bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for novel and specialized mycorrhizal parasitism: the orchid
Gastrodia confusa
gains carbon from saprotrophic
Mycena
Authors: Ogura-Tsujita Yuki , Gebauer Gerhard , Hashimoto Toshimasa , Umata Hidetaka , Yukawa Tomohisa
Published: November 2008

We investigated the physiological ecology of the Asian non-photosynthetic orchid
Gastrodia confusa
. We revealed its mycorrhizal partners by using molecular identification and identified its ultimate nutritional source by analysing carbon and nitrogen natural stable isotope abundances. Molecular identification using internal transcribed spacer and large subunit nrDNA sequences showed that
G. confusa
associates with several species of litter- and wood-decomposer
Mycena
fungi. The carbon and nitrogen isotope signatures of
G. confusa
were analysed together with photosynthetic plant reference samples and samples of the ectomycorrhizal epiparasite
Monotropa uniflora
. We found that
G. confusa
was highly enriched in
13
C but not greatly in
15
N, while
M. uniflora
was highly enriched in both
13
C and
15
N. The
13
C and
15
N signatures of
G. confusa
were the closest to those of the fruit bodies of saprotrophic fungi. Our results demonstrate for the first time using molecular and mass-spectrometric approaches that myco-heterotrophic plants gain carbon through parasitism of wood or litter decaying fungi. Furthermore, we demonstrate that, several otherwise free-living non-mycorrhizal,
Mycena
can be mycorrhizal partners of orchids.
Recognition of other species' aerial alarm calls: speaking the same language or learning another?
Authors: Magrath Robert D , Pitcher Benjamin J , Gardner Janet L
Published: November 2008

Alarm calls given by other species potentially provide a network of information about danger, but little is known about the role of acoustic similarity compared with learning in recognition of heterospecific calls. In particular, the aerial ‘hawk’ alarm calls of passerines provide a textbook example of signal design because many species have converged on a design that thwarts eavesdropping by hawks, and call similarity might therefore allow recognition. We measured the response of fairy-wrens (
Malurus cyaneus
) to playback of acoustically similar scrubwren (
Sericornis frontalis
) aerial alarm calls. First, if call similarity prompts escape independent of learning, then fairy-wrens should flee to playback of scrubwren calls outside their geographical range. However, fairy-wrens fled only in sympatry. Second, if call similarity is necessary for learning heterospecific calls, then fairy-wrens should not respond to sympatric species with different calls. We found, on the contrary, that fairy-wrens fled to the very different aerial alarm calls of a honeyeater (
Phylidonyris novaehollandiae
). Furthermore, response to the honeyeater depended on the specific structure of the call, not acoustic similarity. Overall, call similarity was neither sufficient nor necessary for interspecific recognition, implying learning is essential in the complex task of sifting the acoustic world for cues about danger.
Activation-induced cytidine deaminase-mediated hypermutation in the DT40 cell line
Authors: Arakawa Hiroshi , Buerstedde Jean-Marie
Published: November 2008

Depending on the species and the developmental stage of B cells, activation-induced cytidine deaminase (AID) triggersimmunoglobulin(Ig) gene diversification by gene conversion, hypermutation or switch recombination. The bursal B cell line DT40 usually diversifies its rearrangedIg light chain(IgL) gene by gene conversion, but disruption of theRAD51gene paralogues or deletion of theψVconversion donors induces hypermutation. Although not all aspects of somatic hypermutation can be studied in DT40, the compact size of the chickenIgLlocus and the ability to modify the genome by targeted integration are powerful experimental advantages. We review here how the studies in DT40 contributed to understanding how AID initiatesIggene diversification and how AID-induced uracils are subsequently processed by uracil DNA glycosylase, proliferating cell nuclear antigens and error-prone polymerases. We also discuss the on-going research on theIglocus specificity of hypermutation and the possibility of using hypermutation for the artificial evolution of proteins and regulatory sequences in DT40.
Improving the performance of the amblyopic visual system
Authors: Levi Dennis M , Li Roger W
Published: November 2008

Experience-dependent plasticity is closely linked with the development of sensory function; however, there is also growing evidence for plasticity in the adult visual system. This review re-examines the notion of a sensitive period for the treatment of amblyopia in the light of recent experimental and clinical evidence for neural plasticity. One recently proposed method for improving the effectiveness and efficiency of treatment that has received considerable attention is ‘perceptual learning’. Specifically, both children and adults with amblyopia can improve their perceptual performance through extensive practice on a challenging visual task. The results suggest that perceptual learning may be effective in improving a range of visual performance and, importantly, the improvements may transfer to visual acuity. Recent studies have sought to explore the limits and time course of perceptual learning as an adjunct to occlusion and to investigate the neural mechanisms underlying the visual improvement. These findings, along with the results of new clinical trials, suggest that it might be time to reconsider our notions about neural plasticity in amblyopia.
Cephalopod dynamic camouflage: bridging the continuum between background matching and disruptive coloration
Authors: Hanlon R.T , Chiao C.-C , Mäthger L.M , Barbosa A , Buresch K.C , Chubb C
Published: November 2008

