bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal gelation of commercial whey protein concentrate: influence of pH 4.6 insoluble protein on thermal gelation
Authors: PUYOL PILAR , COTTER PATRICK F , MULVIHILL DANIEL M
Published: August 2007

Thermal gels were prepared from solutions of seven commercial whey protein concentrates (WPCs) and were found to vary considerably in strength, as determined by a compressive rheological measurement method. Further studies were carried out on one WPC (WPC5) which had far superior gelling properties to the other six WPCs and revealed that this WPC had a substantial level of protein that was insoluble (sedimentable) at pH 4.6 on centrifugation at 10000 g for 30 min but not insoluble under similar conditions at pH 7.0. When this pH 4.6 insoluble material was removed the gelling properties of WPC5 decreased considerably. Alkaline treatment (pH 9.0 for 3 hours) of a WPC5 supernatant devoid of pH 4.6 insoluble material resulted in a substantial improvement in gelling properties and generation of further pH 4.6 insoluble material. Gel electrophoresis studies and differential scanning calorimetry confirmed that the pH 4.6 insoluble material recovered from WPC5 and the alkaline treated WPC5 supernatant contained denatured protein which was associated via covalent and non‐covalent interactions. Transmission electron microscopy of thermal gels prepared from WPC5 solutions containing and devoid of pH 4.6 insoluble material indicated that gel micro structure was dependent on the presence or absence of this denatured aggregated protein material in dispersion prior to heat treatment. Overall, the results suggested that the pH 4.6 insoluble, but pH 7.0 soluble, protein present in a WPC5 dispersion influenced gel microstructure on heating in a manner that had a positive influence on gel rheology.
Carboxymethyl cellulose (CMC) as an additive for oil reduction in deep‐fat fried paneer
Authors: SHARMA HARISH KUMAR , SINGHAL REKHA S , KULKARNI PUSHPA R , GHOLAP ACHYUT S
Published: August 2007

The effect of different levels of CMC on the uptake of vegetable oil during the deep‐fat frying of paneer was studied by: (i) direct addition of CMC to the milk and (ii) dipping the paneer cubes into solutions of CMC for different time intervals. The fried paneers were evaluated for chemical composition, hardness and sensory characteristics. Method (i) proved to be beneficial in all respects as compared to (ii), as the absorption of water from the suspensions of CMC destroyed the texture of the paneer.
Viscosity changes during rennet coagulation of Murciano‐Granadina goat milk
Authors: LÓOPEZ M B , JORDÁN M J , GRANADOS M V , FERNÁNDEZ J C , CASTILLO M. , LAENCINA J.
Published: August 2007

The viscosity changes during coagulation of raw and pasteurized Murciano‐Granadina goat milk with 10 rennets and coagulant enzymes were studied using a cylindrical rotational viscometer. The effect of three shear rates (7.32, 14.68, 73.42 s‐1) was analysed in reconstituted milk using 60% chymosin rennet and different enzyme concentrations. The shear rate selected (14.68 s‐1) corresponded to that in which the coagulation time was not modified. At a sheer rate of 73.42 s‐1 there was a significant difference (p < .05) in the milk clotting time determined compared with the shear rates of 7.32 and 14.68 s‐1. At the beginning of the coagulation process there was a decrease in the viscosity value, which was higher in raw milk (22%) than in the two heat treated samples (17% in milk pasteurized at 65°C for 30 min, low temperature long time, and 19% in milk pasteurized at 75°C for 15 s, high temperature short time). After this period the viscosity rose rapidly and reached a value 2.89 times greater than at time 0. A highly significant Pearson correlation (0.952‐0.994) was found between the coagulation time determined by the Berridge method and viscometric measurement in raw and pasteurized milk.
A study of methods for evaluating the integrity of plate type heat exchangers used in the dairy industry
Authors: DOWMAN A A , RATCLIFFE N M
Published: August 2007

An overview of leak testing methods for heat exchangers is presented. The problems associated with the presence of residual liquid during testing were assessed as it was shown experimentally that complete drainage of plate type heat exchangers is very difficult. A theoretical modelling of small leaks in heat exchanger plates was combined with laboratory experiments. The strengths and weaknesses of electrolytic differential analysis and helium leak detection methods are presented. The electrolytic differential analysis method is capable of detecting smaller leak volumes than the helium leak detection method, in the presence of water, assuming α 0.5 μS/cm and 0.1 ppm helium detection limit for the former and latter cases respectively. The test pressure was shown to be a significant factor in the detection of very small holes; this was a particularly important criterion for gas based hole detection methods in the presence of water.
SDT Spring Symposium: Organic milk and dairy products
Authors: O'SULLIVAN ANTHONY
Published: August 2007

objective evaluation of this Symposium results in the following three conclusi

The organic speakers all laboured the view that this new sector is very ‘open’ in terms of helping each other and readily providing information. However, their actual contributions highlighted that they were less open with ‘outsiders’ in mainstream dairying.

In turn, the organic presentations were characterized by (i) paucity of hard facts and lack of technical content, (ii) too much emphasis on the philosophy/ethos of organic production and (iii) associated feelings of superiority over mainstream or conventional agriculture. These considerations were compounded by two speakers not adequately addressing their specific topics and associated briefs.

A niggling concern about the professionalism and commercialism of organic producers and processors, especially when they face the full blast of competition from the major dairy processors in due course.

