RETRACTED ARTICLE: An accurate method to directly measure water strider’s stroke force on the water (Aquarius paludum: Heteroptera: Gerridae)

We measured the force of free pulling water striders, using a hair attached to their backs and a 3D strain gauge force sensor. We showed the repeatability and accuracy of this method. The error of the method was estimated by comparing the projected angles of the force vector on each plane derived from the force data, with those angles derived from video recordings, and was estimated as 12.4%. Females on average were stronger (1.32 mN) than males (0.87 mN), however the ratio of force/weight was not significantly different. Compared with other lighter species, A. paludum seems to be stronger, but the force/weight ratio is actually lower as expected. A. paludum applies about 0.30–0.40 mN/cm with its mid-legs, thus avoiding penetrating the surface tension while propelling itself rapidly over the water. The corresponding author, Dr Pablo Perez Goodwyn, submitted this article [1] to Central European Journal of Biology (CEJB) shortly after submitting the article [2] to Journal of Bionic Engineering (JBE). JBE published it as a research article in June 2008, and in July 2008 the article was published as a communication in CEJB. Since there are significant unacknowledged similarities between the two papers, it has been brought to the attention of the authors that duplicate submission and publication have taken place. The editors of CEJB consider this an infringement of professional ethics and therefore the decision has been made to retract the article published in Central European Journal of Biology. [1] An accurate method to directly measure water strider’s stroke force on the water (Aquarius paludum: Heteroptera: Gerridae), Central European Journal of Biology, Vol. 3, No. 3, 2008, pp. 299–306 [2] Water striders: the biomechanics of water locomotion and functional morphology of the hydrophobic surface (Insecta: Hemiptera-Heteroptera), Journal of Bionic Engineering, Vol. 5, No. 2, 2008, pp. 121-126     

Tuberculosis Exacerbates HIV-1 Infection through IL-10/STAT3-Dependent Tunneling Nanotube Formation in Macrophages

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Identification of Seroreactive Proteins of Leptospira interrogans Serovar Copenhageni Using a High-Density Protein Microarray Approach

Background

Leptospirosis is a widespread zoonotic disease worldwide. The lack of an adequate laboratory test is a major barrier for diagnosis, especially during the early stages of illness, when antibiotic therapy is most effective. Therefore, there is a critical need for an efficient diagnostic test for this life threatening disease.

Methodology

In order to identify new targets that could be used as diagnostic makers for leptopirosis, we constructed a protein microarray chip comprising 61% of Leptospira interrogans proteome and investigated the IgG response from 274 individuals, including 80 acute-phase, 80 convalescent-phase patients and 114 healthy control subjects from regions with endemic, high endemic, and no endemic transmission of leptospirosis. A nitrocellulose line blot assay was performed to validate the accuracy of the protein microarray results.

Principal findings

We found 16 antigens that can discriminate between acute cases and healthy individuals from a region with high endemic transmission of leptospirosis, and 18 antigens that distinguish convalescent cases. Some of the antigens identified in this study, such as LipL32, the non-identical domains of the Lig proteins, GroEL, and Loa22 are already known to be recognized by sera from human patients, thus serving as proof-of-concept for the serodiagnostic antigen discovery approach. Several novel antigens were identified, including the hypothetical protein LIC10215 which showed good sensitivity and specificity rates for both acute- and convalescent-phase patients.

Conclusions

Our study is the first large-scale evaluation of immunodominant antigens associated with naturally acquired leptospiral infection, and novel as well as known serodiagnostic leptospiral antigens that are recognized by antibodies in the sera of leptospirosis cases were identified. The novel antigens identified here may have potential use in both the development of new tests and the improvement of currently available assays for diagnosing this neglected tropical disease. Further research is needed to assess the utility of these antigens in more deployable diagnostic platforms.     

Structural and kinetic analysis of two covalent sialosyl-enzyme intermediates on Trypanosoma rangeli sialidase

Trypanosoma rangeli sialidase is a glycoside hydrolase (family GH33) that catalyzes the cleavage of alpha-2-->3-linked sialic acid residues from sialoglycoconjugates with overall retention of anomeric configuration. Retaining glycosidases usually operate through a ping-pong mechanism, wherein a covalent intermediate is formed between the carbohydrate and an active site carboxylic acid of the enzyme. Sialidases, instead, appear to use a tyrosine as the catalytic nucleophile, leaving the possibility of an essentially different catalytic mechanism. Indeed, a direct nucleophilic role for a tyrosine was shown for the homologous trans-sialidase from Trypanosoma cruzi, although itself not a typical sialidase. Here we present the three-dimensional structures of the covalent glycosyl-enzyme complexes formed by the T. rangeli sialidase with two different mechanism-based inactivators at 1.9 and 1.7 Angstroms resolution. To our knowledge, these are the first reported structures of enzymatically competent covalent intermediates for a strictly hydrolytic sialidase. Kinetic analyses have been carried out on the formation and turnover of both intermediates, showing that structural modifications to these inactivators can be used to modify the lifetimes of covalent intermediates. These results provide further evidence that all sialidases likely operate through a similar mechanism involving the transient formation of a covalently sialylated enzyme. Furthermore, we believe that the ability to "tune" the inactivation and reactivation rates of mechanism-based inactivators toward specific enzymes represents an important step toward developing this class of inactivators into therapeutically useful compounds.     

