNA levels. Viremia of HDV or HBV correlated with poor outcomes. In conclusion, the assembly and secretion of HDV were influenced by the amounts and sequences of HBsAg. For an effective treatment of CHD, reduction of HBsAg production in addition to the suppression of HBV and HDV replication might be crucial.
Binding of ICP4, TATA-Binding Protein, and RNA Polymerase II to Herpes Simplex Virus Type 1 Immediate-Early, Early, and Late Promoters in Virus-Infected Cells
Authors: Sampath Padmavathi , DeLuca Neal A.
Published: December 2007

The binding of herpes simplex virus type 1 ICP4, TATA-binding protein (TBP), and RNA polymerase II (polII) to the promoter regions of representative immediate-early (IE) (ICP0), early (E) (thymidine kinase [tk]), and late (L) (glycoprotein C [gC]) genes on the viral genome was examined as a function of time postinfection, viral DNA replication,
cis
-acting sites for TFIID in the tk and gC promoters, and genetic background of ICP4. The binding of TBP and polII to the IE ICP0 promoter was independent of the presence of ICP4, whereas the binding of TBP and polII to the tk and gC promoters occurred only when ICP4 also bound to the promoters, suggesting that the presence of ICP4 at the promoters of E and L genes in virus-infected cells is crucial for the formation of transcription complexes on these promoters. When the TATA box of the tk promoter or the initiator element (INR) of the gC promoter was mutated, a reduction in the amount of TBP and polII binding was observed. However, a reduction in the amount of ICP4 binding to the promoters was also observed, suggesting that the binding of TBP-containing complexes and ICP4 is cooperative. The binding of ICP4, TBP, and polII was also observed on the gC promoter at early times postinfection or when DNA synthesis was inhibited, suggesting that transcription complexes may be formed early on L promoters and that additional events or proteins are required for expression. The ability to form these early complexes on the gC promoter required the DNA-binding domain but in addition required the carboxyl-terminal 524 amino acids of ICP4, which is missing the virus n208. This region was not required to form TBP- and polII-containing complexes on the tk promoter. n208 activates E but not L genes during viral infection. These data suggest that a region of ICP4 may differentiate between forming TBP- and polII-containing complexes on E and L promoters.
The Nant-y-moch Formation, Plynlimon inlier, West central Wales
Authors: JAMES DAVID MURRAY DENNIS
Published: December 2007

I
n
T
he
C
ourse
of his classic work on the Llandovery graptolite stratigraphy of central Wales, O. T.
Jones (1909)
mapped a large portion of the Ashgill inlier north of Pont Erwyd. Jones erected three sub-divisions of the Ashgill series; in descending stratigraphic order:

Bryn-glas Group

mudstone

Drosgol Group

mudstone, grits and conglomerates

Nant-y-moch Group

mudstones and flags

These Groups were specified with reference to type areas rather than type sections. Graptolites indicative of the
Dicellograptus anceps
Zone were found at one locality in the Nant-y-moch Group (
Jones, 1909
p. 468–69). The boundary between the Drosgol and Nant-y-moch Groups was not shown on the map. In the area examined which was later found to be the southern portion of the plunge culmination, the Nant-y-moch Group was estimated to be about 305 m thick with a reservation that the true thickness might be half this figure.

The Group was next described by Jones & Pugh (1935) in a regional survey of west central Wales which established that these strata are confined to the Plynlimon inlier. The original fossil finds of Jones were augmented by the discovery of
Orthograptus ex. gr. truncatus
(Lapworth) at other levels. A thickness of 718 m (base not exposed) was given (1935, p. 264) which suggests that the entire area of culmination had been studied.

During 1965–67 the writer mapped the Plynlimon inlier on the scale of six inches to one mile, as part of a regional study of the Ashgill basin facies in west central
Geological evolution of the New Hebrides island arc
Authors: MITCHELL ANDREW HARRY GORDON , WARDEN ARTHUR JAMES
Published: December 2007

The New Hebrides islands overlie an eastward-dipping Benioff zone and are bordered by a submarine trench. They consist of volcanic and volcaniclastic rocks, intrusions, mudstones and limestones. Eastern and Western Belts of islands containing Neogene rocks are bisected by a Central Chain of active and recently extinct volcanoes.