However, an overall assessment of this Symposium suggests that it still achieved the main objective set by the Society of providing an independent forum for the domestic organic sector to present its wares to the mainstream UK dairy industry.
The sensory profile and consumer preference for ten speciality cheeses
Authors: LAWLOR J BEN , DELAHUNTY CONOR M
Published: August 2007

The sensory characteristics that determined consumer preference for 10 speciality cheeses were investigated. These cheeses were chosen to reflect a wide range of speciality cheeses now available on the Irish market offering a diverse range of sensory characteristics. Descriptive analysis was carried out by 15 trained assessors who used a vocabulary of 47 terms to quantitatively describe cheese appearance, odour, flavour and texture. Analysis of variance found significant differences between cheeses (p <.05) on the first seven principle components (which accounted for 85% of the explained variation) obtained from Principal Components Analysis of the sensory data. A total of 198 consumers related their preferences for the cheeses on a nine point hedonie scale. Internal preference mapping illustrated individual consumers' preferences for the cheeses. Hierarchical cluster analysis showed that the sampled consumer population was heterogeneous by identifying seven clusters of consumers with different preferences and demonstrated that there exists cr market for the sensory characteristics of each of the cheeses. Partial Least Squares regression was carried out to relate the sensory character of the cheeses with consumer preference scores. Gruyère, the preferred cheese of three clusters of consumers (and the most preferred cheese overall), was distinguished by a ‘fruity’ odour, a ‘balanced’ and ‘sweet’ flavour and a ‘firmness’ texture. Blue Shropshire, the preferred cheese of two clusters of consumers (hut the least liked cheese overall) was characterized by a ‘mouldy’ odour, an ’acidic’, ‘astringent’ and ‘mouldy’ flavour and cr ‘crumbly’ texture. Finally, socioeconomic data were obtained from a consumer questionnaire. These data pointed to some interesting relationships between socioeconomic variables and consumer preferences.
Potential use of homogenized whey protein dispersions and process modification for the manufacture of low fat and reduced fat cheddar type cheeses
Authors: PUNIDADAS P , TUNG M A , FEIRTAG J
Published: August 2007

Interest in cheese with lower fat than regular cheese has grown in recent years due to the changing eating habits of health conscious consumers, but production of such cheeses at low cost, without losing flavour and texture, is a challenge. In this study, modified processes were developed to manufacture low (˜20%) and reduced (˜15%) fat cheddar cheeses. Modifications of cooking time and temperature, along with changes in the amount of starter culture used and the addition of whey proteins, were studied. The results showed that low fat cheese could be manufactured with or without adding homogenized whey proteins, and reduced fat cheese could be manufactured with homogenized whey proteins. This finding reveals that it would be possible to manufacture these cheeses in an existing cheese plant, but that a homogenizer would be required if whey protein is to be added.
An approach to the detection of synthetic milk in dairy milk: 2. Detection of detergents
Authors: PARADKAR MANISH M , SINGHAL REKHA S , KULKARNI PUSHPA R
Published: August 2007

This work reports on methods to detect and estimate anionic detergents, which are important ingredients of synthetic milk formulations, based on the extraction of a detergent‐Methylene Blue complex in chloroform which can be subsequently quantified by measuring the optical density at 653 nm. A base value of 0.52 for optical density was found to represent pure cows' milk. Any result above this value suggested the presence of an anionic detergent in milk.
How Central Is the Genome?
Authors: Werner Eric
Published: August 2007

The Music of Life
. Biology Beyond the Genome.
By Denis Noble
. Oxford University Press, Oxford, 2006. 167 pp. £12.99. ISBN 9780199295739.

Noble develops the analogy between music and living organisms to provide an informal introduction to the concepts and approaches of systems biology.
The Future of Attosecond Spectroscopy
Authors: Bucksbaum Philip H.
Published: August 2007

Attoscience is the study of physical processes that occur in less than a fraction of a cycle of visible light, in times less than a quadrillionth of a second. The motion of electrons inside atoms and molecules that are undergoing photoionization or chemical change falls within this time scale, as does the plasma motion that causes the reflectivity of metals. The techniques to study motion on this scale are based on careful control of strong-field laser-atom interactions. These techniques and new research opportunities in attosecond spectroscopy are reviewed.
Rapid Population Growth of a Critically Endangered Carnivore
Authors: Grenier M. B. , McDonald D. B. , Buskirk S. W.
Published: August 2007

Reintroductions of endangered species are controversial because of high costs and frequent failures. However, the population of black-footed ferrets descended from animals released in Shirley Basin, Wyoming, from 1991 to 1994 has grown rapidly after a decline to a low of five animals in 1997. Beginning around 2000, the population grew rapidly to an estimated 223 (95% confidence interval is 192 to 401) individuals in 2006. Matrix population modeling shows the importance of survival and reproduction during the first year of life, reflecting an uncommon life history for an endangered mammalian carnivore. Recovery of the species may benefit from more opportunistic and widespread releases.
Multifunctional Nanomechanical Systems via Tunably Coupled Piezoelectric Actuation
Authors: Masmanidis Sotiris C. , Karabalin Rassul B. , De Vlaminck Iwijn , Borghs Gustaaf , Freeman Mark R. , Roukes Michael L.
Published: August 2007