Peptides encoded by short ORFs control development and define a new eukaryotic gene family

Despite recent advances in developmental biology, and the sequencing and annotation of genomes, key questions regarding the organisation of cells into embryos remain. One possibility is that uncharacterised genes having nonstandard coding arrangements and functions could provide some of the answers. Here we present the characterisation of tarsal-less (tal), a new type of noncanonical gene that had been previously classified as a putative noncoding RNA. We show that tal controls gene expression and tissue folding in Drosophila, thus acting as a link between patterning and morphogenesis. tal function is mediated by several 33-nucleotide-long open reading frames (ORFs), which are translated into 11-amino-acid-long peptides. These are the shortest functional ORFs described to date, and therefore tal defines two novel paradigms in eukaryotic coding genes: the existence of short, unprocessed peptides with key biological functions, and their arrangement in polycistronic messengers. Our discovery of tal-related short ORFs in other species defines an ancient and noncanonical gene family in metazoans that represents a new class of eukaryotic genes. Our results open a new avenue for the annotation and functional analysis of genes and sequenced genomes, in which thousands of short ORFs are still uncharacterised.     

Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss)

The aim of this study was to evaluate different molecular tools based on the 16S rRNA gene, internal transcribed spacer, and the rpo B gene to examine the bacterial populations present in juvenile rainbow trout intestines. DNA was extracted from both pooled intestinal samples and bacterial strains. Genes were PCR-amplified and analysed using both temporal temperature gradient gel electrophoresis (TTGE) and restriction fragment length polymorphism methods. Because of the high cultivability of the samples, representative bacterial strains were retrieved and we compared the profiles obtained from isolated bacteria with the profile of total bacteria from intestinal contents. Direct analysis based on rpo B-TTGE revealed a simple bacterial composition with two to four bands per sample, while the 16S rRNA gene-TTGE showed multiple bands and comigration for a few species. Sequencing of the 16S rRNA gene- and rpo B-TTGE bands revealed that the intestinal microbiota was dominated by Lactococcus lactis, Citrobacter gillenii, Kluyvera intermedia, Obesumbacterium proteus , and Shewanella marinus . In contrast to 16S rRNA gene-TTGE, rpo B-TTGE profiles derived from bacterial strains produced one band per species. Because the single-copy state of rpo B leads to a single band in TTGE, the rpo B gene is a promising molecular marker for investigating the bacterial community of the rainbow trout intestinal microbiota.     

The dynamics of three shrub species in a fire-prone temperate savanna: the interplay between the seed bank, seed rain and fire regime

A model was developed to assess how the seed rain and fire regime affect seed bank dynamics and seedling establishment of three native shrub species (Acanthostyles buniifolius, Baccharis pingraea and Baccharis dracunculifolia) with different regeneration strategies, in temperate South American savanna. Seed bank and seed rain were quantified for each species under different fire regimes, and their relative roles in regeneration were evaluated. All species had short-term persistent seed banks and high annual variability in seed production. A high proportion of seeds deposited in the seed rain produced seedlings after fire; few entered the soil seed bank. Fire killed a high proportion of the seeds in the soil seed bank. Seedlings derived from the seed rain had a higher probability of surviving for 2 years than seedlings emerging from the soil seed bank. In the absence of fire, establishment depended on germination both from the seed rain and the soil seed bank, whereas with annual fire, establishment was primarily dependent on germination of seeds arriving in the annual seed rain, regardless of species’ regeneration strategies. These results help to explain changes in the vegetation of South American temperate savannas as a result of changes in fire regime and grazing management during the last 50 years. By revealing the crucial roles of the soil seed bank and seed rain in regeneration, this study provides vital information for the development of appropriate management practices to control populations of shrub species with different regeneration strategies in South American temperate savannas.     

Landscape context modulates alien plant invasion in Mediterranean forest edges

Natural habitats in human-altered landscapes are especially vulnerable to biological invasions, especially in their edges. We aim to understand the influence of landscape and local characteristics on biological invasions by exploring the level of plant invasion and alien species traits in forest edges in highly urbanized landscapes. We identified all plant species in 73 paired plots in the edge and 50 m towards the interior of the forest. We explored the association between alien species richness and similarity in species composition between edge and interior plots with landscape and local variables, using generalized linear models and variance partitioning techniques. Then, we performed Fourth-corner analyses to explore the association between alien plant traits and local and landscape variables. In contrast to native species richness, alien species richness was more affected by the surrounding landscape than by the local characteristics of the edge. Road proximity was positively associated with alien species richness and proportion and was its most important correlate, whereas disturbance was negatively associated with native species richness and was its most influential factor. Alien plant traits were also primarily associated with landscape characteristics. For instance, species of Mediterranean origin and introduced for agriculture were associated with higher agriculture use in the landscape. Our findings suggest that risk analyses of habitat vulnerability to invasion must consider the landscape context in order to successfully predict highly invaded areas and identify potentially successful invaders.