In the Western Belt intense early Miocene basaltic and andesitic volcanism resulted in a thick succession consisting largely of quartz-free marine volcaniclastic rocks; intrusion of hornblende andesites and diorites preceded middle Miocene block faulting and uplift. Late Miocene turbidites derived from this succession and rare tufts were faulted and eroded prior to a Pliocene transgression.

In the Eastern Belt undated basalt and andesite lavas were faulted and intruded by gabbros and norites before the middle Miocene. Emplacement of serpentinites containing amphibolite rafts pre-dated accumulation of pillow basalts and breccias of late Miocene to early Pliocene age.

Most islands of the Central Chain consist of late Pliocene to Recent subaerially-erupted basaltic lavas; some islands in the south contain similar basalts and andesites overlying thick Pliocene successions of pillow lavas and volcaniclastic rocks. Massive reef limestones deposited in all three Belts during the late Pliocene and Quaternary now form tilted plateaux and terraces.

The Western Belt was the site of an early Miocene volcanic arc; a parallel submarine trench may have existed either near the Eastern Belt, or to the west of the Western Belt. In many other island arcs volcanic episodes were contemporaneous with those in the Western Belt and Central Chain of the New Hebrides.
Pre-Nubian tectonic trends in Northeastern Sudan
Authors: VAIL JOHN RANDOLPH
Published: December 2007

About 500000 km
2
of the Nubian and Bayuda deserts and Red Sea Hills of Sudan have been investigated by a rapid geological interpretation of trimetrogon aerial photographs supplemented by ground traverses and published and unpublished information. About half the area is covered by unconsolidated sands, Tertiary marine beds along the littoral, Nubian Sandstone Formation and Tertiary to Recent volcanic deposits. The remainder is made of a metamorphosed complex of schists, gneisses and granites intruded by numerous dyke swarms, many of which are related to about 3° post-orogenic ring-complexes. The metamor-phic rocks show well marked bedding and foliation trends which form a heterogeneous orogenic pattern across the entire region. Major structures trend ne, n and Nw in conformity with geological features in neighbouring territories.
Statistical analysis of British Carboniferous conodont faunas
Authors: DRUCE EDRIC C. , RHODES FRANK HAROLD TREVOR , AUSTIN RONALD LEYSHON
Published: December 2007

Three lines of evidence are reviewed that suggest conodont animals contained multielement conodont assemblages in life. Reconstruction of the original multi-element assemblages of conodonts from the Cleistopora (K) and Zaphrentis (Z) Zones of the North Crop of the South Wales Coalfield is attempted using the Centclass programme on a Control Data 3600 computer. Two methods are described which are of use in assemblage reconstruction. Polythetic cluster analysis, first developed for use in ecological surveys, provides dendrograms from which the level of association of individual elements may be determined. This indicates common occurrences of elements and can be supplemented by comparisons of total stratigraphic range and relative frequency of elements. Thirteen groups are recognized which are compared with assemblage models based on assemblages preserved in situ on shale bedding planes. Group 8 compares with a basic duboisellid (Class C) type of assemblage. Groups 5 and 6 do not appear to represent meaningful groups. All other groups represent either complete or partial
Lochreia
type Class A assemblages.
Lower Carboniferous rocks between the Curlew and Ox Mountains, Northwestern Ireland
Authors: DIXON OWEN ARNOLD
Published: December 2007

Rocks in the Ballymote area, occupying one of several broad downwarps of inherited caledonoid trend, provide a crucial link between Viséan successions north of the Highland Boundary line (represented locally by the Ox Mountains) and successions to the south, part of the extensive 'shelf' limestone of central Ireland. The sequence, exceeding 1070 metres (3500 ft) in thickness, ranges in age from early to latest Viséan
21
to
2
) and is succeeded, generally without interruption, by thick upper Carboniferous shales. The succession of different rock types reflects changing controls in the sedimentary environments of a shallow shelf sea. The main episodes (some repeated) include the deposition of locally-derived conglomerates and sandstones in a partly enclosed basin; the accumulation of various thick, clear-water limestones, partly in continuation with adjacent basins; and the influx of muddy detrital sediments from a more distant source.