Individual cuttlefish, octopus and squid have the versatile capability to use body patterns for background matching and disruptive coloration. We define—qualitatively and quantitatively—the chief characteristics of the three major body pattern types used for camouflage by cephalopods: uniform and mottle patterns for background matching, and disruptive patterns that primarily enhance disruptiveness but aid background matching as well. There is great variation within each of the three body pattern types, but by defining their chief characteristics we lay the groundwork to test camouflage concepts by correlating background statistics with those of the body pattern. We describe at least three ways in which background matching can be achieved in cephalopods. Disruptive patterns in cuttlefish possess all four of the basic components of ‘disruptiveness’, supporting Cott's hypotheses, and we provide field examples of disruptive coloration in which the body pattern contrast exceeds that of the immediate surrounds. Based upon laboratory testing as well as thousands of images of camouflaged cephalopods in the field (a sample is provided on a web archive), we note that size, contrast and edges of background objects are key visual cues that guide cephalopod camouflage patterning. Mottle and disruptive patterns are frequently mixed, suggesting that background matching and disruptive mechanisms are often used in the same pattern.
Functional importance of dengue virus maturation: infectious properties of immature virions
Authors: Zybert Izabela A. , van der Ende-Metselaar Heidi , Wilschut Jan , Smit Jolanda M.
Published: November 2008

Prior to the release of flavivirus particles from infected cells, the viral surface protein prM is cleaved to M by the cellular enzyme furin. For dengue virus (DENV), this maturation process appears to be very inefficient since a high proportion of progeny virions contain uncleaved prM. Furthermore, it has been reported that prM-containing DENV particles are infectious. These observations contradict the general assumption that prM processing is required to render virus particles infectious. Therefore, in this study, we reinvestigated the infectious properties of immature DENV virions. DENV particles were produced in furin-deficient LoVo cells. We observed that DENV-infected LoVo cells secrete high numbers of prM-containing particles. Subsequent analysis of the infectious titre revealed that immature particles lack the ability to infect cells, the infectious unit to particle ratio being 10 000-fold reduced compared with that of wild-type virus. Our results indicate that cleavage of prM to M is required for DENV infectivity.
Recombination analysis and structure prediction show correlation between breakpoint clusters and RNA hairpins in the pol gene of human immunodeficiency virus type 1 unique recombinant forms
Authors: Galli Andrea , Lai Alessia , Corvasce Stefano , Saladini Francesco , Riva Chiara , Dehò Lorenzo , Caramma Ilaria , Franzetti Marco , Romano Laura , Galli Massimo , Zazzi Maurizio , Balotta Claudia
Published: November 2008

Recombination is recognized as a primary force in human immunodeficiency virus type 1 (HIV-1) evolution, increasing viral diversity through reshuffling of genomic portions. The strand-switching activity of reverse transcriptase is required to complete HIV-1 replication and can occur randomly throughout the genome, leading to viral recombination. Some recombination hotspots have been identified and found to correlate with RNA structure or sequence features. The aim of this study was to evaluate the presence of recombination hotspots in the pol gene of HIV-1 and to assess their correlation with the underlying RNA structure. Analysis of the recombination pattern and breakpoint distribution in a group of unique recombinant forms (URFs) detected two recombination hotspots in the pol region. Two stable and conserved hairpins were consistently predicted corresponding to the identified hotspots using six different RNA-folding algorithms on the URF parental strains. These findings suggest that such hairpins may play a role in the higher recombination rates detected at these positions.
Inhibition of duck hepatitis B virus infection of liver cells by combined treatment with viral e antigen and carbohydrates
Authors: Maenz Claudia , Loscher Christine , Iwanski Alicja , Bruns Michael
Published: November 2008

The e antigen (eAg) of duck hepatitis B virus (DHBV) is a glycosylated secretory protein with a currently unknown function. We concentrated this antigen from the supernatants of persistently infected primary duck liver cell cultures by ammonium sulphate precipitation, adsorption chromatography over concanavalin A Sepharose, preparative isoelectric focusing and molecular sieve chromatography. The combined treatment of duck liver cells with DHBV eAg (DHBe) concentrate andα-methyl-d-mannopyranoside strongly inhibited DHBV replication atde novoinfection. When DHBe was added to non-infected primary duck liver cells, it was found to be associated with liver sinusoidal endothelial cells. This binding could be inhibited by the addition ofα-methyl-d-mannopyranoside and other sugar molecules. The inhibitory effect of DHBe on infection could play a role in maintaining viral persistence.
Replication promiscuity of DNA-β satellites associated with monopartite begomoviruses; deletion mutagenesis of the Ageratum yellow vein virus DNA-β satellite localizes sequences involved in replication
Authors: Saunders Keith , Briddon Rob W. , Stanley John
Published: November 2008

