bluuebunny/crossref_metadata_2025 huggingface dataset:
Early history of European domestic cattle as revealed by ancient DNA
Authors: Bollongino R , Edwards C.J , Alt K.W , Burger J , Bradley D.G
Published: December 2005

We present an extensive ancient DNA analysis of mainly Neolithic cattle bones sampled from archaeological sites along the route of Neolithic expansion, from Turkey to North-Central Europe and Britain. We place this first reasonable population sample of Neolithic cattle mitochondrial DNA sequence diversity in context to illustrate the continuity of haplotype variation patterns from the first European domestic cattle to the present. Interestingly, the dominant Central European pattern, a starburst phylogeny around the modal sequence, T3, has a Neolithic origin, and the reduced diversity within this cluster in the ancient samples accords with their shorter history of post-domestic accumulation of mutation.
Characterization of the structure and composition of gecko adhesive setae
Authors: Rizzo N.W , Gardner K.H , Walls D.J , Keiper-Hrynko N.M , Ganzke T.S , Hallahan D.L
Published: December 2005

The ability of certain reptiles to adhere to vertical (and hang from horizontal) surfaces has been attributed to the presence of specialized adhesive setae on their feet. Structural and compositional studies of such adhesive setae will contribute significantly towards the design of biomimetic fibrillar adhesive materials. The results of electron microscopy analyses of the structure of such setae are presented, indicating their formation from aggregates of proteinaceous fibrils held together by a matrix and potentially surrounded by a limiting proteinaceous sheath. Microbeam X-ray diffraction analysis has shown conclusively that the only ordered protein constituent in these structures exhibits a diffraction pattern characteristic of β-keratin. Raman microscopy of individual setae, however, clearly shows the presence of additional protein constituents, some of which may be identified as α-keratins. Electrophoretic analysis of solubilized setal proteins supports these conclusions, indicating the presence of a group of low-molecular-weight β-keratins (14–20 kDa), together with α-keratins, and this interpretation is supported by immunological analyses.
On pseudo-rigid bodies
Authors: Steigmann David J
Published: December 2005

The concept of the
pseudo-rigid body
, a model of hypothetical bodies constrained to deform homogeneously, is discussed critically. An analysis is given of a recent attempt, published in this journal, to establish this model on the basis of continuum mechanics.
Riesz basis property of mode shapes for aircraft wing model (subsonic case)
Authors: Shubov Marianna A
Published: December 2005

The present paper is devoted to the Riesz basis property of the mode shapes for an aircraft wing model in an inviscid subsonic airflow. The model has been developed in the Flight Systems Research Center of the University of California at Los Angeles in collaboration with NASA Dryden Flight Research Center. The model has been successfully tested in a series of flight experiments at Edwards Airforce Base, CA, and has been extensively studied numerically. The model is governed by a system of two coupled integro-differential equations and a two parameter family of boundary conditions modelling the action of the self-straining actuators. The system of equations of motion is equivalent to a single operator evolution–convolution equation in the energy space. The Laplace transform of the solution of this equation can be represented in terms of the so-called generalized resolvent operator, which is a finite—meromorphic operator—valued function of the spectral parameter. Its poles are precisely the aeroelastic modes. In the author's previous works, it has been shown that the set of aeroelastic modes asymptotically splits into two disjoint subsets called the
β
-branch and the
δ
-branch, and precise spectral asymptotics with respect to the eigenvalue number have been derived for both branches. The asymptotical approximations for the mode shapes have also been obtained. In the present work, the author proves that the set of the mode shapes forms an unconditional basis (the Riesz basis) in the Hilbert state space of the system. The results of this paper will be important for the reconstruction of the solution of the original initial boundary-value problem from its Laplace transform and for the analysis of the flutter phenomenon in the forthcoming work.
Fine structure of the Vavilov–Cherenkov radiation
Authors: Afanasiev G.N , Lyubchenko M.V , Stepanovsky Yu. P
Published: December 2005

We found relativistic quantum corrections to the one-photon Cherenkov emission. It is proved that, in the absence of dispersion, the Vavilov–Cherenkov radiation fills the whole Cherenkov cone (in the Tamm–Frank theory the Vavilov–Cherenkov radiation for the fixed refractive index is confined to the surface of the Cherenkov cone). The radiation intensity reaches the maximum inside the Cherenkov cone. It turns out that photons with different energies fly at different angles in the interval from zero up to the Cherenkov angle corresponding to the initial charge velocity. The visible light region, where the Vavilov–Cherenkov radiation is usually observed, is surrounded by the low intensity infrared region and by the high intensity one corresponding to high energy photons. The ratio of the radiation intensity at the maximum lying in the Roentgen part of the radiation spectrum to the radiation intensity in its visible part is about 10
4
. Taking into account the medium dispersion leads to the appearance of the striped-like radiation structure inside the Cherenkov cone. Experimental data indicating the existence of a non-zero radiation field inside this cone are discussed. In the past, non-relativistic quantum corrections to the radiation intensity were found by Ginzburg. Yet, he did not analyse their influence for large energy–momentum transfer.
Energetic demand of multiple dependents and the evolution of slow human growth
Authors: Gurven Michael , Walker Robert
Published: December 2005