The rocks contain a succession of rich and diverse benthonic faunas, predominantly of corals and brachiopods, but near the top these give way to several distinctive goniatite-lamellibranch faunas.
Geobiology and the future of Palaeontology
Authors: SYLVESTER-BRADLEY PETER COLLEY
Published: December 2007

The Earth sciences include not only geology, but the hybrid-sciences geophysics, geo­chemistry and geobiology, of which the most complex and least rigorous is geobiology. The future development of geobiology depends on techniques which analyse the complexity and increase the rigour. The most hopeful tech­niques are those which separate each signal in turn from what at first seems to be only noise.
The first Jurassic mammal from Scotland
Authors: WALDMAN MICHAEL , SAVAGE ROBERT JOSEPH GAY
Published: December 2007

R
ecords
of mammals in Mesozoic strata are rare: the earliest are of late Triassic age in Wales, S. Africa and China: two primitive mammal families (Eozo-strodontidae and Kuehneotheridae) are represented in these faunas. There then follows a long time gap until Late Jurassic, when mammals are known from the U.S.A., U.K., Portugal and Tanzania: these faunas include pantotheres, the stock from which almost all the later mammals arose. Between the Late Trias and Late Jurassic, the only known fauna is that of the Middle Jurassic of Stonesfield in Oxfordshire. Thus the discovery of a second site is of great importance: it occurs in the Estuarine Series of Skye in Scotland, and contains a fauna of tritylodonts and docodont mammals. The discovery of this fauna was made in August 1971 by Dr. M. Waldman and Mr. J. B. Dobinson during the course of a search for terrestrial vertebrates in the non-marine strata of Skye.

Stratigraphy

Since
Hugh Miller (1858)
described the occurrence of Jurassic vertebrate fossils on the Isle of Eigg, further vertebrates of similar age have been found in the Hebridean region. The richest material so far recovered has been from the Bathonian (Middle Jurassic) of Eigg (
Hudson 1966
), and the most recent find is that of plesiosaur remains from the Bearreraig Sandstone (Bajocian) near Rigg, Isle of Skye (
Hudson & Morton 1969
). All the Jurassic vertebrate remains known from this area are those of fish and reptiles and occur in a variety of localities. (
Miller 1858
,
Peach 1910
,
Arkell
Diagnosis of marine and non-marine environments from the Cambro-Ordovician sandstones of Jordan
Authors: SELLEY RICHARD CURTIS
Published: December 2007

The Precambrian shields of the Sahara and Arabia are overlain by a thick laterally extensive Cambro-Ordovician sandstone blanket. This is generally divisible into a lower coarse pebbly cross-bedded facies overlain by a finer-grained facies with a characteristic suite of trace fossils.

This paper describes the sedimentology of the Gambro-Ordovician sequence where it crops out in the Southern Desert of Jordan. The lower coarse pebbly facies consists of a complex of channels up to 300 m wide and 15 m deep with occasional shale-filled channels of similar dimensions. Three formations of this facies occur. The lowest overlies a mature pediment with residual inselbergs cut in the Precambrian basement. The succeeding two formations have channelled bases. This facies is attributed to three cycles of pedimentation and sedimentation on braided alluvial outwash plains.

The overlying facies consists of an alternation of medium grained well sorted sandstones and rare shales. The sandstones are devoid of channelling being composed of laterally extensive tabular-planar cross-bedding. The interbedded shales have sheet geometries, in contrast to the shoestring shaped shales of the facies beneath. They consist of laminated silts and microcross-laminated fine sands with a diverse suite of trace fossils.

This upper facies is attributed to deposition on a marine shelf by the alternation of migrating sand shoals and tidal flats.
A concise guide to stratigraphical procedure
Authors: HARLAND W. B. , AGER D. V. , BALL H. W. , BISHOP W. W. , BLOW W. H. , CURRY D. , DEER W. A. , GEORGE T. N. , HOLLAND C. H. , HOLMES S. C. A. , HUGHES N. F. , KENT P. E. , PITCHER W. S. , RAMSBOTTOM W. H. C. , STUBBLEFIELD C. J. , WALLACE PEIGI , WOODLAND A. W.
Published: December 2007

The Stratigraphy Committee of the Geological Society of London presents a revision of its 1969 ‘Recommendations’ which is designed to provide a concise working guide to stratigraphical procedures.

Le Comité de Stratigraphie de la Société Géologique de Londres presente une révision de ses ‘Recommendations’ de 1969 qui est destinée à fournir un guide concis aux methodes stratigraphiques.