Pseudorecombination studies inNicotiana benthamianademonstrate thatAgeratumyellow vein virus (AYVV) andEupatoriumyellow vein virus (EpYVV) can functionally interact with DNA-βsatellites associated with AYVV, EpYVV, cotton leaf curl Multan virus (CLCuMV) and honeysuckle yellow vein virus (HYVV). In contrast, CLCuMV shows some specificity in its ability to interact with distinct satellites and HYVV is able to interact only with its own satellite. Using anN. benthamianaleaf disk assay, we have demonstrated that HYVV is unable totrans-replicate other satellites. To investigate the basis oftrans-replication compatibility, deletion mutagenesis of AYVV DNA-βhas been used to localize the origin of replication to approximately 360 nt, encompassing the ubiquitous nonanucleotide/stem–loop structure, satellite conserved region (SCR) and part of the intergenic region immediately upstream of the SCR. Additional deletions within this intergenic region have identified a region that is essential for replication. The capacity for DNA-βsatellites to functionally interact with distinct geminivirus species and its implications for disease diversification are discussed.
Phylogenetic evidence for homologous recombination within the family Birnaviridae
Authors: Hon Chung-Chau , Lam Tommy Tsan-Yuk , Yip Chi-Wai , Wong Raymond Tsz-Yeung , Shi Mang , Jiang Jingwei , Zeng Fanya , Leung Frederick Chi-Ching
Published: November 2008

Birnaviruses are bi-segmented double-stranded RNA (dsRNA) viruses infecting insects, avian species and a wide range of aquatic species. Although homologous recombination is a common phenomenon in positive-sense RNA viruses, recombination in dsRNA viruses is rarely reported. Here we performed a comprehensive survey on homologous recombination in all available sequences (>1800) of the family Birnaviridae based on phylogenetic incongruence. Although inter-species recombination was not evident, potential intra-species recombination events were detected in aquabirnaviruses and infectious bursal disease virus (IBDV). Eight potential recombination events were identified and the possibility that these events were non-naturally occurring was assessed case by case. Five of the eight events were identified in IBDVs and all of these five events involved live attenuated vaccine strains. This finding suggests that homologous recombination between vaccine and wild-type IBDV strains may have occurred; the potential risk of mass vaccination using live vaccines is discussed. This is the first report of evidence for homologous recombination within the family Birnaviridae.
HepG2 hepatocellular carcinoma cells are a non-permissive system for B19 virus infection
Authors: Bonvicini Francesca , Filippone Claudia , Manaresi Elisabetta , Zerbini Marialuisa , Musiani Monica , Gallinella Giorgio
Published: November 2008

Parvovirus B19 has been associated with liver dysfunction and has been considered a potential aetiological agent of fulminant hepatitis and hepatitis-associated aplastic anaemia. The possible effects of B19 virus infection on the liver have been investigated using HepG2 hepatocellular carcinoma cells as a model system, but the reported results are inconsistent. To investigate this relationship further, this study followed the course of B19 virus infection of HepG2 cells in terms of viral DNA, RNA and protein production by quantitative PCR, RT-PCR and immunofluorescence assays. The data showed that B19 virus is able to bind and possibly enter HepG2 cells, but that viral genome replication or transcription is not supported and that viral proteins are not produced. As far as HepG2 cells can be considered a representative model system, any possible pathogenic role of B19 virus on the liver cannot be ascribed to infection or to a direct cytopathic effect on hepatocytes.
Bombyx mori nucleopolyhedrovirus SNF2 global transactivator homologue (Bm33) enhances viral pathogenicity in B. mori larvae
Authors: Katsuma Susumu , Fujii Tsuguru , Kawaoka Shinpei , Shimada Toru
Published: November 2008

The SNF2 global transactivator gene homologue (Bm33) of Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the genes exclusive to group I NPVs, but its function remains unknown. This study describes the characterization of Bm33. Transcriptional analysis suggested that Bm33 is an early gene, as its transcript was observed at 4 h post-infection in BmNPV-infected BmN cells. To examine the role of Bm33 during BmNPV infection, a Bm33 deletion mutant (BmORF33D) was constructed and its infectivity was characterized in BmN cells and B. mori larvae. BmORF33D did not have any obvious defects in the production of budded viruses (BVs) or occlusion bodies (OBs) in BmN cells compared with wild-type BmNPV. Larval bioassays revealed that deletion of Bm33 did not reduce virus infectivity. However, BmORF33D took approximately 10–15 h longer than wild-type BmNPV to kill B. mori larvae when tested by either BV injection or OB ingestion. These results suggest that Bm33 is not essential for virus growth in vitro or in vivo, but that it accelerates the time of death of B. mori larvae.
Characterization of H9N2 influenza viruses isolated from vaccinated flocks in an integrated broiler chicken operation in eastern China during a 5 year period (1998–2002)
Authors: Zhang Pinghu , Tang Yinghua , Liu Xiaowen , Peng Daxin , Liu Wenbo , Liu Hongqi , Lu Shan , Liu Xiufan
Published: November 2008

