bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Phylogeny and Proposed Classification of the Simian Picornaviruses
Authors: Oberste M. Steven , Maher Kaija , Pallansch Mark A.
Published: October 2010

The simian picornaviruses were isolated from various primate tissues during the development of general tissue culture methods in the 1950s to 1970s or from specimens derived from primates used in biomedical research. Twenty simian picornavirus serotypes are recognized, and all are presently classified within the
Enterovirus
genus. To determine the phylogenetic relationships among all of the simian picornaviruses and to evaluate their classification, we have determined complete VP1 sequences for 19 of the 20 serotypes. Phylogenetic analysis showed that A13, SV19, SV26, SV35, SV43, and SV46 are members of human enterovirus species A, a group that contains enterovirus 71 and 11 of the coxsackie A viruses. SA5 is a member of human enterovirus species B, which contains the echoviruses, coxsackie B viruses, coxsackievirus A9, and enterovirus 69. SV6, N125, and N203 are related to one another and, more distantly, to species A human enteroviruses, but could not be definitely assigned to a species. SV4 and SV28 are closely related to one another and to A-2 plaque virus, but distinct from other enteroviruses, suggesting that these simian viruses are members of a new enterovirus species. SV2, SV16, SV18, SV42, SV44, SV45, and SV49 are related to one another but distinct from viruses in all other picornavirus genera, suggesting that they may comprise a previously unknown genus in
Picornaviridae
. Several simian virus VP1 sequences (N125 and N203; SV4 and SV28; SV19, SV26, and SV35; SV18 and SV44; SV16, SV42, and SV45) are greater than 75% identical to one another (and/or greater than 85% amino acid identity), suggesting that the true number of distinct serotypes among the viruses surveyed is less than 20.
Transcription Regulatory Sequences and mRNA Expression Levels in the Coronavirus Transmissible Gastroenteritis Virus
Authors: Alonso Sara , Izeta Ander , Sola Isabel , Enjuanes Luis
Published: October 2010

The transcription regulatory sequences (TRSs) of the coronavirus transmissible gastroenteritis virus (TGEV) have been characterized by using a helper virus-dependent expression system based on coronavirus-derived minigenomes to study the synthesis of subgenomic mRNAs. The TRSs are located at the 5′ end of TGEV genes and include a highly conserved core sequence (CS), 5′-CUAAAC-3′, that is essential for mediating a 100- to 1,000-fold increase in mRNA synthesis when it is located in the appropriate context. The relevant sequences contributing to TRS activity have been studied by extending the CS 5′ upstream and 3′ downstream. Sequences from virus genes flanking the CS influenced transcription levels from moderate (10- to 20-fold variation) to complete mRNA synthesis silencing, as shown for a canonical CS at nucleotide (nt) 120 from the initiation codon of the S gene that did not lead to the production of the corresponding mRNA. An optimized TRS has been designed comprising 88 nt from the N gene TRS, the CS, and 3 nt 3′ to the M gene CS. Further extension of the 5′-flanking nucleotides (i.e., by 176 nt) decreased subgenomic RNA levels. The expression of a reporter gene (β-glucuronidase) by using the selected TRS led to the production of 2 to 8 μg of protein per 10
6
cells. The presence of an appropriate Kozak context led to a higher level of protein expression. Virus protein levels were shown to be dependent on transcription and translation regulation.
Relative Neurotropism of a Recombinant Rhabdovirus Expressing a Green Fluorescent Envelope Glycoprotein
Authors: van den Pol Anthony N. , Dalton Kevin P. , Rose John K.
Published: October 2010

A new recombinant vesicular stomatitis virus (rVSV) that expresses green fluorescent protein (GFP) on the cytoplasmic domain of the VSV glycoprotein (G protein) was used in the mouse as a model for studying brain infections by a member of the
Mononegavirales
order that can cause permanent changes in behavior. After nasal administration, virus moved down the olfactory nerve, first to periglomerular cells, then past the mitral cell layer to granule cells, and finally to the subventricular zone. Eight days postinoculation, rVSV was eliminated from the olfactory bulb. Little sign of infection could be found outside the olfactory system, suggesting that anterograde or retrograde axonal transport of rVSV was an unlikely mechanism for movement of rVSV out of the bulb. When administered intracerebrally by microinjection, rVSV spread rapidly within the brain, with strong infection at the site of injection and at some specific periventricular regions of the brain, including the dorsal raphe, locus coeruleus, and midline thalamus; the ventricular system may play a key role in rapid rVSV dispersion within the brain. Thus, the lack of VSV movement out of the olfactory system was not due to the absence of potential for infections in other brain regions. In cultures of both mouse and human central nervous system (CNS) cells, rVSV inoculations resulted in productive infection, expression of the G-GFP fusion protein in the dendritic and somatic plasma membrane, and death of all neurons and glia, as detected by ethidium homodimer nuclear staining. Although considered a neurotropic virus, rVSV also infected heart, skin, and kidney cells in dispersed cultures. rVSV showed a preference for immature neurons in vitro, as shown by enhanced viral infection in developing hippocampal cultures and in the outer granule cell layer in slices of developing cerebellum. Together, these data suggest a relative affinity of rVSV for some neuronal types in the CNS, adding to our understanding of the long-lasting changes in rodent behavior found after transient VSV infection.
Analyses of Genotypic Diversity among North, South, and Central American Isolates ofSugarcane Yellow Leaf Virus: Evidence for Colombian Origins and for Intraspecific Spatial Phylogenetic Variation
Authors: Moonan Francis , Mirkov T. Erik
Published: October 2010

