Expression of thiol proteases decreases in tomato ovaries after fruit set induced by pollination or gibberellic acid

The modulation of the expression of thiol proteases during both senescence and development was investigated Proteolytic activity and some thiol proteases were analyzed in unpollinated tomato (Lycopersicon esculentum Mill. cv. Rutgers) ovaries during presenescence and during early fruit development induced by treatment with gibberellic acid (GA) or by natural pollination. Proteolytic activity in extracts was tested on azocasein and by observing degradation of the ribulose-1,5-bisphosphate carboxylase large subunit in western blots. There was no correlation between total activity and protein content. Thiol proteases were analyzed by western blot with antibodies raised against papain and a recombinant tomato C14 thiol protease. A 58-kDa polypeptide was recognized by both antibodies and two more polypeptides of 47 and 36 kDa were detected with the second one. All these polypeptide levels increased in untreated unpollinated ovaries at the presenescent stage. Natural pollination or GA treatment of unpollinated ovaries resulted in decreases of these polypeptides at an early developmental stage. The same pattern was observed for the levels of C14 mRNA. Our results suggest that the expression of C14 thiol protease occurs in unpollinated ovaries at the presenescent stage and that it can be suppressed by factors that induce fruit set and development.     

Reiterated DNA sequences in Rhizobium and Agrobacterium spp.

Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens strain were analyzed for the presence of repetitive DNA. Rhizobium and Agrobacterium spp. are closely related soil bacteria that interact with plants and that belong to the taxonomical family Rhizobiaceae. Rhizobium species establish a nitrogen-fixing symbiosis in the roots of legumes, whereas Agrobacterium species is a pathogen in different plants. The four strains revealed a large number of repeated DNA sequences. The family size was usually small, from 2 to 5 elements, but some presented more than 10 elements. Rhizobium and Agrobacterium spp. contain large plasmids in addition to the chromosomes. Analysis of the two Rhizobium strains indicated that DNA reiteration is not confined to the chromosome or to some plasmids but is a property of the whole genome.     

Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum.

The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determined by the electrophoretic mobilities of eight metabolic enzymes. Nonsymbiotic strains were isolated from the rhizosphere of bean plants and characterized by growth on differential media and at different temperatures, intrinsic antibiotic resistance, the lack of homology to a nifH probe, and their inability to form nodules on bean roots. All the isolates clustered with R. leguminosarum bv. phaseoli reference strains and did not encompass any other Rhizobium taxa. Their rRNA operon restriction fragment length polymorphisms and the nucleotide sequence of a fragment of the 16S rRNA gene were also found to be identical to those of R. leguminosarum bv. phaseoli reference strains. When complemented with an R. leguminosarum bv. phaseoli symbiotic plasmid (p42d), the nonsymbiotic isolates were able to fix nitrogen in symbiosis with bean roots at levels similar to those of the parental strain. The symbiotic isolates were found at a relative frequency of 1 in 40 nonsymbiotic R. leguminosarum strains.     

An RNA Holliday junction? Structural and dynamic considerations of the bacteriophage T4 gene 60 interruption

A novel interrupted gene motif has been reported in which a 50-nucleotide insertion into bacteriophage T4 gene 60 appears to be present in the message at the time of translation, yet it is not translated. We present here a dynamic model for how translation may be occurring in the neighborhood of the interruption. The model involves formation of an RNA structure with similarities to a Holliday junction, followed by migration of the branch point in a strand exchange between message and interruption. The advantage of this model over previous ones is that at no time is a new tRNA required to pair with a discontinuous template.     

Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants

Complete characterization of antibody specificities associated to natural infections is expected to provide a rich source of serologic biomarkers with potential applications in molecular diagnosis, follow-up of chemotherapeutic treatments, and prioritization of targets for vaccine development. Here, we developed a highly-multiplexed platform based on next-generation high-density peptide microarrays to map these specificities in Chagas Disease, an exemplar of a human infectious disease caused by the protozoan Trypanosoma cruzi. We designed a high-density peptide microarray containing more than 175,000 overlapping 15mer peptides derived from T. cruzi proteins. Peptides were synthesized in situ on microarray slides, spanning the complete length of 457 parasite proteins with fully overlapped 15mers (1 residue shift). Screening of these slides with antibodies purified from infected patients and healthy donors demonstrated both a high technical reproducibility as well as epitope mapping consistency when compared with earlier low-throughput technologies. Using a conservative signal threshold to classify positive (reactive) peptides we identified 2,031 disease-specific peptides and 97 novel parasite antigens, effectively doubling the number of known antigens and providing a 10-fold increase in the number of fine mapped antigenic determinants for this disease. Finally, further analysis of the chip data showed that optimizing the amount of sequence overlap of displayed peptides can increase the protein space covered in a single chip by at least ∼threefold without sacrificing sensitivity. In conclusion, we show the power of high-density peptide chips for the discovery of pathogen-specific linear B-cell epitopes from clinical samples, thus setting the stage for high-throughput biomarker discovery screenings and proteome-wide studies of immune responses against pathogens.Detailed knowledge of antigens and epitopes recognized in the context of naturally acquired human infections has important implications for our understanding of immune system responses against pathogens, and of the immunopathogenesis of infectious diseases. This knowledge is also important for practical clinical applications such as the development of improved vaccines, intervention strategies, and diagnostics.In the last decades, significant progress has been made in the discovery of antigens and epitopes thanks to a number of methodologies such as cDNA expression libraries (1), combinatorial peptide libraries (2), and peptide and protein microarrays (3, 4). However, current knowledge of the B-cell antigens and the epitope repertoire recognized by the immune system in human infections is still scarce. Indeed, the Immune Epitope Database (5) currently contains an average of only 10 antigens with mapped B-cell epitopes recognized from naturally acquired human infections for bacterial or eukaryotic pathogens. The reasons for this are many, but can be largely attributed to different limitations in the mentioned screening technologies. Heterologous expression of cDNA libraries has been used to guide antigen discovery, but mapping of epitopes most often lags behind as it is a much more costly exercise. Similarly, combinatorial peptide libraries greatly facilitate the identification of peptides that are specifically recognized by antibodies, but these peptides have sequences that can greatly differ from those of the native epitopes (they are mimotopes), thus making it difficult to identify the original antigens. As a result, we currently have only limited detailed information on the fine specificities of the antibody response against complex pathogens.The number of tools for studying immune responses has recently expanded with the inclusion of peptide and protein microarrays, which have been used to identify pathogen-specific antigens and linear epitopes (6–13). Although whole-protein arrays can successfully identify antigens recognized by antibodies, they present the typical difficulties associated with the production of recombinant proteins in heterologous or in vitro systems, do not provide information on the nature and precise location of the epitope(s) in a protein, and are more likely to suffer from nonspecific antibody binding because of the exposure of a large number of potentially antigenic regions. In contrast, peptide arrays can provide exquisite detail of epitope localization, but until now had other limitations mostly associated with their reduced capacity, preventing the complete scanning of large numbers of candidate proteins.Recent advances in computerized photolithography and photochemistry have led to the development of a novel high-density peptide microarray technology, where individual peptides can be synthesized in situ on a glass slide at high densities (14–17). This technology makes the production of high-density peptide arrays highly cost effective compared with previous approaches, while allowing the interrogation of complex immune responses with unprecedented throughput and mapping precision. Previous applications of this technology were limited to the fine mapping of epitopes in single proteins, using monoclonal antibodies, or using immunized animal sera as the source of polyclonal antibodies (16–18).Using these high-density peptide arrays, we here describe the first large-scale study of fine antibody specificities associated with Chagas Disease, which is an exemplar of a chronic human infectious disease. Chagas Disease, caused by the protozoan Trypanosoma cruzi, is an endemic disease of the Americas, affecting ∼8 million people (19). The parasite invades and replicates within host cells, and briefly enters the bloodstream to reach other target tissues. Initially, the disease goes through an acute stage, characterized by patent parasitaemia and the appearance of antibodies against acute-phase antigens, such as SAPA (20), followed by a delayed specific humoral response. In general, the parasite-specific immune response mounted during T. cruzi infections is insufficient to completely eradicate the pathogen, leading to chronic infection (19). In this chronic stage circulating parasites are difficult to detect, even by extremely sensitive methods such as PCR. Therefore, detection of antibodies against whole-parasite extracts or defined antigens (21, 22) remains the standard for diagnosis of Chagas Disease.In this work, we screened high-density microarray slides containing peptides derived from T. cruzi proteins with mixtures of immunoglobulins purified directly from blood samples of Chagas Disease patients. This led to the identification of novel antigens and the simultaneous mapping of their linear B-cell epitopes, thus demonstrating the capacity and performance of this platform for studying antibody specificities associated with human infectious diseases.     

