A sensitive fluorescence reporter for monitoring quorum sensing regulated protease production in Vibrio harveyi

Many bacteria produce and secrete proteases during host invasion and pathogenesis. Vibrio harveyi, an opportunistic pathogen of shrimp, is known to use a two-component quorum sensing (QS) mechanism for coordination of gene expression including protease secretion at high population densities. We examined the role of V. harveyi's QS signaling molecules, N-(3-hydroxybutanoyl)-l-homoserine lactone (AI-1) and the boron derivative of autoinducer-2 (BAI-2) in extracellular protease production. A fusion protein, M3CLPY (Rajamani et al., 2007), consisting of a large protease sensitive BAI-2 mutant receptor LuxP (~ 38 kDa) flanked by two protease insensitive cyan and yellow variants of GFP (~ 28 kDa each) was utilized as a substrate to detect secreted protease activity. The M3CLPY fusion, with the addition of wild-type V. harveyi (BB120) cell-free culture filtrate showed a time-dependent loss in fluorescence resonance energy transfer (FRET) associated with the cleavage of the LuxP linker protein and hence separation of the two flurophores. This cleavage of LuxP linker protein leading to decreased FRET efficiency was further confirmed by immunoblotting using anti-GFP antibody. The addition of cell-free filtrates from strains defective in one or both of the two-component QS pathways: luxN⁻ (defective in AI-1), luxS⁻ (defective in BAI-2), and luxN⁻/luxS⁻ (defective in both AI-1/BAI-2) showed differential levels of protease production. The observed protease activities were most pronounced in wild-type, followed by the AI-1 defective mutant (BB170) and the least for luxS⁻ mutant (MM30) and luxN⁻/luxS⁻ double mutant (MM32) strains. Incidentally, the lowest protease producing strains MM30 and MM32 were both defective in BAI-2 production. This observation was validated by addition of synthetic BAI-2 to MM30 and MM32 strains to restore protease production. Our results indicate that BAI-2 signaling in the two-component QS pathway plays the key role in regulating extracellular protease production in V. harveyi.     

Hydroxynonenal,toxic carbonyls,and Alzheimer disease

Cytoskeletal disruption is one of the distinguishing characteristics of the vulnerable neurons in Alzheimer disease (AD). It has been suggested that these cytoskeletal changes occur secondarily to covalent modifications of the protein components. Despite the abundance and probable importance of these changes, there has been very little data regarding the identity of the modified proteins or the precise chemistry of the modifications. Here we review a specific type of modification, namely carbonylation of proteins, which has been shown to be a common result of cellular oxidative stress. Hopefully, the following discussion will help elucidate the relationship between oxidative stress, protein modification and the pathogenesis of AD.     

ACUTE EFFECTS OF A RESISTED DYNAMIC WARM-UP PROTOCOL ON JUMPING PERFORMANCE

This study aimed to investigate the kinematic and kinetic changes when resistance is applied in horizontal and vertical directions, produced by using different percentages of body weight, caused by jumping movements during a dynamic warm-up. The group of subjects consisted of 35 voluntary male athletes (19 basketball and 16 volleyball players; age: 23.4 ± 1.4 years, training experience: 9.6 ± 2.7 years; height: 177.2 ± 5.7 cm, body weight: 69.9 ± 6.9 kg) studying Physical Education, who had a jump training background and who were training for 2 hours, on 4 days in a week. A dynamic warm-up protocol containing seven specific resistance movements with specific resistance corresponding to different percentages of body weight (2%, 4%, 6%, 8%, 10%) was applied randomly on non consecutive days. Effects of different warm-up protocols were assessed by pre-/post- exercise changes in jump height in the countermovement jump (CMJ) and the squat jump (SJ) measured using a force platform and changes in hip and knee joint angles at the end of the eccentric phase measured using a video camera. A significant increase in jump height was observed in the dynamic resistance warm-up conducted with different percentages of body weight (p < 0.05). On the other hand, no significant difference in different percentages of body weight states was observed (p > 0.05). In jump movements before and after the warm-up, while no significant difference between the vertical ground reaction forces applied by athletes was observed (p > 0.05), in some cases of resistance, a significant reduction was observed in hip and knee joint angles (p < 0.05). The dynamic resistance warm-up method was found to cause changes in the kinematics of jumping movements, as well as an increase in jump height values. As a result, dynamic warm-up exercises could be applicable in cases of resistance corresponding to 6-10% of body weight applied in horizontal and vertical directions in order to increase the jump performance acutely.     

Design and Characterization of a 52K SNP Chip for Goats

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.     