This study investigates the consequences of the human foraging niche and multiple dependent offspring on the optimal growth trajectory of humans. We test the hypothesis that the human pattern of slow human growth between age at weaning and puberty helps defer the compound energetic demand on parents with multiple dependents, by using growth and demographic data from two foraging societies, the Ache of eastern Paraguay and the Dobe Ju/'hoansi of Botswana and Namibia. We run simulations of observed and potential growth trajectories among sub-adults and their consequent energetic demands on parents given profiles of fertility, mortality, consumption and production. We find that either sub-adult production or food subsidies from other people must substantially increase in order to compensate for the dramatic increase in energetic demand on parents if offspring were to grow faster at younger ages. Our conclusion is that slow human growth followed by a rapid adolescent growth spurt may have facilitated rising human fertility rates and greater investments in neural capital.
Individual advantages to ecological specialization: insights on cognitive constraints from three conspecific taxa
Authors: Egan Scott P , Funk Daniel J
Published: December 2005

The information-processing hypothesis (IPH) posits that specialist herbivores should make host-associated decisions more effectively than generalists and thus enjoy associated fitness advantages that may help explain the evolutionary prevalence of host-specific insects. This is because generalists must evaluate a greater diversity of host plants/cues than specialists and thus face a cognitive challenge that is predicted to constrain the efficiency and accuracy of their choices. Here, we present the first individual-level evaluation of this hypothesis. This involved experimentally quantifying the specificity, efficiency, and accuracy of host selection, as both larvae and adults, for many individuals representing each of three ‘host forms’ of
Neochlamisus bebbianae
leaf beetles. These experiments provided several significant findings: host forms differed in larval specificity, with the more specialized host forms more efficiently and accurately selecting optimal hosts as both larvae and adults. Positive correlations between larval specificity and both efficiency and accuracy across test individuals provided the most direct evidence to date for a biological association between these variables. Our results thus provide strong and consistent support for the IPH at the level of both populations and individuals. Because individual
N. bebbianae
make many host-associated decisions in nature, our results suggest that cognitive constraints may play a major role in the evolutionary dynamics of ongoing ecological specialization and diversification in this species.
Wolbachiainfection suppresses both host defence and parasitoid counter-defence
Authors: Fytrou Anastasia , Schofield Peter G , Kraaijeveld Alex R , Hubbard Stephen F
Published: December 2005

Endosymbiotic bacteria in the genusWolbachiahave been linked to several types of reproductive parasitism, which enhance their own transmission, while their direct effects on the host vary from beneficial to neutral or detrimental. Here, we report negative effects of infection on immunity-related traits ofDrosophila simulansand the parasitoid waspLeptopilina heterotoma. InfectedD. simulansshowed a reduced ability to encapsulate parasitoid eggs, compared to a tetracycline-treated, bacterium-free line. Challenging the two lines with a fungal pathogen,Beauveria bassiana, on the other hand, revealed no differences in survival. Moreover, elimination ofWolbachiawas beneficial for the parasitoid wasp, as eggs laid by uninfected females suffered significantly lower encapsulation rates. We discuss possible origins of these fitness costs and their implications for infection dynamics and the interactions between host species.
Why is stress so deadly? An evolutionary perspective
Authors: Hadany Lilach , Beker Tuvik , Eshel Ilan , Feldman Marcus W
Published: December 2005

The reaction of the body to prolonged stress has many harmful effects. Classical theory assumes that stress responses have evolved due to their short-term selective advantages (‘flight or fight’), and despite their adverse long-term effects. In contrast, we demonstrate that the adverse effects of stress responses may have a selective advantage. Using an analytical model we show that a gene that causes the early death of a relatively unfit individual can increase in frequency in a structured population even if it has no positive effect on that individual. This result offers a new perspective on the relations between stress factors, stress responses and stress-related diseases.
Evolution of long-range myofibrillar crystallinity in insect flight muscle as examined by X-ray cryomicrodiffraction
Authors: Iwamoto Hiroyuki , Inoue Katsuaki , Yagi Naoto
Published: December 2005

Insect flight muscle is known for its crystal-quality regularity of contractile protein arrangement within a sarcomere. We have previously shown by X-ray microdiffraction that the crystal-quality regularity in bumble-bee flight muscle is not confined within a sarcomere, but extends over the entire length of a myofibril (>1000 sarcomeres connected in series). Because of this, the whole myofibril may be regarded as a millimetre-long, natural single protein crystal. Using bright X-ray beams from a synchrotron radiation source, we examined how this long-range crystallinity has evolved among winged insects. We analysed >4600 microdiffraction patterns of quick-frozen myofibrils from 50 insect species, covering all the major winged insect orders. The results show that the occurrence of such long-range crystallinity largely coincides with insect orders with asynchronous muscle operation. However, a few of the more skilled fliers among lower-order insects apparently have developed various degrees of structural regularity, suggesting that the demand for skilful flight has driven the lattice structure towards increased regularity.
Footprints in the sand: independent reduction of subdigital lamellae in the Namib–Kalahari burrowing geckos
Authors: Lamb Trip , Bauer Aaron M
Published: December 2005