Efficient actuation is crucial to obtaining optimal performance from nanoelectromechanical systems (NEMS). We employed epitaxial piezoelectric semiconductors to obtain efficient and fully integrated NEMS actuation, which is based on exploitation of the interaction between piezoelectric strain and built-in charge depletion. The underlying actuation mechanism in these depletion-mediated NEMS becomes important only for devices with dimensions approaching semiconductor depletion lengths. The induced actuation forces are controlled electrically, and resonant excitation approaching single-electron efficiency is demonstrated. The fundamental electromechanical coupling itself can be programmed by heterostructure band engineering, externally controllable charge depletion, and crystallographic orientation. These attributes are combined to realize a prototype, mechanically based, exclusive-or logic element.
Direct Synthesis of Amides from Alcohols and Amines with Liberation of H
2
Authors: Gunanathan Chidambaram , Ben-David Yehoshoa , Milstein David
Published: August 2007

Given the widespread importance of amides in biochemical and chemical systems, an efficient synthesis that avoids wasteful use of stoichiometric coupling reagents or corrosive acidic and basic media is highly desirable. We report a reaction in which primary amines are directly acylated by equimolar amounts of alcohols to produce amides and molecular hydrogen (the only products) in high yields and high turnover numbers. This reaction is catalyzed by a ruthenium complex based on a dearomatized PNN-type ligand [where PNN is 2-(di-
tert
-butylphosphinomethyl)-6-(diethylaminomethyl)pyridine], and no base or acid promoters are required. Use of primary diamines in the reaction leads to bis-amides, whereas with a mixed primary-secondary amine substrate, chemoselective acylation of the primary amine group takes place. The proposed mechanism involves dehydrogenation of hemiaminal intermediates formed by the reaction of an aldehyde intermediate with the amine.
Sporothrix brasiliensis,S. globosa, andS. mexicana, Three NewSporothrixSpecies of Clinical Interest
Authors: Marimon Rita , Cano Josep , Gené Josepa , Sutton Deanna A. , Kawasaki Masako , Guarro Josep
Published: August 2007

Sporothrix schenckiiis the species responsible for sporotrichosis, a fungal infection caused by the traumatic implantation of this dimorphic fungus. Recent molecular studies have demonstrated that this species constitutes a complex of numerous phylogenetic species. Since the delineation of such species could be of extreme importance from a clinical point of view, we have studied a total of 127 isolates, most of which were received asS. schenckii, including the available type strains of species currently considered synonyms, and also some close morphological species. We have phenotypically characterized all these isolates using different culture media, growth rates at different temperatures, and numerous nutritional tests and compared their calmodulin gene sequences. The molecular analysis revealed thatSporothrix albicans,S. inflata, andS. schenckiivar.lurieiare species that are clearly different fromS. schenckii. The combination of these phenetic and genetic approaches allowed us to propose the new speciesSporothrix brasiliensis,S. globosa, andS. mexicana. The key phenotypic features for recognizing these species are the morphology of the sessile pigmented conidia, growth at 30, 35, and 37°C, and the assimilation of sucrose, raffinose, and ribitol.
Targeted PCR for Detection of Vaginal Bacteria Associated with Bacterial Vaginosis
Authors: Fredricks David N. , Fiedler Tina L. , Thomas Katherine K. , Oakley Brian B. , Marrazzo Jeanne M.
Published: August 2007

Several novel bacterial species have been detected in subjects with bacterial vaginosis (BV) by using broad-range PCR assays, but this approach is insensitive for detecting minority species. We developed a series of taxon-directed 16S rRNA gene PCR assays for more sensitive detection of key vaginal bacteria. We sought to determine the prevalence of each species in the vagina, its association with BV, and the utility of PCR for the microbiological diagnosis of BV. Targeted PCR assays were developed for 17 vaginal bacterial species and applied to 264 vaginal-fluid samples from 81 subjects with and 183 subjects without BV. The results were compared to those of two widely accepted methods for diagnosing BV, the use of clinical findings (Amsel criteria) and the interpretation of vaginal-fluid Gram stains (Nugent criteria).
Leptotrichia
/
Sneathia
,
Atopobium vaginae
, an
Eggerthella
-like bacterium,
Megasphaera
species, and three novel bacteria in the order
Clostridiales
are among the bacterial species significantly associated with BV. PCR detection of either a
Megasphaera
species or one of the
Clostridiales
bacteria yielded a sensitivity of 99% and a specificity of 89% for diagnosis of BV compared to the Amsel clinical criteria and a sensitivity of 95.9% and a specificity of 93.7% compared to the Nugent criteria (Gram stain). PCR detection of one or more fastidious bacterial species is a more reliable indicator of BV than detection of bacteria, such as
Gardnerella vaginalis
, previously linked to BV, highlighting the potential of PCR for the diagnosis of BV.
Characterization and Structural Analysis of Novel Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase Involved in the Regulation of Resistance to Nonnucleoside Inhibitors
Authors: Ceccherini-Silberstein Francesca , Svicher Valentina , Sing Tobias , Artese Anna , Santoro Maria Mercedes , Forbici Federica , Bertoli Ada , Alcaro Stefano , Palamara Guido , d'Arminio Monforte Antonella , Balzarini Jan , Antinori Andrea , Lengauer Thomas , Perno Carlo Federico
Published: August 2007

Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y, K223E/Q, and L228H/R) in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase which are involved in the regulation of resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs). These mutations are strongly associated with NNRTI failure and strongly correlate with the classical NNRTI resistance mutations in a data set of 1,904 HIV-1 B-subtypepolsequences from 758 drug-naïve patients, 592 nucleoside reverse transcriptase inhibitor (NRTI)-treated but NNRTI-naïve patients, and 554 patients treated with both NRTIs and NNRTIs. In particular, L74V and H221Y, positively correlated with Y181C, were associated with an increase in Y181C-mediated resistance to nevirapine, while I135M/T mutations, positively correlated with K103N, were associated with an increase in K103N-mediated resistance to efavirenz. In addition, the presence of the I135T polymorphism in NNRTI-naïve patients significantly correlated with the appearance of K103N in cases of NNRTI failure, suggesting that I135T may represent a crucial determinant of NNRTI resistance evolution. Molecular dynamics simulations show that I135T can contribute to the stabilization of the K103N-induced closure of the NNRTI binding pocket by reducing the distance and increasing the number of hydrogen bonds between 103N and 188Y. H221Y also showed negative correlations with type 2 thymidine analogue mutations (TAM2s); its copresence with the TAM2s was associated with a higher level of zidovudine susceptibility. Our study reinforces the complexity of NNRTI resistance and the significant interplay between NRTI- and NNRTI-selected mutations. Mutations beyond those currently known to confer resistance should be considered for a better prediction of clinical response to reverse transcriptase inhibitors and for the development of more efficient new-generation NNRTIs.
Modulation of the Brd4/P-TEFb Interaction by the Human T-Lymphotropic Virus Type 1 Tax Protein
Authors: Cho Won-Kyung , Zhou Meisheng , Jang Moon Kyoo , Huang Keven , Jeong Soo-Jin , Ozato Keiko , Brady John N.
Published: August 2007

Positive transcription elongation factor (P-TEFb), which is composed of CDK9 and cyclin T1, plays an important role in cellular and viral gene expression. Our lab has recently demonstrated that P-TEFb is required for Tax transactivation of the viral long terminal repeat (LTR). P-TEFb is found in two major complexes: the inactive form, which is associated with inhibitory subunits 7SK snRNA and HEXIM1, and the active form, which is associated with, at least in part, Brd4. In this study, we analyzed the effect of Brd4 on human T-lymphotropic virus type 1 (HTLV-1) transcription. Overexpression of Brd4 repressed Tax transactivation of the HTLV-1 LTR in a dose-dependent manner. In vitro binding studies suggest that Tax and Brd4 compete for binding to P-TEFb through direct interaction with cyclin T1. Tax interacts with cyclin T1 amino acids 426 to 533, which overlaps the region responsible for Brd4 binding. In vivo, overexpression of Tax decreased the amount of 7SK snRNA associated with P-TEFb and stimulates serine 2 phosphorylation of the RNA polymerase II carboxyl-terminal domain, suggesting that Tax regulates the functionality of P-TEFb. Our results suggest the possibility that Tax may compete and functionally substitute for Brd4 in P-TEFb regulation.
Rabbitpox Virus and Vaccinia Virus Infection of Rabbits as a Model for Human Smallpox
Authors: Adams Mathew M. , Rice Amanda D. , Moyer R. W.
Published: August 2007

The threat of smallpox release and use as a bioweapon has encouraged the search for new vaccines and antiviral drugs, as well as development of new small-animal models in which their efficacy can be determined. Here, we reinvestigate a rabbit model in which the intradermal infection of rabbits with very low doses of either rabbitpox virus (RPV) or vaccinia virus Western Reserve (VV-WR) recapitulates many of the clinical features of human smallpox. Following intradermal inoculation with RPV, rabbits develop systemic disease characterized by extensive viremia, numerous secondary lesions on the skin and mucocutaneous tissues, severe respiratory disease, death by 9 days postinfection, and, importantly, natural aerosol transmission between animals. Contrary to previous reports, intradermal infection with VV-WR also resulted in a very similar lethal systemic disease in rabbits, again with natural aerosol transmission between animals. When sentinel and index animals were cohoused, transmission rates approached 100% with either virus, with sentinel animals exhibiting a similar, severe disease. Lower rates of transmission were observed when index and sentinel animals were housed in separate cages. Sentinel animals infected with RPV with one exception succumbed to the disease. However, the majority of VV-WR-infected sentinel animals, while becoming seriously ill, survived. Finally, we tested the efficacy of the drug 1-
O
-hexadecyloxypropyl-cidofovir in the RPV/rabbit model and found that an oral dose of 5 mg/kg twice a day for 5 days beginning 1 day before infection was able to completely protect rabbits from lethal disease.
Distinct Intracellular Trafficking of Equine Infectious Anemia Virus and Human Immunodeficiency Virus Type 1 Gag during Viral Assembly and Budding Revealed by Bimolecular Fluorescence Complementation Assays
Authors: Jin Jing , Sturgeon Timothy , Chen Chaoping , Watkins Simon C. , Weisz Ora A. , Montelaro Ronald C.
Published: August 2007