Die stratigraphische Kommission der geologische Gesellschaft in London stellt eine Revision ihrer ‘Empfehlungen’ von 1969 dar, die ein gestrafftes ausreichendes Handbuch zur stratigraphischen Methoden zu geben erstellt wurde.
Hydraulic fracturing and mineralization
Authors: PHILLIPS WILLIAM JOHN
Published: December 2007

The factors relevant to the mechanism of normal faulting and brecciation are discussed. Normal faults develop as the consequence of an increase in the magnitude of the differential stress above the critical limit under the prevailing pore water conditions. The accumulation of a body of hydrothermal solution on the fault zones under pressures greater than the pore water pressure, results in the extension of the faults by hydraulic fracturing. The abrupt drop in the pressure of the hydrothermal solution when fracturing occurs, causes the bursting apart of the rock into which the hydrothermal solution has permeated under high pressure, thus forming angular breccias.

The fracture may be extended by hydraulic fracturing even though the differential stress decreases, provided the pressure of the hydrothermal solution on the fracture plane exceeds the pore water pressure by increasing amounts. Under these conditions the dip of each extension of the normal fault increases, and eventually the fracture develops as a vertical breccia zone.
Modern Arctic glaciers as depositional models for former ice sheets
Authors: BOULTON GEOFFREY STEWART
Published: December 2007

Sedimentary sequences currently forming at the margins of Spitsbergen glaciers are identical in thickness and detail to many Pleistocene and pre-Pleistocene glacigenic sequences. The transport of considerable volumes of englacial debris leads directly to the predominance of supraglacial till deposition, giving hummocky till surfaces and till plains. The association of supraglacial outwash with flow till produces tripartite till/outwash/till sequences, and multitill sequences, which are the result of a single glacier retreat phase.

Complex tectonic structures, often with systematic regional trends are described, which are not the result of ice pushing but of downslope flow and collapse of supraglacial sequences above melting ice.

New classifications are suggested for ice-contact stratified deposits and till, both of which depend upon position of deposition, supraglacial, englacial or subglacial

It is suggested that existing models for the interpretation of ancient tills and the sequences in which they lie are often too simple and lead to erroneous stratigraphic and palaeogeographic conclusions. Till is too often interpreted solely as lodgement till, and it is suggested that many Pleistocene and earlier sequences, currently thought of as products of repeated glacier advance and readvance, may be perfectly normal products of a single retreat phase by a glacier with a thick englacial debris load.

Ways of reconstructing the structural character of ancient ice margins are presented and it is also suggested that the thermal regimes of past ice sheets can be reconstructed from the nature of their deposits. The last Pleistocene ice sheet in Britain is thought to have been composed, at its maximum extent, of cold ice in the marginal zone and temperate ice in the internal zone.
A tectonic mé1ange from the Eastern Taurus Mountains, Turkey
Authors: HALL ROBERT , MASON ROGER
Published: December 2007

The eastern taurus
mountains of Turkey lie on a plate boundary where two areas of continental lithosphere are converging (
McKenzie 1970
), and there is large-scale thrusting (
Ilhan 1971
) comparable with that of the Himalayas (
Gansser 1964
), another region of continental collision.

In the central Taurus there is an extensive tract of greenschist to amphibolite facies metamorphic rocks, the 'Bitlis Massif' (Fig. I). Palaeontological evidence (
Altinli 1966
) and geochronological evidence (Yilmaz 1971)
1
suggest that these rocks were deposited, deformed and metamorphosed in Palaeozoic times. The earlier suggestion that the Bitlis Massif is metamorphosed Mesozoic sediments (Rigo de Righi & Cortesini 1964) can be ruled out in the light of more recent published work. The southern boundary of the Bitlis Massif is tectonic; the metamorphic rocks being thrust over a complex of wildflysch and ophiolites which often has the characteristics of a mélange, as defined by Hsfi (1968). This ophiolite-flysch complex is also thrust over Tertiary and Mesozoic rocks on the northern edge of the Syrian platform. The ophiolite-flysch belt has been regarded as a Tethyan suture (
Smith 1971
) and the Bitlis Massif as the crystalline basement of the over-riding Anatolian Plate (
Peyve 1969
).

An expedition in 1971 found serpentinite-rich mélange well inside the Bitlis Massif. Near the village of Mutki, 27 km west of Bitlis, there is a strip of mélange, 1–3 km wide, trending roughly E–W and fanked by metamorphic rocks to the north and the south. The metamorphic rocks are phyllites, quartzitic phyllites, quartzites and marbles, showing evidence of