Many desert organisms exhibit convergence, and certain physical factors such as windblown sands have generated remarkably similar ecomorphs across divergent lineages. The burrowing geckos
Colopus
,
Chondrodactylus
and
Palmatogecko
occupy dune ecosystems in the Namib and Kalahari deserts of southwest Africa. Considered closely related, they share several putative synapomorphies, including reduced subdigital pads (toe pads) and spinose digital scales. Though recognized as part of Africa's ecologically diverse
Pachydactylus
Group, the burrowing geckos' precise phylogenetic affinities remain elusive. Convergent pedal modification provides a tenable alternative explaining the geckos' derived terrestriality and adaptation to Namib and Kalahari sands. We generated a molecular phylogeny for the
Pachydactylus
Group to examine evolutionary relationships among the burrowing geckos and infer historical patterns of pedal character change. Bayesian and parsimony analyses revealed all three burrowing genera to be deeply nested within
Pachydactylus
, each genus belonging to a separate clade. Strong support for these distinct clades indicates ecomorphological adaptations for burrowing have evolved independently three times in the southern
Pachydactylus
Group. We argue that the physical properties of Namib and Kalahari sands played a principal role in selecting for pedal similarity.
Context-dependent vocal mimicry in a passerine bird
Authors: Goodale Eben , Kotagama Sarath W
Published: December 2005

How do birds select the sounds they mimic, and in what contexts do they use vocal mimicry? Some birds show a preference for mimicking other species' alarm notes, especially in situations when they appear to be alarmed. Yet no study has demonstrated that birds change the call types they mimic with changing contexts. We found that greater racket-tailed drongos (Dicrurus paradiseus) in the rainforest of Sri Lanka mimic the calls of predators and the alarm-associated calls of other species more often than would be expected from the frequency of these sounds in the acoustic environment. Drongos include this alarm-associated mimicry in their own alarm vocalizations, while incorporating other species' songs and contact calls in their own songs. Drongos show an additional level of context specificity by mimicking other species' ground predator-specific call types when mobbing. We suggest that drongos learn other species' calls and their contexts while interacting with these species in mixed flocks. The drongos' behaviour demonstrates that alarm-associated calls can have learned components, and that birds can learn the appropriate usage of calls that encode different types of information.
Disease ecology in the Galápagos Hawk (
Buteo galapagoensis
): host genetic diversity, parasite load and natural antibodies
Authors: Whiteman Noah Kerness , Matson Kevin D , Bollmer Jennifer L , Parker Patricia G
Published: December 2005

An increased susceptibility to disease is one hypothesis explaining how inbreeding hastens extinction in island endemics and threatened species. Experimental studies show that disease resistance declines as inbreeding increases, but data from
in situ
wildlife systems are scarce. Genetic diversity increases with island size across the entire range of an extremely inbred Galápagos endemic bird, providing the context for a natural experiment examining the effects of inbreeding on disease susceptibility. Extremely inbred populations of Galápagos hawks had higher parasite abundances than relatively outbred populations. We found a significant island effect on constitutively produced natural antibody (NAb) levels and inbred populations generally harboured lower average and less variable NAb levels than relatively outbred populations. Furthermore, NAb levels explained abundance of amblyceran lice, which encounter the host immune system. This is the first study linking inbreeding, innate immunity and parasite load in an endemic,
in situ
wildlife population and provides a clear framework for assessment of disease risk in a Galápagos endemic.
Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses
Authors: Oberste M. Steven , Maher Kaija , Williams Alford J. , Dybdahl-Sissoko Naomi , Brown Betty A. , Gookin Michelle S. , Peñaranda Silvia , Mishrik Nada , Uddin Moyez , Pallansch Mark A.
Published: December 2005

The 65 serotypes of human enteroviruses are classified into four species,Human enterovirus(HEV) A to D, based largely on phylogenetic relationships in multiple genome regions. The 3′-non-translated region of enteroviruses is highly conserved within a species but highly divergent between species. From this information, species-specific RT-PCR primers were developed that can be used to rapidly screen collections of enterovirus isolates to identify species of interest. The four primer pairs were 100 % specific when tested against enterovirus prototype strains and panels of isolates of known serotype (a total of 193 isolates). For evaluation in a typical application, the species-specific primers were used to screen 186 previously uncharacterized non-polio enterovirus isolates. The HEV-B primers amplified 68·3 % of isolates, while the HEV-A and HEV-C primers accounted for 9·7 and 11·3 % of isolates, respectively; no isolates were amplified with the HEV-D primers. Twelve isolates (6·5 %) were amplified by more than one primer set and eight isolates (4·3 %) were not amplified by any of the four primer pairs. Serotypes were identified by partial sequencing of the VP1 capsid gene, and in every case sequencing confirmed that the species-specific PCR result was correct; the isolates that were amplified by more than one species-specific primer pair were mixtures of two (11 isolates) or three (one isolate) species of viruses. The eight isolates that were not amplified by the species-specific primers comprised four new serotypes (EV76, EV89, EV90 and EV91) that appear to be unique members of HEV-A based on VP1, 3D and 3′-non-translated region sequences.
Very virulent infectious bursal disease virus: reduced pathogenicity in a rare natural segment-B-reassorted isolate
Authors: Nouën Cyril Le , Rivallan Gaëlle , Toquin Didier , Darlu Pierre , Morin Yannick , Beven Véronique , de Boisseson Claire , Cazaban Christophe , Comte Sylvain , Gardin Yannick , Eterradossi Nicolas
Published: December 2005