Isolation and Genotyping of Acanthamoeba Strains from Soil Sources from Jamaica,West Indies

Acanthamoeba spp. are opportunistic pathogens that are ubiquitous in nature. Many species of this genus are responsible for a fatal encephalitis and keratitis in humans and other animals. Seventy‐two soil samples were collected from the parishes across Jamaica and assessed for the presence of Acanthamoeba spp. Cultivation was carried out on non‐nutrient agar plates seeded with heat killed Escherichia coli. PCR and sequencing of the DF3 region were carried out in order to genotype the isolated strains of Acanthamoeba. Thermotolerance and osmotolerance assays were utilized to investigate the pathogenic potential of the Acanthamoeba isolates. Acanthamoeba spp. was isolated from 63.9% of soil samples. Sequencing of the DF3 region of the 18S rDNA resulted in the identification of genotypes T4, T5, and T11. T4 genotype was most frequently isolated. Most isolates were thermotolerant or both thermotolerant and osmotolerant, indicating that they may present the potential to cause disease in humans and other animals.     

Effectiveness of protein baits on melon fly and oriental fruit fly (Diptera: Tephritidae): attraction and feeding

Attraction and feeding responses of oriental fruit fly, Bactrocera dorsalis (Hendel), and melon fly, Bactrocera cucurbitae (Coquillett), were determined for different protein baits. In separate choice attraction assays for each species, significantly more flies arrived at stations with bait than water, but no differences existed among baits of GF-120 Fruit Fly Bait, GF-120 NF Naturalyte Fruit Fly Bait, Provesta 621 autolyzed yeast extract, and Mazoferm E802. In comparison with B. dorsalis, B. cucurbitae had 2.8 times more responders and a 4.8 times better discrimination between baits and water. In a second attraction assay with only B. dorsalis, volume of bait was negatively correlated to numbers of flies alighting on the bait. Feeding assays for both species demonstrated that time spent feeding and duration on a leaf were both significantly affected by bait type. B. dorsalis fed the longest on Provesta 621, with significantly less feeding on the other baits, and with all baits resulting in more feeding than water. The longest feeding times for B. cucurbitae resulted with Mazoferm E802 and Provesta 621, and all baits except GF-120 NF resulted in eliciting a significantly longer feeding duration than water. In separate toxicology assays for each species, significantly higher mortality resulted from bait formulations containing spinosad compared with blank baits, but no differences existed between GF-120 and GF-120 NF formulations. The differences are discussed between the two Bactrocera species primarily in regard to bait preference, extent of response, and previous work on laboratory flies.     

Novel bait stations for attract-and-kill of pestiferous fruit flies

A novel, visually-attractive bait station was developed in Hawaii for application of insecticidal baits against oriental fruit fly, Bactrocera dorsalis (Hendel), melon fly, Bactrocera cucurbitae (Coquillett), and Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (all Diptera: Tephritidae). The bait station developed represents a supernormal visual stimulus of papaya foliage and takes advantage of the flies' strong response to the high light-reflecting properties of yellow color and of their need for shelter, while fully protecting the bait against rainfall. Field studies revealed that the behavioral response of female fruit flies, in particular C. capitata and B. cucurbitae , to yellow-painted bait stations sprayed with GF-120 NF Naturalyte Fruit Fly Bait was significantly enhanced compared with similarly sprayed bait stations that mimicked the green color of fully grown papaya leaves. Field studies conducted with B. cucurbitae indicated that the period of bait attractiveness can be extended for at least 1 week after bait application due to the rain-fastness properties of the bait stations and the use of a visually-attractive color. Our studies provide the behavioral basis for the development of improved attract-and-kill bait stations for fruit flies in Hawaii. These devices also provide a standardized way of evaluating bait spray formulations, thus allowing for proper comparisons over time, across species, and among geographical areas.     