We have analyzed the genotypic diversity ofSugarcane yellow leaf virus(SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the familyLuteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156–171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a “partial likelihoods assessed through optimization” (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.
Oncoviral Bovine Leukemia Virus G4 and Human T-Cell Leukemia Virus Type 1 p13
II
Accessory Proteins Interact with Farnesyl Pyrophosphate Synthetase
Authors: Lefèbvre Laurent , Vanderplasschen Alain , Ciminale Vincenzo , Heremans Hubertine , Dangoisse Olivier , Jauniaux Jean-Claude , Toussaint Jean-François , Zelnik Vlado , Burny Arsène , Kettmann Richard , Willems Luc
Published: October 2010

G4 and p13
II
are accessory proteins encoded by the X region of bovine leukemia virus and human T-cell leukemia virus type 1 (HTLV-1), respectively. Disruption of the G4 and p13
II
open reading frames interferes with viral spread in animal model systems, indicating that the corresponding proteins play a key role in viral replication. In addition, G4 is oncogenic in primary cell cultures and is absolutely required for efficient onset of leukemogenesis in sheep. To gain insight into the function of these proteins, we utilized the yeast two-hybrid system to identify protein partners of G4. Results revealed that G4 interacts with farnesyl pyrophosphate synthetase (FPPS), a protein involved in the mevalonate/squalene pathway and in synthesis of FPP, a substrate required for prenylation of Ras. The specificity of the interaction was verified by glutathione
S
-transferase (GST) pull-down assays and by coimmunoprecipitation experiments. Furthermore, confocal microscopy showed that the subcellular localization of G4 was profoundly affected by FPPS. The G4 protein itself was not prenylated, at least in rabbit reticulocyte lysate-based assays. The domain of G4 required for binding to FPPS was restricted to an amphipathic α-helix rich in arginine residues. Subtle mutation of this α-helix abrogated G4 oncogenic potential in vitro, providing a biological relevance for FPPS-G4 complex formation in cells. Finally, HTLV-1 p13
II
was also found to specifically interact with FPPS (in yeast as well as in GST pull-down assays) and to colocalize with G4 in mitochondria, suggesting a functional analogy between these oncoviral accessory proteins. Identification of FPPS as a molecular partner for p13
II
and G4 accessory proteins opens new prospects for treatment of retrovirus-induced leukemia.
Heterologous Gene Expression from Transmissible Gastroenteritis Virus Replicon Particles
Authors: Curtis Kristopher M. , Yount Boyd , Baric Ralph S.
Published: October 2010

We have recently isolated a transmissible gastroenteritis virus (TGEV) infectious construct designated TGEV 1000 (B. Yount, K. M. Curtis, and R. S. Baric, J. Virol. 74:10600–10611, 2000). Using this construct, a recombinant TGEV was constructed that replaced open reading frame (ORF) 3A with a heterologous gene encoding green fluorescent protein (GFP). Following transfection of baby hamster kidney (BHK) cells, a recombinant TGEV (TGEV-GFP2) was isolated that replicated efficiently and expressed GFP. Replicon constructs were constructed that lacked either the ORF 3B and E genes or the ORF 3B, E, and M genes [TGEV-Rep(
Avr
II) and TGEV-Rep(
Eco
NI), respectively]. As the E and M proteins are essential for TGEV virion budding, these replicon RNAs should replicate but not result in the production of infectious virus. Following cotransfection of BHK cells with the replicon RNAs carrying
gfp
, GFP expression was evident by fluorescent microscopy and leader-containing transcripts carrying
gfp
were detected by reverse transcription-PCR (RT-PCR). Subsequent passage of cell culture supernatants onto permissive swine testicular (ST) cells did not result in the virus, GFP expression, or the presence of leader-containing subgenomic transcripts, demonstrating the single-hit nature of the TGEV replicon RNAs. To prepare a packaging system to assemble TGEV replicon particles (TGEV VRP), the TGEV E gene was cloned into a Venezuelan equine encephalitis (VEE) replicon expression vector and VEE replicon particles encoding the TGEV E protein were isolated [VEE-TGEV(E)]. BHK cells were either cotransfected with TGEV-Rep(
Avr
II) (E gene deletion) and VEE-TGEV(E) RNA transcripts or transfected with TGEV-Rep(
Avr
II) RNA transcripts and subsequently infected with VEE VRPs carrying the TGEV E gene. In both cases, GFP expression and leader-containing GFP transcripts were detected in transfected cells. Cell culture supernatants, collected ∼36 h posttransfection, were passed onto fresh ST cells where GFP expression was evident ∼18 h postinfection. Leader-containing GFP transcripts containing the ORF 3B and E gene deletions were detected by RT-PCR. Recombinant TGEV was not released from these cultures. Under identical conditions, TGEV-GFP2 spread throughout ST cell cultures, expressed GFP, and formed viral plaques. The development of infectious TGEV replicon particles should assist studies of TGEV replication and assembly as well as facilitate the production of novel swine candidate vaccines.
The Herpes Simplex Virus Type 2 R1 Protein Kinase (ICP10 PK) Blocks Apoptosis in Hippocampal Neurons, Involving Activation of the MEK/MAPK Survival Pathway
Authors: Perkins D. , Pereira E. F. R. , Gober M. , Yarowsky P. J. , Aurelian L.
Published: October 2010