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences

Motivation

Paired-end sequencing protocols, offered by next generation sequencing (NGS) platforms like Illumia, generate a pair of reads for every DNA fragment in a sample. Although this protocol has been utilized for several metagenomics studies, most taxonomic binning approaches classify each of the reads (forming a pair), independently. The present work explores some simple but effective strategies of utilizing pairing-information of Illumina short reads for improving the accuracy of taxonomic binning of metagenomic datasets. The strategies proposed can be used in conjunction with all genres of existing binning methods.

Results

Validation results suggest that employment of these “Binpairs” strategies can provide significant improvements in the binning outcome. The quality of the taxonomic assignments thus obtained are often comparable to those that can only be achieved with relatively longer reads obtained using other NGS platforms (such as Roche).

Availability

An implementation of the proposed strategies of utilizing pairing information is freely available for academic users at https://metagenomics.atc.tcs.com/binning/binpairs.     

Lifestyle and patterns of physical activity in Hadza foragers

Objectives

Physically active lifestyles are associated with several health benefits. Physical activity (PA) levels are low in post-industrial populations, but generally high throughout life in subsistence populations. The Hadza are a subsistence-oriented foraging population in Tanzania known for being physically active, but it is unknown how recent increases in market integration may have altered their PA patterns. In this study, we examine PA patterns for Hadza women and men who engage in different amounts of traditional foraging.

Materials and Methods

One hundred and seventy seven Hadza participants (51% female, 19–87 years) wore an Axivity accelerometer (dominant wrist) for ~6 days during dry season months. We evaluated the effects of age, sex, and lifestyle measures on four PA measures that capture different aspects of the PA profile.

Results

Participants engaged in high levels of both moderate-intensity PA and inactivity. Although PA levels were negatively associated with age, older participants were still highly active. We found no differences in PA between participants living in more traditional “bush” camps and those living in more settled “village” camps. Mobility was positively associated with step counts for female participants, and schooling was positively associated with inactive time for male participants.

Conclusions

The similarity in PA patterns between Hadza participants in different camp types suggests that high PA levels characterize subsistence lifestyles generally. The sex-based difference in the effects of mobility and schooling on PA could be a reflection of the Hadza's gender-based division of labor, or indicate that changes to subsistence-oriented lifestyles impact women and men in different ways.

     

Isolation of Fungi from Heterodera glycines and in vitro Bioassays for Their Antagonism to Eggs

Twenty fungi were assayed in vitro for antagonism to eggs of Heterodera glycines. Eight of the fungi were isolated from cysts or eggs of H. glycines during the current study, one was isolated from Panagrellus redivivus, and eleven were obtained from other researchers or collections. The bioassays were conducted on eggs from nematodes that had been grown monoxenically on excised root tips. Phoma chrysanthemicola, one strain of Verticillium chlamydosporium, and one strain of V. lecanii caused a decrease (P < 0.01, P < 0.05, P < 0.05, respectively) in the number of viable eggs, although no hyphae were observed colonizing live eggs. Trichoderma polysporum infected live eggs but enhanced (P < 0.05) egg survival. Acremonium bacillisporum, Chaetomium sp., Drechmeria coniospora (two strains), Epicoccum sp., Exophiala jeanselmei, Fusarium sp., Neocosmospora vasinfecta, Scytalidium fulvum, Trichoderma harzianum (two strains), V. chlamydosporium (one strain), V. lecanii (three strains), and an unidentified fungus did not measurably affect egg viability, even though hyphae of five of these fungi were seen in live eggs. The bioassay provides a useful step in the selection of a biological control agent for this major nematode pest.     

Structure-neurotoxicity trends of analogues of 1-methyl-4-phenylpyridinium (MPP+), the cytotoxic metabolite of the dopaminergic neurotoxin MPTP

The dopaminergic neurotoxicity of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) derives from its metabolism to 1-methyl-4-phenyl-pyridinium cation (MPP+), which is then selectively accumulated in dopaminergic neurons. In an effort to assess the structural requirements governing MPP+ cytotoxicity, we evaluated dopaminergic toxicity of MPP+ analogues 3 weeks after their microinfusion into rat substantia nigra. We also evaluated the substrate suitability of MPP+ analogues for high-affinity dopamine uptake in striatal synaptosomes by measuring their ability to induce specific dopamine release. The intranigral neurotoxicity of MPP+ analogues in vivo correlates mainly with their in vitro inhibitory activity on mitochondrial respiration, consistent with a compromise in cellular energy production as the principal mechanism of MPTP-induced cell death. This study extends the structure-neurotoxicity data base beyond that obtainable using MPTP analogues, since many of these are not metabolized to pyridinium compounds. Such information is crucial to assess which possible endogenous or exogenous compounds may exert MPTP/MPP(+)-like toxicity.