The purpose of this study was to compare the molecular epidemiology of infectious bursal disease virus (IBDV) segments A and B of 50 natural or vaccine IBDV strains that were isolated or produced between 1972 and 2002 in 17 countries from four continents, with phenotypes ranging from attenuated to very virulent (vv). These strains were subjected to sequence and phylogenetic analysis based on partial sequences of genome segments A and B. Although there is co-evolution of the two genome segments (70 % of strains kept the same genetic relatives in the segment A- and B-defined consensus trees), several strains (26 %) were identified with the incongruence length difference test as exhibiting a significantly different phylogenetic relationship depending on which segment was analysed. This suggested that natural reassortment could have occurred. One of the possible naturally occurring reassortant strains, which exhibited a segment A related to the vvIBDV cluster whereas its segment B was not, was thoroughly sequenced (coding sequence of both segments) and submitted to a standardized experimental characterization of its acute pathogenicity. This strain induced significantly less mortality than typical vvIBDVs; however, the mechanisms for this reduced pathogenicity remain unknown, as no significant difference in the bursal lesions, post-infectious antibody response or virus production in the bursa was observed in challenged chickens.
Comparison of in vitro replication features of H7N3 influenza viruses from wild ducks and turkeys: potential implications for interspecies transmission
Authors: Giannecchini Simone , Campitelli Laura , Calzoletti Laura , De Marco Maria Alessandra , Azzi Alberta , Donatelli Isabella
Published: December 2005

In previous work, it was shown that turkey H7N3 influenza viruses, presumably derived ‘in toto’ from interspecies transmission of duck viruses in Northern Italy, had only 2 aa differences in haemagglutinin and a few amino acid differences as well as a 23 aa deletion in neuraminidase compared with duck viruses. Here, the replication of these duck and turkey viruses in Madin–Darby canine kidney cells was investigated with respect to virus–cell fusion and viral elution from red blood cells. Duck viruses showed similar receptor-binding properties to turkey viruses but possessed a higher pH of fusion activation than the turkey viruses. Conversely, turkey viruses were not able to elute from red blood cells. These data confirm that neuraminidase-stalk deletion impairs the release of virions from cells and also confirm existence of naturally occurring viruses with different pH fusion activities, raising the possibility that these features may play a role in the evolution of influenza viruses in different hosts.
Genetic elements regulating packaging of the Bunyamwera orthobunyavirus genome
Authors: Kohl Alain , Lowen Anice C. , Léonard Vincent H. J. , Elliott Richard M.
Published: December 2005

The genome of Bunyamwera virus (BUN; family Bunyaviridae, genus Orthobunyavirus) comprises three segments of negative-sense, single-stranded RNA. The RNA segments are encapsidated by the viral nucleocapsid (N) protein and form panhandle-like structures through interaction of complementary sequences at their 5′ and 3′ termini. Transcription and replication of a BUN genome analogue (minireplicon), comprising the viral non-coding sequences flanking a reporter gene, requires just the viral RNA polymerase (L protein) and N protein. Here, sequences of Bunyamwera serogroup M segment RNAs were compared and conserved elements within nt 20–33 of the 3′ and 5′ non-coding regions that can affect packaging of minireplicons into virions were identified. RNA-folding models suggest that a conserved sequence within nt 20–33 of the 5′ end of the genome segments maintains conserved structural features necessary for efficient transcription. Competitive packaging experiments using M, L and S segment-derived minireplicons that encode different reporter genes showed variable packaging efficiencies of the three segments. Packaging of a particular segment appeared to be independent of the presence of other segments and, for the S segment, packaging efficiency was unaffected by the inclusion of viral coding sequences in the minireplicon.
Analysis of sequential hepatitis A virus strains reveals coexistence of distinct viral subpopulations
Authors: Costa-Mattioli Mauro , Domingo Esteban , Cristina Juan
Published: December 2005

Hepatitis A
virus (HAV) is a hepatotropic member of the family Picornaviridae. Despite a remarkable antigenic stability, recent results have shown that HAV exists in vivo and in cell culture as distributions of genetically related, non-identical variants, referred to as quasispecies. To gain insight into HAV evolution over time in a specific geographical region, genotype I consensus sequences from strains isolated in France in consecutive years were studied. Phylogenetic neighbour-joining method and a non-hierarchical partition analysis, designed to analyse viral quasispecies, indicate that at least five distinct subpopulations of HAV were identified in the course of the disease episode. Strikingly, over time, different subpopulations cycled in dominance. The coexistence of distinct subpopulations whose frequency varies with time is consistent with quasispecies dynamics, and suggests that variation in the dominant HAV population may provide HAV adaptability without being reflected in significant antigenic variation.
Structural and functional characterization of the coxsackievirus B3 CRE(2C): role of CRE(2C) in negative- and positive-strand RNA synthesis
Authors: van Ooij Mark J. M. , Vogt Dorothee A. , Paul Aniko , Castro Christian , Kuijpers Judith , van Kuppeveld Frank J. M. , Cameron Craig E. , Wimmer Eckard , Andino Raul , Melchers Willem J. G.
Published: December 2005