Herpes simplex virus type 1 (HSV-1) and HSV-2 trigger or counteract apoptosis by a cell-specific mechanism. Our studies are based on previous findings that the protein kinase (PK) domain of the large subunit of HSV-2 ribonucleotide reductase (ICP10) activates the Ras/MEK/MAPK pathway (Smith et al., J. Virol. 74:10417, 2000). Because survival pathways can modulate apoptosis, we used cells that are stably or transiently transfected with ICP10 PK, an HSV-2 mutant deleted in ICP10 PK (ICP10ΔPK) and the MEK-specific inhibitor U0126 to examine the role of ICP10 PK in apoptosis. Apoptosis was induced by staurosporine ord-mannitol in human (HEK293) cells or HEK293 cells stably transfected with the ICP10 PK-negative mutant p139 (JHL15), as determined by morphology, DNA fragmentation, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL), caspase-3 activation, and poly(ADP-ribose) polymerase (PARP) cleavage. HEK293 cells stably transfected with ICP10 (JHLa1) were protected from apoptosis. ICP10 but not p139 protected neuronally differentiated PC12 cells from death due to nerve growth factor withdrawal, and apoptosis (determined by TUNEL) and caspase-3 activation were seen in primary hippocampal cultures infected with ICP10ΔPK but not with HSV-2 or a revertant virus [HSV-2(R)]. The data indicate that ICP10 has antiapoptotic activity under both paradigms and that it requires a functional PK activity. The apoptotic cells in primary hippocampal cultures were neurons, as determined by double immunofluorescence with fluorescein-labeled dUTP (TUNEL) and phycoerythrin-labeled antibodies specific for neuronal proteins (TuJ1 and NF-160). Protection from apoptosis was associated with MEK/MAPK activation, as evidenced by (i) increased levels of activated (phosphorylated) MAPK in HSV-2- but not ICP10ΔPK-infected cultures and (ii) inhibition of MAPK activation by the MEK-specific inhibitor U0126. MEK and MAPK were activated by infection with UV-inactivated but not antibody-neutralized HSV-2, suggesting that activation requires cellular penetration but is independent of de novo viral protein synthesis.
Adenovirus E1A N-Terminal Amino Acid Sequence Requirements for Repression of Transcription In Vitro and In Vivo Correlate with Those Required for E1A Interference with TBP-TATA Complex Formation
Authors: Boyd Janice M. , Loewenstein Paul M. , Tang Qing-quan , Yu Li , Green Maurice
Published: October 2010

The adenovirus (Ad) E1A 243R oncoprotein encodes an N-terminal transcription repression domain that is essential for early viral functions, cell immortalization, and cell transformation. The transcription repression function requires sequences within amino acids 1 to 30 and 48 to 60. To elucidate the roles of the TATA-binding protein (TBP), p300, and the CREB-binding protein (CBP) in the mechanism(s) of E1A repression, we have constructed 29 amino acid substitution mutants and 5 deletion mutants spanning the first 30 amino acids within the E1A 1-80 polypeptide backbone. These mutant E1A polypeptides were characterized with regard to six parameters: the ability to repress transcription in vitro and in vivo, to disrupt TBP-TATA box interaction, and to bind TBP, p300, and CBP. Two regions within E1A residues 1 to 30, amino acids 2 to 6 and amino acid 20, are critical for E1A transcription repression in vitro and in vivo and for the ability to interfere with TBP-TATA interaction. Replacement of 6Cys with Ala in the first region yields the most defective mutant. Replacement of 20Leu with Ala, but not substitutions in flanking residues, yields a substantially defective phenotype. Protein binding assays demonstrate that replacement of 6Cys with Ala yields a mutant completely defective in interaction with TBP, p300, and CBP. Our findings are consistent with a model in which the E1A repression function involves interaction of E1A with p300/CBP and interference with the formation of a TBP-TATA box complex.
E4orf6 Variants with Separate Abilities To Augment Adenovirus Replication and Direct Nuclear Localization of the E1B 55-Kilodalton Protein
Authors: Orlando Joseph S. , Ornelles David A.
Published: October 2010

The E4orf6 protein of group C adenovirus is an oncoprotein that, in association with the E1B 55-kDa protein and by E1B-independent means, promotes virus replication. An arginine-faced amphipathic α-helix in the E4orf6 protein is required for the E4orf6 protein to direct nuclear localization of the E1B 55-kDa protein and to enhance replication of an E4 deletion virus. In this study, E4orf6 protein variants containing arginine substitutions in the amphipathic α-helix were analyzed. Two of the six arginine residues within the α-helix, arginine-241 and arginine-243, were critical for directing nuclear localization of the E1B 55-kDa protein. The four remaining arginine residues appear to provide a net positive charge for the E4orf6 protein to direct nuclear localization of the E1B 55-kDa protein. The molecular determinants of the arginine-faced amphipathic α-helix that were required for the functional interaction between the E4orf6 and E1B 55-kDa proteins seen in the transfected cell differed from those required to support a productive infection. Several E4orf6 protein variants with arginine-to-glutamic acid substitutions that failed to direct nuclear localization of the E1B 55-kDa protein restored replication of an E4 deletion virus. Additionally, a variant containing an arginine-to-alanine substitution at position 243 that directed nuclear localization of the E1B 55-kDa protein failed to enhance virus replication. These results indicate that the ability of the E4orf6 protein to relocalize the E1B 55-kDa protein to the nucleus can be separated from the ability of the E4orf6 protein to support a productive infection.
Increased p50/p50 NF-κB Activation in Human Papillomavirus Type 6- or Type 11-Induced Laryngeal Papilloma Tissue
Authors: Vancurova Ivana , Wu Rong , Miskolci Veronika , Sun Shishinn
Published: October 2010