Retroviral Gag polyproteins are necessary and sufficient for virus budding. Numerous studies of human immunodeficiency virus type 1 (HIV-1) Gag assembly and budding mechanisms have been reported, but relatively little is known about these fundamental pathways among animal lentiviruses. While there may be a general assumption that lentiviruses share common assembly mechanisms, studies of equine infectious anemia virus (EIAV) have indicated alternative cellular pathways and cofactors employed among lentiviruses for assembly and budding. In the current study, we used bimolecular fluorescence complementation to characterize and compare assembly sites and budding efficiencies of EIAV and HIV-1 Gag in both human and rodent cells. The results of these studies demonstrated that replacing the natural RNA nuclear export element (Rev-response element [RRE]) used by HIV-1 and EIAV with the hepatitis B virus posttranscriptional regulatory element (PRE) altered HIV-1, but not EIAV, Gag assembly sites and budding efficiency in human cells. Consistent with this novel observation, different assembly sites were revealed in human cells for Rev-dependent EIAV and HIV-1 Gag polyproteins. In rodent cells, Rev-dependent HIV-1 Gag assembly and budding were blocked, but changing RRE to PRE rescued HIV-1 Gag assembly and budding. In contrast, EIAV Gag polyproteins synthesized from mRNA exported via either Rev-dependent or PRE-dependent mechanisms were able to assemble and bud efficiently in rodent cells. Taken together, our results suggest that lentivirus assembly and budding are regulated by the RNA nuclear export pathway and that alternative cellular pathways can be adapted for lentiviral Gag assembly and budding.
Latent Infection of a New Alphanodavirus in an Insect Cell Line
Authors: Li Tian-Cheng , Scotti Paul D. , Miyamura Tatsuo , Takeda Naokazu
Published: August 2007

Insect BTI-TN-5B1-4 (Tn5) cells have been used extensively with recombinant baculoviruses to express foreign genes. When a recombinant baculovirus containing the hepatitis E virus capsid protein gene was used to infect Tn5 cells, unknown virus particles in addition to the anticipated hepatitis E virus-like particles were produced in the infected cells. The unknown virus particles were 35 nm in diameter and contained RNA that was highly homologous to full-length RNA1 (3,107 bp) and RNA2 (1,383 bp) genomic RNAs of flock house virus. Surprisingly, both RNAs seen in these induced nodavirus particles could be amplified from commercially available Tn5 cells without infection with or induction by a baculovirus. The nucleotide sequences from the purified nodavirus particles and the normal Tn5 cells were identical, demonstrating that the Tn5 cells themselves were latently infected with a nodavirus. However, the generation of nodavirus particles was significantly stimulated by infection with recombinant baculoviruses. Phylogenetic analysis suggested that this new nodavirus belongs to the genus
Alphanodavirus
in the family
Nodaviridae
.
Infectivity and Neutralization of Simian Immunodeficiency Virus with FLAG Epitope Insertion in gp120 Variable Loops
Authors: Laird Melissa E. , Desrosiers Ronald C.
Published: August 2007

A FLAG epitope tag was substituted within variable loop 1 (V1), 2 (V2), or 4 (V4) of the gp120 envelope glycoprotein of simian immunodeficiency virus strain 239 (SIV239) to evaluate the extent to which each variable loop may serve as a target for antibody-mediated neutralization. Two sites within each variable loop of SIV239 were chosen for individual epitope tag insertions. FLAG epitope substitutions were also made in the V1, V2, and V4 loops of a neutralization-sensitive derivative of SIV239, SIV316. Of the 10 FLAG-tagged recombinant viruses analyzed, three (SIV239FV1b, SIV239FV2b, and SIV239FV4a) replicated with kinetics similar to those of the parental strain, SIV239, in both CEMx174 cells and the immortalized rhesus monkey T-cell line 221. The SIV316FV1b and SIV316FV4a FLAG variants replicated with a substantial lag, and the five remaining recombinants did not replicate detectably. Both gp160 and gp120 from replication-competent FLAG variants could be immunoprecipitated from transfected 293T cells by the anti-gp120 rhesus monoclonal antibody (RhMAb) 3.11H, the anti-FLAG MAb M2, and CD4-immunoglobulin, whereas only unprocessed gp160 was detected in 293T cells transfected with replication-defective variants. Furthermore, gp120 was detectably incorporated only into virions that were infectious. SIV239FV1b was sensitive to neutralization by MAb M2, with a 50% inhibitory concentration of 1 μg/ml. Neither SIV239FV2b nor SIV239FV4a was sensitive to M2 neutralization. The ability of the M2 antibody to neutralize SIV239FV1b infectivity was associated with an increased ability of the M2 antibody to detect native, oligomeric SIV239FV1b envelope protein on the surfaces of cells relative to that for the other SIV FLAG variants. Furthermore, SIV239FV1b was globally more sensitive to antibody-mediated neutralization than was parental SIV239 when these strains were screened with a panel of anti-SIV MAbs of various specificities. These results indicate that the V1 loop can serve as an effective target for neutralization on SIV239FV1b. However, antibody-mediated neutralization of this variant, similar to that of other SIV239 variants that have been studied previously, was associated with a global increase in neutralization sensitivity. These results suggest that the variable loops on the neutralization-resistant SIV239 strain are difficult for antibodies to access effectively and that mutations that allow neutralization have global effects on the trimeric envelope glycoprotein structure and accessibility.
DNA Palindromes with a Modest Arm Length of ≳20 Base Pairs Are a Significant Target for Recombinant Adeno-Associated Virus Vector Integration in the Liver, Muscles, and Heart in Mice
Authors: Inagaki Katsuya , Lewis Susanna M. , Wu Xiaolin , Ma Congrong , Munroe David J. , Fuess Sally , Storm Theresa A. , Kay Mark A. , Nakai Hiroyuki
Published: August 2007