A stem–loop element located within the 2C-coding region of the coxsackievirus B3 (CVB3) genome has been proposed to function as a cis-acting replication element (CRE). It is shown here that disruption of this structure indeed interfered with viral RNA replication in vivo and abolished uridylylation of VPg in vitro. Site-directed mutagenesis demonstrated that the previously proposed enteroviral CRE consensus loop sequence, R1NNNAAR2NNNNNNR3, is also applicable to CVB3 CRE(2C) and that a positive correlation exists between the ability of CRE(2C) mutants to serve as template in the uridylylation reaction and the capacity of these mutants to support viral RNA replication. To further investigate the effects of the mutations on negative-strand RNA synthesis, an in vitro translation/replication system containing HeLa S10 cell extracts was used. Similar to the results observed for poliovirus and rhinovirus, it was found that a complete disruption of the CRE(2C) structure interfered with positive-strand RNA synthesis, but not with negative-strand synthesis. All CRE(2C) point mutants affecting the enteroviral CRE consensus loop, however, showed a marked decrease in efficiency to induce negative-strand synthesis. Moreover, a transition (A5G) regarding the first templating adenosine residue in the loop was even unable to initiate complementary negative-strand synthesis above detectable levels. Taken together, these results indicate that the CVB3 CRE(2C) is not only required for the initiation of positive-strand RNA synthesis, but also plays an essential role in the efficient initiation of negative-strand RNA synthesis, a conclusion that has not been reached previously by using the cell-free system.
Screening for CD8 cytotoxic T lymphocytes specific for Gag of human immunodeficiency virus type 1 subtype B′ Henan isolate from China and identification of novel epitopes restricted by the HLA-A2 and HLA-A11 alleles
Authors: Gong Xiaoyan , Gui Xien , Zhang Yuxia , Tien Po
Published: December 2005

The human immunodeficiency virus type 1 (HIV-1) epidemic in China is increasing rapidly at an irrepressible rate. It is caused by HIV-1 subtype B′ in central China. After the full-length genome sequencing of the Henan isolate was performed, the definition of optimal cytotoxic T-lymphocyte (CTL) epitopes across the Henan isolate genome has become crucial for vaccine design. In this study, by using ELISPOT assays with synthetic peptides corresponding to the sequence of the Henan isolate, the identification and analysis of Gag-specific CTL responses among 28 treated and 26 untreated infected paid blood donors (PBDs) from the Henan and Hubei provinces of China are presented. These studies focused on CTL responses restricted by the human leukocyte antigen (HLA)-A2 and -A11 molecules, two of the most prominent HLA-A alleles in the Chinese population. The results suggested that, in the subgroup analysis, the magnitude of response in the infected treated subgroup [median, 93 spot-forming cells (SFCs) per 106 peripheral blood mononuclear cells (PBMCs)] was significantly lower than that in the chronically infected untreated subgroup (median, 221 SFCs per 106 PBMCs), and HLA-A2-restricted treated PBDs had a response of a much higher frequency and magnitude than that of HLA-A11-restricted treated PBDs. Moreover, some novel peptides restricted by the HLA-A2 and -A11 molecules were identified.
Identification of the Bunyamwera bunyavirus transcription termination signal
Authors: Barr John N. , Rodgers John W. , Wertz Gail W.
Published: December 2005

Bunyamwera virus (BUNV) is the prototype of the family Bunyaviridae, which comprises segmented RNA viruses. Each of the BUNV negative-strand segments, small (S), medium (M) and large (L), serves as template for two distinct RNA-synthesis activities: (i) replication to generate antigenomes that are in turn replicated to yield further genomes; and (ii) transcription to generate a single species of mRNA. BUNV mRNAs are truncated at their 3′ ends relative to the genome template, presumably because the BUNV transcriptase terminates transcription before reaching the 5′ terminus of the genomic template. Here, identification of the transcription termination signal responsible for 3′-end truncation of BUNV S-segment mRNA was carried out. It was shown that efficient transcription termination was signalled by a 33 nt sequence within the 5′ non-translated region (NTR) of the S segment. A 6 nt region (3′-GUCGAC-5′) within this sequence was found to play a major role in termination signalling, with other nucleotides possessing individually minor, but collectively significant, signalling ability. By abrogating the signalling ability of these 33 nt, we identified a second, functionally independent termination signal located 32 nt downstream. This downstream signal was 9 nt in length and contained a pentanucleotide sequence, 3′-UGUCG-5′, that overlapped the 6 nt major signalling component of the upstream signal. The pentanucleotide sequence was also found within the 5′ NTR of the BUNV L segment and in several other members of the genus Orthobunyavirus, suggesting that the mechanism responsible for BUNV transcription termination may be common to other orthobunyaviruses.
Variants of Peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant
Authors: Rodio Maria-Elena , Delgado Sonia , Flores Ricardo , Serio Francesco Di
Published: December 2005

Previous characterization of Peach latent mosaic viroid (PLMVd) variants from a single peach calico (PC) isolate showed that PC symptoms are induced by variants with a 12–13 nt insertion at a specific position and folding into a hairpin with a U-rich loop. Here, this study was extended to two other PC isolates. PLMVd variants with insertions similar to those reported previously (type 1), predominated in one isolate (PC-P2). The second (PC-P1), in addition to these variants, contained others with insertions in the same position and of the same size, but with the hairpin capped by a GA-rich loop (type 2). When symptomatic and non-symptomatic tissues from both isolates were used to inoculate GF-305 peach seedlings, they reproduced the phenotype of the inoculum source, indicating that variants differing in pathogenicity are unevenly distributed within single plants. Moreover, characterization of the progeny from inoculations with the PC-P1 source showed that variants with insertions of type 1 and 2 were predominant in the symptomatic and non-symptomatic seedlings, respectively, confirming the association between PC and variants with type 1 but not type 2 insertions. Inoculations with dimeric in vitro transcripts from PLMVd variants with type 1, type 2 and with a chimeric insertion showed that the variant with type 2 insertion was latent and established that the U-rich capping loop has a major role in PC, although the adjacent stem may also have some influence. Insertions can be acquired and lost during infection, suggesting that latent variants can evolve into pathogenic variants and vice versa.
Evolution of Hepatitis B virus in an acute hepatitis B patient co-infected with genotypes B and C
Authors: Chen Bing-Fang , Liu Chun-Jen , Jow Guey-Mei , Chen Pei-Jer , Kao Jia-Horng , Chen Ding-Shinn
Published: December 2005