We have observed elevated NF-κB DNA-binding activity in nuclear extracts from human papillomavirus type 6- and 11-infected laryngeal papilloma tissues. The predominant DNA-binding species is the p50/p50 homodimer. The elevated NF-κB activity could be correlated with a reduced level of cytoplasmic IκBβ and could be associated with the overexpression of p21CIP1/WAF1in papilloma cells. Increased NF-κB activity and cytoplasmic accumulation of p21CIP1/WAF1might counteract death-promoting effects elicited by overexpressed PTEN and reduced activation of Akt and STAT3 previously noted in these tissues.
Integrin αvβ1 Is a Receptor for Foot-and-Mouth Disease Virus
Authors: Jackson Terry , Mould A. Paul , Sheppard Dean , King Andrew M. Q.
Published: October 2010

Infection by field strains of
Foot-and-mouth disease virus
(FMDV) is initiated by binding to certain species of arginine-glycine-aspartic acid (RGD)-dependent integrin including αvβ3 and the epithelial integrin αvβ6. In this report we show that the integrin αvβ1, when expressed as a human/hamster heterodimer on transfected CHOB2 cells, is a receptor for FMDV. Virus binding and infection mediated by αvβ1 was inefficient in the presence of physiological concentrations of calcium and magnesium but were significantly enhanced by reagents that activate the integrin and promote ligand binding. The ability of chimeric α5/αv integrin subunits, in association with the β1 chain, to bind FMDV and mediate infection matched the ligand binding specificity of αvβ1, not α5β1, thus providing further evidence for the receptor role of αvβ1. In addition, data are presented suggesting that amino acid residues near the RGD motif may be important for differentiating between the binding specificities of αvβ1 and αvβ6.
Dissociation of Genome Dimerization from Packaging Functions and Virion Maturation of Human Immunodeficiency Virus Type 1
Authors: Sakuragi Jun-ichi , Iwamoto Aikichi , Shioda Tatsuo
Published: October 2010

The dimer initiation site/dimer linkage sequence (DIS/DLS) region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is thought to play important roles at various stages of the virus life cycle. Recently we showed that the DIS/DLS region affects RNA-RNA interaction in intact virus particles, by demonstrating that duplication of the region in viral RNA caused the production of virus particles containing partially monomeric RNAs. We have extended this finding and succeeded for the first time in creating mutant particles which contain only monomeric RNAs without modifying any viral proteins. In terms of RNA encapsidation ability, virion density, and protein processing, the mutant particles were comparable to wild-type particles. The level of production of viral DNA by the mutant virus construct in infected cells was also comparable to that of the constructs that produced exclusively dimeric RNA, indicating that monomeric viral RNA could be the template for strand transfer. These results indicated that the RNA dimerization of HIV-1 could be separated from viral RNA packaging and was not absolutely required for RNA packaging, virion maturation, and reverse transcription.
Viral Dynamics during Structured Treatment Interruptions of Chronic Human Immunodeficiency Virus Type 1 Infection
Authors: Frost Simon D. W. , Martinez-Picado Javier , Ruiz Lidia , Clotet Bonaventura , Leigh Brown Andrew J.
Published: October 2010

Although antiviral agents which block human immunodeficiency virus (HIV) replication can result in long-term suppression of viral loads to undetectable levels in plasma, long-term therapy fails to eradicate virus, which generally rebounds after a single treatment interruption. Multiple structured treatment interruptions (STIs) have been suggested as a possible strategy that may boost HIV-specific immune responses and control viral replication. We analyze viral dynamics during four consecutive STI cycles in 12 chronically infected patients with a history (>2 years) of viral suppression under highly active antiretroviral therapy. We fitted a simple model of viral rebound to the viral load data from each patient by using a novel statistical approach that allows us to overcome problems of estimating viral dynamics parameters when there are many viral load measurements below the limit of detection. There is an approximate halving of the average viral growth rate between the first and fourth STI cycles, yet the average time between treatment interruption and detection of viral loads in the plasma is approximately the same in the first and fourth interruptions. We hypothesize that reseeding of viral reservoirs during treatment interruptions can account for this discrepancy, although factors such as stochastic effects and the strength of HIV-specific immune responses may also affect the time to viral rebound. We also demonstrate spontaneous drops in viral load in later STIs, which reflect fluctuations in the rates of viral production and/or clearance that may be caused by a complex interaction between virus and target cells and/or immune responses.
Hepatitis C Virus Genotype 1b Core Protein Does Not Exert Immunomodulatory Effects on Virus-Induced Cellular Immunity
Authors: Liu Zhang-Xu , Nishida Hiroshi , He Jian-Wen , Lai Michael M. C. , Feng Ni , Dennert Gunther
Published: October 2010