In the current study, we characterized H9N2 influenza viruses isolated from vaccinated flocks in an integrated broiler chicken operation during a 5 year period (1998–2002). Phylogenetic analysis of the 8 genes of 11 representative viruses showed that they all shared high similarity to that of the first isolate, A/Chicken/Shanghai/F/1998 (Ck/SH/F/98), and clustered to the same lineages. Furthermore, all 11 viruses had a 9 nt deletion between positions 206 and 214 of the neuraminidase gene. These genetic characteristics strongly suggest that these viruses are descendants of the first isolate. In addition, our study also showed that the H9N2 viruses circulating in the operation during this 5 year period were evolving, as shown by antigenic variations between viruses manifested by reactivity with polyclonal antisera and monoclonal antibodies, by haemagglutination with erythrocytes from different animals, by amino acid differences in haemagglutinin and neuraminidase proteins, and by variation in their ability to replicate in the respiratory and intestinal tract and to be transmitted by aerosol. Phylogenetic analysis revealed that the internal genes from some H5N1 viruses of duck origin clustered together with those from H9N2 virus and that the RNP genes of these H5N1 viruses isolated after 2001 are more closely related to the genes of the Ck/SH/F/98-like H9N2 viruses, indicating more recent reassortment events between these two subtypes of viruses. Continuous surveillance of influenza virus in poultry and waterfowl is critical for monitoring the genesis and emergence of potentially pandemic strains in this region.
The human H5N1 influenza A virus polymerase complex is active in vitro over a broad range of temperatures, in contrast to the WSN complex, and this property can be attributed to the PB2 subunit
Authors: Bradel-Tretheway Birgit G. , Kelley Z. , Chakraborty-Sett Shikha , Takimoto Toru , Kim Baek , Dewhurst Stephen
Published: November 2008

Influenza A virus (IAV) replicates in the upper respiratory tract of humans at 33 °C and in the intestinal tract of birds at close to 41 °C. The viral RNA polymerase complex comprises three subunits (PA, PB1 and PB2) and plays an important role in host adaptation. We therefore developed an in vitro system to examine the temperature sensitivity of IAV RNA polymerase complexes from different origins. Complexes were prepared from human lung epithelial cells (A549) using a novel adenoviral expression system. Affinity-purified complexes were generated that contained either all three subunits (PA/PB1/PB2) from the A/Viet/1203/04 H5N1 virus (H/H/H) or the A/WSN/33 H1N1 strain (W/W/W). We also prepared chimeric complexes in which the PB2 subunit was exchanged (H/H/W, W/W/H) or substituted with an avian PB2 from the A/chicken/Nanchang/3-120/01 H3N2 strain (W/W/N). All complexes were functional in transcription, cap-binding and endonucleolytic activity. Complexes containing the H5N1 or Nanchang PB2 protein retained transcriptional activity over a broad temperature range (30–42 °C). In contrast, complexes containing the WSN PB2 protein lost activity at elevated temperatures (39 °C or higher). The E627K mutation in the avian PB2 was not required for this effect. Finally, the avian PB2 subunit was shown to confer enhanced stability to the WSN 3P complex. These results show that PB2 plays an important role in regulating the temperature optimum for IAV RNA polymerase activity, possibly due to effects on the functional stability of the 3P complex.
Evolutionary dynamics of human and avian metapneumoviruses
Authors: de Graaf Miranda , Osterhaus Albert D. M. E. , Fouchier Ron A. M. , Holmes Edward C.
Published: November 2008

Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A–D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations – A1, A2, B1 and B2 – of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119–133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.
Differential Response of Gray Poplar Leaves and Roots Underpins Stress Adaptation during Hypoxia
Authors: Kreuzwieser Jürgen , Hauberg Jost , Howell Katharine A. , Carroll Adam , Rennenberg Heinz , Millar A. Harvey , Whelan James
Published: November 2008

The molecular and physiological responses of gray poplar (Populus × canescens) following root hypoxia were studied in roots and leaves using transcript and metabolite profiling. The results indicate that there were changes in metabolite levels in both organs, but changes in transcript abundance were restricted to the roots. In roots, starch and sucrose degradation were altered under hypoxia, and concurrently, the availability of carbohydrates was enhanced, concomitant with depletion of sucrose from leaves and elevation of sucrose in the phloem. Consistent with the above, glycolytic flux and ethanolic fermentation were stimulated in roots but not in leaves. Various messenger RNAs encoding components of biosynthetic pathways such as secondary cell wall formation (i.e. cellulose and lignin biosynthesis) and other energy-demanding processes such as transport of nutrients were significantly down-regulated in roots but not in leaves. The reduction of biosynthesis was unexpected, as shoot growth was not affected by root hypoxia, suggesting that the up-regulation of glycolysis yields sufficient energy to maintain growth. Besides carbon metabolism, nitrogen metabolism was severely affected in roots, as seen from numerous changes in the transcriptome and the metabolome related to nitrogen uptake, nitrogen assimilation, and amino acid metabolism. The coordinated physiological and molecular responses in leaves and roots, coupled with the transport of metabolites, reveal important stress adaptations to ensure survival during long periods of root hypoxia.
A Relaxed Specificity in Interchain Disulfide Bond Formation Characterizes the Assembly of a Low-Molecular-Weight Glutenin Subunit in the Endoplasmic Reticulum
Authors: Lombardi Alessio , Barbante Alessandra , Cristina Pietro Della , Rosiello Daniele , Castellazzi Chiara Lara , Sbano Luca , Masci Stefania , Ceriotti Aldo
Published: November 2008

