Ethnobiology of snappers (Lutjanidae): target species and suggestions for management

In this study, we sought to investigate the biology (diet and reproduction) and ethnobiology (fishers knowledge and fishing spots used to catch snappers) of five species of snappers (Lutjanidae), including Lutjanus analis, Lutjanus synagris, Lutjanus vivanus, Ocyurus chrysurus, and Romboplites saliens at five sites along the northeast (Riacho Doce, Maceió in Alagoas State, and Porto do Sauípe, Entre Rios at Bahia State) and the southeast (SE) Brazilian coast (Paraty and Rio de Janeiro cities at Rio de Janeiro State, and Bertioga, at São Paulo State.). We collected 288 snappers and interviewed 86 fishermen. The stomach contents of each fish were examined and macroscopic gonad analysis was performed. Snappers are very important for the fisheries of NE Brazil, and our results indicated that some populations, such as mutton snapper (L. analis) and lane snapper (L. synagris), are being caught when they are too young, at early juvenile stages. Local knowledge has been shown to be a powerful tool for determining appropriate policies regarding management of target species, and artisanal fishermen can be included in management processes. Other suggestions for managing the fisheries are discussed, including proposals that could provide motivation for artisanal fishermen to participate in programs to conserve resources, such as co-management approaches that utilize local knowledge, the establishment of fishing seasons, and compensation of fishermen, through 'payment for environmental services'. These suggestions may enhance the participation of local artisanal fishermen in moving to a more realistic and less top-down management approach of the fish population.     

Insights into the structure of the PmrD protein with molecular dynamics simulations

Resistance to cationic antimicrobial peptide polymyxin B from Gram-negative bacteria is accomplished by two-component systems (TCSs), protein complexes PmrA/PmrB and PhoP/PhoQ. PmrD is the first protein identified to mediate the connectivity between two TCSs. The 3D structure of PmrD has been recently solved by NMR and its unique fold was revealed. Here, a molecular dynamics study is presented started from the NMR structure. Numerous hydrophobic and electrostatic interactions were identified to contribute to PmrD's 3D stability. Moreover, the mobility of the five loops that connect the protein's six β-strands has been explored. Solvent-accessible surface area calculation revealed that a Leucine-rich hydrophobic cluster of the protein stabilized the protein's structure.     

Variation in the spectrum of Fusarium species on winter wheat

In 1998–2000 a monitoring of the spectrum of Fusarium species on winter wheat was carried out in the Rhineland. The epidemic spread ofFusarium spp. on wheat plants during growing season was investigated as well as the grain contamination after harvest.F avenaceum was the Fusarium species isolated most frequently followed byF culmorum, F poae andF graminearum. Microdochium nivale occurred considerably only in 1998. Both, susceptibility and plant height of the cultivars were correlated to the incidence of Fusarium species /M nivale on harvested kernels; interactions with cropping intensities were detected. The incidence ofF poae seemed to be independent of the cultivar-specific Fusarium susceptibility. Despite the lack of disease symptoms, between growth stages 45–85 mycelium ofFusarium spp. was detectable in the leaves as well as conidia on the leaf surfaces.     

The yeast kinome displays scale free topology with functional hub clusters

Background  

The availability of interaction databases provides an opportunity for researchers to utilize immense amounts of data exclusively in silico. Recently there has been an emphasis on studying the global properties of biological interactions using network analysis. While this type of analysis offers a wide variety of global insights it has surprisingly not been used to examine more localized interactions based on mechanism. In as such we have particular interest in the role of key topological components in signal transduction cascades as they are vital regulators of healthy and diseased cell states.     

A likelihood method for the detection of selection and recombination using nucleotide sequences

Different regions along nucleotide sequences are often subject to different evolutionary forces. Recombination will result in regions having different evolutionary histories, while selection can cause regions to evolve at different rates. This paper presents a statistical method based on likelihood for detecting such processes by identifying the regions which do not fit with a single phylogenetic topology and nucleotide substitution process along the entire sequence. Subsequent reanalysis of these anomalous regions may then be possible. The method is tested using simulations, and its application is demonstrated using the primate psi eta-globin pseudogene, the V3 region of the envelope gene of HIV-1, and argF sequences from Neisseria bacteria. Reanalysis of anomalous regions is shown to reveal possible immune selection in HIV-1 and recombination in Neisseria. A computer program which implements the method is available.      

Cyclophilin binding to the human immunodeficiency virus type 1 Gag polyprotein is mimicked by an anti-cyclosporine antibody.

Human immunodeficiency virus type 1 is unique among retroviruses in that infectivity requires specific incorporation into virions of the cellular protein cyclophilin A through interactions with the Gag polyprotein. Here we show that monoclonal antibody B11 1.4, which recognizes a cyclophilin-binding epitope on cyclosporine, detects denatured or native human immunodeficiency virus type 1 capsid. B11 1.4 does not recognize the capsids of other retroviruses, and binding is inhibited by cyclosporine or by cyclophilin A.     