The hepatitis C virus (HCV) core protein is among the most conserved proteins in HCV and is known to induce sensitization of cytotoxic T lymphocytes (CTL). Therefore, it is a prime candidate for a component of a potential HCV vaccine. The HCV core protein has, however, been reported to exert multiple effects on cell functions, raising questions as to its suitability for this purpose. This question was investigated here with mice into which replication-deficient adenoviruses expressing core protein of an HCV genotype 1b isolate were injected. We show that induction of cytokines in response to the infection, infiltration of lymphocytes into the infected liver, priming of virus-specific CTL, and liver injury are not modulated by expression of the core protein in the liver. Moreover, no changes in the sensitivity to tumor necrosis factor alpha- or Fas-mediated liver injury are demonstrable. A similar lack of demonstrable effects of the core protein on immune functions has also been obtained using transgenic mice expressing another HCV genotype 1b core protein. It is concluded that the HCV core protein of genotype 1b has no modulatory effects on induction of virus-specific immune responses and may therefore be a suitable component of an HCV vaccine.
Metabolome-Proteome Differentiation Coupled to Microbial Divergence
Authors: Wilmes Paul , Bowen Benjamin P. , Thomas Brian C. , Mueller Ryan S. , Denef Vincent J. , VerBerkmoes Nathan C. , Hettich Robert L. , Northen Trent R. , Banfield Jillian F.
Published: October 2010

Tandem high-throughput proteomics and metabolomics were employed to functionally characterize natural microbial biofilm communities. Distinct molecular signatures exist for each analyzed sample. Deconvolution of the high-resolution molecular data demonstrates that identified proteins and detected metabolites exhibit organism-specific correlation patterns. These patterns are reflective of the functional differentiation of two bacterial species that share the same genus and that co-occur in the sampled microbial communities. Our analyses indicate that the two species have similar niche breadths and are not in strong competition with one another.

IMPORTANCE
Natural microbial assemblages represent dynamic consortia that exhibit extensive complexity at all levels. In the present study, we demonstrate that correlations between protein and metabolite abundances allow the deconvolution of complex molecular data sets into shared and organism-specific contingents. We demonstrate that evolutionary divergence is associated with the restructuring of cellular metabolic networks, which in turn allows bacterial species to occupy distinct ecological niches. The apparent lack of interspecific competition may explain the extensive population-level genetic heterogeneity observed extensively within microbial communities. The reported findings have broad implications for the in-depth investigation of the ecology and evolution of distinct microbial community members and for leveraging the solution of cryptic metabolic processes in the future.
Alcohol based tissue fixation as an alternative for formaldehyde: influence on immunohistochemistry
Authors: van Essen Hendrik F , Verdaasdonk Marina A M , Elshof Sabrina M , de Weger Roel A , van Diest Paul J
Published: October 2010

Background

Formaldehyde is commonly used in histopathology to fix tissue. Not only are the carcinogenic properties of this solution a hazard to the people in the workplace, it is also a major burden on the environment, and it crosslinks molecular groups that hinder immunohistochemistry.

Aims

The influence of two new alcohol based non-crosslinking fixatives on immunohistochemical staining properties was tested on various tissues.

Methods

Fresh tissue samples were cut into three equal pieces, which were then fixed in the alcohol based fixatives Boonfix or RCL2, or in neutral buffered formaldehyde (NBF) as control. After fixation, tissue was routinely processed to paraffin sections. Deparaffinised slides were blocked for endogenous peroxidase and subsequently submitted to the usual NBF based immunohistochemical protocols for 85 different common antibodies either not requiring antigen retrieval (AR), or AR in citrate buffer, EDTA or pepsin.

Results

NBF fixed tissues provided significantly better immunostaining results (84% good staining) than RCL2 (66% good) and Boonfix (60%). The lesser performance of RCL2 and Boonfix was especially caused by pepsin AR which caused significant tissue damage. Omission of pepsin AR resulted in better immunostaining for these antibodies for RCL2 fixed tissues which were overall no longer significantly worse than NBF fixed tissue.

Conclusion

Tissues fixed in non-crosslinking alcohol based fixatives can successfully be immunohistochemically stained for most antibodies following the usual NBF based protocols. Omission of pepsin pretreatment seems to be important to retain proper morphology of immunostained tissues preserved in alcohol based fixatives. Therefore, when switching to less toxic and non-carcinogenic alcohol-based fixatives like RCL2, no major changes in the daily routine of immunohistochemistry are anticipated.
The Right to Fish as an External Benefit of Open Access
Authors: Townsend Ralph E.
Published: October 2010

Work is more than a means to earn income. Work activity is intimately related to the values of a society. This is especially true for occupational communities. Fishing activity may have very profound effects upon the social system. Open access to the resource is one dimension that reinforces this connection. A worker satisfaction bonus is much too narrow a concept to capture the depth of the relationship of social benefits to the open-access institution. To understand the role that the birthright performs, the entire ecological system — biological, economic, political, and social — in which fishermen work and live must be understood.
Removal of Follicle Wall Components from Ovarian Oocytes of the Brook Trout, Salvelinus fontinalis
Authors: Lessman Charles A. , Kavumpurath Soosamma , Habibi Hamid R.
Published: October 2010