Wheat (Triticum spp.) grains contain large protein polymers constituted by two main classes of polypeptides: the high-molecular-weight glutenin subunits and the low-molecular-weight glutenin subunits (LMW-GS). These polymers are among the largest protein molecules known in nature and are the main determinants of the superior technological properties of wheat flours. However, little is known about the mechanisms controlling the assembly of the different subunits and the way they are arranged in the final polymer. Here, we have addressed these issues by analyzing the formation of interchain disulfide bonds between identical and different LMW-GS and by studying the assembly of mutants lacking individual intrachain disulfides. Our results indicate that individual cysteine residues that remain available for disulfide bond formation in the folded monomer can form interchain disulfide bonds with a variety of different cysteine residues present in a companion subunit. These results imply that the coordinated expression of many different LMW-GS in wheat endosperm cells can potentially lead to the formation of a large set of distinct polymeric structures, in which subunits can be arranged in different configurations. In addition, we show that not all intrachain disulfide bonds are necessary for the generation of an assembly-competent structure and that the retention of a LMW-GS in the early secretory pathway is not dependent on polymer formation.
Genetic and Molecular Characterization of theVRN2Loci in Tetraploid Wheat
Authors: Distelfeld Assaf , Tranquilli Gabriela , Li Chengxia , Yan Liuling , Dubcovsky Jorge
Published: November 2008

Winter wheat (Triticum spp.) varieties require long exposures to low temperatures to flower, a process called vernalization. The VRN2 locus includes two completely linked zinc finger-CCT domain genes (ZCCT1 and ZCCT2) that act as flowering repressors down-regulated during vernalization. Deletions or mutations in these two genes result in the elimination of the vernalization requirement in diploid wheat (Triticum monococcum). However, natural allelic variation in these genes has not been described so far in polyploid wheat (tetraploid Triticum turgidum and hexaploid Triticum aestivum). A tetraploid wheat population segregating for both VRN-A2 and VRN-B2 loci facilitated the characterization of different alleles. Comparisons between functional and nonfunctional alleles revealed that both ZCCT1 and ZCCT2 genes are able to confer vernalization requirement and that different ZCCT genes are functional in different genomes. ZCCT1 and ZCCT2 proteins from nonfunctional vrn2 alleles have mutations at arginine amino acids at position 16, 35, or 39 of the CCT domain. These positions are conserved between CCT and HEME ACTIVATOR PROTEIN2 (HAP2) proteins, supporting a model in which the action of CCT domains is mediated by their interactions with HAP2/HAP3/HAP5 complexes. This study also revealed natural variation in gene copy number, including a duplication of the functional ZCCT-B2 gene and deletions or duplications of the complete VRN-B2 locus. Allelic variation at the VRN-B2 locus was associated with a partially dominant effect, which suggests that variation in the number of functional ZCCT genes can be used to expand allelic diversity for heading time in polyploid wheat and, hopefully, improve its adaptation to different environments.
Horizontal gene transfer: sustaining pathogenicity and optimizing host–pathogen interactions
Authors: KADO CLARENCE I.
Published: November 2008

Successful host–pathogen interactions require the presence, maintenance and expression of gene cassettes called ‘pathogenicity islands’ (PAIs) and ‘metabolic islands’ (MAIs) in the respective pathogen. The products of these genes confer on the pathogen the means to recognize their host(s) and to efficiently evade host defences in order to colonize, propagate within the host and eventually disseminate from the host. Virulence effectors secreted by type III and type IV secretion systems, among others, play vital roles in sustaining pathogenicity and optimizing host–pathogen interactions. Complete genome sequences of plant pathogenic bacteria have revealed the presence of PAIs and MAIs. The genes of these islands possess mosaic structures with regions displaying differences in nucleotide composition and codon usage in relation to adjacent genome structures, features that are highly suggestive of their acquisition from a foreign donor. These donors can be other bacteria, as well as lower members of the Archaea and Eukarya. Genes that have moved from the domains Archaea and Eukarya to the domain Bacteria are true cases of horizontal gene transfer. They represent interdomain genetic transfer. Genetic exchange between distinct members of the domain Bacteria, however, represents lateral gene transfer, an intradomain event. Both horizontal and lateral gene transfer events have been used to facilitate survival fitness of the pathogen.
Survival of smaller sport caught chinook, Oncorhynchus tshawytscha (Walbaum), and coho, Oncorhynchus kisutch (Walbaum), salmon from Lake Michigan and its management implications
Authors: SAVITZ J. , BARDYGULA‐NONN L.G. , SIMPSON A. , FUNK G.
Published: November 2008

Abstract The survival of small‐sized (<50.8 cm) chinook salmon, Oncorhynchus tshawytscha (Walbaum), and coho salmon, Oncorhynchus kitsutch (Walbaum), caught by sport fishing was determined to assess the potential for increasing the size limit for these fish. Fishermen were recently catching smaller salmon than in the 1970s, but salmon growth rates had not changed. To be an effective management option, the survival rate of hooked and returned fish must be high. The overall survival rates were high: 76% for chinook salmon and 70% for coho salmon. There was no significant difference in survival of the coho salmon with size of hook used (P = 0.31). Any mortality among fish was generally acute; fish hooked deep in the mouth or gills generally bled and died shortly after capture. Fish hooked in the gills had a significantly greater mortality (P = 0.0002). The overall high survival rate for these species was the result of a small proportion of fish being hooked in the gills or deep in the mouth. Since the survival rate of the salmon was high, the size limit could be increased to allow smaller fish to grow to sizes preferred by sport fishermen.
The effects of perch, Perca fluviatilis L., and bronze bream, Abramis brama (L.), on insect emergence and benthic invertebrate abundance in experimental ponds
Authors: GILES N. , WRIGHT R. M. , SHOESMITH E. A.
Published: November 2008