The interactions between different genotypes ofHepatitis Bvirus(HBV) in co-infected patients remain largely unknown, especially in acute infection. Here, the evolution of HBV strains was studied in an acute, self-limited hepatitis B patient co-infected with genotypes Ba (B2) and C. Virological analyses were performed at four time points after admission: T1 (5 days), T2 (11 days), T3 (22 days) and T4 (260 days). A dominant-genotype change from genotype C to Ba was found after anti-HBV e antigen (anti-HBe) seroconversion. Further clonal and phylogenetic analyses of the pre-S and pre-core/core regions of HBV were carried out to clarify the interactions between genotypes Ba and C. All clones propagated from T1 and T2 were of genotype C. In contrast, clones propagated from T3 (after anti-HBe seroconversion) were of genotype Ba, C and/or recombinant within the pre-S region. At T4, all clones were of genotype Ba with a 123 bp (from nt 3147 of the pre-S1 region to nt 54 of the pre-S2 region) in-frame pre-S deletion and had lost the start codon of the middle envelope protein and the nucleocapsid-binding site. Phylogenetic analysis showed that genetic distance was greater at T3 after seroconversion to anti-HBe. By using SimPlot, the breakpoint of one pre-S recombinant was located at nt 3069–3100 and the other two at nt 49–87. In conclusion, HBV genotype Ba may overtake genotype C as the predominant strain after anti-HBe seroconversion in acute hepatitis B. Recombination within the pre-S region emerged transiently and the pre-S deletion mutant was finally cleared.
Population genetic history of hepatitis C virus 1b infection in China
Authors: Nakano Tatsunori , Lu Ling , He Yunshao , Fu Yongshui , Robertson Betty H. , Pybus Oliver G.
Published: December 2005

Subtype 1b is the most common strain ofHepatitis C virus(HCV) in China. Here, the molecular epidemiology and epidemic history of this strain were investigated by conducting phylogenetic and population genetic analyses of E1 and NS5B gene sequences sampled from nine Chinese cities. The phylogenetic analysis indicated the presence of two clusters of Chinese strains that did not include reference strains from other countries, suggesting that these clusters represent two independent chains of HCV transmission within China. The remaining Chinese isolates were more closely related to reference strains from other countries. The date of origin and past population dynamics of the two groups were investigated using a new population genetic method, the Bayesian skyline plot. The estimated dates of origin of both groups coincide with the period of the Chinese ‘Cultural Revolution’ during the years 1966–1976. Both groups grew at a rapid exponential rate between ∼1970 and ∼1990, after which transmission slowed considerably. Possible explanations for the groups' fast spread and subsequent slowdown are discussed, including parenteral transmission by unsafe injection, iatrogenic transmission by infected blood or blood products and improvements in blood safety since 1990. These results shed light on HCV transmission in China and may help to predict the future burden of HCV-related disease in the country.
Deletion of gene A41L enhances vaccinia virus immunogenicity and vaccine efficacy
Authors: Clark Richard H. , Kenyon Julia C. , Bartlett Nathan W. , Tscharke David C. , Smith Geoffrey L.
Published: December 2005

Vaccinia virus(VACV) is the vaccine that was used to eradicate smallpox and is being developed as a recombinant vaccine for other pathogens. Removal of genes encoding immunomodulatory proteins expressed by VACV may enhance virus immunogenicity and improve its potential as a vaccine. Protein A41 is a candidate for removal, having sequence similarity to the VACV chemokine-binding protein, vCKBP, and an association with reduced inflammation during dermal infection. Here, it is shown that, at low doses, VACV strain Western Reserve (WR) lackingA41L(vΔA41L) was slightly more virulent than wild-type and revertant controls after intranasal infection of BALB/c mice. The primary immune response to vΔA41L was marked by an increase in the percentage of VACV-specific gamma interferon-producing CD8+T cells and enhancement of cytotoxic T-cell responses in the spleen. However, this augmentation of cellular response was not seen in lung infiltrates. Splenic CD8+T-cell responses were also enhanced when VACV strain modified vaccinia virus Ankara (MVA) lackingA41Lwas used to immunize mice. Lastly, immunization with VACV MVA lackingA41Lprovided better protection than control viruses to subsequent challenge with a 300 LD50dose of VACV WR. This study provides insight into the immunomodulatory role of A41 and suggests that MVA lacking A41 may represent a more efficacious vaccine.
Modified vaccinia virus Ankara multiplies in rat IEC-6 cells and limited production of mature virions occurs in other mammalian cell lines
Authors: Okeke Malachy Ifeanyi , Nilssen Øivind , Traavik Terje
Published: December 2005