Fully grown brook trout (Salvelinus fontinalis) ovarian follicles, preincubated in Ca2+-free media, were dissected from other ovarian tissue by use of watchmaker forceps. Manual defolliculation and further Ca2+-free treatments were used to obtain oocytes freed of one or more follicular investments. Combinations of these treatments ultimately resulted in oocytes denuded of somatic cells as demonstrated by scanning electron microscopy. Mechanically denuded brook trout oocytes maintained the ability to undergo progestogen-induced meiotic maturation in vitro. This technique, which avoids use of enzymes that may alter cell surfaces, provides a useful system for the study of interactions between follicle wall components and the oocyte during hormonally induced meiotic maturation in vitro.
Changes to Stock Reduction Analysis Indicated by Schnute's General Theory
Authors: Kimura Daniel K.
Published: October 2010

Recently, J. Schnute generalized the R. B. Deriso age-structured model by using a more general growth curve to derive a more general form of Deriso's delay-difference equation. I have outlined changes in the Stock Reduction Analysis (SRA) model that are required to take advantage of Schnute's more general approach. The proposed changes in the equations do not affect the way SRA is applied, but should reduce bias in the model.
The minor planet (3316) Herzberg
Authors: Aikman G. Christopher L. , Balam David D. , Tatum Jeremy B.
Published: October 2010

We describe the history of the minor planet (3316) Herzberg, and present a new precise orbit for the object from all available observations, including new observations of our own obtained specially for the purpose of this commemorative issue, applying perturbations from all the major planets.
Light element abundance inhomogeneities in globular clusters: probing star formation and evolution in the early Milky Way
Authors: Briley Michael M. , Bell Roger A. , Hesser James E. , Smith Graeme H.
Published: October 2010

Abundance patterns of the elements C, N, and O are sensitive probes of stellar nucleosynthesis processes and, in addition, O abundances are an important input for stellar age determinations. Understanding the nature of the observed distribution of these elements is key to constraining protogalactic star formation history. Patterns deduced from low-resolution spectroscopy of the CN, CH, NH, and CO molecules for low-mass stars in their core-hydrogen or first shell-hydrogen burning phases in the oldest ensembles known, the Galactic globular star clusters, are reviewed. New results for faint stars in NGC 104 (47 Tuc, C0021-723) reveal that the bimodal, anticorrelated pattern of CN and CH strengths found among luminous evolved stars is also present in stars nearing the end of their main-sequence lifetimes. In the absence of known mechanisms to mix newly synthesized elements from the interior to the observable surface layers of such unevolved stars, those particular inhomogeneities imply that the original material from which the stars formed some 15 billion years ago was chemically inhomogeneous in the C and N elements. However, in other clusters, observations of abundance ratios and C isotope ratios suggest that alterations to surface chemical compositions are produced as stars evolve from the main sequence through the red giant branch. Thus, the current observed distributions of C, N, and O among the brightest stars (those also observed most often) may not reflect the true distribution from which the protocluster cloud formed. The picture that is emerging of the C, N, and O abundance patterns within globular clusters may be one which requires a complicated combination of stellar evolutionary and primordial effects for its explanation.
Infrared spectroscopy of molecular hydrogen in astrophysical environments
Authors: Geballe T. R.
Published: October 2010

Forty-five years ago Gerhard Herzberg became the first person to observe lines of the infrared rotation–vibration bands of molecular hydrogen; 20 years ago astronomers first found some of these lines in the interstellar medium. Examples are given of astrophysical environments in which H2 has been detected, with emphasis on their growing importance to astronomy. The rotation–vibration spectrum has been observed in emission following both collisional and radiative excitation processes. Recent detections of absorption by cold interstellar molecular hydrogen, both in the gaseous and the solid states, have expanded knowledge of physical properties of molecular clouds and the physical and chemical processes occurring within them.
Optimization of X-ray laser gain in neonlike germanium plasmas
Authors: Villeneuve D. M. , Enright G. D. , Dunn J. , Fontaine B. La , Baldis H. A. , Kieffer J. C. , Nantel M.
Published: October 2010

X-ray laser action has been studied in a laser-produced plasma composed of germanium atoms ionized to the neonlike state. Laser gains of up to 4.1 cm−1 at 232 Å (1 Å = 10−10 m) were measured. The effect of driver laser parameters such as intensity on target, pulse duration, and pulse rise time have been studied so as to understand the requirements for increased efficiency.
Towards hot solid-density plasmas with ultra-high-intensity sub-picosecond lasers
Authors: Kieffer J. C. , Côté C. Y. , Jiang Z. , Beaudoin Y. , Chaker M. , Peyrusse O.
Published: October 2010

We discuss the various regimes of interaction of a sub-picosecond laser pulse with solid matter that we are exploring with the table top terawatt laser system at the Institut national de la recherche scientifique. The Li-like satellite spectrum (1s2l2l′-1s22l) is used to study (i) the nonstationary and non-Maxwellian physics when the density gradient scale length is large compared with the laser wavelength, and (ii) the transition towards the physics of solid-density plasmas at the local thermodynamical equilibrium when the gradient scale length is ultrashort. We emphasize some exciting perspectives of this new physics and in particular we discuss the generation of hot solid-density plasmas that may have a strong impact in many different areas such as astrophysics, atomic physics, chemistry, and inertial confinement fusion.
Electronic structures and bonding in Rydberg molecules: NH4, H3O and related molecules
Authors: Wang Jian , Boyd Russell J.
Published: October 2010