Abstract The effects of perch, Perca fluviatilis L., and bronze bream, Abramis brama (L.), predation on the production of insects emerging at the water surface and the autumn biomass of benthic macro‐invertebrates were assessed in a series of experimental ponds. The study attempted to discover whether fish affect food availability for diving and dabbling ducks in freshwater habitats. Ten ponds (bisected by fine netting) were used for the study: one was left totally fish‐free, whilst one half of each of three groups of three ponds was stocked with either perch, bream or perch plus bream. The relative abundance of emerging insects (mainly Chironomidae) was significantly reduced in two perch ponds, two perch + bream ponds and two bream ponds. The autumn standing crops of benthic macroinvertebrates were significantly reduced in one perch pond, three bream ponds and one perch plus bream pond. These results support findings of a contemporaneous large bio‐manipulation experiment carried out in two adjacent lakes. During the biomanipulation studies, aquatic invertebrate standing stocks greatly increased after the removal of fish and decreased following restocking.
Status and management of fish populations of Rawal Dam reservoir, Pakistan
Authors: AFZAL M. , RAB A. , AKHTAR N. , YAQOOB M.
Published: November 2008

Abstract Studies were conducted to determine the composition and relative abundance of commercially desirable and less desirable fish populations of Rawal Dam reservoir. Fifteen fish species belonging to 11 genera were identified. The less desirable species were abundant, constituting 62.3%, 84.8% and 78% of the total number of fish sampled on three occasions. Carnivores were represented by two species with very low percentage composition by number or weight. The ratio of total weight of forage fish to that of carnivorous fish indicated an unbalanced population in the lake. The proportion of the fish population at harvestable size suggests a balanced population, but this index may have been overestimated because of a minimum harvestable size.
Diet of the largemouth bass, Micropterus salmoides (Lacepède), in Lake Naivasha, Kenya
Authors: ALOO P. A. , DADZIE S.
Published: November 2008

Abstract The major food items of adult largemouth bass, Micropterus salmoides (Lacepède), in Lake Naivasha, Kenya are not markedly different from those in its native range. Although insects and their larvae are major components of the diet for both temperate and equatorial populations of juvenile bass, the equatorial population also eats Procambarus clarkii (Girard), juvenile fish and aquatic weeds. In temperate populations they also eat crustaceans, rotifers and oligochaetes. The frequency of occurrence of the major prey organisms in the stomachs of M. salmoides varies seasonally with population peaks in these organisms. Similar to North American populations, the Naivasha population feeds during the day between dawn and dusk. In contrast to temperate populations, the population of M. salmoides in this equatorial lake feeds throughout the year, with feeding intensity correlated with water temperature.
Differentiation of striped bass, Morone saxatilis (Walbaum), from a hybrid: effectiveness of training
Authors: HARRELL R. M. , STRAND I. E.
Published: November 2008

Abstract The ability of consumers and fishermen to distinguish‐between wild striped bass, Morone saxatilis (Walbaum), and its hybrids may be important to marketing farm‐raised fish and managing wild stocks. The ability of randomly selected persons to distinguish between wild and hybrid specimens was examined and it was found that a significant improvement in recognition occurred with only minimal training. Average correct response of 70% without training rose to nearly 90% after training. Moreover, the respondents' sex and age were important factors in determining successful identification.
Chemical signals and habitat selection by three zooplankters in Andean Patagonian ponds
Authors: TROCHINE C. , MODENUTTI B. E. , BALSEIRO E. G.
Published: November 2008

1. Zooplankton may react differently to chemical signals produced by macrophytes in shallow systems. They may be attracted by macrophytes, as the plants may be used as a refuge against predators, or the plants may have a repellent effect (e.g. when the plants are a habitat for numerous invertebrate predators or fish). In fishless Patagonian ponds, the structural complexity provided by macrophytes modulates the rate of predation on zooplankton by the invertebrate predator Mesostoma ehrenbergii (Turbellaria).

2. We performed a field study to analyse the coexistence of M. ehrenbergii and three of its prey (two copepods, the calanoid Boeckella gracilis and the cyclopoid Acanthocyclops robustus, and the cladoceran Ceriodaphnia dubia) in four ponds. In two of the ponds, we carried out day and night sampling to evaluate the influence of macrophytes on the distribution of these zooplankters.

3. In laboratory experiments, we analysed the response of the zooplankters to the chemical signals produced by macrophytes (the emergent Juncus pallescens and the submerged Myriophyllum quitense), the predator M. ehrenbergii and the ‘alarm signal’ provided by a homogenate of conspecifics.

4. Our field studies demonstrated the coexistence of M. ehrenbergii and the selected prey in different seasons and that A. robustus and C. dubia choose the vegetated area (a mixed bed of J. pallescens and M. quitense) over the non‐vegetated area. The habitat choice experiments indicated that the presence of M. ehrenbergii may directly affect the habitat selection of B. gracilis, because this zooplankter swam away from the predator. In addition, Mesostoma may indirectly affect the habitat selection of the cyclopoid copepod A. robustus and the cladoceran C. dubia as both zooplankters exhibited a negative response to the alarm signal produced by crushed conspecifics.