Recombinant viruses based on modified vaccinia virus Ankara (MVA) are vaccine candidates against infectious diseases and cancers. Presently, multiplication of MVA has been demonstrated in chicken embryo fibroblast and baby hamster kidney (BHK-21) cells only. The multiplication and morphogenesis of a recombinant (MVA-HANP) and non-recombinant MVA strain in BHK-21 and 12 other mammalian cell lines have now been compared. Rat IEC-6 cells were fully permissive to MVA infection. The virus yield in IEC-6 cells was similar to that obtained in BHK-21 cells at low as well as high multiplicities of infection. Vero cells were semi-permissive to MVA infection. Mature virions were produced in supposedly non-permissive cell lines. The multiplication and morphogenesis of non-recombinant MVA and MVA-HANP were similar. These results are relevant to the production and biosafety of MVA-vectored vaccines.
Importance of the C-terminal domain of soybean mosaic virus coat protein for subunit interactions
Authors: Kang Sung-Hwan , Lim Won-Seok , Hwang Sung-Hyun , Park Jin-Woo , Choi Hong-Soo , Kim Kook-Hyung
Published: December 2005

The potyvirus coat protein (CP) is involved in aphid transmission, cell-to-cell movement and virus assembly, not only by binding to viral RNA, but also by self-interaction or interactions with other factors. In this study, a number of CP mutants ofSoybean mosaic virus(SMV) containing deletions and site-directed mutations were generated and cloned into yeast two-hybrid vectors. Interaction was confirmed by the expression of reporter genes, includingHIS3,ADE2andMEL1, in yeast strain AH109. Deletion of the C-terminal region of the CP caused loss of the CP–CP self-interaction ability detected in CP mutants with the C-terminal region. Alanine substitution at the amino acid positions R190, E191, E212, R245, H246 and R249 disrupted CP–CP interaction, whereas substitutions at the amino acid positions R188, D189, D198, K205, K218 and D250 did not. These results indicate that the C-terminal region of SMV CP may contain a domain(s) or amino acids required for CP–CP interaction and virus assembly.
Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum
Authors: Xie Jun , Wei Dongmei , Jiang Daohong , Fu Yanping , Li Guoqing , Ghabrial Said , Peng Youliang
Published: December 2005

It was previously reported that three dsRNA segments, designated L, M and S, were isolated fromSclerotinia sclerotiorumstrain Ep-1PN and that the M dsRNA segment was coincident with hypovirulence and debilitation of the fungal host. Here, the complete nucleotide sequence of the M dsRNA of 5419 nt, excluding the poly(A) tail, was determined. Sequence analysis revealed the occurrence of a single open reading frame (nt 93–5195) encoding a protein with significant similarity to the replicases of the ‘alphavirus-like’ supergroup of positive-strand RNA viruses. The M dsRNA-encoded putative replicase protein contained the conserved methyl transferase, helicase and RNA-dependent RNA polymerase (RdRp) domains characteristic of the replicases of potex-like plant viruses (flexiviruses) andBotrytis virus F(BVF), a flexuous rod mycovirus infecting the phytopathogenic fungusBotrytis cinerea. Furthermore, convincing evidence is presented showing that ascospore descendents derived from the debilitated strain Ep-1PN were devoid of dsRNA and exhibited normal colony morphology. Moreover, it was demonstrated that the debilitation phenotype was transmitted from the parental debilitated strain to its normal ascospore progeny via hyphal anastomosis. These results suggest that the M dsRNA from strain Ep-1PN is derived from the genomic RNA of a positive-strand RNA virus, which we designatedSclerotiniasclerotiorumdebilitation-associatedRNAvirus (SsDRV). Although phylogenetic analysis of the conserved RdRp motifs verified that SsDRV is closely related to BVF and to the allexiviruses in the familyFlexiviridae, SsDRV is distinct from these viruses, mainly based on the lack of coat protein and movement protein.
Two classes of endogenous small RNAs inTetrahymena thermophila
Authors: Lee Suzanne R. , Collins Kathleen
Published: December 2005

Endogenous small RNAs function in RNA interference (RNAi) pathways to guide RNA cleavage, translational repression, or methylation of DNA or chromatin. InTetrahymena thermophila, developmentally regulated DNA elimination is governed by an RNAi mechanism involving ∼27–30-nucleotide (nt) RNAs. Here we characterize the sequence features of the ∼27–30-nt RNAs and a ∼23–24-nt RNA class representing a second RNAi pathway. The ∼23–24-nt RNAs accumulate strain-specifically manner and map to the genome in clusters that are antisense to predicted genes. These findings reveal the existence of distinct endogenous RNAi pathways in the unicellularT. thermophila, a complexity previously demonstrated only in multicellular organisms.
538. Sorbus Filipes
Authors: McAllister Hugh
Published: December 2005

Summary.  Sorbus filipes Hand.‐Mazz. a low‐growing, red‐flowered mountain ash from western China, is described and illustrated. Its breeding system, cultivation and propagation are discussed.
541. Corylus × Vilmorinii
Authors: Taylor Nigel , Kirkham Tony
Published: December 2005

Summary.  The hybrid hazel, Corylus × vilmorinii Rehder is described and illustrated. Its robust habit and showy catkins make it an interesting and worthwhile tree to cultivate.
Characterization of OCA2 cDNA in different porcine breeds and analysis of its potential effect on skin pigmentation in a red Iberian strain
Authors: Fernández A. , Silió L. , Rodríguez C. , Óvilo C.
Published: December 2005