Yield reduction and mycotoxin contamination of wheat due to<Emphasis Type="Italic">Fusarium culmorum</Emphasis>

The inoculation of wheat ears with 27 isolates ofFusarium culmorum in growth stage 65 reduced 1000-grain weights by 14 to 61%. For the phytopathological characterisation of isolates the virulence on primary wheat leaves and the growth rate an potato-dextrose-agar were assessed. Deoxynivalenol-producing isolates ofF. culmorum reduced the 1000-grain weight more than nivalenol-producing isolates.     

Effect of Preexisting Immunity on an Adenovirus Vaccine Vector: In Vitro Neutralization Assays Fail To Predict Inhibition by Antiviral Antibody In Vivo

A major obstacle to the use of adenovirus vectors derived from common human serotypes, such as human adenovirus 5 (AdHu5), is the high prevalence of virus-neutralizing antibodies in the human population. We previously constructed a variant of chimpanzee adenovirus 68 (AdC68) that maintained the fundamental properties of the carrier but was serologically distinct from AdC68 and resisted neutralization by AdC68 antibodies. In the present study, we tested whether this modified vector, termed AdCDQ, could induce transgene product-specific CD8⁺ T cells in mice with preexisting neutralizing antibody to wild-type AdC68. Contrary to our expectation, the data show conclusively that antibodies that fail to neutralize the AdCDQ mutant vector in vitro nevertheless impair the vector''s capacity to transduce cells and to stimulate a transgene product-specific CD8⁺ T-cell response in vivo. The results thus suggest that in vitro neutralization assays may not reliably predict the effects of virus-specific antibodies on adenovirus vectors in vivo.Adenovirus (Ad) vectors are effective at inducing potent CD8⁺ T-cell responses to immunogens. In animal models, Ad vectors encoding antigens of simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV), used in combination with plasmid-based DNA vectors, generate CD8⁺ T-cell responses that attenuate infection by SIV (9) and by HIV-SIV chimeras (16). In humans, Ad vectors derived from human serotype 5 (AdHu5) are immunogenic and are well tolerated at immunogenic doses; however, in a recent clinical trial, an AdHu5-based HIV-1 vaccine failed to prevent (and may have facilitated) infection (1a). It is not clear whether CD8⁺ T-cell responses will be sufficient to prevent or control HIV infection and disease. However, it seems likely that the induction of effective immune responses against HIV will require multiple doses of antigen, with a priming dose followed by one or more booster immunizations. Prime-boost regimens based on the sequential use of DNA and AdHu5 vectors are being tested clinically, and regimens involving the sequential administration of serologically distinct Ad vectors are being explored in preclinical animal models (1, 5, 8, 9).One major obstacle to the use of vectors derived from AdHu5 and other common human serotypes is the high prevalence of virus-neutralizing antibodies (VNAs) in humans. Preexisting VNAs to the vaccine carrier prevent the vector from transducing target cells, which reduces the amount of vaccine antigen that can be produced and dampens the resultant adaptive immune responses (2, 3, 12). Approximately 40 to 45% of the U.S. population has VNAs to AdHu5, and seroprevalence rates are even higher in Asia and Africa (6, 24).We developed vectors derived from chimpanzee Ads to which humans lack preexisting immunity. When tested in a rodent model, one such vector, AdC68, induces potent transgene product-specific CD8⁺ T-cell responses that can be increased by booster immunizations with serologically distinct Ad vectors (3, 19, 23). However, because the use of multiple serotypes in a prime-boost regimen may prove cumbersome in clinical applications, we have attempted to modify the major neutralizing binding sites within the AdC68 capsid. It has been suggested that the binding sites for Ad-neutralizing antibodies preside primarily within the major capsid protein hexon (4, 10, 14, 15, 17). We defined a single hexon surface loop as the major neutralization site on AdC68 and showed that a mutant vector, AdCDQ, which incorporates a 3-amino-acid mutation within this loop, resists in vitro neutralization by polyclonal antisera obtained from animals immunized against AdC68 (10). Because it is serologically distinct from its parent vector, we expected that AdCDQ could be used in combination with AdC68 in an effective prime-boost regimen.In the present study, we tested whether the AdCDQ vector induces a transgene product-specific CD8⁺ T-cell response in mice with preexisting neutralizing antibody to wild-type AdC68. Contrary to our expectation, the data show conclusively that antibodies that fail to neutralize the AdCDQ vector in vitro nevertheless impair the vector''s capacity to transduce cells and to stimulate a transgene product-specific CD8⁺ T-cell response in vivo. The results thus suggest that in vitro neutralization assays may not reliably predict the effects of virus-specific antibodies on Ad vectors in vivo.