5. The presence of the submerged M. quitense did not affect the horizontal movements of any of the zooplankters studied. In contrast, the emergent macrophyte J. pallescens elicited a positive response of B. gracilis, suggesting that this aquatic plant may act as a predation refuge.

6. Our results suggest that predator avoidance behaviour can occur in fishless environments in response to a tactile invertebrate predator like Mesostoma. In addition, the refuge effect of emergent macrophytes, enhancing the survival of pelagic zooplankters, may act as a key factor in stabilizing predator–prey interactions in fishless Patagonian ponds, as has been widely recorded in northern temperate lakes with fish.
Differing effects of suspended sediments on the performance of native and exotic Daphnia
Authors: SOEKEN‐GITTINGER LORI A. , STOECKEL JAMES A. , HAVEL JOHN E.
Published: November 2008

1. Although large cladocerans are usually uncommon in large rivers, Daphnia lumholtzi (an exotic species in North America) is widespread and occasionally abundant. We collected zooplankton on the Illinois River (Illinois, U.S.A.) in 1995 and 1996 and found that the peak density of D. lumholtzi (25 L−1) typically exceeded that of all native species combined. Maximum density occurred during warm periods (up to 27 °C) when concentrations of inorganic suspended sediments were high (>50 mg L−1).

2. Using a life table experiment, we examined the effects of variation in suspended sediment (0 and 80 mg L−1) and food (104 and 105Ankistrodesmus cells mL−1) on fitness of D. lumholtzi and the native Daphnia parvula. Daphnia lumholtzi had greater survivorship than D. parvula in most treatments and higher life‐time fertility than D. parvula in all treatments. Both species achieved their fastest intrinsic rates of growth in treatments with high food, but their responses to suspended solids differed. The growth rate of D. lumholtzi in high food was slightly increased by higher turbidity, whereas that of D. parvula was depressed.

3. Results suggest that the ability of D. lumholtzi to tolerate suspended solids is an important factor contributing to its success in invading North American rivers.
The expression and function of NKG2D molecule on intrahepatic CD8+ T cells in chronic viral hepatitis
Authors: Kennedy P. T. F. , Gehring A. J. , Nowbath A. , Selden C. , Quaglia A. , Dhillon A. , Dusheiko G. , Bertoletti A.
Published: November 2008

Summary.  The natural killer (NK) cell receptor, NKG2D is a member of the c‐type lectin‐activating receptor family. It is expressed by all NK cells and by a sub‐population of CD8+ T cells. NKG2D engagement with its ligands directly activates NK cells and acts as a co‐stimulator on CD8+ T cells. Recent reports, however, have demonstrated a role for NKG2D in direct T‐cell activation in chronic inflammation. The aim of this study was to investigate the pattern of expression and the functional role of NKG2D on circulating and intrahepatic CD8+ T cells in chronic viral hepatitis. Peripheral blood lymphocytes and intrahepatic lymphocytes from 45 patients with chronic viral hepatitis (HBV and HCV) were studied. Phenotypic NKG2D expression and its functional ability to activate intrahepatic and circulating lymphocytes were analysed. Intrahepatic CD8+ T cells display increased NKG2D expression in chronic viral hepatitis in comparison with circulating CD8+ T cells. NKG2D co‐stimulates intrahepatic CD8+ T cells and hepatitis B virus‐specific CD8+ T cells. However, we could not demonstrate an ability to directly activate CD8+ T cells through the NKG2D signalling pathway alone. NKG2D is up‐regulated on intrahepatic CD8+ T cells in type B and C chronic viral hepatitis; however, its function appears to be restricted to that of a co‐stimulatory molecule.
Primary hepatocytes as targets for Hepatitis C virus replication
Authors: Farquhar M. J. , McKeating J. A.
Published: November 2008

Summary.  Much of our current understanding of hepatits C virus (HCV) replication has hailed from the use of a small number of cloned viral genomes and transformed hepatoma cell lines. Recent evidence suggests that lipoproteins play a key role in the HCV life cycle and virus particles derived from the sera of infected patients exist in association with host lipoproteins. This report will review the literature on HCV replication in primary hepatocytes and transformed cell lines, focusing largely on host factors defining particle entry.
Different stresses, similar morphogenic responses: integrating a plethora of pathways
Authors: POTTERS GEERT , PASTERNAK TARAS P. , GUISEZ YVES , JANSEN MARCEL A. K.
Published: November 2008

Exposure of plants to mild chronic stress can cause induction of specific, stress‐induced morphogenic responses (SIMRs). These responses are characterized by a blockage of cell division in the main meristematic tissues, an inhibition of elongation and a redirected outgrowth of lateral organs. Key elements in the ontogenesis of this phenotype appear to be stress‐affected gradients of reactive oxygen species (ROS), antioxidants, auxin and ethylene. These gradients are present at the the organismal level, but are integrated on the cellular level, affecting cell division, cell elongation and/or cell differentiation. Our analysis of the literature indicates that stress‐induced modulation of plant growth is mediated by a plethora of molecular interactions, whereby different environmental signals can trigger similar morphogenic responses. At least some of the molecular interactions that underlie morphogenic responses appear to be interchangeable. We speculate that this complexity can be viewed in terms of a thermodynamic model, in which not the specific pathway, but the achieved metabolic state is biologically conserved.
Micronutrient status indicators in individuals single‐ or double‐infected with HIV and Wuchereria bancrofti before and after DEC treatment
Authors: Nielsen Nina O. , Simonsen Paul E. , Kæstel Pernille , Krarup Henrik , Magnussen Pascal , Magesa Stephen , Friis Henrik
Published: November 2008