Although the function of the OCA2 gene product has not been totally clarified, variation in OCA2 has been associated with skin and hair pigmentation in human and mouse. However, its contribution to skin colour in domestic species has not been reported. In this study, cDNA and intron 9 sequences of the porcine OCA2 gene have been characterized in several pig populations. The cDNA sequence alignment of 20 animals from eight porcine populations allowed the identification of 10 single nucleotide polymorphisms (SNPs); five of the 10 SNPs were non‐synonymous. The intron 9 sequence alignment of 12 animals belonging to four pig populations revealed four additional SNPs. Skin colour variation was analysed in a red strain of Iberian pigs with segregation of three SNPs forming two OCA2 intragenic haplotypes. Results from this study provide evidence of a suggestive dominant effect of haplotypes on colour intensity and indicate an important contribution of additive polygenic effects (h2 = 0.56 ± 0.21) to the variance of this trait.
Autoantibodies to thrombin directed against both of its cryptic exosites
Authors: Mollica Luigina , Preston Roger J.S. , Chion Alain Chan Kwo , Lees Steve J. , Collins Peter , Lewis Sarah , Lane David A.
Published: December 2005

Immunoglobulin G (IgG) anti‐thrombin autoantibodies (ATA) were purified from the plasma of a patient referred for haematological investigation because of bleeding for 24 h following a dental extraction. The ATA did not inhibit the catalytic activity of thrombin against a chromogenic substrate, suggesting that they did not interact with the active site of thrombin. The ATA did, however, prolong the time required to generate thrombin in plasma, suggesting that they inhibited factor V and factor VIII activation. Surface plasmon resonance (SPR) was used to demonstrate that ATA bound to thrombin with high affinity. Competition of thrombin‐ATA binding, using known thrombin exosite I and II ligands (hirudin, thrombomodulin and heparin), demonstrated that ATA bound to both thrombin exosites. Thrombin residues that are important for ATA binding were identified using a library of 53 recombinant thrombin variants encompassing alanine substitutions of 78 surface‐exposed residues. They were H66, R68, R70 and Y71 in exosite I, and R89, R93, E94, R98, R245 and K248 in exosite II. ATA bound predominantly to exosite II. They did not bind to prothrombin, illustrating the cryptic nature of both exosites exposed and presented as potential antigens following prothrombin conversion to thrombin.
Do habitat models accurately predict the depth distribution of pelagic fishes?
Authors: WARD PETER J. , MYERS RANSOM A.
Published: December 2005

Habitat models are used to correct estimates of fish abundance derived from pelagic longline fishing gear. They combine information on hook depth with the species’ preferences for ambient environmental conditions to adjust the gear's catchability. We compare depth distributions of bigeye tuna (Thunnus obesus) catch predicted by a habitat model with distributions derived from data collected by observers on longliners in the tropical Pacific Ocean. Our analyses show that the habitat model does not accurately predict the depth distribution of bigeye tuna; its predictions are worse than those from models that assume no effect of depth on catches. Statistical models provided superior fits to the observed depth distribution. The poor performance of the habitat model is probably due to (1) problems in estimating hook depth, (2) fine‐scale variations in environmental conditions, (3) incomplete knowledge of habitat preferences and (4) differences between the distribution of bigeye tuna and their vulnerability to longline gear.
Carbon and nitrogen elemental and isotopic patterns in macrofungal sporocarps and trees in semiarid forests of the south‐western USA
Authors: HART S. C. , GEHRING C. A. , SELMANTS P. C. , DECKERT R. J.
Published: December 2005

Previous studies in humid forests have shown that the 13C and 15N isotopic composition differs between ectomycorrhizal (ECM) and saprotrophic (SAP) fungi, and that this ECM–SAP ‘divide’ may provide a useful tool for evaluating fungal trophic status.

We evaluated whether this method could delineate the trophic status of fungi in two semiarid, temperate forests of the south‐western USA. This technique could be particularly valuable in arid regions where the functional roles of fungi can be difficult to assess because of infrequent sporocarp production.

Our data were consistent with the existence of an ECM–SAP divide, although δ13C values were more useful than δ15N values in separating trophic status. Saprotrophic fungi consistently had higher δ13C values than their presumed substrates; however, the degree of 15N enrichment in SAP sporocarps was highly variable. Comparison of 11 sporocarp species common to both sites showed that δ15N values were higher in one of the forests, even though the δ15N values of foliage from common understorey and overstorey trees were similar between forests.

We conclude that assessment of the isotopic compositions of fungal sporocarps and their substrates is helpful for elucidating ecological relationships in semiarid forests.
The role of microarray technologies in the study of soft tissue tumours
Authors: West R B , Van De Rijn M
Published: December 2005

Array technologies (gene array, tissue microarray and others) are being used in a growing number of research projects involving soft tissue tumours. Gene array techniques allow for measurements of RNA expression levels or gene copy number changes for a large number of genes in a single specimen. A complementary technique, tissue microarrays, allows for the measurement of expression of a single gene in a large number of specimens. These techniques and similar ones have created a fundamentally new approach to the investigation of soft tissue tumours. This review addresses some of the advantages, problems, and solutions to those problems that come with these technologies.