Our previous study has shown that recombinant adeno-associated virus (rAAV) vector integrates preferentially in genes, near transcription start sites and CpG islands in mouse liver (H. Nakai, X. Wu, S. Fuess, T. A. Storm, D. Munroe, E. Montini, S. M. Burgess, M. Grompe, and M. A. Kay, J. Virol. 79:3606-3614, 2005). However, the previous method relied on in vivo selection of rAAV integrants and could be employed for the liver but not for other tissues. Here, we describe a novel method for high-throughput rAAV integration site analysis that does not rely on marker gene expression, selection, or cell division, and therefore it can identify rAAV integration sites in nondividing cells without cell manipulations. Using this new method, we identified and characterized a total of 997 rAAV integration sites in mouse liver, skeletal muscle, and heart, transduced with rAAV2 or rAAV8 vector. The results support our previous observations, but notably they have revealed that DNA palindromes with an arm length of ≳20 bp (total length, ≳40 bp) are a significant target for rAAV integration. Up to ∼30% of total integration events occurred in the vicinity of DNA palindromes with an arm length of ≳20 bp. Considering that DNA palindromes may constitute fragile genomic sites, our results support the notion that rAAV integrates at chromosomal sites susceptible to breakage or preexisting breakage sites. The use of rAAV to label fragile genomic sites may provide an important new tool for probing the intrinsic source of ongoing genomic instability in various tissues in animals, studying DNA palindrome metabolism in vivo, and understanding their possible contributions to carcinogenesis and aging.
Innate Recognition Network Driving Herpes Simplex Virus-Induced Corneal Immunopathology: Role of the Toll Pathway in Early Inflammatory Events in Stromal Keratitis
Authors: Sarangi Pranita P. , Kim Bumseok , Kurt-Jones Evelyn , Rouse Barry T.
Published: August 2007

Ocular infection with herpes simplex virus (HSV) sets off an array of events that succeed in clearing virus from the cornea but leaves the tissue with a CD4+T-cell-orchestrated chronic inflammatory lesion that impairs vision. We demonstrate that Toll-like receptor (TLR) signaling forms a part of the recognition system that induces the syndrome that eventually culminates in immunopathology. Accordingly, in a comparison of the outcomes of infection in wild-type (WT) mice and those lacking TLR function, it was apparent that the absence of TLR2 and, to a lesser extent, TLR9 resulted in significantly diminished lesions. Similarly, mice lacking the adapter molecule MyD88 were resistant to lesion development, but such animals were also unable to control infection, with most succumbing to lethal encephalitis. The susceptibility of TLR4−/−animals was also evaluated. These animals developed lesions, which were more severe, more rapidly than did WT animals. We discuss the possible mechanisms by which early recognition of HSV constituents impacts the subsequent development of immunopathological lesions.
Vesicular Stomatitis Virus mRNA Capping Machinery Requires Specific
cis
-Acting Signals in the RNA
Authors: Wang Jennifer T. , McElvain Lauren E. , Whelan Sean P. J.
Published: August 2007

Many viruses of eukaryotes that use mRNA cap-dependent translation strategies have evolved alternate mechanisms to generate the mRNA cap compared to their hosts. The most divergent of these mechanisms are those used by nonsegmented negative-sense (NNS) RNA viruses, which evolved a capping enzyme that transfers RNA onto GDP, rather than GMP onto the 5′ end of the RNA. Working with vesicular stomatitis virus (VSV), a prototype of the NNS RNA viruses, we show that mRNA cap formation is further distinct, requiring a specific
cis
-acting signal in the RNA. Using recombinant VSV, we determined the function of the eight conserved positions of the gene-start sequence in mRNA initiation and cap formation. Alterations to this sequence compromised mRNA initiation and separately formation of the GpppA cap structure. These studies provide genetic and biochemical evidence that the mRNA capping apparatus of VSV evolved an RNA capping machinery that functions in a sequence-specific manner.
Characterization of Human Immunodeficiency Virus Type 1 Replication in Immature and Mature Dendritic Cells Reveals Dissociablecis- andtrans-Infection
Authors: Dong Chunsheng , Janas Alicia M. , Wang Jian-Hua , Olson Wendy J. , Wu Li
Published: August 2007

Dendritic cells (DCs) transmit human immunodeficiency virus type 1 (HIV-1) to CD4+T cells through thetrans- andcis-infection pathways; however, little is known about the relative efficiencies of these pathways and whether they are interdependent. Here we comparecis- andtrans-infections of HIV-1 mediated by immature DCs (iDCs) and mature DCs (mDCs), using replication-competent and single-cycle HIV-1. Monocyte-derived iDCs were differentiated into various types of mDCs by lipopolysaccharide (LPS), tumor necrosis factor alpha (TNF-α), and CD40 ligand (CD40L). iDCs and CD40L-induced mDCs were susceptible to HIV-1 infection and mediated efficient viral transmission to CD4+T cells. Although HIV-1cis-infection was partially restricted in TNF-α-induced mDCs and profoundly blocked in LPS-induced mDCs, these cells efficiently promoted HIV-1trans-infection of CD4+T cells. The postentry restriction of HIV-1 infection in LPS-induced mDCs was identified at the levels of reverse transcription and postintegration, using real-time PCR quantification of viral DNA and integration. Furthermore, nucleofection of DCs with HIV-1 proviral DNA confirmed that impaired gene expression of LPS-induced mDCs was responsible for the postentry restriction of HIV-1 infection. Our results suggest that various DC subsets in vivo may differentially contribute to HIV-1 dissemination via dissociablecis- andtrans-infections.
West Nile Virus Infection Activates the Unfolded Protein Response, Leading to CHOP Induction and Apoptosis
Authors: Medigeshi Guruprasad R. , Lancaster Alissa M. , Hirsch Alec J. , Briese Thomas , Lipkin W. Ian , DeFilippis Victor , Früh Klaus , Mason Peter W. , Nikolich-Zugich Janko , Nelson Jay A.
Published: August 2007