Objective  To identify possible associations between selected micronutrient status indicators (serum ferritin, retinol, β‐carotene, α‐tocopherol, and the acute phase reactant α‐1 antichymotrypsin) and infection with human immunodeficiency virus (HIV) or Wuchereria bancrofti, and to assess the effect of the antifilarial drug diethylcarbamazine (DEC) on the micronutrient status indicators in individuals positive for one or both of the two infections.

Methods  Serum concentrations of ferritin, retinol, β‐carotene, α‐tocopherol and the acute phase reactant α‐1 antichymotrypsin were examined in 59 individuals with HIV, W. bancrofti infection, or both, in Tanga Region, Tanzania, before and 12 weeks after treatment with DEC.

Results  HIV infection, but not W. bancrofti infection, was associated with higher serum ferritin concentrations and lower β‐carotene and α‐tocopherol. Neither HIV infection nor W. bancrofti infection was associated with serum retinol. The four micronutrient status indicators and α‐1 antichymotrypsin were generally lower at 12 weeks after treatment both in the DEC and the placebo groups.

Conclusions  The negative association between HIV infection and the antioxidant vitamins β‐carotene and α‐tocopherol may be due to infection‐induced oxidative stress, whereas W. bancrofti infection seemed not to be associated with oxidative stress. The drop in antioxidant vitamin concentrations after treatment may be due to oxidative stress induced by HIV progression (HIV infected) and inflammation around dead adult worms and microfilariae (W. bancrofti infected) rather than to an effect of DEC.
Determinants of survival in AIDS patients on antiretroviral therapy in a rural centre in the Far‐North Province, Cameroon
Authors: Sieleunou Isidore , Souleymanou Mohamadou , Schönenberger Anne‐Marie , Menten Joris , Boelaert Marleen
Published: November 2008

Objective  To analyse the outcomes of antiretroviral therapy (ART) in routine conditions in a rural hospital in the Far‐North province of Cameroon.

Method  Retrospective cohort study of 1187 patients >15 years who started ART between July 2001 and December 2006. The survival time was estimated by Kaplan–Meier analysis and Cox proportional hazard models were fitted to explain survival.

Results  Upon enrolment, 90.4% patients were in WHO stage III or IV and 56.1% had a BMI <18.5. Median CD4 count was 105 cells/mm³ (IQR 40–173). At the end of the study period, 338/1187 had died and 59/1187 were lost to follow‐up. The survival probability was 77% at 1 year [95% CI: 75–80] and 47% at 5 years [95% CI: 40–55]. The median survival time was 58 months. CD4 count, haemoglobin, BMI, sex and clinical stage at enrolment were independent predictors of mortality.

Conclusion  This study confirms the clinical benefit of ART programs in a remote and resource‐constrained setting operating in routine conditions. The challenge ahead is to secure earlier access to ART and to maintain its longer‐term benefit.
Field evaluation of rapid diagnostic tests for meningococcal meningitis in Niger
Authors: Boisier P. , Elhaj Mahamane A. , Amadou Hamidou A. , Sidikou F. , Djibo S. , Nato F. , Chanteau S.
Published: November 2008

Objective  To evaluate dipstick rapid diagnostic tests (RDTs) for meningococcal meningitis in basic health facilities.

Methods  Health facility staff received a one‐day training. During the meningitis season, they performed RDTs on cerebrospinal fluid (CSF) specimens from suspected cases of meningitis. A frozen aliquot of CSF was later tested using polymerase chain reaction (PCR) to establish the reference diagnosis. RDTs used in health facilities were archived to allow checking the concordance between reported diagnosis and observed results. Reported diagnosis was also compared to PCR diagnosis. A second RDT was performed on each CSF specimen at the reference laboratory.

Results  Using RDTs, health facilities reported 382 negative results (73.9%), 114 NmA (22.1%), 12 NmW135 (2.3%) and nine uninterpretable results (1.7%), the latter corresponding to the misuse of a reagent by three agents. The agreement between reported diagnosis and archived dipsticks was excellent (kappa = 0.98). The agreement between PCR diagnosis and reported RDTs results was strong (kappa = 0.82). In health facilities, the sensitivity of RDTs for N. meningitidis A was Se = 0.91. The kappa coefficient measuring the agreement between RDTs operated in the reference laboratory and RDTs operated in health facilities was κ = 0.78.

Conclusion  We confirmed that dipstick RDTs to identify N. meningitidis serogroups A, C, W135 and Y can be reliably operated by non‐specialized staff in basic health facilities. RDTs proved very useful to recommend vaccination in NmA epidemics, and also to avoid vaccination in epidemics due to serogroups not included in vaccines (NmX).