The electronic structures of the Rydberg and related molecules belonging to the series [Formula: see text], NH4, and [Formula: see text] and H3O+, H3O, and H3O− have been investigated by analysis of the electron densities generated by the Hartree–Fock method (HF), the quadratic configuration interaction method including single and double excitations (QCISD), the coupled-cluster method including double excitations (CCD), and the density functional method with the Becke–Perdew gradient correction functionals (DFT-BP). Adding an electron to the stable cation core ([Formula: see text] and H3O+) results in an increase in the bond length, a larger increase in the distance of the bond critical point (BCP) from the nitrogen atom than from the hydrogen atom, a decrease in the electron density at the bond critical point, and an increase of the Laplacian of the electron density at the BCP. These trends are consistent with a decrease in the electronegativity of the central atom and a weakening of the bond as electrons are added to diffuse Rydberg orbitals. There is little effect, however, when a second electron is added to form the double Rydberg molecules ([Formula: see text] and H3O−). For NH4, the preferred geometry corresponds to a high atomic energy associated with the hydrogen basin, and to a low kinetic energy and a high potential energy in the basin. The high atomic energy associated with the hydrogen basin is attributed to the dominant contribution of the electron–nuclear attraction energy. Similar effects are observed in the Jahn–Teller distorted molecules: [Formula: see text] and [Formula: see text]. The DFT-BP method yields results in qualitative agreement with the results of the QCISD and CCD methods; however, it underestimates the bond strengths of the Rydberg molecules relative to high-level ab initio methods.
An ab initio calculation of the vibronic energies of the CH2+ molecule
Authors: Kraemer W. P. , Jensen Per , Bunker P. R.
Published: October 2010

In this paper we report the results of an ab initio calculation of vibronic (i.e., N = 0) energy levels of the CH2+ molecular ion giving the lowest 19 levels of the ground [Formula: see text] electronic state and the lowest 15 of the first excited Ã2B1 state. The two electronic states become degenerate (2Π) at the linear configuration and their rovibronic levels interact via the Renner effect. The ab initio calculation of the two potential surfaces was performed at 96 nuclear geometries for the ground electronic state, covering energies up to 11 000 cm−1 above equilibrium, and at 86 geometries for the excited state, covering energies up to 30 000 cm−1 above equilibrium. The multireference configuration interaction (MRCI) level of theory was used with molecular orbital bases that were optimized separately for each state by complete-active-space-self-consistent-field (CASSCF) calculations. The vibronic energy levels were calculated variationally from the potential surfaces using the Morse oscillator rigid bender internal dynamics Hamiltonian modified to include the effects of the Renner interaction. We also present calculated vibronic energies for the CD2+ and CHD+ isotopically substituted molecules.
Studies of C 1s → π* triplet states of carbon monoxide, benzene, ethylene, and acetylene
Authors: Francis J. T. , Enkvist C. , Lunell S. , Hitchcock A. P.
Published: October 2010

The (C 1s−1,π*) triplet states of carbon monoxide, benzene, ethylene, and acetylene have been studied using electron energy loss spectroscopy with low-energy (near-threshold) excitation. The singlet–triplet splitting for the (C 1s−1,π*) states of the hydrocarbon species were measured for the first time. Intermediate neglect of differential overlap (spectroscopic) (INDO/S) calculations within the equivalent cores approximation were used to calculate (1s−1, π*) singlet–triplet splittings. The calculated values are in reasonable agreement with the experimental values for the hydrocarbon species but are significantly underestimated for CO. A strong correlation between singlet–triplet splittings and oscillator strengths for the 1s → π* transitions was noted and rationalized in terms of the dependence of both factors on the spatial overlap of 1s and π* wave functions.
Broadening and shifting of the Raman Q branch in pure D2 and D2–He mixtures, I: experimental results and comparison with theory
Authors: Sinclair P. M. , Duggan P. , Flohic M. Le , Forsman J. W. , Drummond J. R. , May A. D.
Published: October 2010

We report the broadening and shifting of the Raman Q-branch lines in D2 and D2–He mixtures, all at 305.2 K. The width and shift of each line were extracted by fitting a simple Lorentzian profile to the experimental data. From a linear fit of the widths and shifts as a function of density we have determined broadening and shifting coefficients with an uncertainty of ±0.5%. None of the existing semiclassical or quantal calculations agree with the measurements at this level of accuracy. It is pointed out that the removal of certain approximations in the calculations should bring theory and experiment into closer agreement.
Simulations of krypton matrix effects on the electronic spectrum of Na2
Authors: Nemukhin A. V. , Grigorenko B. L. , Sergeev G. B.
Published: October 2010

A model for calculation of spectral shifts in small molecules due to matrix environments is developed. The approach is based on the one-electron approximation and combines methods of ab initio quantum chemistry, density functional theory, and molecular dynamics simulations. Applications to Na2Kr62 heteroclusters demonstrate that the model is capable of reproducing spectral shifts of opposite sign for the experimentally studied A–X and B–X transitions in Na2 trapped inside the Kr matrix.
Fourier transform infrared spectroscopy of the BH3 ν2 band
Authors: Kawaguchi K.
Published: October 2010