West Nile virus (WNV)-mediated neuronal death is a hallmark of WNV meningitis and encephalitis. However, the mechanisms of WNV-induced neuronal damage are not well understood. We investigated WNV neuropathogenesis by using human neuroblastoma cells and primary rat hippocampal neurons. We observed that WNV activates multiple unfolded protein response (UPR) pathways, leading to transcriptional and translational induction of UPR target genes. We evaluated the role of the three major UPR pathways, namely, inositol-requiring enzyme 1-dependent splicing of X box binding protein 1 (XBP1) mRNA, activation of activating transcription factor 6 (ATF6), and protein kinase R-like endoplasmic reticulum (ER) kinase-dependent eukaryotic initiation factor 2α (eIF2α) phosphorylation, in WNV-infected cells. We show that XBP1 is nonessential or can be replaced by other UPR pathways in WNV replication. ATF6 was rapidly degraded by proteasomes, consistent with induction of ER stress by WNV. We further observed a transient phosphorylation of eIF2α and induction of the proapoptotic cyclic AMP response element-binding transcription factor homologous protein (CHOP). WNV-infected cells exhibited a number of apoptotic phenotypes, such as (i) induction of growth arrest and DNA damage-inducible gene 34, (ii) activation of caspase-3, and (iii) cleavage of poly(ADP-ribose) polymerase. The expression of WNV nonstructural proteins alone was sufficient to induce CHOP expression. Importantly, WNV grew to significantly higher viral titers in
chop
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mouse embryonic fibroblasts (MEFs) than in wild-type MEFs, suggesting that CHOP-dependent premature cell death represents a host defense mechanism to limit viral replication that might also be responsible for the widespread neuronal loss observed in WNV-infected neuronal tissue.
A Rab-GAP TBC Domain Protein Binds Hepatitis C Virus NS5A and Mediates Viral Replication
Authors: Sklan Ella H. , Staschke Kirk , Oakes Tina M. , Elazar Menashe , Winters Mark , Aroeti Benjamin , Danieli Tsafi , Glenn Jeffrey S.
Published: August 2007

Hepatitis C virus (HCV) is an important cause of liver disease worldwide. Current therapies are inadequate for most patients. Using a two-hybrid screen, we isolated a novel cellular binding partner interacting with the N terminus of HCV nonstructural protein NS5A. This partner contains a TBC Rab-GAP (GTPase-activating protein) homology domain found in all known Rab-activating proteins. As the first described interaction between such a Rab-GAP and a viral protein, this finding suggests a new mechanism whereby viruses may subvert host cell machinery for mediating the endocytosis, trafficking, and sorting of their own proteins. Moreover, depleting the expression of this partner severely impairs HCV RNA replication with no obvious effect on cell viability. These results suggest that pharmacologic disruption of this NS5A-interacting partner can be contemplated as a potential new antiviral strategy against a pathogen affecting nearly 3% of the world's population.
Signal Peptide and Helical Bundle Domains of Virulent Canine Distemper Virus Fusion Protein Restrict Fusogenicity
Authors: Plattet Philippe , Cherpillod Pascal , Wiener Dominique , Zipperle Ljerka , Vandevelde Marc , Wittek Riccardo , Zurbriggen Andreas
Published: August 2007

Persistence in canine distemper virus (CDV) infection is correlated with very limited cell-cell fusion and lack of cytolysis induced by the neurovirulent A75/17-CDV compared to that of the cytolytic Onderstepoort vaccine strain. We have previously shown that this difference was at least in part due to the amino acid sequence of the fusion (F) protein (P. Plattet, J. P. Rivals, B. Zuber, J. M. Brunner, A. Zurbriggen, and R. Wittek, Virology 337:312-326, 2005). Here, we investigated the molecular mechanisms of the neurovirulent CDV F protein underlying limited membrane fusion activity. By exchanging the signal peptide between both F CDV strains or replacing it with an exogenous signal peptide, we demonstrated that this domain controlled intracellular and consequently cell surface protein expression, thus indirectly modulating fusogenicity. In addition, by serially passaging a poorly fusogenic virus and selecting a syncytium-forming variant, we identified the mutation L372W as being responsible for this change of phenotype. Intriguingly, residue L372 potentially is located in the helical bundle domain of the F1subunit. We showed that this mutation drastically increased fusion activity of F proteins of both CDV strains in a signal peptide-independent manner. Due to its unique structure even among morbilliviruses, our findings with respect to the signal peptide are likely to be specifically relevant to CDV, whereas the results related to the helical bundle add new insights to our growing understanding of this class of F proteins. We conclude that different mechanisms involving multiple domains of the neurovirulent A75/17-CDV F protein act in concert to limit fusion activity, preventing lysis of infected cells, which ultimately may favor viral persistence.
Role for the Phosphoprotein P Subunit of the Paramyxovirus Polymerase in Limiting Induction of Host Cell Antiviral Responses
Authors: Dillon Patrick J. , Parks Griffith D.
Published: August 2007