Genetic characterization of indigenous peoples from Oaxaca, Mexico, and its relation to linguistic and geographic isolation

We used 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) to genetically characterize 361 individuals from 11 indigenous populations (Amuzgo, Chinanteco, Chontal, Huave, Mazateco, Mixe, Mixteco, Triqui, Zapoteco del Istmo, Zapoteco del Valle, and Zoque) from Oaxaca, Mexico. We also used previously published data from other Mexican peoples (Maya, Chol, Tepehua, Otomí, and Mestizos from northern and central Mexico) to delineate genetic relations, for a total of 541 individuals. Average heterozygosity (H) was lower in most populations from Oaxaca (range 0.687 in Zoque to 0.756 in Chontal) than values observed in Mestizo populations from Mexico (0.758 and 0.793 in central and northern Mestizo, respectively) but higher than values observed in other Amerindian populations from South America; the same relation was true for the number of alleles (n(a) ). We tested (using the software Structure) whether major geographic or linguistic barriers to gene flow existed among the populations of Oaxaca and found that the populations appeared to constitute one or two genetic groups, suggesting that neither geographic location nor linguistics had an effect on the genetic structure of these culturally and linguistically highly diverse indigenous peoples. Moreover, we found a low but statistically significant between-population differentiation. In addition, the genetic structure of Oaxacan populations did not fit an isolation-by-distance model. Finally, using AMOVA and a Bayesian clustering approach, we did not detect significant geographic or linguistic barriers to gene flow within Oaxaca. These results suggest that the indigenous communities of Oaxaca, although culturally isolated, can be genetically defined as a large, nearly panmictic population in which migration could be a more important population mechanism than genetic drift. Finally, compared with outgroups in Mexico (both indigenous peoples and Mestizos), three groups were apparent. Among them, only the Otomí population from Hidalgo has a different culture and language.     

Membrane changes during different stages of a freeze-thaw protocol for equine semen cryopreservation

Many theories have been postulated concerning the possible effects of cryopreservation on spermatozoa, including suggestions the freeze-thawing process produces membranes that have greater fluidity and are more fusogenic, thus inducing changes similar to those of capacitation. The main objectives of this study were to determine at what stage of the freeze-thaw process membrane changes occur and whether evaluation with chlortetracycline (CTC) stain could predict the freezability of stallion sperm. Sperm viability and state of capacitation were simultaneously evaluated using CTC and Hoechst 33258 (H258) techniques. Membrane function was evaluated using the hypo-osmotic swelling test (HOS) and progressive motility (PM) was evaluated under light microscopy at each stage of a freeze-thaw protocol. Evaluated were raw semen; after dilution and centrifugation; after redilution and equilibration at room temperature; after cooling to 5 degrees C; after super cooling to -15 degrees C; and after thawing. The most pronounced functional damage to membranes and the greatest decrease in PM occurred in samples of all stallions after thawing (P<0.05). Cryopreservation, as evaluated by CTC/H258 staining, significantly (P<0.05) affected sperm membrane integrity after centrifugation, after redilution and equilibration at room temperature and after cooling to 5 degrees C. The HOS and H258 tests gave similar results (R values of approximately 0.75) and correlated inversely with the number of live noncapacitated sperm cells (R values of approximately -0.75). Remarkably, the subpopulation of capacitated live cells was unaffected in all freeze-thawing steps and the number of live acrosome reacted cells increased by a factor of 4. However, it was not possible to determine whether the changing CTC patterns reflect a true capacitation phenomenon or an intermediate destabilized state of the sperm cell membrane. This increase may indicate that the subpopulation of functional sperm cells capable of binding to the zona pellucida increases after freeze-thawing despite the deteriorative effect of this procedure for the entire live sperm population.