The spectrum of the BH3 ν2 band was observed in the 900–1300 cm−1 region with a Fourier transform infrared spectrometer. The borane molecule was produced with a discharge in a B2H6 and He mixture. The observed spectrum was analyzed by including the Coriolis interaction from the ν4 state to determine the molecular constants in the ν2 and ν4 states. The band origins and the Coriolis interaction constant were determined to be ν2 = 1147.4986 (12), ν4 = 1196.66 (12), and D24 = 7.8034 (48) cm−1, with one standard deviation in parentheses. The previous Q-branch assignment of the diode laser spectrum was partly revised.
Analysis of infrared spectra of gaseous TIF
Authors: Ogilvie J. F. , Liao S. C. , Uehara Hiromichi , Horiai Koui
Published: October 2010

Vibration–rotational spectra of 205Tl19F and 203Tl19F in the electronic ground state X0+ were measured in absorption in the range of wave number [Formula: see text] with diode lasers as spectral sources. Analysis of all available data yielded values of coefficients of radial functions for the potential energy and other molecular properties; only eight independently fitted and two constrained parameters sufficed to reproduce satisfactorily and with physical meaning the frequencies and wave numbers of about 890 distinct pure rotational and vibration–rotational transitions. Independent of nuclear mass, the equilibrium internuclear separation Re of TlF is (2.084 3517 ± 0.000 0039) × 10−10 m; the maximum range of validity of radial functions is 1.85 ≤ R/10−10 m ≤ 2.45. Comparing these results with those of InF, we attribute the large magnitude of [Formula: see text] to the finite and isotopically varying nuclear volume of Tl rather than to (adiabatic) effects of nuclear mass, whereas no such effect is detectable for In in InF. Other aspects of nonadiabatic effects for these polar molecules TlF and InF are discussed.
Fluorescence-detected infrared– and Raman–ultraviolet double resonance in acetylene gas: studies of spectroscopy and rotational energy transfer
Authors: Chadwick B. L. , Milce A. P. , Orr B. J.
Published: October 2010

Fluorescence-detected Raman–ultraviolet and infrared–ultraviolet double resonance (DR) spectroscopy enables state-selective studies of rotational and vibrational energy transfer in gas-phase acetylene (C2H2) and its deuterated isotopomers (C2HD, C2D2). The Raman–UV DR approach entails pulsed coherent Raman excitation in the ν2 rovibrational band of C2H2(g), followed by fluorescence-detected rovibronic probing of the resulting rovibrational population distributions. Corresponding IR–UV DR experiments employ a line-tunable, pulsed CO2 laser to excite rovibrational transitions in the 2ν4 band of C2HD(g) and in the (ν4 + ν5) band of C2D2(g), with similar fluorescence-detected rovibronic probing. These time-resolved DR spectroscopic techniques provide rotationally specific information on collision-induced molecular energy transfer in acetylene. This paper extends previous Raman–UV DR spectroscopic studies of C2H2 and presents fresh IR–UV DR spectra of gas-phase C2HD and C2D2, including evidence of a novel two-step excitation sequence in which a single CO2-laser pulse promotes C2D2 by successive transitions in the (ν4 + v5) and (2ν4 + 2ν5−ν4−v5) absorption bands. Kinetic measurements and mechanistic observations are also reported for collision-induced rotational energy transfer in acetylene gas, complementing other investigations of rotationally resolved vibrational energy transfer.
Microwave spectrum and molecular structure of the HS2 radical
Authors: Yamamoto Satoshi , Saito Shuji
Published: October 2010

Rotational spectral lines of the HS2 and DS2 radicals in the 2A″ ground electronic state are detected by a source-modulation microwave spectrometer combined with a free-space cell. The HS2 radical is produced in the cell by discharging a pure H2S gas. The spectrum of DS2 is observed by using a mixture of H2S and D2. The rotational constants, the centrifugal distortion constants, the spin-rotation interaction constants with their centrifugal distortion corrections, and the hyperfine interaction constants for the hydrogen nucleus are determined by least-squares analyses. The harmonic force constants are evaluated from the observed centrifugal distortion constants in combination with the vibrational frequencies reported previously. The zero-point average structure of HS2 is determined from the observed rotational constants of HS2 and DS2 with the aid of the harmonic force constants: rz(S—S) = 1.9650 (7) Å, rz (S—H) = 1.362 (3) Å, and αz (HSS) = 101/7 (4)° (1 Å = 10−10 m). The equilibrium distances for the S—S and S—H bonds are derived to be 1.9606 (7) Å and 1.352 (3) Å, respectively, by assuming the anharmonic constants of the corresponding diatomic molecules.
Branch intensities in the magnetic dipole rotation–vibration spectrum of the oxygen molecule
Authors: Balasubramanian T. K. , Bellary V. P. , Rao K. Narahari
Published: October 2010

The theory of branch line strengths for a magnetic dipole rotation–vibration spectrum in a 3Σ diatomic state is discussed in the context of the oxygen molecule. It is argued that, in contradistinction to the electric dipole case, magnetic dipole rovibrational transitions can occur only through indirect mechanisms. One possible mechanism, that of vibration–rotation interaction, is examined in detail and shown to be unimportant at least in a first-order calculation. The departure of the 3Σ state from a pure Born–Oppenheimer state is treated phenomenologically and shown to result in the appearance of two vibronic transition moments, [Formula: see text] and [Formula: see text] (the former arising only in the second order), in the branch line strength formulae. The available intensity data on O2 are used to generate an intensity listing for lines in the fundamental band.