Six amino acid substitutions in the shared N-terminal region of the P subunit of the viral polymerase and the accessory V protein convert the noncytopathic paramyxovirus simian virus 5 (SV5), which is a poor inducer of host cell responses, into a P/V mutant (P/V-CPI-) that induces high levels of apoptosis, interferon-beta (IFN-beta), and proinflammatory cytokines. In this study, we addressed the question of whether these new mutant phenotypes are due to the presence of an altered P protein or of an altered V protein or of both proteins. By the use of the P/V-CPI- mutant as a backbone, new mutant viruses were engineered to express the wild-type (WT) V protein (+V-wt) or WT P protein (+P-wt) from an additional gene inserted between the HN and L genes. In human epithelial cell lines, the +V-wt virus showed reduced activation of apoptosis and lower secretion of IFN-beta and proinflammatory cytokines compared to the parental P/V-CPI- virus. The presence of a V protein lacking the C-terminal cysteine-rich domain (corresponding to the SV5 I protein) did not reduce these host cell responses to P/V-CPI- infection. Unexpectedly, the +P-wt virus, which expressed a WT P subunit of the viral polymerase, also induced much lower levels of host cell responses than the parental P/V-CPI- mutant. For both +V-wt and +P-wt viruses, reduced levels of IFN-beta synthesis correlated with reduced IRF-3 dimerization and nuclear localization of IRF-3 and NF-κB, suggesting that the WT P and V proteins acted at an early stage in antiviral pathways. Host cell responses induced by the various P/V mutants directly correlated with levels of viral mRNA accumulation but not with steady-state levels of genomic RNA. Our results support the hypothesis that WT P and V proteins limit induction of antiviral responses by controlling the production of key viral inducers. A model is presented for the mechanism by which both the P subunit of the viral polymerase and the V accessory protein contribute to the ability of a paramyxovirus to limit activation of antiviral responses.
A HIGHLY NEUTRON-RICH CLUSTER AND/OR A SUPERHEAVY NUCLEUS IN THE COMPOUND NUCLEUS 238U+238U: A MEAN FIELD STUDY
Authors: GUPTA RAJ K. , PATRA S. K. , STEVENSON P. D. , GREINER WALTER
Published: August 2007

Clustering structures of the various resonance states of the compound nucleus 476184*, formed in 238 U +238 U reaction, are studied within the standard relativistic mean field (RMF) and non-relativistic Skyrme Hartree–Fock formalisms. The formations of various possible clusters and superheavy nuclei as daughter products are discussed. Both the formalisms support clustering phenomenon, the RMF presenting a somewhat more realistic picture. Also, before the asymptotic fissioning state, a kind of triple fission, with the cluster appearing in the neck region of two equal fragments, is obtained as one of the possibilities in RMF formalism.
INCORPORATING HOMOLOGUES INTO SEQUENCE EMBEDDINGS FOR PROTEIN ANALYSIS
Authors: ESKIN ELEAZAR , SNIR SAGI
Published: August 2007

Statistical and learning techniques are becoming increasingly popular for different tasks in bioinformatics. Many of the most powerful statistical and learning techniques are applicable to points in a Euclidean space but not directly applicable to discrete sequences such as protein sequences. One way to apply these techniques to protein sequences is to embed the sequences into a Euclidean space and then apply these techniques to the embedded points. In this work we introduce a biologically motivated sequence embedding, the homology kernel, which takes into account intuitions from local alignment, sequence homology, and predicted secondary structure. This embedding allows us to directly apply learning techniques to protein sequences. We apply the homology kernel in several ways. We demonstrate how the homology kernel can be used for protein family classification and outperforms state-of-the-art methods for remote homology detection. We show that the homology kernel can be used for secondary structure prediction and is competitive with popular secondary structure prediction methods. Finally, we show how the homology kernel can be used to incorporate information from homologous sequences in local sequence alignment.
Subdivision of the Precambrian
Authors: Wright A. E.
Published: August 2007

The Precambrian record is so fragmentary and from such widely contrasting terrains that attempts to erect any formal subdivisions would appear to be premature. The methods that have been used in the Phanerozoic rocks cannot be used for subdividing the Precambrian as they are peculiarly suitable for fossiliferous largely undeformed sedimentary units in which the sedimentary record is relatively full. Isotopic dating methods also become so imprecise over the major portion of Precambrian time that it is only rarely possible to use them to define particular events with the same precision as those dated in the Phanerozoic record, although this is changing with increasing analytical accuracy.

The use of biological criteria for the erection of a chronostratigraphic scale is seen as a future possibility, but the methods of defining the units that are used in the Phanerozoic are thought inappropriate, and the characterization of a particular chronostratigraphic unit (e.g. by the presence of metazoan trace fossils) is seen as more appropriate.

International agreement on the time for particular boundaries in the Precambrian is regarded as an attempt merely to define the terms already in use rather than having any scientific basis. It is possible that future research may reveal global events which are recognized to be unique and these may provide more reliable datum planes to use. If they are also related to changes in the way the earth behaved through time it would be logical to use these as markers for any major subdivisions of Precambrian time. None have
Some key rules for the calibration of the numerical time-scale
Authors: Odin G. S.
Published: August 2007

The building of an acceptable numerical time-scale, in whole or in part, is a complex matter. At the present time, it is often impossible to obtain even a nearly correct figure on which everyone can agree. This is often due to the selective rejection of data which, although considered unsatisfactory by some are accepted by others, and by the existence of data which appear at the time to be mutually incompatible. However, it is possible to draw a series of recommendations which could help in obtaining a result less open to criticism.

As a general scheme, a fully documented time-scale (a certainly megalomaniac aim) can only be obtained after a long itinerary of research comprising essentially four stages: (1) the collection of published data; (2) the evaluation of individual data; (3) the combination of data; (4) the drawing of conclusions: this paper summarizes the author's attitudes to these problems.